Fifth batch of removal of TestClass/-Method use

Change-Id: Id4e8ecf935cc519f529766dc1b3efe1b16b0078d Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Jan 16, 2015 · fb51e91 · fb51e91
1 parent 1f3633c
commit fb51e91
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diff --git a/misc/extra/src/main/java/org/openscience/cdk/Association.java b/misc/extra/src/main/java/org/openscience/cdk/Association.java
@@ -18,8 +18,6 @@
  */
 package org.openscience.cdk;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IAtom;
 
 /**
@@ -33,7 +31,6 @@
  * @cdk.keyword association
  * @cdk.keyword bond
  */
-@TestClass("org.openscience.cdk.AssociationTest")
 public class Association extends ElectronContainer implements java.io.Serializable, Cloneable {
 
     /**
@@ -60,7 +57,6 @@ public class Association extends ElectronContainer implements java.io.Serializab
      * @param atom2 An atom to be associated with another atom
      * @see org.openscience.cdk.Atom
      */
-    @TestMethod("testAssociation_IAtom_IAtom")
     public Association(IAtom atom1, IAtom atom2) {
         atoms = new IAtom[2];
         atoms[0] = atom1;
@@ -73,7 +69,6 @@ public Association(IAtom atom1, IAtom atom2) {
      *
      * @see org.openscience.cdk.Atom
      */
-    @TestMethod("testAssociation")
     public Association() {
         atoms = new Atom[2];
         atomCount = 0;
@@ -86,7 +81,6 @@ public Association() {
      *
      * @see    #setAtoms
      */
-    @TestMethod("testGetAtoms")
     public IAtom[] getAtoms() {
         IAtom[] returnAtoms = new Atom[atomCount];
         System.arraycopy(this.atoms, 0, returnAtoms, 0, returnAtoms.length);
@@ -100,7 +94,6 @@ public IAtom[] getAtoms() {
      *
      * @see    #getAtoms
      */
-    @TestMethod("testSetAtoms")
     public void setAtoms(IAtom[] atoms) {
         this.atoms = atoms;
         notifyChanged();
@@ -111,7 +104,6 @@ public void setAtoms(IAtom[] atoms) {
      *
      * @return The number of Atoms in this Association
      */
-    @TestMethod("testGetAtomCount")
     public int getAtomCount() {
         return atomCount;
     }
@@ -121,7 +113,6 @@ public int getAtomCount() {
      *
      * @return The number of electrons in a Association.
      */
-    @TestMethod("testGetAtomAt")
     @Override
     public Integer getElectronCount() {
         return 0;
@@ -135,7 +126,6 @@ public Integer getElectronCount() {
      *
      * @see     #setAtomAt
      */
-    @TestMethod("testGetAtomAt")
     public IAtom getAtomAt(int position) {
         return atoms[position];
     }
@@ -146,7 +136,6 @@ public IAtom getAtomAt(int position) {
      * @param   atom  The atom to be tested if it participates in this Association
      * @return     true if the atom participates in this Association
      */
-    @TestMethod("testContains")
     public boolean contains(IAtom atom) {
         for (IAtom atom1 : atoms) {
             if (atom1 == atom) {
@@ -164,7 +153,6 @@ public boolean contains(IAtom atom) {
      *
      * @see     #getAtomAt
      */
-    @TestMethod("testSetAtomAt")
     public void setAtomAt(IAtom atom, int position) {
         atoms[position] = atom;
         notifyChanged();
@@ -176,7 +164,6 @@ public void setAtomAt(IAtom atom, int position) {
      *
      * @return    The string representation of this Container
      */
-    @TestMethod("testToString")
     @Override
     public String toString() {
         StringBuilder s = new StringBuilder();

diff --git a/misc/extra/src/main/java/org/openscience/cdk/config/XMLIsotopeFactory.java b/misc/extra/src/main/java/org/openscience/cdk/config/XMLIsotopeFactory.java
@@ -23,8 +23,6 @@
 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.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IIsotope;
@@ -56,7 +54,6 @@
  * @cdk.keyword    isotope
  * @cdk.keyword    element
  */
-@TestClass("org.openscience.cdk.config.XMLIsotopeFactoryTest")
 public class XMLIsotopeFactory extends IsotopeFactory {
 
     private static XMLIsotopeFactory ifac  = null;
@@ -110,7 +107,6 @@ private XMLIsotopeFactory(IChemObjectBuilder builder) throws IOException {
      * @return                             The instance value
      * @exception  IOException  if isotopic data files could not be read.
      */
-    @TestMethod("testGetInstance_IChemObjectBuilder")
     public static XMLIsotopeFactory getInstance(IChemObjectBuilder builder) throws IOException {
         if (ifac == null) {
             ifac = new XMLIsotopeFactory(builder);

