src/META-INF/log4j.cdkdepends src/META-INF/log4j.datafiles src/META-INF/log4j.libdepends src/META-INF/test-log4j.cdkdepends src/META-INF/test-log4j.devellibdepends src/META-INF/test-log4j.libdepends src/test/org/openscience/cdk/coverage/Log4jCoverageTest.java src/test/org/openscience/cdk/modulesuites/Mlog4jTests.java @@ -482,7 +482,7 @@ list="core,ioformats"/> <foreach target="compile-module" param="module" parallel="${parallel}" maxthreads="${threadCount}" - list="data,dict,diff,qm,standard"/> + list="data,dict,diff,qm,standard,log4j"/> <foreach target="compile-module" param="module" trim="yes" parallel="${parallel}" maxthreads="${threadCount}" list="datadebug,nonotify,isomorphism,atomtype,render,valencycheck, @@ -525,7 +525,7 @@ test-pcore,test-sdg,test-forcefield,test-fingerprint, test-ionpot,test-qm,test-isomorphism,test-libiomd,test-dict, test-diff,test-charges,test-inchi,test-formula, - test-render,test-ioformats"/> + test-render,test-ioformats,test-log4j"/> <foreach target="compile-module" param="module" trim="true" parallel="${parallel}" maxthreads="${threadCount}" list="test-data,test-qsaratomic,test-qsarbond, @@ -561,6 +561,7 @@ <includesfile name="${metainf}/builder3dtools.libdepends"/> <includesfile name="${metainf}/charges.libdepends"/> <includesfile name="${metainf}/core.libdepends"/> + <includesfile name="${metainf}/log4j.libdepends"/> <includesfile name="${metainf}/control.libdepends"/> <includesfile name="${metainf}/datadebug.libdepends"/> <includesfile name="${metainf}/data.libdepends"/> @@ -596,6 +597,7 @@ <include name="cdk-builder3dtools.jar"/> <include name="cdk-charges.jar"/> <include name="cdk-core.jar"/> + <include name="cdk-log4j.jar"/> <include name="cdk-dict.jar"/> <include name="cdk-diff.jar"/> <include name="cdk-control.jar"/> @@ -663,6 +665,7 @@ <include name="cdk-builder3d.jar"/> <include name="cdk-builder3dtools.jar"/> <include name="cdk-charges.jar"/> + <include name="cdk-log4j.jar"/> <include name="cdk-core.jar"/> <include name="cdk-control.jar"/> <include name="cdk-datadebug.jar"/> @@ -754,6 +757,7 @@ <includesfile name="${metainf}/test-pcore.libdepends"/> <includesfile name="${metainf}/test-formula.libdepends"/> <includesfile name="${metainf}/test-render.libdepends"/> + <includesfile name="${metainf}/test-log4j.libdepends"/> </fileset> <fileset dir="${dist}/jar"> <include name="cdk-test-annotation.jar"/> @@ -786,6 +790,7 @@ <include name="cdk-test-pcore.jar"/> <include name="cdk-test-formula.jar"/> <include name="cdk-test-render.jar"/> + <include name="cdk-test-log4j.jar"/> </fileset> </unjar> @@ -995,7 +1000,7 @@ smarts,fingerprint,smiles,qsar,qsaratomic,qsarbond, qsarmolecular,qsarionpot,qsarprotein,pdb,pcore,inchi, structgen,libiomd,libiocml,formula,render,extra,sdg, - ioformats"/> + ioformats,log4j"/> </target> <target id="limitations" name="limitations" depends="noJunit, dist-all" build.xml @@ -114,6 +114,7 @@ <antcall target="doccheck-module"><param name="module" value="interfaces"/></antcall> <antcall target="doccheck-module"><param name="module" value="core"/></antcall> <antcall target="doccheck-module"><param name="module" value="data"/></antcall> + <antcall target="doccheck-module"><param name="module" value="log4j"/></antcall> <antcall target="doccheck-module"><param name="module" value="datadebug"/></antcall> <antcall target="doccheck-module"><param name="module" value="nonotify"/></antcall> <antcall target="doccheck-module"><param name="module" value="standard"/></antcall> javadoc.xml @@ -33,6 +33,7 @@ <!-- the other modules --> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="interfaces"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="core"/></antcall> + <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="log4j"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="standard"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="atomtype"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom"/><param name="module" value="io"/></antcall> @@ -86,6 +87,7 @@ <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-charges"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-diff"/></antcall> <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-qm"/></antcall> + <antcall target="test-module"><param name="pmd.test" value="custom-test"/><param name="module" value="test-log4j"/></antcall> </target> <target id="test-module" name="test-module" pmd.xml @@ -2,5 +2,4 @@ org/openscience/cdk/config/data/*_atomtypes.txt org/openscience/cdk/config/data/*_atomtypes.xml org/openscience/cdk/config/data/isotopes.xml org/openscience/cdk/config/data/chemicalElements.xml -org/openscience/cdk/config/data/log4j.properties org/openscience/cdk/dict/data/cdk-atom-types.owl src/META-INF/core.datafiles @@ -1,3 +1,2 @@ vecmath1.2-1.14.jar -log4j.jar jgrapht-0.6.0.jar src/META-INF/isomorphism.libdepends @@ -1,4 +1,3 @@ -log4j.jar jgrapht-0.6.0.jar vecmath1.2-1.14.jar xom-1.1.jar src/META-INF/reaction.libdepends @@ -1,3 +1,2 @@ vecmath1.2-1.14.jar -log4j.jar jgrapht-0.6.0.jar src/META-INF/standard.libdepends @@ -12,3 +12,4 @@ cdk-testdata.jar cdk-atomtype.jar cdk-valencycheck.jar cdk-pdb.jar +cdk-log4j.jar src/META-INF/test-core.cdkdepends @@ -27,7 +27,8 @@ package org.openscience.cdk; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>An PeriodicTableElement class is instantiated with at least the atom symbol: @@ -66,7 +67,8 @@ public class PeriodicTableElement extends Element */ private static final long serialVersionUID = -2508810950266128526L; - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PeriodicTableElement.class); /** The name for this element. */ protected String name; @@ -130,7 +132,6 @@ public class PeriodicTableElement extends Element public PeriodicTableElement(String symbol) { this.symbol = symbol; - logger = new LoggingTool(this); } /** * Returns the name of this element. src/main/org/openscience/cdk/PeriodicTableElement.java @@ -65,7 +65,6 @@ public class CDKAtomTypeMatcher implements IAtomTypeMatcher { private static Map<Integer,Map<IChemObjectBuilder,CDKAtomTypeMatcher>> factories = new Hashtable<Integer,Map<IChemObjectBuilder,CDKAtomTypeMatcher>>(1); - // private static LoggingTool logger = new LoggingTool(CDKAtomTypeMatcher.class); private CDKAtomTypeMatcher(IChemObjectBuilder builder, int mode) { factory = AtomTypeFactory.getInstance( src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java @@ -37,7 +37,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.tools.AtomTypeTools; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Class implements methods to assign mmff94 atom types for a specific atom in an molecule. @@ -49,7 +50,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class MM2AtomTypeMatcher implements IAtomTypeMatcher { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MM2AtomTypeMatcher.class); IBond.Order maxBondOrder = IBond.Order.SINGLE; private AtomTypeFactory factory = null; @@ -68,7 +70,6 @@ public class MM2AtomTypeMatcher implements IAtomTypeMatcher { * Constructor for the MMFF94AtomTypeMatcher object. */ public MM2AtomTypeMatcher() { - logger = new LoggingTool(this); atomTypeTools=new AtomTypeTools(); } src/main/org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java @@ -37,7 +37,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.tools.AtomTypeTools; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Class implements methods to assign mmff94 atom types for a specific atom in @@ -51,7 +52,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class MMFF94AtomTypeMatcher implements IAtomTypeMatcher { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MMFF94AtomTypeMatcher.class); IBond.Order maxBondOrder = IBond.Order.SINGLE; private AtomTypeFactory factory = null; @@ -72,7 +74,6 @@ public class MMFF94AtomTypeMatcher implements IAtomTypeMatcher { * Constructor for the MMFF94AtomTypeMatcher object. */ public MMFF94AtomTypeMatcher() { - logger = new LoggingTool(this); atomTypeTools=new AtomTypeTools(); } src/main/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; /** @@ -48,13 +49,13 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; public class StructGenAtomTypeGuesser implements IAtomTypeGuesser { private static AtomTypeFactory factory = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(StructGenAtomTypeGuesser.class); /** * Constructor for the StructGenMatcher object. */ public StructGenAtomTypeGuesser() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/atomtype/StructGenAtomTypeGuesser.java @@ -26,7 +26,8 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; /** @@ -46,13 +47,13 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; public class StructGenMatcher implements IAtomTypeMatcher { private static AtomTypeFactory factory = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(StructGenMatcher.class); /** * Constructor for the StructGenMatcher object. */ public StructGenMatcher() { - logger = new LoggingTool(this); } @TestMethod("testFindMatchingAtomType_IAtomContainer") src/main/org/openscience/cdk/atomtype/StructGenMatcher.java @@ -23,6 +23,11 @@ */ package org.openscience.cdk.charges; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -44,15 +49,11 @@ import org.openscience.cdk.reaction.type.HyperconjugationReaction; import org.openscience.cdk.reaction.type.SharingAnionReaction; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.StructureResonanceGenerator; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import java.io.IOException; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * <p>The calculation of the Gasteiger (PEPE) partial charges is based on * {@cdk.cite Saller85}. This class doesn't implement the original method of the Marsili but the @@ -90,7 +91,8 @@ public class GasteigerPEPEPartialCharges implements IChargeCalculator { private double fS = 0.37; - private LoggingTool logger = new LoggingTool(GasteigerPEPEPartialCharges.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(GasteigerPEPEPartialCharges.class); /** * Constructor for the GasteigerPEPEPartialCharges object src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java @@ -24,18 +24,24 @@ */ package org.openscience.cdk.charges; +import java.io.IOException; + +import javax.vecmath.Point3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.AtomTypeFactory; import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IElement; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import java.io.IOException; - /** * The calculation of the inductive partial atomic charges and equalization of * effective electronegativities is based on {@cdk.cite CHE03}. @@ -54,7 +60,8 @@ public class InductivePartialCharges implements IChargeCalculator { private static double[] pauling; private IsotopeFactory ifac = null; private AtomTypeFactory factory = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(InductivePartialCharges.class); /** @@ -73,7 +80,6 @@ public class InductivePartialCharges implements IChargeCalculator { 1.9, 2.2, 2.2, 2.2, 1.9, 1.7, 1.7, 1.8, 1.9, 2.1, 2.5, 0.7, 0.9, 1.1, 1.3, 1.5, 1.7, 1.9, 2.2, 2.2, 2.2, 2.4, 1.9, 1.8, 1.8, 1.9, 2.0, 2.2, 0, 0.7, 0.9, 1.1}; } - logger = new LoggingTool(this); } src/main/org/openscience/cdk/charges/InductivePartialCharges.java @@ -35,7 +35,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; @@ -54,13 +55,13 @@ import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; */ @TestClass("org.openscience.cdk.charges.PolarizabilityTest") public class Polarizability { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Polarizability.class); /** * Constructor for the Polarizability object */ public Polarizability() { - logger = new LoggingTool(this); } private void addExplicitHydrogens(IAtomContainer container) { src/main/org/openscience/cdk/charges/Polarizability.java @@ -36,7 +36,8 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IPseudoAtom; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * General class for defining AtomTypes. This class itself does not define the @@ -94,7 +95,8 @@ public class AtomTypeFactory { private final static String XML_EXTENSION = "xml"; private final static String OWL_EXTENSION = "owl"; - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomTypeFactory.class); private static Map<String, AtomTypeFactory> tables = null; private List<IAtomType> atomTypes = null; @@ -104,9 +106,6 @@ public class AtomTypeFactory { * */ private AtomTypeFactory(String configFile, IChemObjectBuilder builder) { - if (logger == null) { - logger = new LoggingTool(this); - } atomTypes = new ArrayList<IAtomType>(100); readConfiguration(configFile, builder); } @@ -116,9 +115,6 @@ public class AtomTypeFactory { * */ private AtomTypeFactory(InputStream ins, String format, IChemObjectBuilder builder) { - if (logger == null) { - logger = new LoggingTool(this); - } atomTypes = new ArrayList<IAtomType>(100); readConfiguration(ins, format, builder); } src/main/org/openscience/cdk/config/AtomTypeFactory.java @@ -23,17 +23,18 @@ */ package org.openscience.cdk.config; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.List; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.atomtypes.AtomTypeReader; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IChemObjectBuilder; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.List; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * AtomType resource that reads the atom type configuration from an XML file. @@ -49,10 +50,10 @@ public class CDKBasedAtomTypeConfigurator implements IAtomTypeConfigurator { private String configFile = "org.openscience.cdk.config.data.structgen_atomtypes.xml"; private InputStream ins = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CDKBasedAtomTypeConfigurator.class); public CDKBasedAtomTypeConfigurator() { - logger = new LoggingTool(this); } @TestMethod("testSetInputStream_InputStream") src/main/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java @@ -23,18 +23,19 @@ */ package org.openscience.cdk.config; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.List; + import org.openscience.cdk.PeriodicTableElement; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.elements.ElementPTReader; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IElement; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.List; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Used to store and return data of a particular chemicalElement. As this class is a @@ -55,7 +56,8 @@ public class ElementPTFactory private static ElementPTFactory efac = null; private List<PeriodicTableElement> elements = null; private boolean debug = false; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ElementPTFactory.class); /** * Private constructor for the ElementPTFactory object. @@ -64,7 +66,6 @@ public class ElementPTFactory */ private ElementPTFactory() throws IOException { - logger = new LoggingTool(this); logger.info("Creating new ElementPTFactory"); InputStream ins = null; src/main/org/openscience/cdk/config/ElementPTFactory.java @@ -23,18 +23,23 @@ */ package org.openscience.cdk.config; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; -import org.openscience.cdk.config.isotopes.IsotopeReader; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.tools.LoggingTool; - import java.io.IOException; import java.io.InputStream; import java.util.ArrayList; import java.util.HashMap; import java.util.List; +import org.openscience.cdk.annotations.TestClass; +import org.openscience.cdk.annotations.TestMethod; +import org.openscience.cdk.config.isotopes.IsotopeReader; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IChemObjectBuilder; +import org.openscience.cdk.interfaces.IElement; +import org.openscience.cdk.interfaces.IIsotope; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; + /** * Used to store and return data of a particular isotope. As this class is a * singleton class, one gets an instance with: @@ -70,7 +75,8 @@ public class IsotopeFactory private List<IIsotope> isotopes = null; private HashMap<String, IIsotope> majorIsotopes = null; private boolean debug = false; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IsotopeFactory.class); /** * Private constructor for the IsotopeFactory object. @@ -80,7 +86,6 @@ public class IsotopeFactory * @param builder The builder from which we the factory will be generated */ private IsotopeFactory(IChemObjectBuilder builder) throws IOException { - logger = new LoggingTool(this); logger.info("Creating new IsotopeFactory"); InputStream ins; src/main/org/openscience/cdk/config/IsotopeFactory.java @@ -20,17 +20,18 @@ */ package org.openscience.cdk.config; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.List; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.atomtypes.OWLAtomTypeReader; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IChemObjectBuilder; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.List; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * AtomType resource that reads the atom type configuration from an OWL file. @@ -42,10 +43,10 @@ import java.util.List; public class OWLBasedAtomTypeConfigurator implements IAtomTypeConfigurator { private InputStream ins = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLBasedAtomTypeConfigurator.class); public OWLBasedAtomTypeConfigurator() { - logger = new LoggingTool(this); } @TestMethod("testSetInputStream_InputStream") src/main/org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java @@ -23,20 +23,21 @@ */ package org.openscience.cdk.config.atomtypes; +import java.util.ArrayList; +import java.util.List; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.interfaces.IAtomType; -import org.openscience.cdk.interfaces.IAtomType.Hybridization; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObjectBuilder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.interfaces.IAtomType.Hybridization; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.Attributes; import org.xml.sax.helpers.DefaultHandler; -import java.util.ArrayList; -import java.util.List; - /** * SAX Handler for the AtomTypeReader. * @@ -64,7 +65,8 @@ public class AtomTypeHandler extends DefaultHandler { private final int SCALAR_PIBONDCOUNT=13; private final int SCALAR_LONEPAIRCOUNT=14; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomTypeHandler.class); private String currentChars; private List<IAtomType> atomTypes; private int scalarType; @@ -79,7 +81,6 @@ public class AtomTypeHandler extends DefaultHandler { * @param build The IChemObjectBuilder used to create the IAtomType's. */ public AtomTypeHandler(IChemObjectBuilder build) { - logger = new LoggingTool(this); builder = build; } src/main/org/openscience/cdk/config/atomtypes/AtomTypeHandler.java @@ -27,20 +27,21 @@ */ package org.openscience.cdk.config.atomtypes; +import java.io.IOException; +import java.io.Reader; +import java.util.ArrayList; +import java.util.List; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IChemObjectBuilder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.XMLReader; -import java.io.IOException; -import java.io.Reader; -import java.util.ArrayList; -import java.util.List; - /** * XML Reader for the CDKBasedAtomTypeConfigurator. * @@ -54,7 +55,8 @@ public class AtomTypeReader { private XMLReader parser; private Reader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomTypeReader.class); /** * Instantiates the XML based AtomTypeReader. @@ -67,7 +69,6 @@ public class AtomTypeReader { } private void init() { - logger = new LoggingTool(this); boolean success = false; // If JAXP is prefered (comes with Sun JVM 1.4.0 and higher) if (!success) { src/main/org/openscience/cdk/config/atomtypes/AtomTypeReader.java @@ -28,7 +28,8 @@ import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IChemObjectBuilder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.Attributes; import org.xml.sax.helpers.DefaultHandler; @@ -43,7 +44,8 @@ public class OWLAtomTypeHandler extends DefaultHandler { private final String NS_ATOMTYPE = "http://cdk.sf.net/ontologies/atomtypes#"; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLAtomTypeHandler.class); private String currentChars; private List<IAtomType> atomTypes; private IAtomType currentAtomType; @@ -57,7 +59,6 @@ public class OWLAtomTypeHandler extends DefaultHandler { * @param build The IChemObjectBuilder used to create the IAtomType's. */ public OWLAtomTypeHandler(IChemObjectBuilder build) { - logger = new LoggingTool(this); builder = build; } src/main/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java @@ -24,19 +24,20 @@ */ package org.openscience.cdk.config.atomtypes; +import java.io.IOException; +import java.io.Reader; +import java.util.HashMap; +import java.util.Map; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.OWLBasedAtomTypeConfigurator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.XMLReader; -import java.io.IOException; -import java.io.Reader; -import java.util.HashMap; -import java.util.Map; - /** * XML Reader for the {@link OWLBasedAtomTypeConfigurator}. * @@ -48,7 +49,8 @@ public class OWLAtomTypeMappingReader { private XMLReader parser; private Reader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLAtomTypeReader.class); /** * Instantiates the XML based AtomTypeReader. @@ -62,7 +64,6 @@ public class OWLAtomTypeMappingReader { } private void init() { - logger = new LoggingTool(this); boolean success = false; // If JAXP is preferred (comes with Sun JVM 1.4.0 and higher) if (!success) { src/main/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java @@ -34,7 +34,8 @@ import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.OWLBasedAtomTypeConfigurator; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IChemObjectBuilder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.XMLReader; @@ -50,7 +51,8 @@ public class OWLAtomTypeReader { private XMLReader parser; private Reader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLAtomTypeReader.class); /** * Instantiates the XML based AtomTypeReader. @@ -63,7 +65,6 @@ public class OWLAtomTypeReader { } private void init() { - logger = new LoggingTool(this); boolean success = false; // If JAXP is preferred (comes with Sun JVM 1.4.0 and higher) if (!success) { src/main/org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java @@ -23,15 +23,16 @@ */ package org.openscience.cdk.config.elements; +import java.util.ArrayList; +import java.util.List; + import org.openscience.cdk.PeriodicTableElement; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.Attributes; import org.xml.sax.helpers.DefaultHandler; -import java.util.ArrayList; -import java.util.List; - /** * Reads an element list in CML2 format. An example definition is: * <pre> @@ -65,7 +66,8 @@ public class ElementPTHandler extends DefaultHandler private final int SCALAR_RADVDW = 9; private final int SCALAR_PAULE = 10; private int scalarType; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ElementPTHandler.class); private String currentChars; private List<PeriodicTableElement> elements; @@ -75,7 +77,6 @@ public class ElementPTHandler extends DefaultHandler public ElementPTHandler() { - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/config/elements/ElementPTHandler.java @@ -33,7 +33,8 @@ import java.util.ArrayList; import java.util.List; import org.openscience.cdk.PeriodicTableElement; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.XMLReader; @@ -55,7 +56,8 @@ public class ElementPTReader { private XMLReader parser; private Reader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ElementPTReader.class); /** * Instantiates a new reader that parses the XML from the given <code>input</code>. @@ -68,7 +70,6 @@ public class ElementPTReader { } private void init() { - logger = new LoggingTool(this); boolean success = false; // If JAXP is prefered (comes with Sun JVM 1.4.0 and higher) if (!success) { src/main/org/openscience/cdk/config/elements/ElementPTReader.java @@ -23,17 +23,18 @@ */ package org.openscience.cdk.config.isotopes; +import java.util.ArrayList; +import java.util.List; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IIsotope; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.Attributes; import org.xml.sax.helpers.DefaultHandler; -import java.util.ArrayList; -import java.util.List; - /** * Reads an isotope list in CML2 format. An example definition is: * <pre> @@ -57,7 +58,8 @@ import java.util.List; @TestClass("org.openscience.cdk.config.isotopes.IsotopeHandlerTest") public class IsotopeHandler extends DefaultHandler { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IsotopeHandler.class); private String currentChars; private List<IIsotope> isotopes; @@ -73,7 +75,6 @@ public class IsotopeHandler extends DefaultHandler { * @param builder The IChemObjectBuilder used to create new IIsotope's. */ public IsotopeHandler(IChemObjectBuilder builder) { - logger = new LoggingTool(this); this.builder = builder; } src/main/org/openscience/cdk/config/isotopes/IsotopeHandler.java @@ -27,20 +27,21 @@ */ package org.openscience.cdk.config.isotopes; +import java.io.IOException; +import java.io.InputStream; +import java.util.ArrayList; +import java.util.List; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IIsotope; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.XMLReader; -import java.io.IOException; -import java.io.InputStream; -import java.util.ArrayList; -import java.util.List; - /** * Reader that instantiates an XML parser and customized handler to process * the isotope information in the CML2 isotope data file. The Reader first @@ -59,7 +60,8 @@ public class IsotopeReader { private XMLReader parser; private InputStream input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IsotopeReader.class); private IChemObjectBuilder builder; /** @@ -75,7 +77,6 @@ public class IsotopeReader { } private void init() { - logger = new LoggingTool(this); boolean success = false; // If JAXP is prefered (comes with Sun JVM 1.4.0 and higher) if (!success) { src/main/org/openscience/cdk/config/isotopes/IsotopeReader.java @@ -20,18 +20,24 @@ */ package org.openscience.cdk.debug; -import org.openscience.cdk.formula.AdductFormula; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.tools.LoggingTool; - import java.util.Iterator; +import org.openscience.cdk.formula.AdductFormula; +import org.openscience.cdk.interfaces.IAdductFormula; +import org.openscience.cdk.interfaces.IChemObjectBuilder; +import org.openscience.cdk.interfaces.IIsotope; +import org.openscience.cdk.interfaces.IMolecularFormula; +import org.openscience.cdk.interfaces.IMolecularFormulaSet; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; + /** * @cdk.module datadebug */ public class DebugAdductFormula extends AdductFormula implements IAdductFormula { - private LoggingTool logger = new LoggingTool(DebugAdductFormula.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAdductFormula.class); public DebugAdductFormula() { super(); src/main/org/openscience/cdk/debug/DebugAdductFormula.java @@ -20,14 +20,25 @@ */ package org.openscience.cdk.debug; -import org.openscience.cdk.AminoAcid; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; - import java.util.List; import java.util.Map; +import org.openscience.cdk.AminoAcid; +import org.openscience.cdk.interfaces.IAminoAcid; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomParity; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IChemObjectBuilder; +import org.openscience.cdk.interfaces.IChemObjectChangeEvent; +import org.openscience.cdk.interfaces.IChemObjectListener; +import org.openscience.cdk.interfaces.IElectronContainer; +import org.openscience.cdk.interfaces.ILonePair; +import org.openscience.cdk.interfaces.ISingleElectron; +import org.openscience.cdk.interfaces.IBond.Order; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; + /** * Debugging data class. * @@ -40,7 +51,8 @@ public class DebugAminoAcid extends AminoAcid private static final long serialVersionUID = 4092864536013855890L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public void addAtomParity(IAtomParity parity) { logger.debug("Adding atom parity: ", parity); src/main/org/openscience/cdk/debug/DebugAminoAcid.java @@ -33,7 +33,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IElement; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -46,7 +47,8 @@ public class DebugAtom extends Atom implements IAtom { private static final long serialVersionUID = 188945429187084868L; - LoggingTool logger = new LoggingTool(DebugAtom.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtom.class); public DebugAtom() { super(); src/main/org/openscience/cdk/debug/DebugAtom.java @@ -35,7 +35,8 @@ import org.openscience.cdk.interfaces.IElectronContainer; import org.openscience.cdk.interfaces.ILonePair; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -49,7 +50,8 @@ public class DebugAtomContainer extends AtomContainer private static final long serialVersionUID = 7584711255625778345L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public DebugAtomContainer() { super(); src/main/org/openscience/cdk/debug/DebugAtomContainer.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,7 +43,8 @@ public class DebugAtomContainerSet extends AtomContainerSet private static final long serialVersionUID = -8358480615782437454L; - LoggingTool logger = new LoggingTool(DebugAtomContainerSet.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainerSet.class); public void addListener(IChemObjectListener col) { logger.debug("Adding listener: ", col); src/main/org/openscience/cdk/debug/DebugAtomContainerSet.java @@ -23,7 +23,8 @@ package org.openscience.cdk.debug; import org.openscience.cdk.AtomParity; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomParity; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -41,7 +42,8 @@ public class DebugAtomParity extends AtomParity super(centralAtom, first, second, third, fourth, parity); } - LoggingTool logger = new LoggingTool(DebugAtomParity.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomParity.class); public IAtom getAtom() { logger.debug("Getting atom: ", super.getAtom()); src/main/org/openscience/cdk/debug/DebugAtomParity.java @@ -29,7 +29,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IElement; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -43,7 +44,8 @@ public class DebugAtomType extends AtomType private static final long serialVersionUID = 1427549696666679540L; - LoggingTool logger = new LoggingTool(DebugAtomType.