Separating out cdk-extra from the cdk-io modules

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

build.xml

@@ -585,7 +585,7 @@
             list="test"/>
         <foreach target="compile-module" param="module" trim="true"
             parallel="${parallel}" maxthreads="${threadCount}"
-            list="test-interfaces,test-libiocml,test-qsar,test-data,test-io,test-core,
+            list="test-interfaces,test-data,test-libiocml,test-qsar,test-io,test-core,
         	      test-valencycheck,test-smarts,test-standard,test-reaction,
                   test-pcore,test-sdg,test-forcefield,test-fingerprint,
                   test-ionpot,test-qm,test-isomorphism,test-libiomd,test-dict,

src/META-INF/test-inchi.cdkdepends

@@ -1,5 +1,6 @@
 cdk-annotation.jar
 cdk-data.jar
+cdk-test-data.jar
 cdk-core.jar
 cdk-interfaces.jar
 cdk-io.jar
@@ -10,4 +11,3 @@ cdk-test.jar
 cdk-inchi.jar
 cdk-smiles.jar
 cdk-silent.jar
-cdk-extra.jar

src/META-INF/test-ioformats.cdkdepends

@@ -8,7 +8,6 @@ cdk-iordf.jar
 cdk-smiles.jar
 cdk-pdb.jar
 cdk-libiocml.jar
-cdk-extra.jar
 cdk-data.jar
 cdk-test.jar
 cdk-testdata.jar

src/META-INF/test-libiocml.cdkdepends

@@ -3,7 +3,7 @@ cdk-core.jar
 cdk-interfaces.jar
 cdk-standard.jar
 cdk-data.jar
-cdk-extra.jar
+cdk-test-data.jar
 cdk-io.jar
 cdk-test-io.jar
 cdk-ioformats.jar

src/META-INF/test-libiomd.cdkdepends

@@ -3,7 +3,6 @@ cdk-core.jar
 cdk-interfaces.jar
 cdk-standard.jar
 cdk-data.jar
-cdk-extra.jar
 cdk-libiomd.jar
 cdk-io.jar
 cdk-libiocml.jar

src/META-INF/test-qsarcml.devellibdepends

@@ -1 +1 @@
-junit-4.11.jar
+junit-4.10.jar

src/META-INF/test-smiles.cdkdepends

@@ -4,13 +4,13 @@ cdk-atomtype.jar
 cdk-core.jar
 cdk-standard.jar
 cdk-data.jar
+cdk-test-data.jar
 cdk-datadebug.jar
 cdk-silent.jar
 cdk-io.jar
 cdk-ioformats.jar
 cdk-valencycheck.jar
 cdk-smiles.jar
-cdk-extra.jar
 cdk-test.jar
 cdk-test-core.jar
 cdk-sdg.jar

src/test/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java

@@ -36,7 +36,7 @@
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.*;
 import org.openscience.cdk.smiles.SmilesParser;
-import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.templates.TestMoleculeFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 import static org.junit.Assert.assertFalse;
@@ -174,7 +174,7 @@ public void testGetInChIToStructure_String_IChemObjectBuilder_NullList() throws
     @Test public void testInChIGenerator_AromaticBonds() throws CDKException {
 
         // create a fairly complex aromatic molecule
-        IAtomContainer tetrazole = MoleculeFactory.makeTetrazole();
+        IAtomContainer tetrazole = TestMoleculeFactory.makeTetrazole();
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(tetrazole);
         CDKHueckelAromaticityDetector.detectAromaticity(tetrazole);
 

src/test/org/openscience/cdk/io/SMILESWriterTest.java

@@ -32,7 +32,7 @@
 import org.openscience.cdk.AtomContainerSet;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.io.listener.PropertiesListener;
-import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.templates.TestMoleculeFactory;
 
 /**
  * TestCase for the writer for SMILES files.
@@ -55,7 +55,7 @@ public class SMILESWriterTest extends ChemObjectIOTest {
 
     @Test public void testWriteSMILESFile() throws Exception {
         StringWriter stringWriter = new StringWriter();
-        IAtomContainer benzene = MoleculeFactory.makeBenzene();
+        IAtomContainer benzene = TestMoleculeFactory.makeBenzene();
         SMILESWriter smilesWriter = new SMILESWriter(stringWriter);
         smilesWriter.write(benzene);
         smilesWriter.close();
@@ -64,7 +64,7 @@ public class SMILESWriterTest extends ChemObjectIOTest {
 