diff --git a/misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeHandler.java b/misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeHandler.java
@@ -21,8 +21,6 @@
 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.IIsotope;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.tools.ILoggingTool;
@@ -50,7 +48,6 @@
  * @cdk.module  extra
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.config.isotopes.IsotopeHandlerTest")
 public class IsotopeHandler extends DefaultHandler {
 
     private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(IsotopeHandler.class);
@@ -68,7 +65,6 @@ public class IsotopeHandler extends DefaultHandler {
      *
      * @param builder The IChemObjectBuilder used to create new IIsotope's.
      */
-    @TestMethod("testIsotopeHandler_IChemObjectBuilder")
     public IsotopeHandler(IChemObjectBuilder builder) {
         this.builder = builder;
     }
@@ -78,7 +74,6 @@ public IsotopeHandler(IChemObjectBuilder builder) {
      *
      * @return A List object with all isotopes
      */
-    @TestMethod("testGetIsotopes")
     public List<IIsotope> getIsotopes() {
         return isotopes;
     }
@@ -87,14 +82,12 @@ public List<IIsotope> getIsotopes() {
 
     /** {@inheritDoc} */
     @Override
-    @TestMethod("testStartDocument")
     public void startDocument() {
         isotopes = new ArrayList<IIsotope>();
     }
 
     /** {@inheritDoc} */
     @Override
-    @TestMethod("testEndElement_String_String_String")
     public void endElement(String uri, String local, String raw) {
         logger.debug("end element: ", raw);
         if ("isotope".equals(local)) {
@@ -120,7 +113,6 @@ public void endElement(String uri, String local, String raw) {
 
     /** {@inheritDoc} */
     @Override
-    @TestMethod("testEndElement_String_String_String")
     public void startElement(String uri, String local, String raw, Attributes atts) {
         currentChars = "";
         dictRef = "";
@@ -143,7 +135,6 @@ public void startElement(String uri, String local, String raw, Attributes atts)
 
     /** {@inheritDoc} */
     @Override
-    @TestMethod("testCharacters_arraychar_int_int")
     public void characters(char chars[], int start, int length) {
         currentChars += new String(chars, start, length);
     }

diff --git a/misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeReader.java b/misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeReader.java
@@ -29,8 +29,6 @@
 
 import javax.xml.parsers.ParserConfigurationException;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.tools.ILoggingTool;
@@ -52,7 +50,6 @@
  *
  * @author     Egon Willighagen
  */
-@TestClass("org.openscience.cdk.config.isotopes.IsotopeReaderTest")
 public class IsotopeReader {
 
     private XMLReader           parser;
@@ -67,7 +64,6 @@ public class IsotopeReader {
      * @param input   InputStream with the XML source
      * @param builder The {@link IChemObjectBuilder} used to create new IIsotope's.
      */
-    @TestMethod("testIsotopeReader_InputStream_IChemObjectBuilder")
     public IsotopeReader(InputStream input, IChemObjectBuilder builder) {
         this.init();
         this.input = input;
@@ -126,7 +122,6 @@ private void init() {
      * @return a List of Isotope's. Returns an empty list is some reading error
      *         occurred.
      */
-    @TestMethod("testReadIsotopes,testReadIsotopes2")
     public List<IIsotope> readIsotopes() {
         List<IIsotope> isotopes = new ArrayList<IIsotope>();
         try {

diff --git a/misc/extra/src/main/java/org/openscience/cdk/geometry/alignment/KabschAlignment.java b/misc/extra/src/main/java/org/openscience/cdk/geometry/alignment/KabschAlignment.java
@@ -22,8 +22,6 @@
 
 import javax.vecmath.Point3d;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
 import org.openscience.cdk.config.Isotopes;
 import org.openscience.cdk.config.IsotopeFactory;
 import org.openscience.cdk.exception.CDKException;
@@ -92,7 +90,6 @@
  * @cdk.dictref      blue-obelisk:alignmentKabsch
  * @cdk.githash
  */
-@TestClass("org.openscience.cdk.geometry.alignment.KabschAlignmentTest")
 public class KabschAlignment {
 
     private ILoggingTool logger = LoggingToolFactory.createLoggingTool(KabschAlignment.class);
@@ -234,7 +231,6 @@ public KabschAlignment(IAtom[] al1, IAtom[] al2, double[] wts) throws CDKExcepti
      *            so that the RMDS is minimized to the coordinates of the first one
      * @throws CDKException if the number of atom's are not the same in the two AtomContainer's
      */
-    @TestMethod("testAlign")
     public KabschAlignment(IAtomContainer ac1, IAtomContainer ac2) throws CDKException {
         if (ac1.getAtomCount() != ac2.getAtomCount()) {
             throw new CDKException("The AtomContainer's being aligned must have the same number of atoms");
@@ -283,7 +279,6 @@ public KabschAlignment(IAtomContainer ac1, IAtomContainer ac2, double[] wts) thr
      * This method aligns to set of atoms which should have been specified
      * prior to this call
      */
-    @TestMethod("testAlign")
     public void align() {
 