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomType.class); public DebugAtomType(String elementSymbol) { super(elementSymbol); src/main/org/openscience/cdk/debug/DebugAtomType.java @@ -39,7 +39,8 @@ import org.openscience.cdk.interfaces.IMonomer; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IStrand; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -53,7 +54,8 @@ public class DebugBioPolymer extends BioPolymer private static final long serialVersionUID = 5349870327516864575L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public void addAtomParity(IAtomParity parity) { logger.debug("Adding atom parity: ", parity); src/main/org/openscience/cdk/debug/DebugBioPolymer.java @@ -31,7 +31,8 @@ import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -45,7 +46,8 @@ public class DebugBond extends Bond private static final long serialVersionUID = -2330398179697796261L; - LoggingTool logger = new LoggingTool(DebugBond.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugBond.class); public DebugBond() { super(); src/main/org/openscience/cdk/debug/DebugBond.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,7 +43,8 @@ public class DebugChemFile extends ChemFile private static final long serialVersionUID = -5575043161897814279L; - LoggingTool logger = new LoggingTool(DebugChemFile.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugChemFile.class); public DebugChemFile() { super(); src/main/org/openscience/cdk/debug/DebugChemFile.java @@ -31,7 +31,8 @@ import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.interfaces.IRingSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -45,7 +46,8 @@ public class DebugChemModel extends ChemModel private static final long serialVersionUID = -920209300005079592L; - LoggingTool logger = new LoggingTool(DebugChemModel.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugChemModel.class); public void addListener(IChemObjectListener col) { logger.debug("Adding listener: ", col); src/main/org/openscience/cdk/debug/DebugChemModel.java @@ -27,7 +27,8 @@ import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -41,7 +42,8 @@ public class DebugChemObject extends ChemObject private static final long serialVersionUID = -8547443535884526365L; - LoggingTool logger = new LoggingTool(DebugChemObject.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugChemObject.class); public DebugChemObject(IChemObject object) { super(object); src/main/org/openscience/cdk/debug/DebugChemObject.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,7 +43,8 @@ public class DebugChemSequence extends ChemSequence private static final long serialVersionUID = -628120469241907704L; - LoggingTool logger = new LoggingTool(DebugChemSequence.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugChemSequence.class); public void addListener(IChemObjectListener col) { logger.debug("Adding listener: ", col); src/main/org/openscience/cdk/debug/DebugChemSequence.java @@ -38,7 +38,8 @@ import org.openscience.cdk.interfaces.IElectronContainer; import org.openscience.cdk.interfaces.ILonePair; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -52,16 +53,15 @@ public class DebugCrystal extends Crystal private static final long serialVersionUID = -1749989529794094087L; - LoggingTool logger; + static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugCrystal.class); public DebugCrystal() { super(); - logger = new LoggingTool(DebugCrystal.class); } public DebugCrystal(IAtomContainer container) { super(container); - logger = new LoggingTool(DebugCrystal.class); } public void addAtomParity(IAtomParity parity) { src/main/org/openscience/cdk/debug/DebugCrystal.java @@ -27,7 +27,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IElectronContainer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -41,7 +42,8 @@ public class DebugElectronContainer extends ElectronContainer private static final long serialVersionUID = 5309193617982266230L; - LoggingTool logger = new LoggingTool(DebugElectronContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugElectronContainer.class); public Integer getElectronCount() { logger.debug("Getting electron count: ", super.getElectronCount()); src/main/org/openscience/cdk/debug/DebugElectronContainer.java @@ -27,7 +27,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IElement; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -41,7 +42,8 @@ public class DebugElement extends Element private static final long serialVersionUID = -8520499563841667066L; - LoggingTool logger = new LoggingTool(DebugElement.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugElement.class); public DebugElement() { super(); src/main/org/openscience/cdk/debug/DebugElement.java @@ -36,7 +36,8 @@ import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much @@ -51,7 +52,8 @@ public class DebugFragmentAtom extends FragmentAtom { private static final long serialVersionUID = 0L; - LoggingTool logger = new LoggingTool(DebugFragmentAtom.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugFragmentAtom.class); public DebugFragmentAtom() { super(); src/main/org/openscience/cdk/debug/DebugFragmentAtom.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IIsotope; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,7 +43,8 @@ public class DebugIsotope extends Isotope private static final long serialVersionUID = -2659188100080921299L; - LoggingTool logger = new LoggingTool(DebugIsotope.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugIsotope.class); public DebugIsotope(String elementSymbol) { super(elementSymbol); src/main/org/openscience/cdk/debug/DebugIsotope.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.ILonePair; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,7 +43,8 @@ public class DebugLonePair extends LonePair private static final long serialVersionUID = 5683399496728893341L; - LoggingTool logger = new LoggingTool(DebugLonePair.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugLonePair.class); public DebugLonePair() { super(); src/main/org/openscience/cdk/debug/DebugLonePair.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IMapping; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,11 +43,11 @@ public class DebugMapping extends Mapping private static final long serialVersionUID = -3785399530153469835L; - LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugMapping.class); public DebugMapping(IChemObject objectOne, IChemObject objectTwo) { super(objectOne, objectTwo); - logger = new LoggingTool(DebugMapping.class); } public void addListener(IChemObjectListener col) { src/main/org/openscience/cdk/debug/DebugMapping.java @@ -26,14 +26,16 @@ import org.openscience.cdk.formula.MolecularFormula; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IIsotope; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module datadebug */ public class DebugMolecularFormula extends MolecularFormula implements IMolecularFormula { - private LoggingTool logger = new LoggingTool(DebugMolecularFormula.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugMolecularFormula.class); public IMolecularFormula add(IMolecularFormula formula) { logger.debug("Adding formula: ", formula); src/main/org/openscience/cdk/debug/DebugMolecularFormula.java @@ -26,14 +26,16 @@ import org.openscience.cdk.formula.MolecularFormulaSet; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IMolecularFormula; import org.openscience.cdk.interfaces.IMolecularFormulaSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module datadebug */ public class DebugMolecularFormulaSet extends MolecularFormulaSet implements IMolecularFormulaSet { - private LoggingTool logger = new LoggingTool(DebugMolecularFormulaSet.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugMolecularFormulaSet.class); public DebugMolecularFormulaSet() { super(); src/main/org/openscience/cdk/debug/DebugMolecularFormulaSet.java @@ -36,7 +36,8 @@ import org.openscience.cdk.interfaces.ILonePair; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -50,7 +51,8 @@ public class DebugMolecule extends Molecule private static final long serialVersionUID = -7263404200270132412L; - LoggingTool logger = new LoggingTool(DebugMolecule.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugMolecule.class); public DebugMolecule() { super(); src/main/org/openscience/cdk/debug/DebugMolecule.java @@ -30,7 +30,8 @@ import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -44,7 +45,8 @@ public class DebugMoleculeSet extends MoleculeSet private static final long serialVersionUID = -2925577323304207688L; - LoggingTool logger = new LoggingTool(DebugMoleculeSet.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugMoleculeSet.class); public void addListener(IChemObjectListener col) { logger.debug("Adding listener: ", col); src/main/org/openscience/cdk/debug/DebugMoleculeSet.java @@ -36,7 +36,8 @@ import org.openscience.cdk.interfaces.ILonePair; import org.openscience.cdk.interfaces.IMonomer; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -50,7 +51,8 @@ public class DebugMonomer extends Monomer private static final long serialVersionUID = -7312839949399572435L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public void addAtomParity(IAtomParity parity) { logger.debug("Adding atom parity: ", parity); src/main/org/openscience/cdk/debug/DebugMonomer.java @@ -25,7 +25,8 @@ import javax.vecmath.Point3d; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IPDBAtom; import org.openscience.cdk.protein.data.PDBAtom; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -39,7 +40,8 @@ public class DebugPDBAtom extends PDBAtom implements IPDBAtom { private static final long serialVersionUID = -2432127382224382452L; - LoggingTool logger = new LoggingTool(DebugPDBAtom.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugPDBAtom.class); public DebugPDBAtom(IElement element) { super(element); src/main/org/openscience/cdk/debug/DebugPDBAtom.java @@ -22,7 +22,8 @@ package org.openscience.cdk.debug; import org.openscience.cdk.interfaces.IPDBMonomer; import org.openscience.cdk.protein.data.PDBMonomer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -35,7 +36,8 @@ public class DebugPDBMonomer extends PDBMonomer implements IPDBMonomer { private static final long serialVersionUID = -5156111560946745699L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public void setICode(String newICode) { logger.debug("Setting I Code: ", newICode); src/main/org/openscience/cdk/debug/DebugPDBMonomer.java @@ -25,7 +25,8 @@ import java.util.Collection; import org.openscience.cdk.interfaces.IBioPolymer; import org.openscience.cdk.interfaces.IPDBStructure; import org.openscience.cdk.protein.data.PDBPolymer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -39,7 +40,8 @@ public class DebugPDBPolymer extends PDBPolymer implements IBioPolymer { private static final long serialVersionUID = -8485559594520919850L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public Collection getStructures() { logger.debug("Getting Structure: ", super.getStructures()); src/main/org/openscience/cdk/debug/DebugPDBPolymer.java @@ -21,7 +21,8 @@ package org.openscience.cdk.debug; import org.openscience.cdk.protein.data.PDBStructure; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -35,7 +36,8 @@ public class DebugPDBStructure extends PDBStructure { private static final long serialVersionUID = 1934748703085969097L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public Character getEndChainID() { logger.debug("Getting End Chain ID: ", super.getEndChainID()); src/main/org/openscience/cdk/debug/DebugPDBStructure.java @@ -38,7 +38,8 @@ import org.openscience.cdk.interfaces.IMonomer; import org.openscience.cdk.interfaces.IPolymer; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -52,7 +53,8 @@ public class DebugPolymer extends Polymer private static final long serialVersionUID = -1459933635059023539L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public void addAtomParity(IAtomParity parity) { logger.debug("Adding atom parity: ", parity); src/main/org/openscience/cdk/debug/DebugPolymer.java @@ -33,7 +33,8 @@ import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IPseudoAtom; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -47,7 +48,8 @@ public class DebugPseudoAtom extends PseudoAtom private static final long serialVersionUID = -5935090219383862070L; - LoggingTool logger = new LoggingTool(DebugPseudoAtom.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugPseudoAtom.class); public DebugPseudoAtom() { super(); src/main/org/openscience/cdk/debug/DebugPseudoAtom.java @@ -29,7 +29,8 @@ import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReaction; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -43,7 +44,8 @@ public class DebugReaction extends Reaction private static final long serialVersionUID = -8958358842308217875L; - LoggingTool logger = new LoggingTool(DebugReaction.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugReaction.class); public DebugReaction() { super(); src/main/org/openscience/cdk/debug/DebugReaction.java @@ -27,7 +27,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IReactionScheme; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -40,7 +41,8 @@ public class DebugReactionScheme extends ReactionScheme private static final long serialVersionUID = 705803374163613819L; - LoggingTool logger = new LoggingTool(DebugReactionScheme.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugReactionScheme.class); public void addListener(IChemObjectListener col) { logger.debug("Adding listener: ", col); src/main/org/openscience/cdk/debug/DebugReactionScheme.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,7 +43,8 @@ public class DebugReactionSet extends ReactionSet private static final long serialVersionUID = 1620489912540131959L; - LoggingTool logger = new LoggingTool(DebugReactionSet.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugReactionSet.class); public void addListener(IChemObjectListener col) { logger.debug("Adding listener: ", col); src/main/org/openscience/cdk/debug/DebugReactionSet.java @@ -37,7 +37,8 @@ import org.openscience.cdk.interfaces.ILonePair; import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -51,7 +52,8 @@ public class DebugRing extends Ring private static final long serialVersionUID = -6420813246421544803L; - LoggingTool logger = new LoggingTool(DebugRing.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugRing.class); public DebugRing() { super(); src/main/org/openscience/cdk/debug/DebugRing.java @@ -25,7 +25,8 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -39,7 +40,8 @@ public class DebugRingSet extends RingSet private static final long serialVersionUID = -4144201128508373352L; - LoggingTool logger = new LoggingTool(DebugRingSet.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugRingSet.class); public DebugRingSet() { super(); src/main/org/openscience/cdk/debug/DebugRingSet.java @@ -28,7 +28,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObjectChangeEvent; import org.openscience.cdk.interfaces.IChemObjectListener; import org.openscience.cdk.interfaces.ISingleElectron; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -42,7 +43,8 @@ public class DebugSingleElectron extends SingleElectron private static final long serialVersionUID = -2895377834940311825L; - LoggingTool logger = new LoggingTool(DebugSingleElectron.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugSingleElectron.class); public DebugSingleElectron() { super(); src/main/org/openscience/cdk/debug/DebugSingleElectron.java @@ -38,7 +38,8 @@ import org.openscience.cdk.interfaces.IMonomer; import org.openscience.cdk.interfaces.ISingleElectron; import org.openscience.cdk.interfaces.IStrand; import org.openscience.cdk.interfaces.IBond.Order; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Debugging data class. @@ -52,7 +53,8 @@ public class DebugStrand extends Strand private static final long serialVersionUID = 1794588804926192427L; - LoggingTool logger = new LoggingTool(DebugAtomContainer.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DebugAtomContainer.class); public void addAtomParity(IAtomParity parity) { logger.debug("Adding atom parity: ", parity); src/main/org/openscience/cdk/debug/DebugStrand.java @@ -28,17 +28,18 @@ */ package org.openscience.cdk.dict; -import org.openscience.cdk.tools.LoggingTool; -import org.xml.sax.InputSource; -import org.xml.sax.SAXException; -import org.xml.sax.XMLReader; -import org.xml.sax.helpers.XMLReaderFactory; - import java.io.IOException; import java.io.Reader; import java.util.Enumeration; import java.util.Hashtable; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; +import org.xml.sax.InputSource; +import org.xml.sax.SAXException; +import org.xml.sax.XMLReader; +import org.xml.sax.helpers.XMLReaderFactory; + /** * Dictionary with entries. * @@ -61,7 +62,8 @@ public class Dictionary { } public static Dictionary unmarshal(Reader reader) { - LoggingTool logger = new LoggingTool(Dictionary.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Dictionary.class); DictionaryHandler handler = new DictionaryHandler(); XMLReader parser = null; try { src/main/org/openscience/cdk/dict/Dictionary.java @@ -28,13 +28,14 @@ */ package org.openscience.cdk.dict; -import org.openscience.cdk.tools.LoggingTool; - import java.io.InputStreamReader; import java.io.Reader; import java.util.Enumeration; import java.util.Hashtable; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; + /** * Database of dictionaries listing entries with compounds, fragments * and entities. @@ -50,7 +51,8 @@ public class DictionaryDatabase { public final static String DICTREFPROPERTYNAME = "org.openscience.cdk.dict"; - private LoggingTool logger; + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DictionaryDatabase.class); private String[] dictionaryNames = { "chemical", "elements", "descriptor-algorithms","reaction-processes" @@ -62,8 +64,6 @@ public class DictionaryDatabase { private Hashtable<String, Dictionary> dictionaries; public DictionaryDatabase() { - logger = new LoggingTool(this); - // read dictionaries distributed with CDK dictionaries = new Hashtable<String, Dictionary>(); for (int i=0; i<dictionaryNames.length; i++) { src/main/org/openscience/cdk/dict/DictionaryDatabase.java @@ -38,7 +38,8 @@ import nu.xom.Element; import nu.xom.Elements; import nu.xom.ParsingException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Dictionary with entries build from an OWL file. @@ -61,7 +62,8 @@ public class OWLFile extends Dictionary { } public static Dictionary unmarshal(Reader reader) { - LoggingTool logger = new LoggingTool(OWLFile.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLFile.class); Dictionary dict = new OWLFile(); try { Builder parser = new Builder(); @@ -105,7 +107,8 @@ public class OWLFile extends Dictionary { } public static Entry unmarshal(Element entry, String ownNS) { - LoggingTool logger = new LoggingTool(OWLFile.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLFile.class); // create a new entry by ID Attribute id = entry.getAttribute("ID", rdfNS); src/main/org/openscience/cdk/dict/OWLFile.java @@ -40,7 +40,8 @@ import nu.xom.Element; import nu.xom.Elements; import nu.xom.ParsingException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Dictionary with entries build from an OWL React. @@ -70,7 +71,8 @@ public class OWLReact extends Dictionary { * @return The Dictionary */ public static Dictionary unmarshal(Reader reader) { - LoggingTool logger = new LoggingTool(OWLReact.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLReact.class); Dictionary dict = new OWLReact(); try { Builder parser = new Builder(); @@ -114,7 +116,8 @@ public class OWLReact extends Dictionary { } public static EntryReact unmarshal(Element entry, String ownNS) { - LoggingTool logger = new LoggingTool(OWLReact.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OWLReact.class); // create a new entry by ID Attribute id = entry.getAttribute("ID", rdfNS); src/main/org/openscience/cdk/dict/OWLReact.java @@ -24,6 +24,14 @@ */ package org.openscience.cdk.fingerprint; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -36,11 +44,10 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IPseudoAtom; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import java.util.*; - /** * Generates a fingerprint for a given AtomContainer. Fingerprints are * one-dimensional bit arrays, where bits are set according to a the @@ -99,7 +106,8 @@ public class Fingerprinter implements IFingerprinter { static int debugCounter = 0; - private static LoggingTool logger = new LoggingTool(Fingerprinter.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Fingerprinter.class); private static final Map<String, String> queryReplace = new HashMap<String, String>() { src/main/org/openscience/cdk/fingerprint/Fingerprinter.java @@ -24,14 +24,15 @@ */ package org.openscience.cdk.fingerprint; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; -import org.openscience.cdk.tools.LoggingTool; - import java.util.ArrayList; import java.util.BitSet; import java.util.List; +import org.openscience.cdk.annotations.TestClass; +import org.openscience.cdk.annotations.TestMethod; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; + /** * Tool with helper methods for IFingerprint. * @@ -44,7 +45,8 @@ import java.util.List; @TestClass("org.openscience.cdk.fingerprint.FingerprinterToolTest") public class FingerprinterTool { - private final static LoggingTool logger = new LoggingTool(FingerprinterTool.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(FingerprinterTool.class); /** * Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1. If src/main/org/openscience/cdk/fingerprint/FingerprinterTool.java @@ -24,6 +24,15 @@ */ package org.openscience.cdk.fingerprint; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Iterator; +import java.util.List; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -35,16 +44,8 @@ import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.smiles.smarts.SMARTSQueryTool; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.ArrayList; -import java.util.BitSet; -import java.util.Iterator; -import java.util.List; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This fingerprinter generates 166 bit MACCS keys. @@ -70,8 +71,8 @@ import java.util.List; */ @TestClass("org.openscience.cdk.fingerprint.MACCSFingerprinterTest") public class MACCSFingerprinter implements IFingerprinter { - private static LoggingTool logger - = new LoggingTool(MACCSFingerprinter.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MACCSFingerprinter.class); private MaccsKey[] keys = null; @TestMethod("testFingerprint") src/main/org/openscience/cdk/fingerprint/MACCSFingerprinter.java @@ -29,7 +29,8 @@ import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IIsotope; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; /** @@ -50,7 +51,8 @@ public class IsotopePatternGenerator{ private IsotopeFactory isoFactory; private IsotopePattern abundance_Mass = null; - private LoggingTool logger = new LoggingTool(IsotopePatternGenerator.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IsotopePatternGenerator.class); /** Minimal abundance of the isotopes to be added in the combinatorial search.*/ private double minAbundance = .1; src/main/org/openscience/cdk/formula/IsotopePatternGenerator.java @@ -43,7 +43,8 @@ import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IIsotope; import org.openscience.cdk.interfaces.IMolecularFormula; import org.openscience.cdk.interfaces.IMolecularFormulaSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; import org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator; @@ -69,7 +70,8 @@ import org.openscience.cdk.tools.manipulator.MolecularFormulaRangeManipulator; @TestClass("org.openscience.cdk.formula.MassToFormulaToolTest") public class MassToFormulaTool { - private LoggingTool logger = new LoggingTool(MassToFormulaTool.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MassToFormulaTool.class); private IChemObjectBuilder builder; src/main/org/openscience/cdk/formula/MassToFormulaTool.java @@ -33,7 +33,8 @@ import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.formula.rules.IRule; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p> Validate a molecular formula given in IMolecularformula object. The @@ -49,7 +50,8 @@ import org.openscience.cdk.tools.LoggingTool; @TestClass("org.openscience.cdk.formula.MolecularFormulaCheckerTest") public class MolecularFormulaChecker { - private LoggingTool logger = new LoggingTool(MolecularFormulaChecker.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MolecularFormulaChecker.class); /** List of IRules to be applied in the validation.*/ @@ -109,8 +111,6 @@ public class MolecularFormulaChecker { */ @TestMethod("testIsValid_IMolecularFormula") public IMolecularFormula isValid(IMolecularFormula formula){ - logger = new LoggingTool(this); - logger.info("Generating the validity of the molecular formula"); if(formula.getIsotopeCount() == 0){ src/main/org/openscience/cdk/formula/MolecularFormulaChecker.java @@ -27,7 +27,8 @@ import java.io.IOException; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This class validate if the charge in the IMolecularFormula correspond with * a specific value. As default it is defined as neutral == 0.0. @@ -53,8 +54,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class ChargeRule implements IRule{ - - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ChargeRule.class); private double charge = 0.0; @@ -65,7 +66,6 @@ public class ChargeRule implements IRule{ * @throws ClassNotFoundException If an error occurs during tom typing */ public ChargeRule() { - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/formula/rules/ChargeRule.java @@ -32,7 +32,8 @@ import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IIsotope; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; /** @@ -62,7 +63,8 @@ import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; public class ElementRule implements IRule{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ElementRule.class); private MolecularFormulaRange mfRange; @@ -73,7 +75,6 @@ public class ElementRule implements IRule{ * @throws ClassNotFoundException If an error occurs during tom typing */ public ElementRule(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/formula/rules/ElementRule.java @@ -33,7 +33,8 @@ import org.openscience.cdk.formula.IsotopePatternGenerator; import org.openscience.cdk.formula.IsotopePatternManipulator; import org.openscience.cdk.formula.IsotopePatternSimilarity; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This class validate if the Isotope Pattern from a given IMolecularFormula * correspond with other to compare. @@ -60,7 +61,8 @@ import org.openscience.cdk.tools.LoggingTool; public class IsotopePatternRule implements IRule{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IsotopePatternRule.class); /** Accuracy on the mass measuring isotope pattern*/ private double toleranceMass = 0.001; @@ -81,8 +83,6 @@ public class IsotopePatternRule implements IRule{ isotopeGe = new IsotopePatternGenerator(0.01); is = new IsotopePatternSimilarity(); is.seTolerance(toleranceMass); - - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/formula/rules/IsotopePatternRule.java @@ -30,7 +30,8 @@ import java.util.Iterator; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IElement; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; /** * This class validate if the occurrence of the IElements in the IMolecularFormula, for @@ -74,7 +75,8 @@ public class MMElementRule implements IRule{ private HashMap<String, Integer> hashMap; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MMElementRule.class); /** A enumeration of the possible mass range * according the rules */ @@ -104,8 +106,6 @@ public class MMElementRule implements IRule{ * @throws ClassNotFoundException If an error occurs during tom typing */ public MMElementRule(){ - logger = new LoggingTool(this); - // initiate Hashmap default this.hashMap = getWisley_500(); } src/main/org/openscience/cdk/formula/rules/MMElementRule.java @@ -25,7 +25,8 @@ package org.openscience.cdk.formula.rules; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; /** * This class validate if the rule of nitrogen is kept. @@ -55,13 +56,13 @@ import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; public class NitrogenRule implements IRule{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(NitrogenRule.class); /** * Constructor for the NitrogenRule object. */ public NitrogenRule() { - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/formula/rules/NitrogenRule.java @@ -23,16 +23,21 @@ */ package org.openscience.cdk.formula.rules; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IIsotope; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; -import java.util.*; - /** * <p>Ring Double Bond Equivalents (RDBE) or * Double Bond Equivalents (DBE) are calculated from valence values of @@ -64,7 +69,8 @@ public class RDBERule implements IRule{ private static Map<String,int[]> oxidationStateTable = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RDBERule.class); private double min = -0.5; private double max = 30; @@ -72,7 +78,6 @@ public class RDBERule implements IRule{ * Constructor for the RDBE object. */ public RDBERule() { - logger = new LoggingTool(this); createTable(); } src/main/org/openscience/cdk/formula/rules/RDBERule.java @@ -27,7 +27,8 @@ import java.io.IOException; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IMolecularFormula; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; /** * This class validate if the mass from an IMolecularFormula is @@ -61,7 +62,8 @@ import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; public class ToleranceRangeRule implements IRule{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ToleranceRangeRule.class); private double mass = 0.0; @@ -74,7 +76,6 @@ public class ToleranceRangeRule implements IRule{ * @throws ClassNotFoundException If an error occurs during tom typing */ public ToleranceRangeRule(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/formula/rules/ToleranceRangeRule.java @@ -24,6 +24,19 @@ */ package org.openscience.cdk.geometry; +import java.awt.Dimension; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.TreeMap; + +import javax.vecmath.Point2d; +import javax.vecmath.Point3d; +import javax.vecmath.Vector2d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; @@ -31,15 +44,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; -import org.openscience.cdk.tools.LoggingTool; - -import javax.vecmath.Point2d; -import javax.vecmath.Point3d; -import javax.vecmath.Vector2d; -import javax.vecmath.Vector3d; -import java.awt.