Adding descriptor initialisation for those which require it.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jul 31, 2013 · 284f1ef · 284f1ef
1 parent a097d37
commit 284f1ef
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Showing 5 changed files with 35 additions and 13 deletions.
diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java
@@ -67,11 +67,14 @@ public class AcidicGroupCountDescriptor extends AbstractMolecularDescriptor impl
      * Creates a new {@link AcidicGroupCountDescriptor}.
      */
     @TestMethod("testConstructor")
-    public AcidicGroupCountDescriptor(IChemObjectBuilder builder) throws CDKException {
+    public AcidicGroupCountDescriptor() {
+        this.checkAromaticity = true;
+    }
+
+    @Override public void initialise(IChemObjectBuilder builder) {
         for (String smarts : SMARTS_STRINGS) {
             tools.add(new SMARTSQueryTool(smarts, builder));
         }
-        this.checkAromaticity = true;
     }
 
     /** {@inheritDoc} */
@@ -117,6 +120,11 @@ public String[] getDescriptorNames() {
     /** {@inheritDoc} */
     @TestMethod("testCalculate_IAtomContainer")
     public DescriptorValue calculate(IAtomContainer atomContainer) {
+
+        if(tools.isEmpty()) {
+            throw new IllegalStateException("descriptor is not initalised, invoke 'initalise' first");
+        }
+
         // do aromaticity detection
         if (this.checkAromaticity) {
             try {

diff --git a/src/main/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptor.java b/src/main/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptor.java
@@ -64,7 +64,10 @@ public class BasicGroupCountDescriptor extends AbstractMolecularDescriptor imple
      * Creates a new {@link BasicGroupCountDescriptor}.
      */
     @TestMethod("testConstructor")
-    public BasicGroupCountDescriptor(IChemObjectBuilder builder) throws CDKException {
+    public BasicGroupCountDescriptor() {
+    }
+
+    @Override public void initialise(IChemObjectBuilder builder) {
         for (String smarts : SMARTS_STRINGS) {
             tools.add(new SMARTSQueryTool(smarts, builder));
         }
@@ -101,6 +104,11 @@ public String[] getDescriptorNames() {
     /** {@inheritDoc} */
     @TestMethod("testCalculate_IAtomContainer")
     public DescriptorValue calculate(IAtomContainer atomContainer) {
+
+        if(tools.isEmpty()) {
+            throw new IllegalStateException("descriptor is not initalised, invoke 'initalise' first");
+        }
+
         try {
             int count = 0;
             for (SMARTSQueryTool tool : tools) {

diff --git a/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java
@@ -44,14 +44,9 @@ public DescriptorTest() {}
 
     public void setDescriptor(Class<? extends T> descriptorClass) throws Exception {
 		if (descriptor == null) {
-            try {
-                Constructor<? extends T> defaultConstructor = descriptorClass.getConstructor();
-                this.descriptor = defaultConstructor.newInstance();
-            } catch (NoSuchMethodException ex) {
-                // no default constructor, try with an IChemObjectBuilder...
-                Constructor<? extends T> builderConstructor = descriptorClass.getConstructor(IChemObjectBuilder.class);
-                this.descriptor = builderConstructor.newInstance(DefaultChemObjectBuilder.getInstance());
-            }
+            Constructor<? extends T> defaultConstructor = descriptorClass.getConstructor();
+            this.descriptor = defaultConstructor.newInstance();
+            this.descriptor.initialise(DefaultChemObjectBuilder.getInstance());
 		}
 	}
 

diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptorTest.java
@@ -43,7 +43,12 @@ public void setUp() throws Exception {
     }
 
     @Test public void testConstructor() throws Exception {
-        Assert.assertNotNull(new AcidicGroupCountDescriptor(DefaultChemObjectBuilder.getInstance()));
+        Assert.assertNotNull(new AcidicGroupCountDescriptor());
+    }
+
+    @Test(expected = IllegalStateException.class)
+    public void uninitalisedError() {
+        new BasicGroupCountDescriptor().calculate(new AtomContainer());
     }
 
     @Test public void testOneAcidGroup() throws Exception {

diff --git a/src/test/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java b/src/test/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java
@@ -21,6 +21,7 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -41,7 +42,7 @@ public void setUp() throws Exception {
     }
 
     @Test public void testConstructor() throws Exception {
-        Assert.assertNotNull(new BasicGroupCountDescriptor(DefaultChemObjectBuilder.getInstance()));
+        Assert.assertNotNull(new BasicGroupCountDescriptor());
     }
 
     @Test public void testAmine() throws Exception {
@@ -54,6 +55,11 @@ public void setUp() throws Exception {
         Assert.assertEquals(1, result.intValue());
     }
 
+    @Test(expected = IllegalStateException.class)
+    public void uninitalisedError() {
+        new BasicGroupCountDescriptor().calculate(new AtomContainer());
+    }
+
     /**
      * @cdk.inchi InChI=1S/C2H4N2/c1-4-2-3/h2-3H,1H2
      */