Updated with sanity checks if descriptor calculation fails.

bioclipse · Dec 29, 2011 · d860996 · d860996
1 parent 603a3cc
commit d860996
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Showing 4 changed files with 27 additions and 10 deletions.
diff --git a/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/business/IQsarManager.java b/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/business/IQsarManager.java
@@ -21,7 +21,7 @@
 import net.bioclipse.core.PublishedMethod;
 import net.bioclipse.core.Recorded;
 import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.Dataset;
+import net.bioclipse.core.domain.DenseDataset;
 import net.bioclipse.core.domain.IMolecule;
 import net.bioclipse.managers.business.IBioclipseManager;
 import net.bioclipse.qsar.DescriptorType;
@@ -225,7 +225,7 @@ IDescriptorResult calculate( IMolecule mol, String ontologyID,
                      		"list of molecules " +
                         "using the default provider.")
     @Recorded
-    Dataset calculate( List<IMolecule> mols,
+    DenseDataset calculate( List<IMolecule> mols,
                                             List<String> descriptors )
                                                       throws BioclipseException;
 
@@ -235,7 +235,7 @@ Dataset calculate( List<IMolecule> mols,
                                      "list of molecules " +
                                      "using the selected provider.")
     @Recorded
-    Dataset calculate( List<IMolecule> mols,
+    DenseDataset calculate( List<IMolecule> mols,
                                             List<String> descriptors,
                                             String provider )
                                                       throws BioclipseException;

diff --git a/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/business/QsarManager.java b/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/business/QsarManager.java
@@ -27,7 +27,7 @@
 import net.bioclipse.cdk.business.ICDKManager;
 import net.bioclipse.cdk.domain.ICDKMolecule;
 import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.Dataset;
+import net.bioclipse.core.domain.DenseDataset;
 import net.bioclipse.core.domain.IMolecule;
 import net.bioclipse.core.domain.IStringMatrix;
 import net.bioclipse.core.util.LogUtils;
@@ -805,7 +805,7 @@ public IDescriptorResult calculate(IMolecule mol, String descriptor) throws Bioc
 	 * @throws BioclipseException 
 	 * @throws BioclipseException 
 	 */
-	public Dataset calculate(List<IMolecule> mols, List<String> descriptors) throws BioclipseException{
+	public DenseDataset calculate(List<IMolecule> mols, List<String> descriptors) throws BioclipseException{
 
 		//Just propagate with provider as null
 		return calculate( mols, descriptors, null );
@@ -818,7 +818,7 @@ public Dataset calculate(List<IMolecule> mols, List<String> descriptors) throws
 	 * @throws BioclipseException 
 	 * @throws BioclipseException 
 	 */
-	public Dataset calculate(List<IMolecule> mols, List<String> descriptors, String provider) throws BioclipseException{
+	public DenseDataset calculate(List<IMolecule> mols, List<String> descriptors, String provider) throws BioclipseException{
 
 		Map<IMolecule, List<DescriptorImpl>> calculationMap=new HashMap<IMolecule, List<DescriptorImpl>>();
 
@@ -889,7 +889,16 @@ private QsarDataset calculate(
 
 //		DescriptorCalculationResult dcalres=new DescriptorCalculationResult(resultMap);
 
-
+		//Some sanity checks, if all results fail then throw exception.
+		for (IMolecule mol : resultMap.keySet()){
+			for (IDescriptorResult dres : resultMap.get(mol)){
+				if (dres.getErrorMessage()!=null){
+					System.out.println("Errors exist in descriptor result: " + dres);
+					throw new BioclipseException("Error in descriptor generation for molecule: " + mol);
+					//TODO: we could also simply remove this molecule if we would like to
+				}
+			}
+		}
 
 		return new QsarDataset(resultMap);
 	}

diff --git a/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/descriptor/DescriptorResult.java b/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/descriptor/DescriptorResult.java
@@ -64,7 +64,7 @@ public void setValues(Float[] values) {
 
 	@Override
     public String toString() {
-
+	    if (errorMessage!=null) return "ERROR: " + errorMessage;
 	    if (labels==null || labels.length<=0) return "null";
 	    IQsarManager qsar=Activator.getDefault().getJavaQsarManager();
 

diff --git a/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/descriptor/QsarDataset.java b/plugins/net.bioclipse.qsar/src/net/bioclipse/qsar/descriptor/QsarDataset.java
@@ -8,10 +8,10 @@
 import net.bioclipse.cdk.business.ICDKManager;
 import net.bioclipse.cdk.domain.ICDKMolecule;
 import net.bioclipse.core.business.BioclipseException;
-import net.bioclipse.core.domain.Dataset;
+import net.bioclipse.core.domain.DenseDataset;
 import net.bioclipse.core.domain.IMolecule;
 
-public class QsarDataset extends Dataset{
+public class QsarDataset extends DenseDataset{
 
 	Map<IMolecule, List<IDescriptorResult>> qsarResults;
 
@@ -32,6 +32,10 @@ public QsarDataset(Map<IMolecule, List<IDescriptorResult>> resultMap) {
 		//Loop over all descriptors in get first mol (all are same)
 		IMolecule fmol = (IMolecule) resultMap.keySet().toArray()[0];
 		for (IDescriptorResult dres : resultMap.get( fmol )){
+			if (dres.getErrorMessage()!=null){
+				System.out.println("Errors exist in descriptor result: " + dres);
+				continue;
+			}
 			for (String label : dres.getLabels()){
 				colHeaders.add(label);
 			}
@@ -47,6 +51,10 @@ public QsarDataset(Map<IMolecule, List<IDescriptorResult>> resultMap) {
 			rowHeaders.add("Molecule-" + mol);
 			List<IDescriptorResult> lst = resultMap.get( mol );
 			for (IDescriptorResult dres : lst){
+				if (dres.getErrorMessage()!=null){
+					System.out.println("Errors exist in descriptor result: " + dres);
+					continue;
+				}
 				for (Float value : dres.getValues()){
 					rowValues.add(value);
 				}