*; -import java.util.*; -import java.util.List; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * A set of static utility classes for geometric calculations and operations. @@ -58,7 +64,8 @@ import java.util.List; */ public class GeometryTools { - private static LoggingTool logger = new LoggingTool(GeometryTools.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(GeometryTools.class); /** * Adds an automatically calculated offset to the coordinates of all atoms src/main/org/openscience/cdk/geometry/GeometryTools.java @@ -31,7 +31,8 @@ import javax.vecmath.Point3d; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Calculator of radial distribution functions. The RDF has bins defined around @@ -64,7 +65,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class RDFCalculator { - private static LoggingTool logger = new LoggingTool(RDFCalculator.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RDFCalculator.class); private double startCutoff; private double cutoff; src/main/org/openscience/cdk/geometry/RDFCalculator.java @@ -29,7 +29,8 @@ import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import Jama.EigenvalueDecomposition; import Jama.Matrix; @@ -96,7 +97,8 @@ import Jama.Matrix; @TestClass("org.openscience.cdk.geometry.alignment.KabschAlignmentTest") public class KabschAlignment { - private LoggingTool logger = new LoggingTool(KabschAlignment.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(KabschAlignment.class); private double[][] U; private double rmsd = -1.0; src/main/org/openscience/cdk/geometry/alignment/KabschAlignment.java @@ -20,17 +20,19 @@ package org.openscience.cdk.geometry.surface; +import java.util.ArrayList; +import java.util.Iterator; + +import javax.vecmath.Point3d; + import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.PeriodicTable; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import java.util.ArrayList; -import java.util.Iterator; - /** * A class representing the solvent acessible surface area surface of a molecule. * @@ -55,7 +57,8 @@ import java.util.Iterator; * @cdk.bug 1846421 */ public class NumericalSurface { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(NumericalSurface.class); double solvent_radius = 1.4; int tesslevel = 4; IAtom[] atoms; @@ -73,7 +76,6 @@ public class NumericalSurface { */ public NumericalSurface(IAtomContainer atomContainer) { this.atoms = AtomContainerManipulator.getAtomArray(atomContainer); - logger = new LoggingTool(this); } /** * Constructor to initialize the surface calculation with user specified values. @@ -91,7 +93,6 @@ public class NumericalSurface { this.solvent_radius = solvent_radius; this.atoms = AtomContainerManipulator.getAtomArray(atomContainer); this.tesslevel = tesslevel; - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/geometry/surface/NumericalSurface.java @@ -32,7 +32,8 @@ package org.openscience.cdk.graph; import java.util.Iterator; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * The permutation code here is based on a pseudo code example @@ -52,7 +53,8 @@ public abstract class AtomContainerPermutor implements Iterator int[] bookkeeping; Object[] objects; - private static LoggingTool logger = new LoggingTool(AtomContainerPermutor.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomContainerPermutor.class); AtomContainer atomContainer; src/main/org/openscience/cdk/graph/AtomContainerPermutor.java @@ -31,7 +31,8 @@ import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.graph.matrix.ConnectionMatrix; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * An algorithm for topological symmetry. @@ -53,7 +54,8 @@ public class EquivalentClassPartitioner private int layerNumber; private int nodeNumber; private static double LOST=0.000000000001; - private org.openscience.cdk.tools.LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(EquivalentClassPartitioner.class); /** @@ -77,7 +79,6 @@ public class EquivalentClassPartitioner nodeMatrix=new double[nodeNumber][layerNumber+1]; bondMatrix=new double[nodeNumber][layerNumber]; weight=new double[nodeNumber+1]; - logger = new LoggingTool(this); } src/main/org/openscience/cdk/graph/invariant/EquivalentClassPartitioner.java @@ -24,6 +24,8 @@ */ package org.openscience.cdk.graph.invariant; +import java.util.Iterator; + import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.NoSuchAtomException; import org.openscience.cdk.graph.PathTools; @@ -32,9 +34,8 @@ import org.openscience.cdk.graph.invariant.exception.IndexOutOfBoundsException; import org.openscience.cdk.graph.matrix.ConnectionMatrix; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.tools.LoggingTool; - -import java.util.Iterator; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Collection of methods for the calculation of topological indices of a @@ -44,7 +45,8 @@ import java.util.Iterator; */ public class HuLuIndexTool { - private final static LoggingTool logger = new LoggingTool(HuLuIndexTool.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HuLuIndexTool.class); /** * Calculates the extended adjacency matrix index. src/main/org/openscience/cdk/graph/invariant/HuLuIndexTool.java @@ -50,7 +50,8 @@ import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.tools.DataFeatures; import org.openscience.cdk.tools.IDCreator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Converts a Molecule into CDK source code that would build the same @@ -75,7 +76,8 @@ import org.openscience.cdk.tools.LoggingTool; public class CDKSourceCodeWriter extends DefaultChemObjectWriter { private BufferedWriter writer; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CDKSourceCodeWriter.class); private BooleanIOSetting write2DCoordinates; private BooleanIOSetting write3DCoordinates; @@ -86,7 +88,6 @@ public class CDKSourceCodeWriter extends DefaultChemObjectWriter { * @param out The Writer to write to */ public CDKSourceCodeWriter(Writer out) { - logger = new LoggingTool(this); initIOSettings(); try { setWriter(out); src/main/org/openscience/cdk/io/CDKSourceCodeWriter.java @@ -39,19 +39,20 @@ import java.util.StringTokenizer; import javax.vecmath.Point3d; import javax.vecmath.Vector3d; +import org.openscience.cdk.annotations.TestClass; +import org.openscience.cdk.annotations.TestMethod; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.geometry.CrystalGeometryTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.ICrystal; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.geometry.CrystalGeometryTools; import org.openscience.cdk.io.formats.CIFFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This is not a reader for the CIF and mmCIF crystallographic formats. @@ -76,7 +77,8 @@ import org.openscience.cdk.tools.LoggingTool; public class CIFReader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CIFReader.class); private ICrystal crystal = null; // cell parameters @@ -94,7 +96,6 @@ public class CIFReader extends DefaultChemObjectReader { */ public CIFReader(Reader input) { this.input = new BufferedReader(input); - this.logger = new LoggingTool(this); } public CIFReader(InputStream input) { src/main/org/openscience/cdk/io/CIFReader.java @@ -43,7 +43,8 @@ import org.openscience.cdk.io.cml.CMLResolver; import org.openscience.cdk.io.cml.ICMLModule; import org.openscience.cdk.io.formats.CMLFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.SAXParseException; @@ -70,7 +71,8 @@ public class CMLReader extends DefaultChemObjectReader { private Map<String,ICMLModule> userConventions = new HashMap<String,ICMLModule>(); - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CMLReader.class); /** * Reads CML from an java.io.InputStream, for example the FileInputStream. @@ -121,8 +123,6 @@ public class CMLReader extends DefaultChemObjectReader { } private void init() { - logger = new LoggingTool(this); - url = ""; // make sure it is not null boolean success = false; src/main/org/openscience/cdk/io/CMLReader.java @@ -65,7 +65,8 @@ import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.io.setting.StringIOSetting; import org.openscience.cdk.libio.cml.Convertor; import org.openscience.cdk.libio.cml.ICMLCustomizer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Serializes a {@link IMoleculeSet} or a {@link IMolecule} object to CML 2 code. @@ -122,7 +123,8 @@ public class CMLWriter extends DefaultChemObjectWriter { private BooleanIOSetting indent; private BooleanIOSetting xmlDeclaration; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CMLWriter.class); private static List<ICMLCustomizer> customizers = null; @@ -140,14 +142,12 @@ public class CMLWriter extends DefaultChemObjectWriter { writer.write(anInt); } }; - logger = new LoggingTool(this); initIOSettings(); } public CMLWriter(OutputStream output) { this.output = output; writer = null; - logger = new LoggingTool(this); initIOSettings(); } src/main/org/openscience/cdk/io/CMLWriter.java @@ -23,19 +23,32 @@ */ package org.openscience.cdk.io; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.Reader; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.Symbols; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IChemFile; +import org.openscience.cdk.interfaces.IChemModel; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.interfaces.IChemSequence; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.CTXFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; -import java.io.*; - /** * Reader that extracts information from the IDENT, NAME, ATOMS and BONDS * blocks in CTX files. @@ -47,12 +60,12 @@ import java.io.*; public class CTXReader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CTXReader.class); private IChemFile file; public CTXReader() { - logger = new LoggingTool(this); file = null; } src/main/org/openscience/cdk/io/CTXReader.java @@ -20,19 +20,30 @@ */ package org.openscience.cdk.io; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.Reader; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.CrystalGeometryTools; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IChemFile; +import org.openscience.cdk.interfaces.IChemModel; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.interfaces.IChemSequence; +import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.io.formats.CrystClustFormat; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.math.FortranFormat; -import org.openscience.cdk.tools.LoggingTool; - -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.io.*; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module extra @@ -42,10 +53,10 @@ import java.io.*; public class CrystClustReader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CrystClustReader.class); public CrystClustReader() { - logger = new LoggingTool(this); } public CrystClustReader(Reader input) { src/main/org/openscience/cdk/io/CrystClustReader.java @@ -20,6 +20,15 @@ */ package org.openscience.cdk.io; +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.OutputStream; +import java.io.OutputStreamWriter; +import java.io.StringWriter; +import java.io.Writer; + +import javax.vecmath.Vector3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; @@ -30,11 +39,8 @@ import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.io.formats.CrystClustFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; - -import javax.vecmath.Vector3d; -import java.io.*; -//import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Rather stupid file format used for storing crystal information. @@ -49,7 +55,8 @@ import java.io.*; public class CrystClustWriter extends DefaultChemObjectWriter { private BufferedWriter writer; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CrystClustWriter.class); /** * Constructs a new CrystClustWriter class. Output will be stored in the Writer @@ -58,7 +65,6 @@ public class CrystClustWriter extends DefaultChemObjectWriter { * @param out Writer to redirect the output to. */ public CrystClustWriter(Writer out) { - logger = new LoggingTool(this); try { if (out instanceof BufferedWriter) { writer = (BufferedWriter)out; src/main/org/openscience/cdk/io/CrystClustWriter.java @@ -43,7 +43,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.Gaussian03Format; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * A reader for Gaussian03 output. @@ -73,11 +74,11 @@ import org.openscience.cdk.tools.LoggingTool; public class Gaussian03Reader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Gaussian03Reader.class);; public Gaussian03Reader(Reader reader) { input = new BufferedReader(reader); - logger = new LoggingTool(this); } public Gaussian03Reader(InputStream input) { src/main/org/openscience/cdk/io/Gaussian03Reader.java @@ -51,7 +51,8 @@ import org.openscience.cdk.io.formats.Gaussian98Format; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; /** @@ -78,7 +79,8 @@ import org.openscience.cdk.tools.manipulator.ChemModelManipulator; public class Gaussian98Reader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Gaussian98Reader.class);; private int atomCount = 0; private String lastRoute = ""; @@ -131,7 +133,6 @@ public class Gaussian98Reader extends DefaultChemObjectReader { * @param input source of Gaussian98 data */ public Gaussian98Reader(Reader input) { - logger = new LoggingTool(this); if (input instanceof BufferedReader) { this.input = (BufferedReader) input; } else { src/main/org/openscience/cdk/io/Gaussian98Reader.java @@ -47,7 +47,8 @@ import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.GhemicalMMFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Reads Ghemical (<a href="http://www.uku.fi/~thassine/ghemical/"> @@ -62,11 +63,11 @@ import org.openscience.cdk.tools.LoggingTool; @TestClass("org.openscience.cdk.io.GhemicalMMReaderTest") public class GhemicalMMReader extends DefaultChemObjectReader { - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(GhemicalMMReader.class); private BufferedReader input = null; public GhemicalMMReader(Reader input) { - this.logger = new LoggingTool(this); this.input = new BufferedReader(input); } src/main/org/openscience/cdk/io/GhemicalMMReader.java @@ -44,7 +44,7 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.HINFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Writer that outputs in the HIN format. @@ -65,7 +65,6 @@ public class HINWriter extends DefaultChemObjectWriter { * @param out the stream to write the HIN file to. */ public HINWriter(Writer out) { - LoggingTool logger = new LoggingTool(this); try { if (out instanceof BufferedWriter) { writer = (BufferedWriter) out; @@ -73,7 +72,8 @@ public class HINWriter extends DefaultChemObjectWriter { writer = new BufferedWriter(out); } } catch (Exception exc) { - logger.debug(exc.toString()); + LoggingToolFactory.createLoggingTool(HINWriter.class) + .debug(exc.toString()); } } src/main/org/openscience/cdk/io/HINWriter.java @@ -41,7 +41,8 @@ import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.io.formats.INChIFormat; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.inchi.INChIHandler; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.XMLReader; @@ -72,7 +73,8 @@ public class INChIReader extends DefaultChemObjectReader { private XMLReader parser; private InputStream input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(INChIReader.class); /** * Construct a INChI reader from a InputStream object. @@ -111,7 +113,6 @@ public class INChIReader extends DefaultChemObjectReader { * Initializes this reader. */ private void init() { - logger = new LoggingTool(this); boolean success = false; // If JAXP is prefered (comes with Sun JVM 1.4.0 and higher) if (!success) { src/main/org/openscience/cdk/io/INChIReader.java @@ -51,7 +51,8 @@ import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLRXNFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Reads a molecule from an MDL RXN file {@cdk.cite DAL92}. @@ -68,7 +69,8 @@ import org.openscience.cdk.tools.LoggingTool; public class MDLRXNReader extends DefaultChemObjectReader { BufferedReader input = null; - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLReader.class); /** * Contructs a new MDLReader that can read Molecule from a given Reader. @@ -79,7 +81,6 @@ public class MDLRXNReader extends DefaultChemObjectReader { this(in, Mode.RELAXED); } public MDLRXNReader(Reader in, Mode mode) { - logger = new LoggingTool(this); if (in instanceof BufferedReader) { input = (BufferedReader)in; } else { src/main/org/openscience/cdk/io/MDLRXNReader.java @@ -50,7 +50,8 @@ import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLRXNFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Reads a molecule from an MDL RXN file {@cdk.cite DAL92}. @@ -69,7 +70,8 @@ import org.openscience.cdk.tools.LoggingTool; public class MDLRXNV2000Reader extends DefaultChemObjectReader { BufferedReader input = null; - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLRXNV2000Reader.class); /** * Contructs a new MDLReader that can read Molecule from a given Reader. @@ -80,7 +82,6 @@ public class MDLRXNV2000Reader extends DefaultChemObjectReader { this(in, Mode.RELAXED); } public MDLRXNV2000Reader(Reader in, Mode mode) { - logger = new LoggingTool(this); if (in instanceof BufferedReader) { input = (BufferedReader)in; } else { src/main/org/openscience/cdk/io/MDLRXNV2000Reader.java @@ -40,7 +40,8 @@ import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLRXNV3000Format; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Class that implements the new MDL mol format introduced in August 2002. @@ -61,13 +62,13 @@ import org.openscience.cdk.tools.LoggingTool; public class MDLRXNV3000Reader extends DefaultChemObjectReader { BufferedReader input = null; - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLRXNV3000Reader.class); public MDLRXNV3000Reader(Reader in) { this(in, Mode.RELAXED); } public MDLRXNV3000Reader(Reader in, Mode mode) { - logger = new LoggingTool(this); if (in instanceof BufferedReader) { input = (BufferedReader)in; } else { src/main/org/openscience/cdk/io/MDLRXNV3000Reader.java @@ -51,7 +51,8 @@ import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; @@ -76,7 +77,8 @@ import org.openscience.cdk.tools.LoggingTool; public class MDLRXNWriter extends DefaultChemObjectWriter { private BufferedWriter writer; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLRXNWriter.class); private int reactionNumber; public Map rdFields=null; @@ -88,7 +90,6 @@ public class MDLRXNWriter extends DefaultChemObjectWriter { * @param out The Writer to write to */ public MDLRXNWriter(Writer out){ - logger = new LoggingTool(this); try { if (out instanceof BufferedWriter) { writer = (BufferedWriter)out; src/main/org/openscience/cdk/io/MDLRXNWriter.java @@ -54,7 +54,8 @@ import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Reads a molecule from the original MDL MOL or SDF file {@cdk.cite DAL92}. An SD files @@ -85,7 +86,8 @@ import org.openscience.cdk.tools.LoggingTool; public class MDLReader extends DefaultChemObjectReader { BufferedReader input = null; - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLReader.class); private BooleanIOSetting forceReadAs3DCoords; @@ -117,8 +119,7 @@ public class MDLReader extends DefaultChemObjectReader { } public MDLReader(Reader in, Mode mode) { - super.mode = mode; - logger = new LoggingTool(this); + super.mode = mode; input = new BufferedReader(in); initIOSettings(); } src/main/org/openscience/cdk/io/MDLReader.java @@ -56,7 +56,8 @@ import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLV2000Format; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -95,7 +96,8 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; public class MDLV2000Reader extends DefaultChemObjectReader { BufferedReader input = null; - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLV2000Reader.class); private BooleanIOSetting forceReadAs3DCoords; private BooleanIOSetting interpretHydrogenIsotopes; @@ -125,7 +127,6 @@ public class MDLV2000Reader extends DefaultChemObjectReader { this(in, Mode.RELAXED); } public MDLV2000Reader(Reader in, Mode mode) { - logger = new LoggingTool(this); input = new BufferedReader(in); initIOSettings(); super.mode = mode; src/main/org/openscience/cdk/io/MDLV2000Reader.java @@ -51,7 +51,8 @@ import org.openscience.cdk.interfaces.IPseudoAtom; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLV3000Format; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; /** @@ -71,7 +72,8 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; public class MDLV3000Reader extends DefaultChemObjectReader { BufferedReader input = null; - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLV3000Reader.class); private Pattern keyValueTuple; private Pattern keyValueTuple2; @@ -82,7 +84,6 @@ public class MDLV3000Reader extends DefaultChemObjectReader { this(in, Mode.RELAXED); } public MDLV3000Reader(Reader in, Mode mode) { - logger = new LoggingTool(this); input = new BufferedReader(in); initIOSettings(); super.mode = mode; src/main/org/openscience/cdk/io/MDLV3000Reader.java @@ -56,7 +56,8 @@ import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -77,7 +78,8 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @TestClass("org.openscience.cdk.io.MDLWriterTest") public class MDLWriter extends DefaultChemObjectWriter { - private final static LoggingTool logger = new LoggingTool(MDLWriter.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLWriter.class); private BooleanIOSetting forceWriteAs2DCoords; src/main/org/openscience/cdk/io/MDLWriter.java @@ -51,7 +51,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.Mol2Format; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; /** @@ -70,7 +71,8 @@ import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; public class Mol2Reader extends DefaultChemObjectReader { BufferedReader input = null; - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Mol2Reader.class); /** * Contructs a new MDLReader that can read Molecule from a given Reader. @@ -78,7 +80,6 @@ public class Mol2Reader extends DefaultChemObjectReader { * @param in The Reader to read from */ public Mol2Reader(Reader in) { - logger = new LoggingTool(this); input = new BufferedReader(in); } src/main/org/openscience/cdk/io/Mol2Reader.java @@ -26,7 +26,6 @@ import java.io.OutputStream; import java.io.OutputStreamWriter; import java.io.StringWriter; import java.io.Writer; -import java.util.Iterator; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; @@ -40,7 +39,8 @@ import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.Mol2Format; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * An output Writer that writes molecular data into the @@ -56,7 +56,8 @@ import org.openscience.cdk.tools.LoggingTool; public class Mol2Writer extends DefaultChemObjectWriter { private BufferedWriter writer; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Mol2Writer.class); private SybylAtomTypeMatcher matcher; public Mol2Writer() { @@ -68,7 +69,6 @@ public class Mol2Writer extends DefaultChemObjectWriter { * @param out the stream to write the Mol2 file to. */ public Mol2Writer(Writer out) { - logger = new LoggingTool(this); try { if (out instanceof BufferedWriter) { writer = (BufferedWriter)out; src/main/org/openscience/cdk/io/Mol2Writer.java @@ -47,7 +47,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.PubChemASNFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Reads an object from ASN formated input for PubChem Compound entries. The following @@ -63,7 +64,8 @@ import org.openscience.cdk.tools.LoggingTool; public class PCCompoundASNReader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PCCompoundASNReader.class); IMolecule molecule = null; Map atomIDs = null; @@ -75,7 +77,6 @@ public class PCCompoundASNReader extends DefaultChemObjectReader { */ public PCCompoundASNReader(Reader input) { this.input = new BufferedReader(input); - logger = new LoggingTool(this); } public PCCompoundASNReader(InputStream input) { src/main/org/openscience/cdk/io/PCCompoundASNReader.java @@ -64,7 +64,8 @@ import org.openscience.cdk.protein.data.PDBMonomer; import org.openscience.cdk.protein.data.PDBPolymer; import org.openscience.cdk.protein.data.PDBStrand; import org.openscience.cdk.protein.data.PDBStructure; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; /** @@ -88,7 +89,8 @@ import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; @TestClass("org.openscience.cdk.io.PDBReaderTest") public class PDBReader extends DefaultChemObjectReader { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PDBReader.class); private BufferedReader _oInput; // The internal used BufferedReader private BooleanIOSetting useRebondTool; private BooleanIOSetting readConnect; @@ -125,7 +127,6 @@ public class PDBReader extends DefaultChemObjectReader { * */ public PDBReader(Reader oIn) { - logger = new LoggingTool(this.getClass()); _oInput = new BufferedReader(oIn); initIOSettings(); pdbFactory = null; src/main/org/openscience/cdk/io/PDBReader.java @@ -56,7 +56,8 @@ import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.PMPFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Reads an frames from a PMP formated input. @@ -78,7 +79,8 @@ public class PMPReader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PMPReader.class); /* Keep a copy of the PMP model */ private IAtomContainer modelStructure; @@ -108,7 +110,6 @@ public class PMPReader extends DefaultChemObjectReader { */ public PMPReader(Reader input) { this.input = new BufferedReader(input); - logger = new LoggingTool(this); this.lineNumber = 0; /* compile patterns */ src/main/org/openscience/cdk/io/PMPReader.java @@ -31,7 +31,8 @@ import java.util.zip.GZIPInputStream; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.IChemFormatMatcher; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * A factory for creating ChemObjectReaders. The type of reader @@ -52,7 +53,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class ReaderFactory { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ReaderFactory.class); private FormatFactory formatFactory = null; private int headerLength = 8192; @@ -71,7 +73,6 @@ public class ReaderFactory { * @param headerLength length of the header in number of chars */ public ReaderFactory(int headerLength) { - logger = new LoggingTool(this); formatFactory = new FormatFactory(headerLength); this.headerLength = headerLength; } src/main/org/openscience/cdk/io/ReaderFactory.java @@ -49,7 +49,8 @@ import org.openscience.cdk.io.formats.SDFFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.smiles.InvPair; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -63,7 +64,8 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @TestClass("org.openscience.cdk.io.SDFWriterTest") public class SDFWriter extends DefaultChemObjectWriter { - private final static LoggingTool logger = new LoggingTool(SDFWriter.