     @Test public void testWriteAromatic() throws Exception {
         StringWriter stringWriter = new StringWriter();
-        IAtomContainer benzene = MoleculeFactory.makeBenzene();
+        IAtomContainer benzene = TestMoleculeFactory.makeBenzene();
         SMILESWriter smilesWriter = new SMILESWriter(stringWriter);
 
         Properties prop = new Properties();

src/test/org/openscience/cdk/io/cml/CML2WriterTest.java

@@ -61,7 +61,7 @@
 import org.openscience.cdk.silent.ChemModel;
 import org.openscience.cdk.silent.Crystal;
 import org.openscience.cdk.silent.Reaction;
-import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.templates.TestMoleculeFactory;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 
@@ -79,7 +79,7 @@ public class CML2WriterTest extends CDKTestCase {
 
     @Test public void testCMLWriterBenzene() throws Exception {
 		StringWriter writer = new StringWriter();
-		IAtomContainer molecule = MoleculeFactory.makeBenzene();
+		IAtomContainer molecule = TestMoleculeFactory.makeBenzene();
         CDKHueckelAromaticityDetector.detectAromaticity(molecule);
         CMLWriter cmlWriter = new CMLWriter(writer);
 

src/test/org/openscience/cdk/io/cml/CMLRoundTripTest.java

@@ -58,7 +58,7 @@
 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.templates.TestMoleculeFactory;
 import org.openscience.cdk.tools.ILoggingTool;
 import org.openscience.cdk.tools.LoggingToolFactory;
 import org.openscience.cdk.tools.manipulator.BondManipulator;
@@ -561,7 +561,7 @@ public void testAtomStereoParity() throws Exception {
     }
 
     @Test public void testDescriptorValue() throws Exception {
-        IAtomContainer molecule = MoleculeFactory.makeBenzene();
+        IAtomContainer molecule = TestMoleculeFactory.makeBenzene();
 
     	String[] propertyName = {"testKey1","testKey2"};
     	String[] propertyValue = {"testValue1","testValue2"};
@@ -582,7 +582,7 @@ public void testAtomStereoParity() throws Exception {
      * @throws Exception
      */
     @Test public void testAromaticity() throws Exception {
-        IAtomContainer molecule = MoleculeFactory.makeBenzene();
+        IAtomContainer molecule = TestMoleculeFactory.makeBenzene();
     	for (IBond bond : molecule.bonds()) {
     		bond.setFlag(CDKConstants.ISAROMATIC, true);
     	}
@@ -597,7 +597,7 @@ public void testAtomStereoParity() throws Exception {
     }
 
     @Test public void testAtomAromaticity() throws Exception {
-        IAtomContainer molecule = MoleculeFactory.makeBenzene();
+        IAtomContainer molecule = TestMoleculeFactory.makeBenzene();
     	for (IAtom atom : molecule.atoms()) {
     		atom.setFlag(CDKConstants.ISAROMATIC, true);
     	}
@@ -618,7 +618,7 @@ public void testAtomStereoParity() throws Exception {
     	String[] key = {"customAtomProperty1","customAtomProperty2"};
     	String[] value = {"true","false"};
 
-    	IAtomContainer mol = MoleculeFactory.makeBenzene();
+    	IAtomContainer mol = TestMoleculeFactory.makeBenzene();
         for (Iterator<IAtom> it = mol.atoms().iterator(); it.hasNext();) {
            IAtom a = it.next();
            for (int i=0; i < key.length;i++)
@@ -648,7 +648,7 @@ public void testAtomStereoParity() throws Exception {
     @Test public void testBondProperty() throws Exception {
     	String[] key = {"customBondProperty1","customBondProperty2"};
     	String[] value = {"true","false"};
-    	IAtomContainer mol = MoleculeFactory.makeBenzene();
+    	IAtomContainer mol = TestMoleculeFactory.makeBenzene();
         for (Iterator<IBond> it = mol.bonds().iterator(); it.hasNext();) {
            IBond b = it.next();
            for (int i=0; i < key.length;i++)
@@ -679,7 +679,7 @@ public void testAtomStereoParity() throws Exception {
     	String[] key = {"customMoleculeProperty1","customMoleculeProperty2"};
     	String[] value = {"true","false"};
 
