Fixed debugging, removed sysouts

bioclipse · Dec 13, 2012 · c0d2820 · c0d2820
1 parent 42e11a7
commit c0d2820
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/PCMSignLibSvmPrediction.java b/plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/PCMSignLibSvmPrediction.java
@@ -113,6 +113,8 @@ protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
 			String protName = protNames.get(ix);
 			List<Double> protDesc = protDescList.get(ix);
 
+			logger.debug("Predicting PCM for: " + protName);
+
 			//Take proteins one by ones
 			List<svm_node> protSvmNodes = new ArrayList<svm_node>();
 			for (int i=0; i< protDesc.size();i++){

diff --git a/plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMPrediction.java b/plugins/net.bioclipse.ds.libsvm/src/net/bioclipse/ds/libsvm/SignaturesLibSVMPrediction.java
@@ -250,8 +250,8 @@ public List<? extends ITestResult> predictLibSVM(ICDKMolecule cdkmol,
 				node.index = signSvmModel.getModelSignatures().indexOf(currentSignature)+1; // libsvm assumes that the index starts at one.
 				node.value = (Double) predModel.getMoleculeSignatures().get(currentSignature);
 
-				System.out.println(currentSignature + " ==> " 
-				+ node.index + "=" + node.value);
+//				System.out.println(currentSignature + " ==> " 
+//				+ node.index + "=" + node.value);
 
 			}
 		}
@@ -281,8 +281,6 @@ public List<? extends ITestResult> predictLibSVM(ICDKMolecule cdkmol,
 			prediction = signSvmModel.predict(svmPredictionArray);
 
 		}
-		System.out.println("--> PREDICTION: " + prediction);
-
 
 		//Create the result for the classification, overwrite name later if we have sign signature
 		AtomResultMatch match = new PosNegIncMatch("No significant signature", 
@@ -295,7 +293,8 @@ public List<? extends ITestResult> predictLibSVM(ICDKMolecule cdkmol,
 			return returnError("No classlabels found in model", "Classlabels are null for model");
 		}
 		String predictedClassLabel = classLabels.get(intPrediction);
-		System.out.println("predictedClassLabel=" + predictedClassLabel);
+
+		logger.debug("PCM Prediction: " + prediction + ", predictedClassLabel=" + predictedClassLabel);
 
 		//If this is higher than posVal in list, set POSITIVE color
 		int posIX = classLabels.indexOf(positiveValue);