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SDFWriter.class); private BufferedWriter writer; private BooleanIOSetting writerProperties; src/main/org/openscience/cdk/io/SDFWriter.java @@ -48,7 +48,8 @@ import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This Reader reads files which has one SMILES string on each @@ -73,7 +74,8 @@ public class SMILESReader extends DefaultChemObjectReader { private BufferedReader input = null; private SmilesParser sp = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SMILESReader.class); /* * construct a new reader from a Reader type object @@ -81,7 +83,6 @@ public class SMILESReader extends DefaultChemObjectReader { * @param input reader from which input is read */ public SMILESReader(Reader input) { - logger = new LoggingTool(this); this.input = new BufferedReader(input); sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); } src/main/org/openscience/cdk/io/SMILESReader.java @@ -45,7 +45,8 @@ import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; import org.openscience.cdk.smiles.SmilesGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Writes the SMILES strings to a plain text file. @@ -58,7 +59,8 @@ import org.openscience.cdk.tools.LoggingTool; @TestClass("org.openscience.cdk.io.SMILESWriterTest") public class SMILESWriter extends DefaultChemObjectWriter { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SMILESWriter.class); private BufferedWriter writer; /** @@ -67,7 +69,6 @@ public class SMILESWriter extends DefaultChemObjectWriter { * @param out The Writer to write to */ public SMILESWriter(Writer out) { - logger = new LoggingTool(this); try { if (out instanceof BufferedWriter) { writer = (BufferedWriter)out; src/main/org/openscience/cdk/io/SMILESWriter.java @@ -49,7 +49,8 @@ import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.ShelXFormat; import org.openscience.cdk.math.FortranFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** @@ -73,7 +74,8 @@ import org.openscience.cdk.tools.LoggingTool; public class ShelXReader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ShelXReader.class); /** * Create an ShelX file reader. @@ -82,7 +84,6 @@ public class ShelXReader extends DefaultChemObjectReader { */ public ShelXReader(Reader input) { this.input = new BufferedReader(input); - this.logger = new LoggingTool(this); } public ShelXReader(InputStream input) { src/main/org/openscience/cdk/io/ShelXReader.java @@ -64,7 +64,6 @@ import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; public class ShelXWriter extends DefaultChemObjectWriter { private BufferedWriter writer; - //private LoggingTool logger; /** * Constructs a new ShelXWriter class. Output will be stored in the Writer @@ -73,7 +72,6 @@ public class ShelXWriter extends DefaultChemObjectWriter { * @param out Writer to redirect the output to. */ public ShelXWriter(Writer out) { - //logger = new LoggingTool(this); try { if (out instanceof BufferedWriter) { writer = (BufferedWriter)out; src/main/org/openscience/cdk/io/ShelXWriter.java @@ -49,7 +49,8 @@ import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.VASPFormat; import org.openscience.cdk.math.FortranFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Read output files generated with the VASP software. @@ -62,7 +63,8 @@ import org.openscience.cdk.tools.LoggingTool; @TestClass("org.openscience.cdk.io.VSPReaderTest") public class VASPReader extends DefaultChemObjectReader { - private LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(VASPReader.class); // This variable is used to parse the input file protected StringTokenizer st = new StringTokenizer("", "");; @@ -88,7 +90,6 @@ public class VASPReader extends DefaultChemObjectReader { * @param input a <code>Reader</code> value */ public VASPReader(Reader input) { - logger = new LoggingTool(this); if (input instanceof BufferedReader) { this.inputBuffer = (BufferedReader)input; } else { src/main/org/openscience/cdk/io/VASPReader.java @@ -39,7 +39,8 @@ import java.util.Map; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Helper tool to create IChemObjectWriters. @@ -52,7 +53,8 @@ public class WriterFactory { private final static String IO_FORMATS_LIST = "io-formats.set"; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(WriterFactory.class); private static List<IChemFormat> formats = null; @@ -62,7 +64,6 @@ public class WriterFactory { * Constructs a ChemObjectIOInstantionTests. */ public WriterFactory() { - logger = new LoggingTool(this); registeredReaders = new HashMap<String, Class<IChemObjectWriter>>(); } src/main/org/openscience/cdk/io/WriterFactory.java @@ -51,7 +51,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.XYZFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Reads an object from XYZ formated input. @@ -67,7 +68,8 @@ import org.openscience.cdk.tools.LoggingTool; public class XYZReader extends DefaultChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(XYZReader.class); /** * Construct a new reader from a Reader type object. @@ -76,7 +78,6 @@ public class XYZReader extends DefaultChemObjectReader { */ public XYZReader(Reader input) { this.input = new BufferedReader(input); - logger = new LoggingTool(this); } public XYZReader(InputStream input) { src/main/org/openscience/cdk/io/XYZReader.java @@ -42,7 +42,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.XYZFormat; import org.openscience.cdk.tools.FormatStringBuffer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module io @@ -56,7 +57,8 @@ import org.openscience.cdk.tools.LoggingTool; public class XYZWriter extends DefaultChemObjectWriter { private BufferedWriter writer; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(XYZWriter.class); private FormatStringBuffer fsb; /** @@ -65,7 +67,6 @@ public class XYZWriter extends DefaultChemObjectWriter { * @param out the stream to write the XYZ file to. */ public XYZWriter(Writer out) { - logger = new LoggingTool(this); fsb = new FormatStringBuffer("%-8.6f"); try { if (out instanceof BufferedWriter) { src/main/org/openscience/cdk/io/XYZWriter.java @@ -54,7 +54,8 @@ import org.openscience.cdk.interfaces.IPseudoAtom; import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.interfaces.IStrand; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.BondManipulator; import org.xml.sax.Attributes; @@ -72,7 +73,7 @@ import org.xml.sax.Attributes; **/ public class CMLCoreModule implements ICMLModule { - protected org.openscience.cdk.tools.LoggingTool logger; + protected ILoggingTool logger; protected final String SYSTEMID = "CML-1999-05-15"; // protected IChemicalDocumentObject cdo; @@ -148,12 +149,12 @@ public class CMLCoreModule implements ICMLModule { boolean cartesianAxesSet = false; public CMLCoreModule(IChemFile chemFile) { - logger = new LoggingTool(this); + logger = LoggingToolFactory.createLoggingTool(CMLCoreModule.class); this.currentChemFile = chemFile; } public CMLCoreModule(ICMLModule conv) { - logger = new LoggingTool(this); + logger = LoggingToolFactory.createLoggingTool(CMLCoreModule.class); inherit(conv); } src/main/org/openscience/cdk/io/cml/CMLCoreModule.java @@ -25,7 +25,8 @@ */ package org.openscience.cdk.io.cml; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.ErrorHandler; import org.xml.sax.SAXException; import org.xml.sax.SAXParseException; @@ -41,7 +42,8 @@ import org.xml.sax.SAXParseException; **/ public class CMLErrorHandler implements ErrorHandler { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CMLErrorHandler.class); public boolean reportErrors = true; public boolean abortOnErrors = false; @@ -51,7 +53,6 @@ public class CMLErrorHandler implements ErrorHandler { * class to output errors and warnings to. **/ public CMLErrorHandler() { - logger = new LoggingTool(this); logger.info("instantiated"); } src/main/org/openscience/cdk/io/cml/CMLErrorHandler.java @@ -25,7 +25,8 @@ import java.util.Hashtable; import java.util.Map; import org.openscience.cdk.interfaces.IChemFile; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.Attributes; import org.xml.sax.helpers.DefaultHandler; @@ -45,7 +46,8 @@ import org.xml.sax.helpers.DefaultHandler; public class CMLHandler extends DefaultHandler { private ICMLModule conv; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CMLHandler.class); private boolean debug = true; private Map<String,ICMLModule> userConventions; @@ -59,7 +61,6 @@ public class CMLHandler extends DefaultHandler { * @param chemFile The document in which data is stored **/ public CMLHandler(IChemFile chemFile) { - logger = new LoggingTool(this); conv = new CMLCoreModule(chemFile); userConventions = new Hashtable<String,ICMLModule>(); xpath = new CMLStack(); src/main/org/openscience/cdk/io/cml/CMLHandler.java @@ -25,7 +25,8 @@ import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.EntityResolver; import org.xml.sax.InputSource; @@ -41,10 +42,10 @@ import org.xml.sax.InputSource; **/ public class CMLResolver implements EntityResolver { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CMLResolver.class); public CMLResolver() { - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/io/cml/CMLResolver.java @@ -26,7 +26,8 @@ package org.openscience.cdk.io.cml; import org.openscience.cdk.interfaces.IChemFile; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.Attributes; /** @@ -42,17 +43,16 @@ public class JMOLANIMATIONConvention extends CMLCoreModule { private int current; private String frame_energy; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(JMOLANIMATIONConvention.class); public JMOLANIMATIONConvention(IChemFile chemFile) { super(chemFile); - logger = new LoggingTool(this); current = UNKNOWN; } public JMOLANIMATIONConvention(ICMLModule conv) { super(conv); - logger = new LoggingTool(this); } public void startElement(CMLStack xpath, String uri, String local, String raw, Attributes atts) { src/main/org/openscience/cdk/io/cml/JMOLANIMATIONConvention.java @@ -29,7 +29,8 @@ import java.util.regex.Pattern; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Tool to help process INChI 1.12beta content. @@ -39,10 +40,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class INChIContentProcessorTool { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(INChIContentProcessorTool.class);; public INChIContentProcessorTool() { - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/io/inchi/INChIContentProcessorTool.java @@ -28,7 +28,8 @@ import org.openscience.cdk.ChemModel; import org.openscience.cdk.ChemSequence; import org.openscience.cdk.Molecule; import org.openscience.cdk.MoleculeSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.Attributes; import org.xml.sax.helpers.DefaultHandler; @@ -52,7 +53,8 @@ import org.xml.sax.helpers.DefaultHandler; */ public class INChIHandler extends DefaultHandler { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(INChIHandler.class); private INChIContentProcessorTool inchiTool; private ChemFile chemFile; @@ -68,7 +70,6 @@ public class INChIHandler extends DefaultHandler { * Constructor for the IChIHandler. **/ public INChIHandler() { - logger = new LoggingTool(this); inchiTool = new INChIContentProcessorTool(); } src/main/org/openscience/cdk/io/inchi/INChIHandler.java @@ -48,7 +48,8 @@ import org.openscience.cdk.io.formats.MDLV3000Format; import org.openscience.cdk.io.listener.IChemObjectIOListener; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Iterating MDL SDF reader. It allows to iterate over all molecules @@ -84,7 +85,8 @@ import org.openscience.cdk.tools.LoggingTool; public class IteratingMDLReader extends DefaultIteratingChemObjectReader implements IChemObjectIOListener { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingMDLReader.class); private String currentLine; private IChemFormat currentFormat; private final ReaderFactory factory = new ReaderFactory(); @@ -103,7 +105,6 @@ public class IteratingMDLReader extends DefaultIteratingChemObjectReader impleme * @param builder The builder */ public IteratingMDLReader(Reader in, IChemObjectBuilder builder) { - logger = new LoggingTool(this); this.builder = builder; setReader(in); initIOSettings(); src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java @@ -41,7 +41,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.PCCompoundASNReader; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.PubChemSubstancesASNFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -61,7 +62,8 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; public class IteratingPCCompoundASNReader extends DefaultIteratingChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingPCCompoundASNReader.class); private IChemObjectBuilder builder; private boolean nextAvailableIsKnown; @@ -77,7 +79,6 @@ public class IteratingPCCompoundASNReader extends DefaultIteratingChemObjectRead * @param in The Reader to read from */ public IteratingPCCompoundASNReader(Reader in, IChemObjectBuilder builder) { - logger = new LoggingTool(this); this.builder = builder; setReader(in); } src/main/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReader.java @@ -27,6 +27,13 @@ */ package org.openscience.cdk.io.iterator; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.Reader; +import java.util.NoSuchElementException; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.annotations.TestClass; @@ -37,10 +44,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.*; -import java.util.NoSuchElementException; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Iterating SMILES file reader. It allows to iterate over all molecules @@ -64,7 +69,8 @@ import java.util.NoSuchElementException; public class IteratingSMILESReader extends DefaultIteratingChemObjectReader { private BufferedReader input; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingSMILESReader.class); private String currentLine; private SmilesParser sp = null; @@ -82,7 +88,6 @@ public class IteratingSMILESReader extends DefaultIteratingChemObjectReader { */ @TestMethod("testSMILESFileWithNames") public IteratingSMILESReader(Reader in, IChemObjectBuilder builder) { - logger = new LoggingTool(this); sp = new SmilesParser(builder); setReader(in); } src/main/org/openscience/cdk/io/iterator/IteratingSMILESReader.java @@ -33,7 +33,8 @@ import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObjectBuilder; import org.openscience.cdk.interfaces.IPseudoAtom; import org.openscience.cdk.io.cml.CMLHandler; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * CDO object needed as interface with the JCFL library for reading CML @@ -62,7 +63,8 @@ public class EventCMLHandler extends CMLHandler { private IBond.Stereo bond_stereo; private String bond_id; - protected LoggingTool logger; + protected static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(EventCMLHandler.class); private DefaultEventChemObjectReader eventReader; @@ -73,7 +75,6 @@ public class EventCMLHandler extends CMLHandler { public EventCMLHandler(DefaultEventChemObjectReader eventReader, IChemObjectBuilder builder) { super(builder.newChemFile()); - logger = new LoggingTool(this); this.eventReader = eventReader; this.builder = builder; clearData(); src/main/org/openscience/cdk/io/iterator/event/EventCMLHandler.java @@ -40,7 +40,8 @@ import org.openscience.cdk.io.cml.CMLResolver; import org.openscience.cdk.io.formats.CMLFormat; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.listener.IReaderListener; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.SAXParseException; @@ -66,7 +67,8 @@ public class EventCMLReader extends DefaultEventChemObjectReader { private IChemObjectBuilder builder; private EventCMLHandler cdo; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(EventCMLReader.class);; /** * Define this CMLReader to take the input from a java.io.Reader @@ -101,8 +103,6 @@ public class EventCMLReader extends DefaultEventChemObjectReader { } private void init() { - logger = new LoggingTool(this); - boolean success = false; // If JAXP is prefered (comes with Sun JVM 1.4.0 and higher) if (!success) { src/main/org/openscience/cdk/io/iterator/event/EventCMLReader.java @@ -43,7 +43,8 @@ import org.openscience.cdk.io.ReaderEvent; import org.openscience.cdk.io.listener.IChemObjectIOListener; import org.openscience.cdk.io.listener.IReaderListener; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Random access to text files of compounds. @@ -59,7 +60,8 @@ public abstract class RandomAccessReader extends DefaultRandomAccessChemObjectReader implements IRandomAccessChemObjectReader<IChemObject> { - protected static LoggingTool logger = new LoggingTool(RandomAccessReader.class); + protected static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RandomAccessReader.class); protected RandomAccessFile raFile; protected IOSetting[] headerOptions = null; private final String filename; src/main/org/openscience/cdk/io/random/RandomAccessReader.java @@ -31,7 +31,8 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.isomorphism.mcss.RMap; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module standard @@ -39,7 +40,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class AtomMappingTools { - private static LoggingTool logger = new LoggingTool(AtomMappingTools.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomMappingTools.class); /** * Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest src/main/org/openscience/cdk/isomorphism/AtomMappingTools.java @@ -36,7 +36,8 @@ import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; import org.openscience.cdk.isomorphism.matchers.IQueryAtom; import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer; import org.openscience.cdk.isomorphism.mcss.RMap; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This matches recursive smarts atoms. @@ -47,7 +48,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class RecursiveSmartsAtom extends SMARTSAtom { private static final long serialVersionUID = 1L; - private final static LoggingTool logger = new LoggingTool( + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool( RecursiveSmartsAtom.class); /** * AtomContainer of the target molecule to which this recursive smarts query trying to match src/main/org/openscience/cdk/isomorphism/matchers/smarts/RecursiveSmartsAtom.java @@ -28,6 +28,13 @@ */ package org.openscience.cdk.layout; +import java.util.Comparator; +import java.util.List; +import java.util.Vector; + +import javax.vecmath.Point2d; +import javax.vecmath.Vector2d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.BondTools; @@ -38,15 +45,10 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point2d; -import javax.vecmath.Vector2d; -import java.util.Comparator; -import java.util.List; -import java.util.Vector; - /** * Methods for generating coordinates for atoms in various situations. They can * be used for Automated Structure Diagram Generation or in the interactive @@ -61,7 +63,8 @@ public class AtomPlacer { public final static boolean debug = true; - private static LoggingTool logger = new LoggingTool(AtomPlacer.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomPlacer.class); /** * The molecule to be laid out. To be assigned from outside src/main/org/openscience/cdk/layout/AtomPlacer.java @@ -35,7 +35,8 @@ import javax.vecmath.Point2d; import org.openscience.cdk.geometry.GeometryTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This is a wrapper class for some existing methods in AtomPlacer. It helps @@ -53,7 +54,8 @@ public class HydrogenPlacer { public final static boolean debug1 = false; public void placeHydrogens2D(IAtomContainer atomContainer, double bondLength){ - LoggingTool logger = new LoggingTool(this); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HydrogenPlacer.class); logger.debug("Entering Hydrogen Placement..."); IAtom atom = null; for (int f = 0; f < atomContainer.getAtomCount();f++) @@ -79,7 +81,8 @@ public class HydrogenPlacer { } public void placeHydrogens2D(IAtomContainer atomContainer, IAtom atom, double bondLength){ - LoggingTool logger = new LoggingTool(this); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HydrogenPlacer.class); //double startAngle = 0.0; //double addAngle = 0.0; src/main/org/openscience/cdk/layout/HydrogenPlacer.java @@ -40,7 +40,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IRingSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Helper class for Structure Diagram Generation. Resolves atom or bond @@ -56,14 +57,14 @@ import org.openscience.cdk.tools.LoggingTool; public class OverlapResolver { - private org.openscience.cdk.tools.LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OverlapResolver.class); double bondLength = 1.5; int maxSteps = 10000; public OverlapResolver() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/layout/OverlapResolver.java @@ -40,7 +40,8 @@ import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -55,7 +56,8 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; public class RingPlacer { final static boolean debug = false; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RingPlacer.class); private IMolecule molecule; @@ -70,7 +72,6 @@ public class RingPlacer */ public RingPlacer() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/layout/RingPlacer.java @@ -44,7 +44,8 @@ import org.openscience.cdk.interfaces.IRing; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.ringsearch.RingPartitioner; import org.openscience.cdk.ringsearch.SSSRFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerSetManipulator; import org.openscience.cdk.tools.manipulator.RingSetManipulator; @@ -79,7 +80,8 @@ import org.openscience.cdk.tools.manipulator.RingSetManipulator; public class StructureDiagramGenerator { - private LoggingTool logger = new LoggingTool(StructureDiagramGenerator.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(StructureDiagramGenerator.class); private static TemplateHandler DEFAULT_TEMPLATE_HANDLER = null; src/main/org/openscience/cdk/layout/StructureDiagramGenerator.java @@ -48,7 +48,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.CMLReader; import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; import org.openscience.cdk.isomorphism.mcss.RMap; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -68,7 +69,8 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; public class TemplateHandler { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(TemplateHandler.class); private List<IAtomContainer> templates = null; @@ -78,7 +80,6 @@ public class TemplateHandler */ public TemplateHandler(IChemObjectBuilder builder) { - logger = new LoggingTool(this); templates = new ArrayList<IAtomContainer>(); loadTemplates(builder); } src/main/org/openscience/cdk/layout/TemplateHandler.java @@ -57,7 +57,8 @@ import org.openscience.cdk.interfaces.IReactionScheme; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.interfaces.IStrand; import org.openscience.cdk.tools.IDCreator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; import org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator; import org.xmlcml.cml.base.CMLElement; @@ -96,7 +97,8 @@ public class Convertor { public final static String NS_CML = "http://www.xml-cml.org/schema"; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Convertor.class); private final static String CUSTOMIZERS_LIST = "libio-cml-customizers.set"; private static Map<String, ICMLCustomizer> customizers = null; @@ -113,7 +115,6 @@ public class Convertor { * @param prefix Namespace prefix to use. If null, then no prefix is used; */ public Convertor(boolean useCMLIDs, String prefix) { - logger = new LoggingTool(this); this.useCMLIDs = useCMLIDs; this.prefix = prefix; setupCustomizers(); src/main/org/openscience/cdk/libio/cml/Convertor.java @@ -30,7 +30,8 @@ package org.openscience.cdk.math.qm; import org.openscience.cdk.math.Matrix; import org.openscience.cdk.math.Vector; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Calculates the orbitals and orbital energies of electron systems @@ -46,7 +47,8 @@ public class ClosedShellJob private Orbitals orbitals; private Vector E; - private LoggingTool log = new LoggingTool(ClosedShellJob.class); + private static ILoggingTool log = + LoggingToolFactory.createLoggingTool(ClosedShellJob.class); private int iterations = 0; src/main/org/openscience/cdk/math/qm/ClosedShellJob.java @@ -30,7 +30,8 @@ package org.openscience.cdk.math.qm; import org.openscience.cdk.math.Matrix; import org.openscience.cdk.math.Vector; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Calculates the orbitals and orbital energies of electron systems @@ -46,7 +47,8 @@ public class OneElectronJob private Orbitals orbitals; private Vector E; - private LoggingTool log = new LoggingTool(OneElectronJob.class); + private static ILoggingTool log = + LoggingToolFactory.createLoggingTool(OneElectronJob.class); /** * Constructs a one electron job src/main/org/openscience/cdk/math/qm/OneElectronJob.java @@ -55,8 +55,6 @@ import org.openscience.cdk.interfaces.IAtomType; */ public class MM2BasedParameterSetReader { -// private final LoggingTool logger = new LoggingTool(MM2BasedParameterSetReader.class); - private String configFile = "org/openscience/cdk/modeling/forcefield/data/mm2.prm"; private InputStream ins = null; private Map<String, Object> parameterSet; src/main/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java @@ -44,7 +44,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.layout.AtomPlacer; import org.openscience.cdk.ringsearch.RingPartitioner; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.RingSetManipulator; /** @@ -85,7 +86,8 @@ public class ModelBuilder3D { String forceFieldName = "mm2"; - private LoggingTool logger = new LoggingTool(ModelBuilder3D.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ModelBuilder3D.class); /** * Constructor for the ModelBuilder3D object. src/main/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java @@ -49,12 +49,10 @@ import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.io.iterator.IteratingMDLReader; import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; -import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; -import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator; import org.openscience.cdk.isomorphism.mcss.RMap; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; -import org.openscience.cdk.ringsearch.RingPartitioner; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.RingSetManipulator; @@ -71,7 +69,8 @@ import org.openscience.cdk.tools.manipulator.RingSetManipulator; public class TemplateHandler3D { private static final IChemObjectBuilder builder = NoNotificationChemObjectBuilder.getInstance(); - private static final LoggingTool logger = new LoggingTool(TemplateHandler3D.class); + private static final ILoggingTool logger = + LoggingToolFactory.createLoggingTool(TemplateHandler3D.class); IMolecule molecule; IRingSet sssr; src/main/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java @@ -85,9 +85,7 @@ public class AngleBending { /** * Constructor for the AngleBending object */ - public AngleBending() { - //logger = new LoggingTool(this); - } + public AngleBending() {} public void setAngleBendingFlag(boolean flag){ angleBending=flag; src/main/org/openscience/cdk/modeling/forcefield/AngleBending.java @@ -67,15 +67,10 @@ public class BondStretching { double[][] dDeltar = null; double[][][] ddDeltar = null; - //private LoggingTool logger; - - /** * Constructor for the BondStretching object */ - public BondStretching() { - //logger = new LoggingTool(this); - } + public BondStretching() {} /** src/main/org/openscience/cdk/modeling/forcefield/BondStretching.java @@ -22,7 +22,8 @@ package org.openscience.cdk.modeling.forcefield; import javax.vecmath.GVector; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** @@ -41,14 +42,14 @@ public class ConjugateGradientMethod { boolean orthogonalDirectionsProperty = true; GVector diffgk_gkminus1 = null; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ConjugateGradientMethod.class); /** * Constructor for the ConjugateGradientMethod object */ public ConjugateGradientMethod() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/ConjugateGradientMethod.java @@ -70,14 +70,10 @@ public class ElectrostaticInteractions { double[] iQ = null; double electrostatic14interactionsScale = 0.75; // Scale factor for 1-4 interactions. To take in the future from mmff94.prm files. - //private LoggingTool logger; - /** * Constructor for the ElectrostaticInteractions object */ - public ElectrostaticInteractions() { - //logger = new LoggingTool(this); - } + public ElectrostaticInteractions() {} /** src/main/org/openscience/cdk/modeling/forcefield/ElectrostaticInteractions.java @@ -20,12 +20,11 @@ */ package org.openscience.cdk.modeling.forcefield; +import javax.vecmath.GVector; + import org.openscience.cdk.Molecule; import org.openscience.cdk.graph.ConnectivityChecker; -import javax.vecmath.GVector; -//import org.openscience.cdk.tools.LoggingTool; - /** * To work with the coordinates of the molecule, like get the 3d coordinates of the atoms or * calculate the distance between two atoms. @@ -42,19 +41,13 @@ public class ForceField extends GeometricMinimizer{ boolean cgm_flag=true; boolean nrm_flag=true; - //private LoggingTool logger; - - /** * Constructor for the ForceField object */ - public ForceField() { - //logger = new LoggingTool(this); - } + public ForceField() {} public ForceField(Molecule molecule) throws Exception { setMolecule(molecule, false); - //logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/ForceField.java @@ -26,8 +26,6 @@ import org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator; import javax.vecmath.GMatrix; import javax.vecmath.GVector; -import java.util.Hashtable; -//import org.openscience.cdk.tools.LoggingTool; import java.util.Map; @@ -79,7 +77,6 @@ public class GeometricMinimizer { double infiniteNorm; NewtonRaphsonMethod nrm = new NewtonRaphsonMethod(); - //private LoggingTool logger; IMolecule molecule; @@ -87,9 +84,7 @@ public class GeometricMinimizer { /** * Constructor for the GeometricMinimizer object */ - public GeometricMinimizer() { - //logger = new LoggingTool(this); - } + public GeometricMinimizer() {} public void setMolecule(IMolecule mol, boolean clone) throws Exception { src/main/org/openscience/cdk/modeling/forcefield/GeometricMinimizer.java @@ -22,7 +22,8 @@ package org.openscience.cdk.modeling.forcefield; import javax.vecmath.GVector; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** @@ -53,14 +54,14 @@ public class LineSearch { double fxLS = 0; double lambdabOld = 0; double tol = 0.0001; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(LineSearch.class); /** * Constructor for the LineSearch object */ public LineSearch() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/LineSearch.java @@ -22,7 +22,7 @@ package org.openscience.cdk.modeling.forcefield; import javax.vecmath.GVector; -//import org.openscience.cdk.tools.LoggingTool; + /** * * @@ -85,9 +85,6 @@ public class LineSearchForTheWolfeConditions { private double d2; private double alphaiplus1; - //private LoggingTool logger; - - public LineSearchForTheWolfeConditions(IPotentialFunction pfUser, String method) { this.pf = pfUser; if ((method == "sdm") | (method == "cgm")) {c2 = 0.07;} src/main/org/openscience/cdk/modeling/forcefield/LineSearchForTheWolfeConditions.java @@ -20,15 +20,12 @@ */ package org.openscience.cdk.modeling.forcefield; -import java.util.Hashtable; import java.util.Map; import javax.vecmath.GMatrix; import javax.vecmath.GVector; import org.openscience.cdk.interfaces.IAtomContainer; -//import org.openscience.cdk.tools.LoggingTool; - /** * MMFF94 energy function. @@ -50,8 +47,6 @@ public class MMFF94EnergyFunction implements IPotentialFunction { GMatrix energyHessian = null; double[] forHessian = null; - //private LoggingTool logger; - BondStretching bs = new BondStretching(); AngleBending ab = new AngleBending(); StretchBendInteractions sbi = new StretchBendInteractions(); @@ -72,8 +67,6 @@ public class MMFF94EnergyFunction implements IPotentialFunction { t.setMMFF94TorsionsParameters(molecule, mmff94Tables); vdwi.setMMFF94VanDerWaalsParameters(molecule, mmff94Tables); ei.setMMFF94ElectrostaticParameters(molecule, mmff94Tables); - - //logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/MMFF94EnergyFunction.java @@ -27,7 +27,8 @@ package org.openscience.cdk.modeling.forcefield; import javax.vecmath.GMatrix; import javax.vecmath.GVector; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import Jama.Matrix; @@ -44,14 +45,13 @@ import Jama.Matrix; public class NewtonRaphsonMethod { GVector gradientPerInverseHessianVector = null; Matrix matrixForDeterminatCalculation = null; - private LoggingTool logger; - + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(NewtonRaphsonMethod.class); /** * Constructor for the NR object */ public NewtonRaphsonMethod() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/NewtonRaphsonMethod.java @@ -20,8 +20,6 @@ */ package org.openscience.cdk.modeling.forcefield; -//import org.openscience.cdk.tools.LoggingTool; - /** * Cutoffs and Smoothing Functions. @@ -36,15 +34,11 @@ public class SmoothingFunctions { double cutoffr0 = 5; // For Smoothing function (s) double cutoffr1 = 6; // For Smoothing function (s) double dampingFactor = 1; // For Smoothing function (s) - //private LoggingTool logger; - /** * Constructor for the SmoothingFunctions object */ - public SmoothingFunctions() { - //logger = new LoggingTool(this); - } + public SmoothingFunctions() {} /** src/main/org/openscience/cdk/modeling/forcefield/SmoothingFunctions.java @@ -22,8 +22,6 @@ package org.openscience.cdk.modeling.forcefield; import javax.vecmath.GVector; -//import org.openscience.cdk.tools.LoggingTool; - /** * Find a direction from a point of the coordinates space using the steepest descents approach. @@ -36,12 +34,8 @@ import javax.vecmath.GVector; */ public class SteepestDescentsMethod { GVector sk = null; - //private LoggingTool logger; - - public SteepestDescentsMethod() { - //logger = new LoggingTool(this); - } + public SteepestDescentsMethod() {} /** src/main/org/openscience/cdk/modeling/forcefield/SteepestDescentsMethod.java @@ -33,7 +33,8 @@ import org.openscience.cdk.modeling.builder3d.MMFF94ParametersCall; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.descriptors.atomic.PeriodicTablePositionDescriptor; import org.openscience.cdk.qsar.result.IntegerResult; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -74,7 +75,8 @@ public class StretchBendInteractions { BondStretching bs = new BondStretching(); AngleBending ab = new AngleBending(); - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(StretchBendInteractions.class); GVector moleculeCurrentCoordinates = null; boolean[] changeAtomCoordinates = null; @@ -85,7 +87,6 @@ public class StretchBendInteractions { * Constructor for the StretchBendInteractions object */ public StretchBendInteractions() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/StretchBendInteractions.java @@ -75,9 +75,6 @@ public class Torsions { IBond[] bondConnectedBefore = null; IBond[] bondConnectedAfter = null; - - //private LoggingTool logger; - GVector moleculeCurrentCoordinates = null; boolean[] changeAtomCoordinates = null; int changedCoordinates; @@ -87,7 +84,6 @@ public class Torsions { * Constructor for the Torsions object */ public Torsions() { - //logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/Torsions.java @@ -98,13 +98,10 @@ public class VanDerWaalsInteractions { double[] ivdw = null; double vdwScale14 = 1; // Scale factor for 1-4 interactions. To take in the future from mmff94.prm files. - //private LoggingTool logger; - /** * Constructor for the VanDerWaalsInteractions object */ public VanDerWaalsInteractions() { - //logger = new LoggingTool(this); } src/main/org/openscience/cdk/modeling/forcefield/VanDerWaalsInteractions.java @@ -23,6 +23,13 @@ */ package org.openscience.cdk.pharmacophore; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; + +import javax.vecmath.Point3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.annotations.TestClass; @@ -37,13 +44,8 @@ import org.openscience.cdk.isomorphism.matchers.IQueryAtom; import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer; import org.openscience.cdk.isomorphism.mcss.RMap; import org.openscience.cdk.smiles.smarts.SMARTSQueryTool; -import org.openscience.cdk.tools.LoggingTool; - -import javax.vecmath.Point3d; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Identifies atoms whose 3D arrangement matches a specified pharmacophore query. @@ -139,7 +141,8 @@ import java.util.List; */ @TestClass("org.openscience.cdk.pharmacophore.PharmacophoreMatcherTest") public class PharmacophoreMatcher { - private LoggingTool logger = new LoggingTool(PharmacophoreMatcher.