         Matrix tmp;
@@ -427,7 +422,6 @@ public void align() {
      * @return The RMSD for this alignment
      * @see #align
      */
-    @TestMethod("testAlign")
     public double getRMSD() {
         return (this.rmsd);
     }
@@ -438,7 +432,6 @@ public double getRMSD() {
      * @return A double[][] representing the rotation matrix
      * @see #align
      */
-    @TestMethod("testAlign")
     public double[][] getRotationMatrix() {
         return (this.U);
     }

diff --git a/misc/extra/src/main/java/org/openscience/cdk/index/CASNumber.java b/misc/extra/src/main/java/org/openscience/cdk/index/CASNumber.java
@@ -23,9 +23,6 @@
 
 package org.openscience.cdk.index;
 
-import org.openscience.cdk.annotations.TestClass;
-import org.openscience.cdk.annotations.TestMethod;
-
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -49,7 +46,6 @@
  * @cdk.keyword CAS number
  * @cdk.require java1.4+
  */
-@TestClass("org.openscience.cdk.index.CASNumberTest")
 public class CASNumber {
 
     /**
@@ -60,7 +56,6 @@ public class CASNumber {
      * @cdk.keyword validation
      * @return true if a valid CAS number, false otherwise
      */
-    @TestMethod("testInvalidCheckDigits,testValidNumbers")
     public static boolean isValid(String casNumber) {
         boolean overall = true;
         /*

diff --git a/misc/extra/src/main/java/org/openscience/cdk/io/CrystClustReader.java b/misc/extra/src/main/java/org/openscience/cdk/io/CrystClustReader.java
@@ -27,8 +27,6 @@
 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;
@@ -48,7 +46,6 @@
  * @cdk.githash
  * @cdk.iooptions
  */
-@TestClass("org.openscience.cdk.io.CrystClustReaderTest")
 public class CrystClustReader extends DefaultChemObjectReader {
 
     private BufferedReader      input;
@@ -69,13 +66,11 @@ public CrystClustReader(InputStream input) {
         this(new InputStreamReader(input));
     }
 
-    @TestMethod("testGetFormat")
     @Override
     public IResourceFormat getFormat() {
         return CrystClustFormat.getInstance();
     }
 
-    @TestMethod("testSetReader_Reader")
     @Override
     public void setReader(Reader reader) throws CDKException {
         if (reader instanceof BufferedReader) {
@@ -85,13 +80,11 @@ public void setReader(Reader reader) throws CDKException {
         }
     }
 
-    @TestMethod("testSetReader_InputStream")
     @Override
     public void setReader(InputStream input) throws CDKException {
         setReader(new InputStreamReader(input));
     }
 
-    @TestMethod("testAccepts")
     @Override
     public boolean accepts(Class<? extends IChemObject> classObject) {
         if (IChemFile.class.equals(classObject)) return true;
@@ -239,7 +232,6 @@ private IChemFile readChemFile(IChemFile file) throws CDKException {
         return file;
     }
 
-    @TestMethod("testClose")
     @Override
     public void close() throws IOException {
         input.close();

diff --git a/misc/extra/src/main/java/org/openscience/cdk/io/CrystClustWriter.java b/misc/extra/src/main/java/org/openscience/cdk/io/CrystClustWriter.java
@@ -27,8 +27,6 @@
 
 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.exception.UnsupportedChemObjectException;
 import org.openscience.cdk.interfaces.IAtom;
@@ -50,7 +48,6 @@
  * @cdk.githash
  * @cdk.iooptions
  */
-@TestClass("org.openscience.cdk.io.CrystClustWriterTest")
 public class CrystClustWriter extends DefaultChemObjectWriter {
 
     private BufferedWriter      writer;
@@ -82,7 +79,6 @@ public CrystClustWriter() {
         this(new StringWriter());
     }
 
-    @TestMethod("testGetFormat")
     @Override
     public IResourceFormat getFormat() {
         return CrystClustFormat.getInstance();
@@ -102,7 +98,6 @@ public void setWriter(OutputStream output) throws CDKException {
         setWriter(new OutputStreamWriter(output));
     }
 
-    @TestMethod("testAccepts")
     @Override
     public boolean accepts(Class<? extends IChemObject> classObject) {
         Class<?>[] interfaces = classObject.getInterfaces();
@@ -132,7 +127,6 @@ public void write(IChemObject object) throws UnsupportedChemObjectException {
     /**
      * Flushes the output and closes this object.
      */
-    @TestMethod("testClose")
     @Override
     public void close() throws IOException {
         writer.close();