-    	IAtomContainer mol = MoleculeFactory.makeAdenine();
+    	IAtomContainer mol = TestMoleculeFactory.makeAdenine();
     	for (int i=0; i < key.length;i++) {
     		mol.setProperty(key[i], value[i]);
     	}

src/test/org/openscience/cdk/smiles/SmilesGeneratorTest.java

@@ -61,7 +61,7 @@
 import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
 import org.openscience.cdk.layout.HydrogenPlacer;
 import org.openscience.cdk.layout.StructureDiagramGenerator;
-import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.templates.TestMoleculeFactory;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
 /**
@@ -78,7 +78,7 @@ public class SmilesGeneratorTest extends CDKTestCase {
 	@Test
     public void testSmilesGenerator()
 	{
-	    IAtomContainer mol2 = MoleculeFactory.makeAlphaPinene();
+	    IAtomContainer mol2 = TestMoleculeFactory.makeAlphaPinene();
 		SmilesGenerator sg = new SmilesGenerator();
 		fixCarbonHCount(mol2);
 		String smiles2 = sg.createSMILES(mol2);
@@ -92,7 +92,7 @@ public void testSmilesGenerator()
 	 */
 	@Test public void testEthylPropylPhenantren()
 	{
-	    IAtomContainer mol1 = MoleculeFactory.makeEthylPropylPhenantren();
+	    IAtomContainer mol1 = TestMoleculeFactory.makeEthylPropylPhenantren();
         SmilesGenerator sg = new SmilesGenerator();
 		fixCarbonHCount(mol1);
 		String smiles1 = sg.createSMILES(mol1);
@@ -107,7 +107,7 @@ public void testSmilesGenerator()
 	 */
 	@Test public void testPropylCycloPropane()
 	{
-	    IAtomContainer mol1 = MoleculeFactory.makePropylCycloPropane();
+	    IAtomContainer mol1 = TestMoleculeFactory.makePropylCycloPropane();
         SmilesGenerator sg = new SmilesGenerator();
 		fixCarbonHCount(mol1);
 		String smiles1 = sg.createSMILES(mol1);
@@ -817,7 +817,7 @@ private void fixCarbonHCount(IAtomContainer mol) {
 	}
 
     @Test public void testIndole() throws Exception {
-        IAtomContainer mol = MoleculeFactory.makeIndole();
+        IAtomContainer mol = TestMoleculeFactory.makeIndole();
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
         CDKHueckelAromaticityDetector.detectAromaticity(mol);
 
@@ -828,7 +828,7 @@ private void fixCarbonHCount(IAtomContainer mol) {
     }
 
     @Test public void testPyrrole() throws Exception {
-        IAtomContainer mol = MoleculeFactory.makePyrrole();
+        IAtomContainer mol = TestMoleculeFactory.makePyrrole();
         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
         CDKHueckelAromaticityDetector.detectAromaticity(mol);
 
@@ -986,14 +986,14 @@ public void testBug3040273() throws Exception {
 
 
     @Test public void testCreateSMILESWithoutCheckForMultipleMolecules_withDetectAromaticity() throws CDKException{
-        IAtomContainer benzene = MoleculeFactory.makeBenzene();
+        IAtomContainer benzene = TestMoleculeFactory.makeBenzene();
         SmilesGenerator sg = new SmilesGenerator(false);
         String smileswithoutaromaticity = sg.createSMILESWithoutCheckForMultipleMolecules(benzene, false, new boolean[benzene.getBondCount()]);
         Assert.assertEquals("C=1C=CC=CC=1", smileswithoutaromaticity);
     }
 
     @Test public void testCreateSMILESWithoutCheckForMultipleMolecules_withoutDetectAromaticity() throws CDKException{
-        IAtomContainer benzene = MoleculeFactory.makeBenzene();
+        IAtomContainer benzene = TestMoleculeFactory.makeBenzene();
         SmilesGenerator sg = new SmilesGenerator(true);
         String smileswitharomaticity = sg.createSMILESWithoutCheckForMultipleMolecules(benzene, false, new boolean[benzene.getBondCount()]);
         Assert.assertEquals("c1ccccc1", smileswitharomaticity);

src/test/org/openscience/cdk/smiles/SmilesParserTest.java

@@ -50,7 +50,7 @@
 import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
 import org.openscience.cdk.layout.StructureDiagramGenerator;
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
-import org.openscience.cdk.templates.MoleculeFactory;
+import org.openscience.cdk.templates.TestMoleculeFactory;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
@@ -917,7 +917,7 @@ public void testSFBug956921() throws Exception {
 	@org.junit.Test (timeout=1000)
 	public void testSFBug1274464() throws Exception {
 		IAtomContainer fromSmiles = new	SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles("C1=CC=CC=C1");
-		IAtomContainer fromFactory =	MoleculeFactory.makeBenzene();
+		IAtomContainer fromFactory =	TestMoleculeFactory.makeBenzene();
 		CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(fromFactory.getBuilder());
 		Iterator<IAtom> atoms = fromFactory.atoms().iterator();
 		CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(fromFactory.getBuilder());