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PharmacophoreMatcher.class); private PharmacophoreQuery pharmacophoreQuery = null; private List<List<PharmacophoreAtom>> matchingPAtoms = null; private List<List<IBond>> matchingPBonds = null; src/main/org/openscience/cdk/pharmacophore/PharmacophoreMatcher.java @@ -20,18 +20,6 @@ */ package org.openscience.cdk.protein; -import org.openscience.cdk.ChemFile; -import org.openscience.cdk.config.AtomTypeFactory; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.io.ISimpleChemObjectReader; -import org.openscience.cdk.io.ReaderFactory; -import org.openscience.cdk.protein.data.PDBAtom; -import org.openscience.cdk.tools.GridGenerator; -import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.tools.PeriodicTable; -import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; - -import javax.vecmath.Point3d; import java.io.BufferedWriter; import java.io.FileReader; import java.io.FileWriter; @@ -43,6 +31,26 @@ import java.util.List; import java.util.Map; import java.util.Vector; +import javax.vecmath.Point3d; + +import org.openscience.cdk.ChemFile; +import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IBioPolymer; +import org.openscience.cdk.interfaces.IChemFile; +import org.openscience.cdk.interfaces.IChemModel; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.interfaces.IChemSequence; +import org.openscience.cdk.interfaces.IMoleculeSet; +import org.openscience.cdk.io.ISimpleChemObjectReader; +import org.openscience.cdk.io.ReaderFactory; +import org.openscience.cdk.protein.data.PDBAtom; +import org.openscience.cdk.tools.GridGenerator; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; +import org.openscience.cdk.tools.PeriodicTable; +import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; + /** * The detection of pocket and cavities in a bioPolymer is done similar to the program * LIGSITE {@cdk.cite MH1997}. @@ -58,7 +66,8 @@ import java.util.Vector; */ public class ProteinPocketFinder { - private final LoggingTool logger = new LoggingTool(ProteinPocketFinder.class); + private final ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ProteinPocketFinder.class); int solvantValue = 0; int proteinInterior = -1; src/main/org/openscience/cdk/protein/ProteinPocketFinder.java @@ -20,9 +20,23 @@ */ package org.openscience.cdk.qsar; +import java.io.File; +import java.io.IOException; +import java.lang.reflect.Modifier; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Enumeration; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Set; +import java.util.jar.JarEntry; +import java.util.jar.JarFile; + import nu.xom.Attribute; import nu.xom.Element; import nu.xom.Elements; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.dict.Dictionary; @@ -32,8 +46,8 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.tools.LoggingTool; - +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import java.io.File; import java.io.IOException; import java.lang.reflect.Modifier; @@ -47,7 +61,6 @@ import java.util.Set; import java.util.jar.JarEntry; import java.util.jar.JarFile; - /** * A class that provides access to automatic descriptor calculation and more. * <p/> @@ -90,7 +103,8 @@ public class DescriptorEngine { private List<String> classNames = null; private List<IDescriptor> descriptors = null; private List<DescriptorSpecification> speclist = null; - private static LoggingTool logger = new LoggingTool(DescriptorEngine.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DescriptorEngine.class); /** * Instantiates the DescriptorEngine. src/main/org/openscience/cdk/qsar/DescriptorEngine.java @@ -24,6 +24,8 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.io.IOException; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.AtomTypeFactory; @@ -35,9 +37,8 @@ import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleResult; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.IOException; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This class return the covalent radius of a given atom. @@ -67,8 +68,8 @@ import java.io.IOException; public class CovalentRadiusDescriptor implements IAtomicDescriptor { private AtomTypeFactory factory = null; - private LoggingTool logger; - + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CovalentRadiusDescriptor.class); /** * Constructor for the CovalentRadiusDescriptor object. @@ -77,7 +78,6 @@ public class CovalentRadiusDescriptor implements IAtomicDescriptor { * @throws ClassNotFoundException if an error occurs during tom typing */ public CovalentRadiusDescriptor() throws IOException, ClassNotFoundException { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptor.java @@ -24,6 +24,10 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.io.IOException; + +import javax.vecmath.Point3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.AtomTypeFactory; @@ -35,10 +39,8 @@ import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleResult; -import org.openscience.cdk.tools.LoggingTool; - -import javax.vecmath.Point3d; -import java.io.IOException; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Inductive atomic hardness of an atom in a polyatomic system can be defined @@ -94,7 +96,8 @@ public class InductiveAtomicHardnessDescriptor implements IAtomicDescriptor { private static final String[] names = {"indAtomHardnesss"}; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(InductiveAtomicHardnessDescriptor.class); private AtomTypeFactory factory = null; @@ -105,7 +108,6 @@ public class InductiveAtomicHardnessDescriptor implements IAtomicDescriptor { *@exception ClassNotFoundException Description of the Exception */ public InductiveAtomicHardnessDescriptor() throws IOException, ClassNotFoundException { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java @@ -25,6 +25,10 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.io.IOException; + +import javax.vecmath.Point3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.AtomTypeFactory; @@ -36,10 +40,8 @@ import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleResult; -import org.openscience.cdk.tools.LoggingTool; - -import javax.vecmath.Point3d; -import java.io.IOException; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Inductive atomic softness of an atom in a polyatomic system can be defined @@ -95,7 +97,8 @@ public class InductiveAtomicSoftnessDescriptor implements IAtomicDescriptor { private static final String[] names = {"indAtomSoftness"}; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(InductiveAtomicSoftnessDescriptor.class); private AtomTypeFactory factory = null; @@ -106,7 +109,6 @@ public class InductiveAtomicSoftnessDescriptor implements IAtomicDescriptor { *@exception ClassNotFoundException Description of the Exception */ public InductiveAtomicSoftnessDescriptor() throws IOException, ClassNotFoundException { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptor.java @@ -71,7 +71,6 @@ public class PeriodicTablePositionDescriptor implements IAtomicDescriptor { * Constructor for the PeriodicTablePositionDescriptor object */ public PeriodicTablePositionDescriptor() { - //logger = new LoggingTool(this); if (periodicTable == null) { periodicTable = new Hashtable<String, Integer>(); periodicTable.put("H", 1); src/main/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptor.java @@ -21,6 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -30,21 +37,20 @@ import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates G3R proton descriptors used in neural networks for H1 * NMR shift. @@ -84,7 +90,8 @@ public class RDFProtonDescriptor_G3R implements IAtomicDescriptor { private IAtomContainerSet varAtomContainerSet = null; - private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_G3R.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RDFProtonDescriptor_G3R.class); private static String[] descriptorNames; src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java @@ -21,6 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -30,21 +37,20 @@ import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GDR proton descriptors used in neural networks for H1 NMR shift. * <p/> @@ -78,7 +84,8 @@ public class RDFProtonDescriptor_GDR implements IAtomicDescriptor { private IRingSet varRingSet = null; private IAtomContainerSet varAtomContainerSet = null; - private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GDR.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RDFProtonDescriptor_GDR.class); private final int gdr_desc_length = 7; private static String[] descriptorNames; src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java @@ -21,6 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -30,21 +37,20 @@ import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GHR proton descriptors used in neural networks for H1 NMR shift. @@ -79,7 +85,8 @@ public class RDFProtonDescriptor_GHR implements IAtomicDescriptor { private IRingSet varRingSet = null; private IAtomContainerSet varAtomContainerSet = null; - private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GHR.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RDFProtonDescriptor_GHR.class); private static String[] descriptorNames; private final int ghr_desc_length = 15; src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java @@ -21,6 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org._3pq.jgrapht.Edge; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; @@ -32,21 +39,20 @@ import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.MoleculeGraphs; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift. * <p/> @@ -80,7 +86,8 @@ public class RDFProtonDescriptor_GHR_topol implements IAtomicDescriptor { private IRingSet varRingSet = null; private IAtomContainerSet varAtomContainerSet = null; - private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GHR_topol.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RDFProtonDescriptor_GHR_topol.class); private final int ghr_topol_desc_length = 15; /** src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java @@ -21,6 +21,13 @@ */ package org.openscience.cdk.qsar.descriptors.atomic; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; @@ -30,21 +37,20 @@ import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomContainerSet; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import javax.vecmath.Point3d; -import javax.vecmath.Vector3d; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * This class calculates GDR proton descriptors used in neural networks for H1 NMR shift. * <p/> @@ -78,7 +84,8 @@ public class RDFProtonDescriptor_GSR implements IAtomicDescriptor { private IRingSet varRingSet = null; private IAtomContainerSet varAtomContainerSet = null; - private final static LoggingTool logger = new LoggingTool(RDFProtonDescriptor_GSR.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RDFProtonDescriptor_GSR.class); private final int gsr_desc_length = 7; src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java @@ -24,12 +24,19 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; +import java.lang.reflect.Method; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.atomtype.EStateAtomTypeMatcher; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; @@ -39,12 +46,11 @@ import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.AtomicProperties; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.BondManipulator; -import java.lang.reflect.Method; - /** * This class calculates ALOGP (Ghose-Crippen LogKow) and the * Ghose-Crippen molar refractivity @cdk.cite{GHOSE1986} @cdk.cite{GHOSE1987}. @@ -93,7 +99,8 @@ import java.lang.reflect.Method; */ @TestClass("org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptorTest") public class ALOGPDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ALOGPDescriptor.class); IAtomContainer atomContainer; IRingSet rs; @@ -362,8 +369,6 @@ public class ALOGPDescriptor implements IMolecularDescriptor { public ALOGPDescriptor() throws CDKException { - logger = new LoggingTool(this); - try { ap = AtomicProperties.getInstance(); } catch (Exception e) { src/main/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java @@ -37,7 +37,8 @@ import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Sum of the atomic polarizabilities (including implicit hydrogens). @@ -75,7 +76,8 @@ import org.openscience.cdk.tools.LoggingTool; @TestClass("org.openscience.cdk.qsar.descriptors.molecular.APolDescriptorTest") public class APolDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(APolDescriptor.class); /* Atomic polarizabilities ordered by atomic number from 1 to 102. */ private static double[] polarizabilities; private static final String[] names = {"apol"}; @@ -84,7 +86,6 @@ public class APolDescriptor implements IMolecularDescriptor { * Constructor for the APolDescriptor object. */ public APolDescriptor() { - logger = new LoggingTool(this); if (polarizabilities == null) { polarizabilities = new double[] {0, 0.666793, 0.204956, 24.3, 5.6, 3.03, 1.76, 1.1, 0.802, 0.557, 0.3956, 23.6, 10.6, 6.8, 5.38, 3.63, 2.9, 2.18, 1.6411, src/main/org/openscience/cdk/qsar/descriptors/molecular/APolDescriptor.java @@ -23,8 +23,6 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; -import Jama.EigenvalueDecomposition; -import Jama.Matrix; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.annotations.TestClass; @@ -46,10 +44,14 @@ import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.LonePairElectronChecker; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; +import Jama.EigenvalueDecomposition; +import Jama.Matrix; + /** * Eigenvalue based descriptor noted for its utility in chemical diversity. * Described by Pearlman et al. {@cdk.cite PEA99}. @@ -127,7 +129,8 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; */ @TestClass("org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptorTest") public class BCUTDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(BCUTDescriptor.class); // the number of negative & positive eigenvalues // to return for each class of BCUT descriptor @@ -136,8 +139,6 @@ public class BCUTDescriptor implements IMolecularDescriptor { private boolean checkAromaticity; public BCUTDescriptor() { - logger = new LoggingTool(this); - // set the default number of BCUT's this.nhigh = 1; this.nlow = 1; src/main/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java @@ -38,7 +38,8 @@ import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Sum of the absolute value of the difference between atomic polarizabilities @@ -72,7 +73,8 @@ import org.openscience.cdk.tools.LoggingTool; */ @TestClass("org.openscience.cdk.qsar.descriptors.molecular.BPolDescriptorTest") public class BPolDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(BPolDescriptor.class); /* Atomic polarizabilities ordered by atomic number from 1 to 102. */ private static double[] polarizabilities; private static final String[] names = {"bpol"}; @@ -81,7 +83,6 @@ public class BPolDescriptor implements IMolecularDescriptor { * Constructor for the APolDescriptor object */ public BPolDescriptor() { - logger = new LoggingTool(this); // atomic polarizabilities ordered by atomic number from 1 to 102 if (polarizabilities == null) { polarizabilities = new double[] {0, 0.666793, 0.204956, 24.3, 5.6, 3.03, 1.76, src/main/org/openscience/cdk/qsar/descriptors/molecular/BPolDescriptor.java @@ -32,7 +32,8 @@ import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Calculates 29 Charged Partial Surface Area (CPSA) descriptors. @@ -151,10 +152,10 @@ public class CPSADescriptor implements IMolecularDescriptor { "THSA", "TPSA", "RHSA", "RPSA" }; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CPSADescriptor.class); public CPSADescriptor() { - logger = new LoggingTool(this); } @TestMethod("testGetSpecification") src/main/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java @@ -20,6 +20,8 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; +import java.util.List; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; @@ -32,11 +34,8 @@ import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.qsar.result.IntegerArrayResult; import org.openscience.cdk.qsar.result.IntegerArrayResultType; -import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.BondManipulator; -import java.util.List; - /** * Topological descriptor characterizing the carbon connectivity. * <p/> @@ -86,7 +85,6 @@ public class CarbonTypesDescriptor implements IMolecularDescriptor { }; public CarbonTypesDescriptor() { - LoggingTool logger = new LoggingTool(this); } @TestMethod("testGetSpecification") src/main/org/openscience/cdk/qsar/descriptors/molecular/CarbonTypesDescriptor.java @@ -25,6 +25,10 @@ package org.openscience.cdk.qsar.descriptors.molecular; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -46,14 +50,11 @@ import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.ringsearch.SSSRFinder; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; - /** * Evaluates chi chain descriptors. @@ -93,7 +94,8 @@ import java.util.List; */ @TestClass("org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptorTest") public class ChiChainDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ChiChainDescriptor.class); private SmilesParser sp; private static final String[] names = { @@ -103,7 +105,6 @@ public class ChiChainDescriptor implements IMolecularDescriptor { public ChiChainDescriptor() { - logger = new LoggingTool(this); sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); } src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptor.java @@ -25,6 +25,9 @@ package org.openscience.cdk.qsar.descriptors.molecular; +import java.util.Iterator; +import java.util.List; + import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -44,13 +47,11 @@ import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; -import java.util.Iterator; -import java.util.List; - /** * Evaluates chi cluster descriptors. * <p/> @@ -87,7 +88,8 @@ import java.util.List; */ @TestClass("org.openscience.cdk.qsar.descriptors.molecular.ChiClusterDescriptorTest") public class ChiClusterDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ChiClusterDescriptor.class); private SmilesParser sp; private static final String[] names = { @@ -96,7 +98,6 @@ public class ChiClusterDescriptor implements IMolecularDescriptor { }; public ChiClusterDescriptor() { - logger = new LoggingTool(this); sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); } src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptor.java @@ -24,6 +24,9 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; +import java.util.Iterator; +import java.util.List; + import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -43,13 +46,11 @@ import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; -import java.util.Iterator; -import java.util.List; - /** * Evaluates chi path cluster descriptors. * <p/> @@ -85,7 +86,8 @@ import java.util.List; */ @TestClass("org.openscience.cdk.qsar.descriptors.molecular.ChiPathClusterDescriptorTest") public class ChiPathClusterDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ChiPathClusterDescriptor.class); private SmilesParser sp; private static final String[] names = { @@ -94,7 +96,6 @@ public class ChiPathClusterDescriptor implements IMolecularDescriptor { }; public ChiPathClusterDescriptor() { - logger = new LoggingTool(this); sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); } src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptor.java @@ -24,6 +24,10 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; +import java.util.ArrayList; + +import javax.vecmath.Point3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.IsotopeFactory; @@ -37,10 +41,8 @@ import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; - -import javax.vecmath.Point3d; -import java.util.ArrayList; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** @@ -89,7 +91,8 @@ import java.util.ArrayList; @TestClass("org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptorTest") public class GravitationalIndexDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(GravitationalIndexDescriptor.class); private class pair { int x, y; @@ -107,7 +110,6 @@ public class GravitationalIndexDescriptor implements IMolecularDescriptor { }; public GravitationalIndexDescriptor() { - logger = new LoggingTool(this); } @TestMethod("testGetSpecification") src/main/org/openscience/cdk/qsar/descriptors/molecular/GravitationalIndexDescriptor.java @@ -24,7 +24,8 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; -import Jama.Matrix; +import javax.vecmath.Point3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; @@ -37,10 +38,11 @@ import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.PeriodicTable; -import javax.vecmath.Point3d; +import Jama.Matrix; /** * Evaluates length over breadth descriptors. @@ -66,14 +68,14 @@ import javax.vecmath.Point3d; */ @TestClass("org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptorTest") public class LengthOverBreadthDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(LengthOverBreadthDescriptor.class); private static final String[] names = {"LOBMAX", "LOBMIN"}; /** * Constructor for the LengthOverBreadthDescriptor object. */ public LengthOverBreadthDescriptor() { - logger = new LoggingTool(this); } src/main/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptor.java @@ -19,8 +19,8 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; -import Jama.EigenvalueDecomposition; -import Jama.Matrix; +import javax.vecmath.Point3d; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.IsotopeFactory; @@ -35,10 +35,12 @@ import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; -import javax.vecmath.Point3d; +import Jama.EigenvalueDecomposition; +import Jama.Matrix; /** * A descriptor that calculates the moment of inertia and radius of gyration. @@ -88,17 +90,14 @@ import javax.vecmath.Point3d; @TestClass("org.openscience.cdk.qsar.descriptors.molecular.MomentOfInertiaDescriptorTest") public class MomentOfInertiaDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MomentOfInertiaDescriptor.class); private static final String[] names = { "MOMI-X", "MOMI-Y", "MOMI-Z", "MOMI-XY", "MOMI-XZ", "MOMI-YZ", "MOMI-R" }; - public MomentOfInertiaDescriptor() { - logger = new LoggingTool(this); - } - @TestMethod("testGetSpecification") public DescriptorSpecification getSpecification() { return new DescriptorSpecification( src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java @@ -23,8 +23,11 @@ */ package org.openscience.cdk.qsar.descriptors.molecular; -import Jama.EigenvalueDecomposition; -import Jama.Matrix; +import java.util.HashMap; +import java.util.Map; + +import javax.vecmath.Point3d; + import org.openscience.cdk.Molecule; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -37,11 +40,11 @@ import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.DoubleArrayResultType; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; -import javax.vecmath.Point3d; -import java.util.HashMap; -import java.util.Map; +import Jama.EigenvalueDecomposition; +import Jama.Matrix; /** @@ -127,12 +130,12 @@ import java.util.Map; @TestClass("org.openscience.cdk.qsar.descriptors.molecular.WHIMDescriptorTest") public class WHIMDescriptor implements IMolecularDescriptor { - LoggingTool logger; + static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(WHIMDescriptor.class); String type = ""; Map<String,Double> hashatwt, hashvdw, hasheneg, hashpol; public WHIMDescriptor() { - logger = new LoggingTool(this); this.type = "unity"; // default weighting scheme // set up the values from TOD98 src/main/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java @@ -24,6 +24,17 @@ package org.openscience.cdk.qsar.descriptors.protein; +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; + import org.openscience.cdk.Monomer; import org.openscience.cdk.Strand; import org.openscience.cdk.annotations.TestMethod; @@ -35,13 +46,8 @@ import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.qsar.result.IDescriptorResult; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.*; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** @@ -114,7 +120,8 @@ import java.util.*; * @see IBioPolymer */ public class TaeAminoAcidDescriptor implements IMolecularDescriptor { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(TaeAminoAcidDescriptor.class); private Map<String, Double[]> TAEParams = new HashMap<String, Double[]>(); private int ndesc = 147; @@ -176,8 +183,6 @@ public class TaeAminoAcidDescriptor implements IMolecularDescriptor { } public TaeAminoAcidDescriptor() { - logger = new LoggingTool(this); - nametrans.put("a", "ala"); nametrans.put("c", "cys"); nametrans.put("d", "asp"); src/main/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java @@ -24,13 +24,19 @@ package org.openscience.cdk.qsar.model.R; +import java.io.BufferedReader; +import java.io.BufferedWriter; +import java.io.File; +import java.io.FileWriter; +import java.io.InputStreamReader; +import java.io.StringWriter; + import org.omegahat.R.Java.REvaluator; import org.omegahat.R.Java.ROmegahatInterpreter; import org.openscience.cdk.qsar.model.IModel; import org.openscience.cdk.qsar.model.QSARModelException; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.*; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** Base class for modeling classes that use R as the backend. * @@ -85,7 +91,8 @@ public abstract class RModel implements IModel { * A boolean that indicates whether the R/Java subsystem has been initialized or not. */ private static boolean doneInit = false; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RModel.class); private void loadRFunctions(REvaluator evaluator) { String scriptLocator = "org/openscience/cdk/qsar/model/data/cdkSJava.R"; @@ -160,8 +167,6 @@ public abstract class RModel implements IModel { * @param args A String[] containing the command line parameters as elements */ public RModel(String[] args) { - logger = new LoggingTool(this); - String initRFromString = System.getProperty("initRFromString"); boolean useDisk = true; if (initRFromString != null && initRFromString.equals("true")) { @@ -194,8 +199,6 @@ public abstract class RModel implements IModel { */ public RModel() { String[] args = {"--vanilla","-q", "--slave"}; - logger = new LoggingTool(this); - String initRFromString = System.getProperty("initRFromString"); boolean useDisk = true; if (initRFromString != null && initRFromString.equals("true")) { src/main/org/openscience/cdk/qsar/model/R/RModel.java @@ -24,15 +24,16 @@ package org.openscience.cdk.qsar.model.R2; +import java.io.File; +import java.util.HashMap; + import org.openscience.cdk.qsar.model.QSARModelException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.rosuda.JRI.RBool; import org.rosuda.JRI.REXP; import org.rosuda.JRI.RList; -import java.io.File; -import java.util.HashMap; - /** * A modeling class that provides a computational neural network regression model. * <p/> @@ -127,7 +128,8 @@ public class CNNRegressionModel extends RModel { private double[][] modelPredict = null; - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CNNRegressionModel.class); private void setDefaults() { // lets set the default values of the arguments that are specified @@ -171,8 +173,6 @@ public class CNNRegressionModel extends RModel { */ public CNNRegressionModel() throws QSARModelException { super(); - logger = new LoggingTool(this); - params = new HashMap(); int currentID = CNNRegressionModel.globalID; CNNRegressionModel.globalID++; @@ -205,8 +205,6 @@ public class CNNRegressionModel extends RModel { */ public CNNRegressionModel(double[][] x, double[] y, int size) throws QSARModelException { super(); - logger = new LoggingTool(this); - params = new HashMap(); int currentID = CNNRegressionModel.globalID; CNNRegressionModel.globalID++; @@ -259,8 +257,6 @@ public class CNNRegressionModel extends RModel { */ public CNNRegressionModel(double[][] x, double[][] y, int size) throws QSARModelException { super(); - logger = new LoggingTool(this); - params = new HashMap(); int currentID = CNNRegressionModel.globalID; CNNRegressionModel.globalID++; src/main/org/openscience/cdk/qsar/model/R2/CNNRegressionModel.java @@ -23,14 +23,15 @@ */ package org.openscience.cdk.qsar.model.R2; +import java.io.File; +import java.util.HashMap; + import org.openscience.cdk.qsar.model.QSARModelException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.rosuda.JRI.REXP; import org.rosuda.JRI.RList; -import java.io.File; -import java.util.HashMap; - /** * A modeling class that provides a linear least squares regression model. * <p/> @@ -115,7 +116,8 @@ public class LinearRegressionModel extends org.openscience.cdk.qsar.model.R2.RMo private RList modelPredict = null; - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(LinearRegressionModel.class); /** * Constructs a LinearRegressionModel object. @@ -130,7 +132,6 @@ public class LinearRegressionModel extends org.openscience.cdk.qsar.model.R2.RMo */ public LinearRegressionModel() throws QSARModelException { super(); - logger = new LoggingTool(this); params = new HashMap(); int currentID = LinearRegressionModel.globalID; org.openscience.cdk.qsar.model.R2.LinearRegressionModel.globalID++; src/main/org/openscience/cdk/qsar/model/R2/LinearRegressionModel.java @@ -38,7 +38,8 @@ import java.util.Set; import org.openscience.cdk.qsar.model.IModel; import org.openscience.cdk.qsar.model.QSARModelException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.rosuda.JRI.REXP; import org.rosuda.JRI.RList; import org.rosuda.JRI.RMainLoopCallbacks; @@ -118,7 +119,8 @@ public abstract class RModel implements IModel { * A boolean that indicates whether the R/Java subsystem has been initialized or not. */ private static boolean doneInit = false; - private static LoggingTool logger = new LoggingTool(RModel.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RModel.class); private void checkEnvironmentVariables() throws QSARModelException { String rhome = System.getenv("R_HOME"); src/main/org/openscience/cdk/qsar/model/R2/RModel.java @@ -36,7 +36,8 @@ import org.openscience.cdk.dict.DictionaryDatabase; import org.openscience.cdk.dict.EntryReact; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.reaction.type.parameters.IParameterReact; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>The base class for all chemical reactions objects in this cdk. @@ -51,7 +52,8 @@ import org.openscience.cdk.tools.LoggingTool; */ @TestClass("org.openscience.cdk.reaction.ReactionEngineTest") public class ReactionEngine{ - private static LoggingTool logger = new LoggingTool(ReactionEngine.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ReactionEngine.class); private Dictionary dictionary; public HashMap<String, Object> paramsMap; src/main/org/openscience/cdk/reaction/ReactionEngine.java @@ -43,7 +43,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.AdductionLPMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.AdductionProtonLPReactionTest") public class AdductionProtonLPReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AdductionProtonLPReaction.class); /** * Constructor of the AdductionProtonLPReaction object. * */ public AdductionProtonLPReaction(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java @@ -44,7 +44,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.AdductionPBMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.AdductionProtonPBReactionTest") public class AdductionProtonPBReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AdductionProtonPBReaction.class); /** * Constructor of the AdductionProtonPBReaction object. * */ public AdductionProtonPBReaction(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/reaction/type/AdductionProtonPBReaction.java @@ -43,7 +43,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.AdductionLPMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.AdductionSodiumLPReactionTest") public class AdductionSodiumLPReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AdductionSodiumLPReaction.class); /** * Constructor of the AdductionSodiumLPReaction object. * */ public AdductionSodiumLPReaction(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java @@ -43,7 +43,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate mass spectrum process. @@ -80,14 +81,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.CarbonylEliminationReactionTest") public class CarbonylEliminationReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CarbonylEliminationReaction.class); /** * Constructor of the CarbonylEliminationReaction object. * */ public CarbonylEliminationReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the CarbonylEliminationReaction object. src/main/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java @@ -43,7 +43,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RemovingSEofNBMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which make an electron impact for for Non-Bonding Electron Lost. @@ -80,7 +81,8 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.ElectronImpactNBEReactionTest") public class ElectronImpactNBEReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ElectronImpactNBEReaction.class); /** * Constructor of the ElectronImpactNBEReaction object. @@ -88,7 +90,6 @@ public class ElectronImpactNBEReaction extends ReactionEngine implements IReacti */ public ElectronImpactNBEReaction(){ super(); - logger = new LoggingTool(this); } /** * Gets the specification attribute of the ElectronImpactNBEReaction object. src/main/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java @@ -44,7 +44,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which make an electron impact for pi-Bond Dissociation.</p> @@ -80,14 +81,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.ElectronImpactPDBReactionTest") public class ElectronImpactPDBReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ElectronImpactPDBReaction.class); /** * Constructor of the ElectronImpactPDBReaction object. * */ public ElectronImpactPDBReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the ElectronImpactPDBReaction object. src/main/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RemovingSEofBMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which make an electron impact for Sigma Bond Dissociation.</p> @@ -79,14 +80,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.ElectronImpactSDBReactionTest") public class ElectronImpactSDBReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ElectronImpactSDBReaction.class); /** * Constructor of the ElectronImpactSDBReaction object. * */ public ElectronImpactSDBReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the ElectronImpactSDBReaction object. src/main/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which a bond is broken displacing the electron to one of the @@ -88,14 +89,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.HeterolyticCleavagePBReactionTest") public class HeterolyticCleavagePBReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HeterolyticCleavagePBReaction.class); /** * Constructor of the HeterolyticCleavagePBReaction object. * */ public HeterolyticCleavagePBReaction(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which a bond is broken displacing the electron to one of the @@ -88,14 +89,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.HeterolyticCleavageSBReactionTest") public class HeterolyticCleavageSBReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HeterolyticCleavageSBReaction.class); /** * Constructor of the HeterolyticCleavageSBReaction object. * */ public HeterolyticCleavageSBReaction(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.HomolyticCleavageMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which breaks the bond homogeneously leading to radical ions. @@ -81,13 +82,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.HomolyticCleavageReactionTest") public class HomolyticCleavageReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HomolyticCleavageReaction.class); + /** * Constructor of the HomolyticCleavageReaction object. * */ public HomolyticCleavageReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the HomolyticCleavageReaction object. src/main/org/openscience/cdk/reaction/type/HomolyticCleavageReaction.java @@ -43,7 +43,8 @@ import org.openscience.cdk.reaction.ReactionEngine; import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>HyperconjugationReaction is the stabilizing interaction that results @@ -81,14 +82,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.HyperconjugationReactionTest") public class HyperconjugationReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HyperconjugationReaction.class); /** * Constructor of the HyperconjugationReaction object * */ public HyperconjugationReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the HyperconjugationReaction object src/main/org/openscience/cdk/reaction/type/HyperconjugationReaction.java @@ -46,7 +46,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.BondManipulator; @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.PiBondingMovementReactionTest") public class PiBondingMovementReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PiBondingMovementReaction.class); /** * Constructor of the PiBondingMovementReaction object * */ public PiBondingMovementReaction(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java @@ -43,7 +43,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate mass spectrum process. Homolitic dissocitation. @@ -80,14 +81,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReactionTest") public class RadicalChargeSiteInitiationHReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalChargeSiteInitiationReaction.class); /** * Constructor of the RadicalChargeSiteInitiationHReaction object * */ public RadicalChargeSiteInitiationHReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalChargeSiteInitiationHReaction object src/main/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReaction.java @@ -44,7 +44,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate mass spectrum process. Homolitic dissocitation. @@ -81,14 +82,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReactionTest") public class RadicalChargeSiteInitiationReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalChargeSiteInitiationReaction.class); /** * Constructor of the RadicalChargeSiteInitiationReaction object * */ public RadicalChargeSiteInitiationReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalChargeSiteInitiationReaction object src/main/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReaction.java @@ -51,7 +51,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -88,14 +89,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteHrAlphaReactionTest") public class RadicalSiteHrAlphaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteHrAlphaReaction.class); /** * Constructor of the RadicalSiteHrAlphaReaction object * */ public RadicalSiteHrAlphaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteHrAlphaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java @@ -51,7 +51,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -88,14 +89,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteHrBetaReactionTest") public class RadicalSiteHrBetaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteHrBetaReaction.class); /** * Constructor of the RadicalSiteHrBetaReaction object * */ public RadicalSiteHrBetaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteHrBetaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java @@ -51,7 +51,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -88,14 +89,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteHrDeltaReactionTest") public class RadicalSiteHrDeltaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteHrDeltaReaction.class); /** * Constructor of the RadicalSiteHrDeltaReaction object * */ public RadicalSiteHrDeltaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteHrDeltaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java @@ -51,7 +51,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -88,14 +89,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteHrGammaReactionTest") public class RadicalSiteHrGammaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteHrGammaReaction.class); /** * Constructor of the RadicalSiteHrGammaReaction object * */ public RadicalSiteHrGammaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteHrGammaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java @@ -43,7 +43,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate mass spectrum process. Homolitic dissocitation. @@ -80,14 +81,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteInitiationHReactionTest") public class RadicalSiteInitiationHReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteInitiationHReaction.class); /** * Constructor of the RadicalSiteInitiationHReaction object * */ public RadicalSiteInitiationHReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteInitiationHReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java @@ -44,7 +44,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RadicalSiteIonizationMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate mass spectrum process. Homolitic dissocitation. @@ -81,14 +82,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteInitiationReactionTest") public class RadicalSiteInitiationReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteInitiationReaction.class); /** * Constructor of the RadicalSiteInitiationReaction object * */ public RadicalSiteInitiationReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteInitiationReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java @@ -52,7 +52,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -89,14 +90,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteRrAlphaReactionTest") public class RadicalSiteRrAlphaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteRrAlphaReaction.class); /** * Constructor of the RadicalSiteRrAlphaReaction object * */ public RadicalSiteRrAlphaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteRrAlphaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java @@ -52,7 +52,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -89,14 +90,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteRrBetaReactionTest") public class RadicalSiteRrBetaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteRrBetaReaction.class); /** * Constructor of the RadicalSiteRrBetaReaction object * */ public RadicalSiteRrBetaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteRrBetaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java @@ -52,7 +52,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -89,14 +90,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteRrDeltaReactionTest") public class RadicalSiteRrDeltaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteRrDeltaReaction.class); /** * Constructor of the RadicalSiteRrDeltaReaction object * */ public RadicalSiteRrDeltaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteRrDeltaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java @@ -52,7 +52,8 @@ import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.HOSECodeGenerator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -89,14 +90,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RadicalSiteRrGammaReactionTest") public class RadicalSiteRrGammaReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RadicalSiteRrGammaReaction.class); /** * Constructor of the RadicalSiteRrGammaReaction object * */ public RadicalSiteRrGammaReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RadicalSiteRrGammaReaction object src/main/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate in movement resonance. * This reaction could be represented as [A-]-B=C => A=B-[C-]. Due to @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.RearrangementAnionReactionTest") public class RearrangementAnionReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RearrangementAnionReaction.class); /** * Constructor of the RearrangementAnionReaction object * */ public RearrangementAnionReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RearrangementAnionReaction object src/main/org/openscience/cdk/reaction/type/RearrangementAnionReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate in movement resonance. @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.RearrangementCationReactionTest") public class RearrangementCationReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RearrangementCationReaction.class); /** * Constructor of the RearrangementCharge2Reaction object * */ public RearrangementCationReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RearrangementCationReaction object src/main/org/openscience/cdk/reaction/type/RearrangementCationReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate in movement resonance. * This reaction could be represented as |A-B=C => [A+]=B-[C-]. Due to @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.RearrangementLonePairReactionTest") public class RearrangementLonePairReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RearrangementLonePairReaction.class); /** * Constructor of the RearrangementLonePairReaction object * */ public RearrangementLonePairReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RearrangementLonePairReaction object src/main/org/openscience/cdk/reaction/type/RearrangementLonePairReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.RearrangementChargeMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -85,14 +86,14 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; **/ @TestClass(value="org.openscience.cdk.reaction.type.RearrangementRadicalReactionTest") public class RearrangementRadicalReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RearrangementRadicalReaction.class); /** * Constructor of the RearrangementRadicalReaction object * */ public RearrangementRadicalReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the RearrangementRadicalReaction object src/main/org/openscience/cdk/reaction/type/RearrangementRadicalReaction.java @@ -44,7 +44,8 @@ import org.openscience.cdk.reaction.ReactionEngine; import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate in movement resonance. @@ -81,14 +82,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.SharingAnionReactionTest") public class SharingAnionReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SharingAnionReaction.class); /** * Constructor of the SharingAnionReaction object. * */ public SharingAnionReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the SharingAnionReaction object. src/main/org/openscience/cdk/reaction/type/SharingAnionReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate in movement resonance. @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.SharingChargeDBReactionTest") public class SharingChargeDBReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SharingChargeDBReaction.class); /** * Constructor of the SharingChargeDBReaction object. * */ public SharingChargeDBReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the SharingChargeDBReaction object src/main/org/openscience/cdk/reaction/type/SharingChargeDBReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.HeterolyticCleavageMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate in movement resonance. @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.SharingChargeSBReactionTest") public class SharingChargeSBReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SharingChargeSBReaction.class); /** * Constructor of the SharingChargeSBReaction object. * */ public SharingChargeSBReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the SharingChargeSBReaction object src/main/org/openscience/cdk/reaction/type/SharingChargeSBReaction.java @@ -44,7 +44,8 @@ import org.openscience.cdk.reaction.ReactionEngine; import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which participate in movement resonance. @@ -81,14 +82,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.SharingLonePairReactionTest") public class SharingLonePairReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SharingLonePairReaction.class); /** * Constructor of the SharingLonePairReaction object. * */ public SharingLonePairReaction(){ - logger = new LoggingTool(this); } /** * Gets the specification attribute of the SharingLonePairReaction object. src/main/org/openscience/cdk/reaction/type/SharingLonePairReaction.java @@ -45,7 +45,8 @@ import org.openscience.cdk.reaction.ReactionSpecification; import org.openscience.cdk.reaction.mechanism.TautomerizationMechanism; import org.openscience.cdk.reaction.type.parameters.IParameterReact; import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>IReactionProcess which produces a tautomerization chemical reaction. @@ -83,14 +84,14 @@ import org.openscience.cdk.tools.LoggingTool; **/ @TestClass(value="org.openscience.cdk.reaction.type.TautomerizationReactionTest") public class TautomerizationReaction extends ReactionEngine implements IReactionProcess{ - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(TautomerizationReaction.class); /** * Constructor of the TautomerizationReaction object. * */ public TautomerizationReaction(){ - logger = new LoggingTool(this); } /** src/main/org/openscience/cdk/reaction/type/TautomerizationReaction.java @@ -33,15 +33,14 @@ import java.awt.event.ActionEvent; import java.util.Hashtable; import javax.swing.AbstractAction; +import javax.swing.JFrame; import javax.swing.JMenuItem; import javax.swing.JPopupMenu; -import javax.swing.JFrame; -import org.openscience.cdk.interfaces.IChemObject; -//import org.openscience.cdk.applications.jchempaint.JChemPaintMenuBar; -//import org.openscience.cdk.applications.jchempaint.JChemPaintPanel; import org.openscience.cdk.controller.CDKPopupMenu; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Superclass of all JChemPaint GUI actions @@ -71,7 +70,8 @@ public class JCPAction2D extends AbstractAction /** * Description of the Field */ - protected static LoggingTool logger = null; + protected static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(JCPAction2D.class); private Hashtable actions = null; private Hashtable popupActions = null; @@ -103,11 +103,7 @@ public class JCPAction2D extends AbstractAction public JCPAction2D(JFrame jcpPanel, String type, boolean isPopupAction) { super(); - //logger.debug("JCPAction->type: " + type); - if (JCPAction2D.logger == null) - { - JCPAction2D.logger = new LoggingTool(this); - } + logger.debug("JCPAction->type: " + type); if (this.actions == null) { this.actions = new Hashtable(); src/main/org/openscience/cdk/renderer/JCPAction2D.java @@ -25,17 +25,23 @@ */ package org.openscience.cdk.ringsearch; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.ConnectivityChecker; import org.openscience.cdk.graph.SpanningTree; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.tools.LoggingTool; - -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Finds the Set of all Rings. This is an implementation of the algorithm @@ -64,7 +70,8 @@ import java.util.List; @TestClass("org.openscience.cdk.ringsearch.AllRingsFinderTest") public class AllRingsFinder { - private final LoggingTool logger = new LoggingTool(AllRingsFinder.class); + private final ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AllRingsFinder.class); public boolean debug = false; private long timeout = 5000; src/main/org/openscience/cdk/ringsearch/AllRingsFinder.java @@ -38,7 +38,8 @@ import org.openscience.cdk.Ring; import org.openscience.cdk.RingSet; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.RingSetManipulator; /** @@ -59,15 +60,12 @@ import org.openscience.cdk.tools.manipulator.RingSetManipulator; */ public class FiguerasSSSRFinder { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(FiguerasSSSRFinder.class); int trimCounter = 0; private static final String PATH = "org.openscience.cdk.ringsearch.FiguerasSSSRFinderRFinder.PATH"; - public FiguerasSSSRFinder() { - logger = new LoggingTool(this); - } - /** * Finds the Smallest Set of Smallest Rings. * src/main/org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java @@ -27,22 +27,33 @@ */ package org.openscience.cdk.smiles; -import org.openscience.cdk.*; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; + +import org.openscience.cdk.Atom; +import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.Molecule; +import org.openscience.cdk.Ring; +import org.openscience.cdk.RingSet; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.atomtype.CDKAtomTypeMatcher; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.interfaces.IAtomType.Hybridization; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.ringsearch.SSSRFinder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.RingManipulator; - -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; /** * Tool that tries to deduce bond orders based on connectivity and hybridization * for a number of common ring systems. @@ -59,7 +70,8 @@ import java.util.List; public class DeduceBondSystemTool { private AllRingsFinder allRingsFinder; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DeduceBondSystemTool.class); private List<Integer[]> listOfRings = null; @@ -70,7 +82,6 @@ public class DeduceBondSystemTool { */ public DeduceBondSystemTool() { allRingsFinder = new AllRingsFinder(); - logger = new LoggingTool(this); } public boolean isOK(IMolecule m) throws CDKException { src/main/org/openscience/cdk/smiles/DeduceBondSystemTool.java @@ -25,6 +25,11 @@ */ package org.openscience.cdk.smiles; +import java.util.Enumeration; +import java.util.Iterator; +import java.util.Stack; +import java.util.StringTokenizer; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -32,18 +37,21 @@ import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.atomtype.CDKAtomTypeMatcher; import org.openscience.cdk.exception.InvalidSmilesException; import org.openscience.cdk.graph.ConnectivityChecker; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IChemObjectBuilder; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; +import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IAtomType.Hybridization; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; import org.openscience.cdk.tools.manipulator.BondManipulator; -import java.util.Enumeration; -import java.util.Iterator; -import java.util.Stack; -import java.util.StringTokenizer; - /** * Parses a SMILES {@cdk.cite SMILESTUT} string and an AtomContainer. The full * SSMILES subset {@cdk.cite SSMILESTUT} and the '%' tag for more than 10 rings @@ -77,7 +85,8 @@ public class SmilesParser { private final static String HAS_HARDCODED_HYDROGEN_COUNT = "SmilesParser.HasHardcodedHydrogenCount"; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SmilesParser.class); private CDKHydrogenAdder hAdder; private int status = 0; @@ -90,7 +99,6 @@ public class SmilesParser { */ public SmilesParser(IChemObjectBuilder builder) { - logger = new LoggingTool(this); this.builder = builder; try { hAdder = CDKHydrogenAdder.getInstance(builder); src/main/org/openscience/cdk/smiles/SmilesParser.java @@ -20,6 +20,12 @@ */ package org.openscience.cdk.smiles.smarts; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; @@ -40,15 +46,10 @@ import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.ringsearch.SSSRFinder; import org.openscience.cdk.smiles.smarts.parser.SMARTSParser; import org.openscience.cdk.smiles.smarts.parser.TokenMgrError; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - /** * This class provides a easy to use wrapper around SMARTS matching * functionality. <p/> User code that wants to do SMARTS matching should use @@ -134,7 +135,8 @@ import java.util.Map; */ @TestClass("org.openscience.cdk.smiles.smarts.SMARTSQueryToolTest") public class SMARTSQueryTool { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SMARTSQueryTool.class); private String smarts; private IAtomContainer atomContainer = null; private QueryAtomContainer query = null; @@ -142,7 +144,6 @@ public class SMARTSQueryTool { private List<List<Integer>> matchingAtoms = null; public SMARTSQueryTool(String smarts) throws CDKException { - logger = new LoggingTool(this); this.smarts = smarts; try { initializeQuery(); src/main/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java @@ -33,7 +33,6 @@ PARSER_BEGIN(SMARTSParser) * Foundation, 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. * (or see http://www.gnu.org/copyleft/lesser.html) */ - package org.openscience.cdk.smiles.smarts.parser; import java.io.StringReader; @@ -41,7 +40,6 @@ import java.util.Stack; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; -import org.openscience.cdk.tools.LoggingTool; /** * This parser implements a nearly complete subset of the SMARTS syntax as defined on src/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt @@ -19,6 +19,9 @@ */ package org.openscience.cdk.smiles.smarts.parser.visitor; +import java.util.ArrayList; +import java.util.List; + import org.openscience.cdk.CDKConstants; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; @@ -27,12 +30,83 @@ import org.openscience.cdk.isomorphism.matchers.IQueryAtom; import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer; import org.openscience.cdk.isomorphism.matchers.IQueryBond; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; -import org.openscience.cdk.isomorphism.matchers.smarts.*; -import org.openscience.cdk.smiles.smarts.parser.