Invert class prob if RHO negative + minor cleanup

bioclipse · May 22, 2012 · ec938bc · ec938bc
1 parent efa9780
commit ec938bc
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Showing 3 changed files with 11 additions and 3 deletions.
diff --git a/plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/DenseCDKRModelMatcher.java b/plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/DenseCDKRModelMatcher.java
@@ -137,7 +137,6 @@ protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
 	        //Parse result and create testresults
 	        double posProb = Double.parseDouble(ret.substring(4));
 	        System.out.println("Parsed prediction prob: " + posProb);
-
 
 			int overallPrediction;
 	        if (posProb>=0.5)

diff --git a/plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/SparseSignaturesRModelMatcher.java b/plugins/net.bioclipse.ds.r/src/net/bioclipse/ds/r/SparseSignaturesRModelMatcher.java
@@ -100,6 +100,15 @@ protected List<? extends ITestResult> doRunTest(ICDKMolecule cdkmol,
         //Parse result and create testresults
         double posProb = Double.parseDouble(output.substring(4));
 
+        //Check what rho is, if negative then invert predictions
+        //FIXME
+		output = R.eval("cas.svm$rho");
+		if (output.substring(4).startsWith("-")){
+			System.out.println("RHO IS NEG - INVERT!");
+			posProb=1-posProb;
+		}
+
+
 		int overallPrediction;
         if (posProb>=0.5)
         	overallPrediction = ITestResult.POSITIVE;

diff --git a/...t.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/business/SignaturesManager.java b/...t.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/business/SignaturesManager.java
@@ -134,7 +134,7 @@ public Map<IMolecule, AtomSignatures> generate(List<? extends IMolecule> mols,
 
 				AtomSignatures as = generate( mol , height);
 
-				logger.debug("Mol=" + mol + ", height=" + height + ", SIGNS=" + as.getSignatures());
+//				logger.debug("Mol=" + mol + ", height=" + height + ", SIGNS=" + as.getSignatures());
 
 				if (as.getSignatures() == null || as.getSignatures().size()<=0)
 					logger.error( "No signatures generated for for molecule: " 
@@ -367,7 +367,7 @@ public SparseDataset generateSparseDataset(List<? extends IMolecule> mols, List<
 
 		}
 
-		logger.debug("SIGNS: " + allSignaturesList);
+//		logger.debug("SIGNS: " + allSignaturesList);
 
 		//Set up the dataset
 		LinkedHashMap<Point, Integer> values = new LinkedHashMap<Point, Integer>();