*; -import org.openscience.cdk.tools.LoggingTool; - -import java.util.ArrayList; -import java.util.List; +import org.openscience.cdk.isomorphism.matchers.smarts.AliphaticAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.AliphaticSymbolAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.AnyAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond; +import org.openscience.cdk.isomorphism.matchers.smarts.AromaticAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond; +import org.openscience.cdk.isomorphism.matchers.smarts.AromaticQueryBond; +import org.openscience.cdk.isomorphism.matchers.smarts.AromaticSymbolAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.AtomicNumberAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.ChiralityAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.ExplicitConnectionAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.FormalChargeAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.HybridizationNumberAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.HydrogenAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.ImplicitHCountAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.LogicalOperatorBond; +import org.openscience.cdk.isomorphism.matchers.smarts.MassAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.NonCHHeavyAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond; +import org.openscience.cdk.isomorphism.matchers.smarts.PeriodicGroupNumberAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.RecursiveSmartsAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.RingBond; +import org.openscience.cdk.isomorphism.matchers.smarts.RingIdentifierAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.RingMembershipAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond; +import org.openscience.cdk.isomorphism.matchers.smarts.SmallestRingAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.StereoBond; +import org.openscience.cdk.isomorphism.matchers.smarts.TotalConnectionAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.TotalHCountAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom; +import org.openscience.cdk.isomorphism.matchers.smarts.TotalValencyAtom; +import org.openscience.cdk.smiles.smarts.parser.ASTAliphatic; +import org.openscience.cdk.smiles.smarts.parser.ASTAnyAtom; +import org.openscience.cdk.smiles.smarts.parser.ASTAromatic; +import org.openscience.cdk.smiles.smarts.parser.ASTAtom; +import org.openscience.cdk.smiles.smarts.parser.ASTAtomicMass; +import org.openscience.cdk.smiles.smarts.parser.ASTAtomicNumber; +import org.openscience.cdk.smiles.smarts.parser.ASTCharge; +import org.openscience.cdk.smiles.smarts.parser.ASTChirality; +import org.openscience.cdk.smiles.smarts.parser.ASTElement; +import org.openscience.cdk.smiles.smarts.parser.ASTExplicitAtom; +import org.openscience.cdk.smiles.smarts.parser.ASTExplicitConnectivity; +import org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndBond; +import org.openscience.cdk.smiles.smarts.parser.ASTExplicitHighAndExpression; +import org.openscience.cdk.smiles.smarts.parser.ASTGroup; +import org.openscience.cdk.smiles.smarts.parser.ASTHybrdizationNumber; +import org.openscience.cdk.smiles.smarts.parser.ASTImplicitHCount; +import org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndBond; +import org.openscience.cdk.smiles.smarts.parser.ASTImplicitHighAndExpression; +import org.openscience.cdk.smiles.smarts.parser.ASTLowAndBond; +import org.openscience.cdk.smiles.smarts.parser.ASTLowAndExpression; +import org.openscience.cdk.smiles.smarts.parser.ASTNonCHHeavyAtom; +import org.openscience.cdk.smiles.smarts.parser.ASTNotBond; +import org.openscience.cdk.smiles.smarts.parser.ASTNotExpression; +import org.openscience.cdk.smiles.smarts.parser.ASTOrBond; +import org.openscience.cdk.smiles.smarts.parser.ASTOrExpression; +import org.openscience.cdk.smiles.smarts.parser.ASTPeriodicGroupNumber; +import org.openscience.cdk.smiles.smarts.parser.ASTReaction; +import org.openscience.cdk.smiles.smarts.parser.ASTRecursiveSmartsExpression; +import org.openscience.cdk.smiles.smarts.parser.ASTRingConnectivity; +import org.openscience.cdk.smiles.smarts.parser.ASTRingIdentifier; +import org.openscience.cdk.smiles.smarts.parser.ASTRingMembership; +import org.openscience.cdk.smiles.smarts.parser.ASTSimpleBond; +import org.openscience.cdk.smiles.smarts.parser.ASTSmallestRingSize; +import org.openscience.cdk.smiles.smarts.parser.ASTSmarts; +import org.openscience.cdk.smiles.smarts.parser.ASTStart; +import org.openscience.cdk.smiles.smarts.parser.ASTTotalConnectivity; +import org.openscience.cdk.smiles.smarts.parser.ASTTotalHCount; +import org.openscience.cdk.smiles.smarts.parser.ASTValence; +import org.openscience.cdk.smiles.smarts.parser.Node; +import org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants; +import org.openscience.cdk.smiles.smarts.parser.SMARTSParserVisitor; +import org.openscience.cdk.smiles.smarts.parser.SimpleNode; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * An AST tree visitor. It builds an instance of <code>QueryAtomContainer</code> @@ -146,7 +220,8 @@ public class SmartsQueryVisitor implements SMARTSParserVisitor { return atom; } - private final static LoggingTool logger = new LoggingTool( + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool( SmartsQueryVisitor.class); /** src/main/org/openscience/cdk/smiles/smarts/parser/visitor/SmartsQueryVisitor.java @@ -30,7 +30,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.math.MathTools; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; /** @@ -49,7 +50,8 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; */ public class RandomGenerator { - LoggingTool logger = new LoggingTool(RandomGenerator.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RandomGenerator.class); private IMolecule proposedStructure = null; private IMolecule molecule = null; src/main/org/openscience/cdk/structgen/RandomGenerator.java @@ -35,7 +35,8 @@ import org.openscience.cdk.graph.ConnectivityChecker; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.SaturationChecker; import org.openscience.cdk.tools.manipulator.BondManipulator; @@ -69,7 +70,8 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; */ public class SingleStructureRandomGenerator { - LoggingTool logger = new LoggingTool(SingleStructureRandomGenerator.class); + ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SingleStructureRandomGenerator.class); IAtomContainer atomContainer; SaturationChecker satCheck; src/main/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java @@ -33,7 +33,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.math.MathTools; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; /** @@ -49,7 +50,8 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; */ public class VicinitySampler { - private final static LoggingTool logger = new LoggingTool(VicinitySampler.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(VicinitySampler.class); int molCounter = 0; src/main/org/openscience/cdk/structgen/VicinitySampler.java @@ -28,7 +28,8 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.ConnectivityChecker; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.SaturationChecker; import org.openscience.cdk.tools.manipulator.BondManipulator; @@ -63,7 +64,8 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; */ public class PartialFilledStructureMerger { - private LoggingTool logger = new LoggingTool(PartialFilledStructureMerger.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PartialFilledStructureMerger.class); IAtomContainer atomContainer; SaturationChecker satCheck; src/main/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java @@ -33,7 +33,8 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.io.CMLReader; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AminoAcidManipulator; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @@ -49,7 +50,8 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class AminoAcids { - private static final LoggingTool logger = new LoggingTool(AminoAcids.class); + private static final ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AminoAcids.class); /** * Creates matrix with info about the bonds in the amino acids. src/main/org/openscience/cdk/templates/AminoAcids.java @@ -39,7 +39,8 @@ import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.MDLReader; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * This class contains methods for generating simple organic molecules. @@ -49,11 +50,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class MoleculeFactory { - private static LoggingTool logger = null; - - static { - logger = new LoggingTool(MoleculeFactory.class); - } + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MoleculeFactory.class); public static Molecule makeAlphaPinene() { Molecule mol = new Molecule(); src/main/org/openscience/cdk/templates/MoleculeFactory.java @@ -46,7 +46,8 @@ import org.openscience.cdk.tools.manipulator.RingSetManipulator; public class AtomTypeTools { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomTypeTools.class); HOSECodeGenerator hcg=null; SmilesGenerator sg=null; @@ -54,7 +55,6 @@ public class AtomTypeTools { * Constructor for the MMFF94AtomTypeMatcher object. */ public AtomTypeTools() { - logger = new LoggingTool(this); hcg = new HOSECodeGenerator(); } src/main/org/openscience/cdk/tools/AtomTypeTools.java @@ -25,21 +25,25 @@ */ package org.openscience.cdk.tools; +import java.util.ArrayList; +import java.util.List; +import java.util.Vector; + import org.openscience.cdk.AtomContainer; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.ConnectivityChecker; import org.openscience.cdk.graph.PathTools; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.ringsearch.RingPartitioner; import org.openscience.cdk.ringsearch.SSSRFinder; import org.openscience.cdk.smiles.SmilesGenerator; -import java.util.ArrayList; -import java.util.List; -import java.util.Vector; - /** * Generate ring and Murcko-like fragments. * <ul> @@ -70,7 +74,8 @@ import java.util.Vector; **/ public class GenerateFragments { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(GenerateFragments.class); private List murckoFragments =null; private List ringFragments=null; @@ -81,10 +86,6 @@ public class GenerateFragments { private boolean smilesToUpperCase=false; //private IChemObjectBuilder builder; - public GenerateFragments() { - logger = new LoggingTool(this); - } - /** * generates ring fragments from SSSR and RingPartitioner method * @param molecule src/main/org/openscience/cdk/tools/GenerateFragments.java @@ -63,7 +63,8 @@ import org.openscience.cdk.ringsearch.SSSRFinder; public class HOSECodeGenerator implements java.io.Serializable { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HOSECodeGenerator.class); private static final long serialVersionUID = -4353471818831864513L; @@ -165,8 +166,6 @@ public class HOSECodeGenerator implements java.io.Serializable @TestMethod("test1Sphere") public HOSECodeGenerator() { - logger = new LoggingTool(this); - sphereNodes = new ArrayList<TreeNode>(); sphereNodesWithAtoms = new ArrayList<IAtom>(); nextSphereNodes = new ArrayList<TreeNode>(); src/main/org/openscience/cdk/tools/HOSECodeGenerator.java @@ -19,14 +19,14 @@ */ package org.openscience.cdk.tools; -import org.apache.log4j.Logger; -import org.openscience.cdk.annotations.TestClass; -import org.openscience.cdk.annotations.TestMethod; - import java.io.BufferedReader; import java.io.PrintWriter; import java.io.StringReader; +import org.apache.log4j.Logger; +import org.openscience.cdk.annotations.TestClass; +import org.openscience.cdk.annotations.TestMethod; + /** * Useful for logging messages. Often used as a class static variable instantiated like: * <pre> @@ -82,7 +82,7 @@ import java.io.StringReader; * * <p>The class uses log4j as a backend if available, and System.out otherwise. * - * @cdk.module core + * @cdk.module log4j * @cdk.githash * @cdk.builddepends log4j.jar */ @@ -93,7 +93,7 @@ public class LoggingTool implements ILoggingTool { private boolean toSTDOUT = false; private Logger log4jLogger; - private LoggingTool logger; + private static ILoggingTool logger; private String classname; private int stackLength; // NOPMD src/main/org/openscience/cdk/tools/LoggingTool.java @@ -44,16 +44,10 @@ import org.openscience.cdk.interfaces.ILonePair; */ public class LonePairElectronChecker { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(LonePairElectronChecker.class); private static AtomTypeFactory factory; - /** - * Constructor of the LonePairElectronChecker object. - */ - public LonePairElectronChecker() { - logger = new LoggingTool(LonePairElectronChecker.class); - } - private void createAtomTypeFactory(IChemObjectBuilder builder) { if (factory == null) { factory = AtomTypeFactory.getInstance( src/main/org/openscience/cdk/tools/LonePairElectronChecker.java @@ -48,7 +48,8 @@ import java.util.Map; */ public class ProteinBuilderTool { - private static LoggingTool logger = new LoggingTool(ProteinBuilderTool.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ProteinBuilderTool.class); /** * Builds a protein by connecting a new amino acid at the N-terminus of the src/main/org/openscience/cdk/tools/ProteinBuilderTool.java @@ -69,11 +69,8 @@ public class SaturationChecker implements IValencyChecker, IDeduceBondOrderTool AtomTypeFactory structgenATF; - private LoggingTool logger; - - public SaturationChecker() { - logger = new LoggingTool(this); - } + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SaturationChecker.class); /** * @param builder the ChemObjectBuilder implementation used to construct the AtomType's. src/main/org/openscience/cdk/tools/SaturationChecker.java @@ -54,7 +54,8 @@ public class SmilesValencyChecker implements IValencyChecker, IDeduceBondOrderTo private String atomTypeList = null; protected AtomTypeFactory structgenATF; - protected LoggingTool logger; + protected static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SmilesValencyChecker.class); public SmilesValencyChecker() { this("org/openscience/cdk/dict/data/cdk-atom-types.owl"); @@ -62,7 +63,6 @@ public class SmilesValencyChecker implements IValencyChecker, IDeduceBondOrderTo public SmilesValencyChecker(String atomTypeList) { this.atomTypeList = atomTypeList; - logger = new LoggingTool(this); logger.info("Using configuration file: ", atomTypeList); } src/main/org/openscience/cdk/tools/SmilesValencyChecker.java @@ -79,7 +79,8 @@ import org.openscience.cdk.reaction.type.parameters.SetReactionCenter; @TestClass("org.openscience.cdk.tools.StructureResonanceGeneratorTest") public class StructureResonanceGenerator { - private LoggingTool logger = new LoggingTool(StructureResonanceGenerator.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(StructureResonanceGenerator.class); private List<IReactionProcess> reactionsList = new ArrayList<IReactionProcess>(); /**Generate resonance structure without looking at the symmetry*/ private boolean lookingSymmetry; src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java @@ -28,17 +28,17 @@ */ package org.openscience.cdk.tools.manipulator; +import java.io.IOException; +import java.util.Comparator; + import org.openscience.cdk.annotations.TestClass; import org.openscience.cdk.annotations.TestMethod; import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.IOException; -import java.util.Comparator; -import java.util.Iterator; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * <p>Compares two IAtomContainers for order with the following criteria with decreasing priority:</p> @@ -60,7 +60,8 @@ import java.util.Iterator; public class AtomContainerComparator implements Comparator { /** Configure LoggingTool */ - private LoggingTool logger = new LoggingTool(AtomContainerComparator.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(AtomContainerComparator.class); /** Creates a new instance of AtomContainerComparator */ public AtomContainerComparator() { src/main/org/openscience/cdk/tools/manipulator/AtomContainerComparator.java @@ -30,18 +30,19 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.interfaces.IAtom; -import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; -import org.openscience.cdk.interfaces.IElement; -import org.openscience.cdk.interfaces.IIsotope; -import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.Molecule; import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.Reaction; import org.openscience.cdk.config.AtomTypeFactory; import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IElement; +import org.openscience.cdk.interfaces.IIsotope; +import org.openscience.cdk.interfaces.IMoleculeSet; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; /** @@ -53,11 +54,8 @@ import org.openscience.cdk.tools.manipulator.BondManipulator; */ public class BasicValidator extends AbstractValidator { - private static LoggingTool logger; - - static { - logger = new LoggingTool(BasicValidator.class); - } + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(BasicValidator.class); public BasicValidator() { } src/main/org/openscience/cdk/validate/BasicValidator.java @@ -27,9 +27,10 @@ package org.openscience.cdk.validate; import java.util.Iterator; import java.util.Map; -import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.dict.DictionaryDatabase; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Validates the existence of references to dictionaries. @@ -40,11 +41,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class DictionaryValidator extends AbstractValidator { - private static LoggingTool logger; - - static { - logger = new LoggingTool(DictionaryValidator.class); - } + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(DictionaryValidator.class); private DictionaryDatabase db; src/main/org/openscience/cdk/validate/DictionaryValidator.java @@ -40,7 +40,8 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Engine that performs the validation by traversing the IChemObject @@ -58,11 +59,11 @@ import org.openscience.cdk.tools.LoggingTool; public class ValidatorEngine implements IValidator { private Map<String,IValidator> validators; - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ValidatorEngine.class); public ValidatorEngine() { validators = new Hashtable<String,IValidator>(); - logger = new LoggingTool(this); } public void addValidator(IValidator validator) { src/main/org/openscience/cdk/validate/ValidatorEngine.java @@ -28,7 +28,6 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; @@ -46,10 +45,6 @@ import java.util.Iterator; */ public class CDKTestCase { - static { - LoggingTool.configureLog4j(); - } - /** * Determines if slow JUnit tests are to be run. You can set this * from the command line when running Ant: src/test/org/openscience/cdk/CDKTestCase.java @@ -38,7 +38,8 @@ import org.openscience.cdk.io.MDLV2000Reader; import org.openscience.cdk.nonotify.NNMolecule; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.tools.AtomTypeTools; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; /** @@ -50,14 +51,13 @@ import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; */ public class MM2AtomTypeMatcherTest extends AbstractAtomTypeTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MM2AtomTypeMatcherTest.class); private static IMolecule testMolecule = null; private static Map<String, Integer> testedAtomTypes = new HashMap<String, Integer>(); @BeforeClass public static void setUp() throws Exception { - logger = new LoggingTool(MM2AtomTypeMatcherTest.class); - if (testMolecule == null) { // read the test file and percieve atom types AtomTypeTools att=new AtomTypeTools(); src/test/org/openscience/cdk/atomtype/MM2AtomTypeMatcherTest.java @@ -43,7 +43,8 @@ import org.openscience.cdk.io.MDLV2000Reader; import org.openscience.cdk.nonotify.NNMolecule; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.tools.AtomTypeTools; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; /** @@ -55,7 +56,8 @@ import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; */ public class MMFF94AtomTypeMatcherTest extends AbstractAtomTypeTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MMFF94AtomTypeMatcherTest.class); private final IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance(); private static IMolecule testMolecule = null; @@ -63,8 +65,6 @@ public class MMFF94AtomTypeMatcherTest extends AbstractAtomTypeTest { private static Map<String, Integer> testedAtomTypes = new HashMap<String, Integer>(); @BeforeClass public static void setUpTestMolecule() throws Exception { - logger = new LoggingTool(MMFF94AtomTypeMatcherTest.class); - if (testMolecule == null) { //logger.debug("**** START ATOMTYPE TEST ******"); AtomTypeTools att=new AtomTypeTools(); src/test/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcherTest.java @@ -32,14 +32,15 @@ import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; - +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-fingerprint */ public class EStateFingerprinterTest extends AbstractFingerprinterTest { - private static LoggingTool logger = new LoggingTool(EStateFingerprinterTest.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(EStateFingerprinterTest.class); public IFingerprinter getFingerprinter() { return new EStateFingerprinter(); src/test/org/openscience/cdk/fingerprint/EStateFingerprinterTest.java @@ -40,7 +40,8 @@ import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.io.MDLRXNV2000Reader; import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.templates.MoleculeFactory; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-standard @@ -48,7 +49,8 @@ import org.openscience.cdk.tools.LoggingTool; public class FingerprinterTest extends AbstractFingerprinterTest { boolean standAlone = false; - private static LoggingTool logger = new LoggingTool(FingerprinterTest.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(FingerprinterTest.class); public IFingerprinter getFingerprinter() { return new Fingerprinter(); src/test/org/openscience/cdk/fingerprint/FingerprinterTest.java @@ -30,6 +30,7 @@ import java.util.BitSet; import org.junit.Assert; import org.junit.Test; +import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; @@ -38,14 +39,16 @@ import org.openscience.cdk.io.MDLV2000Reader; import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-standard */ public class GraphOnlyFingerprinterTest extends AbstractFingerprinterTest { - private static LoggingTool logger = new LoggingTool(FingerprinterTest.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(FingerprinterTest.class); public IFingerprinter getFingerprinter() { return new GraphOnlyFingerprinter(); src/test/org/openscience/cdk/fingerprint/GraphOnlyFingerprinterTest.java @@ -34,7 +34,8 @@ import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** @@ -42,7 +43,8 @@ import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; */ public class MACCSFingerprinterTest extends AbstractFingerprinterTest { - private static LoggingTool logger = new LoggingTool(MACCSFingerprinterTest.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MACCSFingerprinterTest.class); public IFingerprinter getFingerprinter() { return new MACCSFingerprinter(); src/test/org/openscience/cdk/fingerprint/MACCSFingerprinterTest.java @@ -26,6 +26,8 @@ */ package org.openscience.cdk.fingerprint; +import java.util.BitSet; + import org.junit.Assert; import org.junit.Before; import org.junit.Test; @@ -38,18 +40,14 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.CDKHydrogenAdder; -import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import java.util.BitSet; - /** * @cdk.module test-fingerprint */ public class PubchemFingerprinterTest extends AbstractFingerprinterTest { SmilesParser parser; - private static LoggingTool logger = new LoggingTool(PubchemFingerprinterTest.class); public IFingerprinter getFingerprinter() { return new PubchemFingerprinter(); src/test/org/openscience/cdk/fingerprint/PubchemFingerprinterTest.java @@ -48,7 +48,8 @@ import org.openscience.cdk.io.MDLReader; import org.openscience.cdk.io.MDLV2000Reader; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.LonePairElectronChecker; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; @@ -62,11 +63,11 @@ public class ConjugatedPiSystemsDetectorTest extends CDKTestCase private static IChemObjectBuilder builder; private static LonePairElectronChecker lpcheck; - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ConjugatedPiSystemsDetectorTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(ConjugatedPiSystemsDetectorTest.class); builder = NoNotificationChemObjectBuilder.getInstance(); lpcheck = new LonePairElectronChecker(); } src/test/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java @@ -28,7 +28,8 @@ import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.layout.StructureDiagramGenerator; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** *@author steinbeck @@ -37,7 +38,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class SmilesParserTest { - private LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SmilesParserTest.class); boolean standAlone = false; private SmilesParser sp; @@ -48,7 +50,6 @@ public class SmilesParserTest { */ public SmilesParserTest(String name) { sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); - logger = new LoggingTool(this); } public void testSMILES() { src/test/org/openscience/cdk/gui/smiles/SmilesParserTest.java @@ -40,7 +40,8 @@ import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading CTX files using a test file. @@ -51,10 +52,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class CTXReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CTXReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(CTXReaderTest.class); setSimpleChemObjectReader(new CTXReader(), "data/ctx/methanol_with_descriptors.ctx"); } src/test/org/openscience/cdk/io/CTXReaderTest.java @@ -35,7 +35,8 @@ import org.junit.Test; import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.IResourceFormat; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Tests whether all Reader and Writer classes can be instantiated. @@ -48,7 +49,8 @@ public class ChemObjectIOInstantionTests extends CDKTestCase { private final static String IO_FORMATS_LIST = "io-formats.set"; - private static LoggingTool logger = new LoggingTool(ChemObjectIOInstantionTests.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ChemObjectIOInstantionTests.class); private static List<IChemFormat> formats = null; src/test/org/openscience/cdk/io/ChemObjectIOInstantionTests.java @@ -37,7 +37,8 @@ import org.junit.Test; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL mol files using one test file. @@ -48,10 +49,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class CrystClustReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CrystClustReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(CrystClustReaderTest.class); setSimpleChemObjectReader(new CrystClustReader(), "data/crystclust/estron.crystclust"); } src/test/org/openscience/cdk/io/CrystClustReaderTest.java @@ -38,7 +38,8 @@ import org.openscience.cdk.ChemObject; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IChemFile; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -50,10 +51,10 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class HINReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HINReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(HINReaderTest.class); setSimpleChemObjectReader(new HINReader(), "data/hin/benzene.hin"); } src/test/org/openscience/cdk/io/HINReaderTest.java @@ -34,7 +34,8 @@ import org.junit.BeforeClass; import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading INChI plain text files. @@ -46,10 +47,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class INChIPlainTextReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(INChIPlainTextReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(INChIPlainTextReaderTest.class); setSimpleChemObjectReader(new INChIPlainTextReader(), "data/inchi/guanine.inchi"); } src/test/org/openscience/cdk/io/INChIPlainTextReaderTest.java @@ -35,7 +35,8 @@ import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading INChI files using one test file. @@ -47,10 +48,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class INChIReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(INChIReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(INChIReaderTest.class); setSimpleChemObjectReader(new INChIReader(), "data/inchi/guanine.inchi.xml"); } src/test/org/openscience/cdk/io/INChIReaderTest.java @@ -48,7 +48,8 @@ import org.openscience.cdk.nonotify.NNChemFile; import org.openscience.cdk.nonotify.NNChemModel; import org.openscience.cdk.nonotify.NNReaction; import org.openscience.cdk.nonotify.NNReactionSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL RXN files using one test file. @@ -59,10 +60,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class MDLRXNReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLRXNReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(MDLRXNReaderTest.class); setSimpleChemObjectReader(new MDLRXNReader(), "data/mdl/reaction-1.rxn"); } src/test/org/openscience/cdk/io/MDLRXNReaderTest.java @@ -35,7 +35,8 @@ import org.openscience.cdk.Reaction; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.io.IChemObjectReader.Mode; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL RXN files using one test file. @@ -46,10 +47,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class MDLRXNV2000ReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLRXNV2000ReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(MDLRXNV2000ReaderTest.class); setSimpleChemObjectReader(new MDLRXNV2000Reader(), "data/mdl/0024.stg02.rxn"); } src/test/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java @@ -38,7 +38,8 @@ import org.openscience.cdk.Reaction; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.io.IChemObjectReader.Mode; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL RXN files using one test file. @@ -49,10 +50,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class MDLRXNV3000ReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLRXNV3000ReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(MDLRXNV3000ReaderTest.class); setSimpleChemObjectReader(new MDLRXNV3000Reader(), "data/mdl/reaction_v3.rxn"); } src/test/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java @@ -41,7 +41,8 @@ import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.nonotify.NNMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -55,10 +56,10 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class MDLReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(MDLReaderTest.class); setSimpleChemObjectReader(new MDLReader(), "data/mdl/Strychnine_nichtOK.mol"); } src/test/org/openscience/cdk/io/MDLReaderTest.java @@ -53,7 +53,8 @@ import org.openscience.cdk.interfaces.IPseudoAtom; import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.io.listener.PropertiesListener; import org.openscience.cdk.nonotify.NNMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @@ -68,10 +69,10 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class MDLV2000ReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLV2000ReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(MDLV2000ReaderTest.class); setSimpleChemObjectReader(new MDLV2000Reader(), "data/mdl/bug682233.mol"); } src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java @@ -35,7 +35,8 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.nonotify.NNMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL V3000 mol files using one test file. @@ -47,10 +48,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class MDLV3000ReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDLV3000ReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(MDLV3000ReaderTest.class); setSimpleChemObjectReader(new MDLV3000Reader(), "data/mdl/molV3000.mol"); } src/test/org/openscience/cdk/io/MDLV3000ReaderTest.java @@ -50,7 +50,8 @@ import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; /** @@ -62,10 +63,10 @@ import org.openscience.cdk.tools.manipulator.ChemModelManipulator; */ public class Mol2ReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(Mol2ReaderTest.class); @BeforeClass public static void setup() { - logger = new LoggingTool(Mol2ReaderTest.class); setSimpleChemObjectReader(new Mol2Reader(), "data/mol2/fromWebsite.mol2"); } src/test/org/openscience/cdk/io/Mol2ReaderTest.java @@ -34,7 +34,8 @@ import org.openscience.cdk.CDKConstants; import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -42,11 +43,10 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class PCCompoundASNReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PCCompoundASNReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(PCCompoundASNReaderTest.class); - System.out.println("Foo"); setSimpleChemObjectReader(new PCCompoundASNReader(), "data/asn/pubchem/cid1.asn"); } src/test/org/openscience/cdk/io/PCCompoundASNReaderTest.java @@ -34,17 +34,18 @@ import org.junit.BeforeClass; import org.junit.Test; import org.openscience.cdk.Molecule; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-io */ public class PCCompoundXMLReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PCCompoundXMLReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(PCCompoundXMLReaderTest.class); setSimpleChemObjectReader(new PCCompoundXMLReader(), "data/asn/pubchem/cid1145.xml"); } src/test/org/openscience/cdk/io/PCCompoundXMLReaderTest.java @@ -32,17 +32,18 @@ import org.junit.Test; import org.openscience.cdk.Molecule; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IPseudoAtom; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-io */ public class PCSubstanceXMLReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(PCSubstanceXMLReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(Mol2ReaderTest.class); setSimpleChemObjectReader(new Mol2Reader(), "data/asn/pubchem/sid577309.xml"); } src/test/org/openscience/cdk/io/PCSubstanceXMLReaderTest.java @@ -34,7 +34,8 @@ import org.junit.BeforeClass; import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.MoleculeSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL mol files using one test file. @@ -45,10 +46,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class SMILESReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SMILESReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(SMILESReaderTest.class); setSimpleChemObjectReader(new SMILESReader(), "data/smiles/smiles.smi"); } src/test/org/openscience/cdk/io/SMILESReaderTest.java @@ -35,17 +35,18 @@ import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.Crystal; import org.openscience.cdk.geometry.CrystalGeometryTools; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-io */ public class ShelXReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ShelXReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(ShelXReaderTest.class); setSimpleChemObjectReader(new ShelXReader(), "data/shelx/frame_1.res"); } src/test/org/openscience/cdk/io/ShelXReaderTest.java @@ -33,17 +33,18 @@ import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; import org.openscience.cdk.ChemFile; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-extra */ public class VASPReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(VASPReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(VASPReaderTest.class); setSimpleChemObjectReader(new VASPReader(), "data/vasp/LiMoS2_optimisation_ISIF3.vasp"); } src/test/org/openscience/cdk/io/VASPReaderTest.java @@ -31,7 +31,8 @@ import org.junit.BeforeClass; import org.junit.Test; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading XYZ files using a test file. @@ -42,10 +43,10 @@ import org.openscience.cdk.tools.LoggingTool; */ public class XYZReaderTest extends SimpleChemObjectReaderTest { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(XYZReaderTest.class); @BeforeClass public static void setup() throws Exception { - logger = new LoggingTool(XYZReaderTest.class); setSimpleChemObjectReader(new XYZReader(), "data/xyz/viagra.xyz"); } src/test/org/openscience/cdk/io/XYZReaderTest.java @@ -28,7 +28,6 @@ import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; import org.openscience.cdk.ChemFile; -import org.openscience.cdk.tools.LoggingTool; /** * @cdk.module test-io src/test/org/openscience/cdk/io/ZMatrixReaderTest.java @@ -56,7 +56,8 @@ import org.openscience.cdk.io.ISimpleChemObjectReader; import org.openscience.cdk.io.PDBReader; import org.openscience.cdk.nonotify.NNChemFile; import org.openscience.cdk.protein.data.PDBPolymer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -68,7 +69,8 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class CML2Test extends CDKTestCase { - private static LoggingTool logger = new LoggingTool(CML2Test.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CML2Test.class); @Test public void testFile3() throws Exception { String filename = "data/cml/3.cml"; src/test/org/openscience/cdk/io/cml/CML2Test.java @@ -36,9 +36,9 @@ import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.Molecule; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.ReactionScheme; import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector; import org.openscience.cdk.config.Elements; @@ -66,7 +66,8 @@ import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor; import org.openscience.cdk.templates.MoleculeFactory; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading CML 2 files using a few test files @@ -77,7 +78,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class CML2WriterTest extends CDKTestCase { - private static LoggingTool logger = new LoggingTool(CML2WriterTest.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CML2WriterTest.class); @Test public void testCMLWriterBenzene() throws Exception { StringWriter writer = new StringWriter(); src/test/org/openscience/cdk/io/cml/CML2WriterTest.java @@ -58,7 +58,8 @@ import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IMolecularDescriptor; import org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor; import org.openscience.cdk.templates.MoleculeFactory; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.BondManipulator; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @@ -72,11 +73,11 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class CMLRoundTripTest extends CDKTestCase { - private static LoggingTool logger; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CMLRoundTripTest.class); private static Convertor convertor; @BeforeClass public static void setup() { - logger = new LoggingTool(CMLRoundTripTest.class); convertor = new Convertor(false, ""); convertor.registerCustomizer(new QSARCustomizer()); } src/test/org/openscience/cdk/io/cml/CMLRoundTripTest.java @@ -39,7 +39,8 @@ import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.io.CMLReader; import org.openscience.cdk.libio.cml.Convertor; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Helper tool for round tripping CDK classes via CML. @@ -50,7 +51,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class CMLRoundTripTool extends CDKTestCase { - private static LoggingTool logger = new LoggingTool(CMLRoundTripTool.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(CMLRoundTripTool.class); private static Convertor convertor = new Convertor(true, null); /** src/test/org/openscience/cdk/io/cml/CMLRoundTripTool.java @@ -39,7 +39,8 @@ import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.CMLReader; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for reading CML files using a few test files @@ -50,7 +51,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class JChemPaintTest extends CDKTestCase { - private LoggingTool logger = new org.openscience.cdk.tools.LoggingTool(this); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(JChemPaintTest.class); /** * This one tests a CML2 file. src/test/org/openscience/cdk/io/cml/JChemPaintTest.java @@ -42,7 +42,8 @@ import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; import org.openscience.cdk.io.CMLReader; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for reading CML files using a few test files @@ -53,7 +54,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class JmolTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(JmolTest.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(JmolTest.class); /** * Now come the actual tests... src/test/org/openscience/cdk/io/cml/JmolTest.java @@ -38,7 +38,8 @@ import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.CMLReader; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for reading CML files using a few test files @@ -49,7 +50,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class JumboTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(JumboTest.class); /** * Now come the actual tests... src/test/org/openscience/cdk/io/cml/JumboTest.java @@ -1,14 +1,14 @@ package org.openscience.cdk.io.iterator; +import java.io.InputStream; + import org.junit.Assert; -import org.junit.BeforeClass; import org.junit.Test; +import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.ConformerContainer; import org.openscience.cdk.DefaultChemObjectBuilder; -import org.openscience.cdk.CDKTestCase; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.InputStream; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL mol files using one test file. @@ -19,12 +19,8 @@ import java.io.InputStream; */ public class IteratingMDLConformerReaderTest extends CDKTestCase { - private static LoggingTool logger; - - @BeforeClass - public static void setup() { - logger = new LoggingTool(IteratingMDLConformerReaderTest.class); - } + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingMDLConformerReaderTest.class); @Test public void testSDF() throws Exception { src/test/org/openscience/cdk/io/iterator/IteratingMDLConformerReaderTest.java @@ -43,7 +43,8 @@ import org.openscience.cdk.io.formats.MDLV2000Format; import org.openscience.cdk.io.listener.IChemObjectIOListener; import org.openscience.cdk.io.listener.PropertiesListener; import org.openscience.cdk.io.setting.IOSetting; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading MDL mol files using one test file. @@ -53,7 +54,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class IteratingMDLReaderTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingMDLReaderTest.class); @Test public void testSDF() throws Exception { String filename = "data/mdl/test2.sdf"; src/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java @@ -28,17 +28,19 @@ import java.io.InputStream; import org.junit.Assert; import org.junit.Test; +import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.Molecule; -import org.openscience.cdk.CDKTestCase; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-io */ public class IteratingPCCompoundASNReaderTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingPCCompoundASNReaderTest.class); @Test public void testList() throws Exception { String filename = "data/asn/pubchem/list.asn"; src/test/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReaderTest.java @@ -29,18 +29,20 @@ import java.io.InputStreamReader; import org.junit.Assert; import org.junit.Test; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-io */ public class IteratingPCCompoundXMLReaderTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingPCCompoundXMLReaderTest.class); @Test public void testList() throws Exception { String filename = "data/asn/pubchem/aceticAcids38.xml"; src/test/org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReaderTest.java @@ -29,11 +29,12 @@ import java.io.InputStreamReader; import org.junit.Assert; import org.junit.Test; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IChemModel; import org.openscience.cdk.interfaces.IChemSequence; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; /** @@ -41,7 +42,8 @@ import org.openscience.cdk.tools.manipulator.ChemModelManipulator; */ public class IteratingPCSubstancesXMLReaderTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingPCSubstancesXMLReaderTest.class); @Test public void testTaxols() throws Exception { String filename = "data/asn/pubchem/taxols.xml"; src/test/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReaderTest.java @@ -27,18 +27,18 @@ * */ package org.openscience.cdk.io.iterator; +import java.io.InputStream; + import org.junit.Assert; -import org.junit.Before; import org.junit.Test; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.Molecule; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.Molecule; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.InputStream; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * TestCase for the reading SMILES mol files using one test file. @@ -48,12 +48,8 @@ import java.io.InputStream; */ public class IteratingSMILESReaderTest extends CDKTestCase { - private static LoggingTool logger; - - @Before - public void setup() { - logger = new LoggingTool(IteratingSMILESReaderTest.class); - } + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(IteratingSMILESReaderTest.class); @Test public void testSMILESFileWithNames() throws Exception { src/test/org/openscience/cdk/io/iterator/IteratingSMILESReaderTest.java @@ -28,11 +28,12 @@ import java.io.File; import org.junit.Assert; import org.junit.Test; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * Test for {@link RandomAccessSDFReader}. @@ -42,7 +43,8 @@ import org.openscience.cdk.tools.LoggingTool; */ public class RandomAccessTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(RandomAccessTest.class); @Test public void test() throws Exception { String filename = "src/test/data/mdl/test2.sdf"; src/test/org/openscience/cdk/io/random/RandomAccessTest.java @@ -31,14 +31,15 @@ import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.Bond; +import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; import org.openscience.cdk.Molecule; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.geometry.GeometryTools; import org.openscience.cdk.io.MDLReader; import org.openscience.cdk.io.IChemObjectReader.Mode; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-sdg @@ -46,7 +47,8 @@ import org.openscience.cdk.tools.LoggingTool; public class HydrogenPlacerTest extends CDKTestCase { public boolean standAlone = false; - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(HydrogenPlacerTest.class); /** * @cdk.bug 933572 src/test/org/openscience/cdk/layout/HydrogenPlacerTest.java @@ -28,16 +28,16 @@ import java.io.InputStream; import java.util.Vector; import org.junit.Assert; -import org.junit.BeforeClass; import org.junit.Test; -import org.openscience.cdk.Molecule; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.Molecule; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.io.CMLReader; import org.openscience.cdk.nonotify.NNChemFile; import org.openscience.cdk.smiles.SmilesParser; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -55,17 +55,11 @@ public class OverlapResolverTest extends CDKTestCase { * Description of the Field */ public boolean standAlone = false; - private static LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(OverlapResolverTest.class); StructureDiagramGenerator sdg = null; /** - * The JUnit setup method - */ - @BeforeClass public static void setUp() throws Exception { - logger = new LoggingTool(OverlapResolverTest.class); - } - - /** * A unit test for JUnit * *@exception Exception Description of the Exception src/test/org/openscience/cdk/layout/OverlapResolverTest.java @@ -25,8 +25,8 @@ import java.io.InputStream; import org.junit.Assert; import org.junit.BeforeClass; import org.junit.Test; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.interfaces.IAtomContainerSet; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IMolecule; @@ -35,7 +35,8 @@ import org.openscience.cdk.io.MDLReader; import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.templates.MoleculeFactory; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-sdg @@ -46,7 +47,8 @@ import org.openscience.cdk.tools.LoggingTool; public class TemplateHandlerTest extends CDKTestCase { public boolean standAlone = false; - private static LoggingTool logger = null; + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(TemplateHandlerTest.class); private static SmilesParser sp = null; private static StructureDiagramGenerator sdg = null; @@ -55,7 +57,6 @@ public class TemplateHandlerTest extends CDKTestCase { * The JUnit setup method */ @BeforeClass public static void setUp() throws Exception { - logger = new LoggingTool(TemplateHandlerTest.class); sdg = new StructureDiagramGenerator(); sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); } src/test/org/openscience/cdk/layout/TemplateHandlerTest.java @@ -33,8 +33,8 @@ import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.ChemFile; import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.ChemFile; import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.interfaces.IChemFile; import org.openscience.cdk.interfaces.IMolecule; @@ -42,7 +42,8 @@ import org.openscience.cdk.io.CMLReader; import org.openscience.cdk.io.CMLWriter; import org.openscience.cdk.io.cml.MDMoleculeConvention; import org.openscience.cdk.libio.cml.MDMoleculeCustomizer; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** @@ -50,7 +51,8 @@ import org.openscience.cdk.tools.manipulator.ChemFileManipulator; */ public class MDMoleculeTest extends CDKTestCase { - private LoggingTool logger = new LoggingTool(this); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(MDMoleculeTest.class); /** * Test an MDMolecule with residues and charge groups src/test/org/openscience/cdk/libio/md/MDMoleculeTest.java @@ -20,8 +20,6 @@ */ package org.openscience.cdk.modeling.forcefield; -import java.io.File; -import java.io.FileWriter; import java.io.InputStream; import java.util.Map; @@ -37,10 +35,10 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.MDLV2000Reader; -import org.openscience.cdk.io.MDLWriter; import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; @@ -68,7 +66,8 @@ public class ForceFieldTests extends CDKTestCase { String input; - private LoggingTool logger = new LoggingTool(ForceFieldTests.class); + private ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ForceFieldTests.class); private boolean standAlone = false; /** src/test/org/openscience/cdk/modeling/forcefield/ForceFieldTests.java @@ -48,7 +48,6 @@ import org.openscience.cdk.graph.SpanningTreeTest; import org.openscience.cdk.graph.matrix.AdjacencyMatrixTest; import org.openscience.cdk.tools.DataFeaturesTest; import org.openscience.cdk.tools.LoggingToolFactoryTest; -import org.openscience.cdk.tools.LoggingToolTest; import org.openscience.cdk.tools.manipulator.BondManipulatorTest; /** @@ -88,7 +87,6 @@ import org.openscience.cdk.tools.manipulator.BondManipulatorTest; CDKExceptionTest.class, NoSuchAtomExceptionTest.class, NoSuchAtomTypeExceptionTest.class, - LoggingToolTest.class, LoggingToolFactoryTest.class, BondManipulatorTest.class, AdjacencyMatrixTest.class, src/test/org/openscience/cdk/modulesuites/McoreTests.java @@ -48,7 +48,7 @@ public class RingPartitionerTest extends CDKTestCase { static boolean standAlone = false; - //private LoggingTool logger = null; + //private static ILoggingTool logger = null; src/test/org/openscience/cdk/ringsearch/RingPartitionerTest.java @@ -20,27 +20,33 @@ */ package org.openscience.cdk.ringsearch; +import java.io.InputStream; +import java.util.Iterator; + import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.DefaultChemObjectBuilder; import org.openscience.cdk.CDKTestCase; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.io.IChemObjectReader.Mode; +import org.openscience.cdk.DefaultChemObjectBuilder; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IChemObject; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IRing; +import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.io.MDLV2000Reader; +import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.templates.MoleculeFactory; -import org.openscience.cdk.tools.LoggingTool; - -import java.io.InputStream; -import java.util.Iterator; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-standard */ public class SSSRFinderTest extends CDKTestCase { - private final LoggingTool logger = new LoggingTool(SSSRFinderTest.class); + private final ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SSSRFinderTest.class); public SSSRFinderTest() { super(); src/test/org/openscience/cdk/ringsearch/SSSRFinderTest.java @@ -1,27 +1,26 @@ package org.openscience.cdk.similarity; +import java.io.IOException; +import java.io.InputStream; +import java.util.List; + import org.junit.Assert; import org.junit.Test; +import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemObject; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.io.MDLV2000Reader; +import org.openscience.cdk.io.IChemObjectReader.Mode; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; -import java.io.IOException; -import java.io.InputStream; -import java.util.List; - /** * @cdk.module test-fingerprint */ public class DistanceMomentTest extends CDKTestCase { boolean standAlone = false; - //private static LoggingTool logger = new LoggingTool(TanimotoTest.class); private IAtomContainer loadMolecule(String path) throws Exception { InputStream ins = this.getClass().getClassLoader().getResourceAsStream(path); src/test/org/openscience/cdk/similarity/DistanceMomentTest.java @@ -20,6 +20,9 @@ */ package org.openscience.cdk.smiles.smarts.parser; +import java.io.InputStream; +import java.util.List; + import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.CDKTestCase; @@ -34,12 +37,10 @@ import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.smiles.smarts.SMARTSQueryTool; -import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; -import java.io.InputStream; -import java.util.List; - /** * JUnit test routines for the SMARTS substructure search. * @@ -49,7 +50,8 @@ import java.util.List; */ public class SMARTSSearchTest extends CDKTestCase { - private static LoggingTool logger = new LoggingTool(SMARTSSearchTest.class); + private static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(SMARTSSearchTest.class); private int[] match(String smarts, String smiles) throws Exception { SMARTSQueryTool sqt = new SMARTSQueryTool(smarts); src/test/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java @@ -20,13 +20,31 @@ */ package org.openscience.cdk.tools; +import java.io.InputStream; +import java.util.Iterator; +import java.util.List; + +import javax.vecmath.Point2d; + import org.junit.Assert; import org.junit.Test; -import org.openscience.cdk.*; +import org.openscience.cdk.Atom; +import org.openscience.cdk.Bond; +import org.openscience.cdk.CDKConstants; +import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.ChemFile; +import org.openscience.cdk.ChemObject; +import org.openscience.cdk.Molecule; import org.openscience.cdk.atomtype.CDKAtomTypeMatcher; import org.openscience.cdk.config.Elements; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IAtomType; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IChemFile; +import org.openscience.cdk.interfaces.IMolecularFormula; +import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.MDLV2000Reader; import org.openscience.cdk.nonotify.NNAtom; import org.openscience.cdk.nonotify.NNMolecule; @@ -36,11 +54,6 @@ import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator; -import javax.vecmath.Point2d; -import java.io.InputStream; -import java.util.Iterator; -import java.util.List; - /** * Tests CDK's hydrogen adding capabilities in terms of * example molecules. @@ -52,7 +65,6 @@ import java.util.List; */ public class CDKHydrogenAdderTest extends CDKTestCase { -// private final static LoggingTool logger = new LoggingTool(CDKHydrogenAdderTest.class); private final static CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(NoNotificationChemObjectBuilder.getInstance()); private final static CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(NoNotificationChemObjectBuilder.getInstance()); src/test/org/openscience/cdk/tools/CDKHydrogenAdderTest.java @@ -23,10 +23,9 @@ package org.openscience.cdk.tools; import org.junit.Assert; import org.junit.Test; import org.openscience.cdk.CDKTestCase; -import org.openscience.cdk.tools.LoggingTool; /** - * @cdk.module test-core + * @cdk.module test-log4j */ public class LoggingToolTest extends CDKTestCase { src/test/org/openscience/cdk/tools/LoggingToolTest.java @@ -20,30 +20,48 @@ */ package org.openscience.cdk.tools.manipulator; -import org.junit.Assert; -import org.junit.Before; -import org.junit.Test; -import org.openscience.cdk.*; -import org.openscience.cdk.interfaces.*; -import org.openscience.cdk.io.IChemObjectReader.Mode; -import org.openscience.cdk.io.MDLReader; -import org.openscience.cdk.CDKTestCase; -import org.openscience.cdk.tools.IDCreator; -import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.tools.manipulator.ChemFileManipulator; - import java.io.InputStream; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Set; +import org.junit.Assert; +import org.junit.Before; +import org.junit.Test; +import org.openscience.cdk.Atom; +import org.openscience.cdk.Bond; +import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.ChemFile; +import org.openscience.cdk.ChemModel; +import org.openscience.cdk.ChemObject; +import org.openscience.cdk.ChemSequence; +import org.openscience.cdk.Molecule; +import org.openscience.cdk.MoleculeSet; +import org.openscience.cdk.Reaction; +import org.openscience.cdk.ReactionSet; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IChemFile; +import org.openscience.cdk.interfaces.IChemModel; +import org.openscience.cdk.interfaces.IChemSequence; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; +import org.openscience.cdk.interfaces.IReaction; +import org.openscience.cdk.interfaces.IReactionSet; +import org.openscience.cdk.io.MDLReader; +import org.openscience.cdk.io.IChemObjectReader.Mode; +import org.openscience.cdk.tools.IDCreator; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; + /** * @cdk.module test-standard */ public class ChemFileManipulatorTest extends CDKTestCase { - private final static LoggingTool logger = new LoggingTool(ChemFileManipulatorTest.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ChemFileManipulatorTest.class); IMolecule molecule1 = null; IMolecule molecule2 = null; src/test/org/openscience/cdk/tools/manipulator/ChemFileManipulatorTest.java @@ -20,30 +20,46 @@ */ package org.openscience.cdk.tools.manipulator; +import java.io.InputStream; +import java.util.HashSet; +import java.util.List; +import java.util.Set; + import org.junit.Assert; import org.junit.Before; import org.junit.Test; -import org.openscience.cdk.*; -import org.openscience.cdk.interfaces.*; +import org.openscience.cdk.Atom; +import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.Bond; +import org.openscience.cdk.CDKTestCase; +import org.openscience.cdk.ChemModel; +import org.openscience.cdk.ChemObject; +import org.openscience.cdk.Molecule; +import org.openscience.cdk.MoleculeSet; +import org.openscience.cdk.Reaction; +import org.openscience.cdk.ReactionSet; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBond; +import org.openscience.cdk.interfaces.IChemModel; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.interfaces.IMoleculeSet; +import org.openscience.cdk.interfaces.IReaction; +import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.io.MDLRXNV2000Reader; import org.openscience.cdk.io.MDLV2000Reader; import org.openscience.cdk.io.IChemObjectReader.Mode; -import org.openscience.cdk.CDKTestCase; import org.openscience.cdk.tools.IDCreator; -import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.tools.manipulator.ChemModelManipulator; - -import java.io.InputStream; -import java.util.HashSet; -import java.util.List; -import java.util.Set; +import org.openscience.cdk.tools.ILoggingTool; +import org.openscience.cdk.tools.LoggingToolFactory; /** * @cdk.module test-standard */ public class ChemModelManipulatorTest extends CDKTestCase { - private final static LoggingTool logger = new LoggingTool(ChemModelManipulatorTest.class); + private final static ILoggingTool logger = + LoggingToolFactory.createLoggingTool(ChemModelManipulatorTest.class); IMolecule molecule1 = null; IMolecule molecule2 = null; src/test/org/openscience/cdk/tools/manipulator/ChemModelManipulatorTest.java src/META-INF/atomtype.libdepends src/META-INF/core.libdepends c6c8d38a9373064cdec5f9bcadcfc92200486493 Egon Willighagen egonw@users.sourceforge.net http://github.com/egonw/cdk/commit/112f64d6a08feb07cf8c133211a65e3a03a794ca 112f64d6a08feb07cf8c133211a65e3a03a794ca 2009-11-03T19:59:57-08:00 2009-07-03T13:56:30-07:00 Moved the log4j.jar depending LoggingTool into a separate module Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> 955eb52a7fcbbd9d779f0036da9b93b9bf2f818a Rajarshi Guha rajarshi.guha@gmail.com