Added a p-value cutoff for signature alerts

bioclipse · Dec 21, 2010 · 9f07d8e · 9f07d8e
1 parent 859fd40
commit 9f07d8e
Showing 1 changed file with 11 additions and 8 deletions.
diff --git a/plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/SignatureAlertsMatcher.java b/plugins/net.bioclipse.ds.common/src/net/bioclipse/ds/matcher/SignatureAlertsMatcher.java
@@ -38,7 +38,6 @@
 import net.bioclipse.ds.model.DSException;
 import net.bioclipse.ds.model.IDSTest;
 import net.bioclipse.ds.model.ITestResult;
-import net.bioclipse.ds.model.result.SimpleResult;
 import net.bioclipse.ds.signatures.Activator;
 import net.bioclipse.ds.signatures.business.ISignaturesManager;
 import net.bioclipse.ds.signatures.prop.calc.AtomSignatures;
@@ -57,6 +56,8 @@ public class SignatureAlertsMatcher extends AbstractDSTest implements IDSTest{
 
     private static final String FILE_PROPERTY_PARAM="file";
 
+	private static final double P_VALUE_CUTOFF = 0.05;
+
     //Model, from height to list of significant signatures
 	Map<Integer, List<SignificantSignature>> significantSignatures;
 	Map<Integer, List<String>> significantSignatureStrings;
@@ -165,12 +166,14 @@ else if (line.startsWith("significantSignature")){
 					}
 
 					//Create and add signatures to list
-					SignificantSignature signsign=new SignificantSignature(
-  					  sign, nrpos, nrtot, pvalue, accuracy, activeCall, height);
-					signsignlist.add(signsign);
-					signsignStringlist.add(sign);
-//					logger.debug("  Added SignSignature: " + signsign);
-					signCount++;
+					if (pvalue<=P_VALUE_CUTOFF){
+						SignificantSignature signsign=new SignificantSignature(
+								sign, nrpos, nrtot, pvalue, accuracy, activeCall, height);
+						signsignlist.add(signsign);
+						signsignStringlist.add(sign);
+						//					logger.debug("  Added SignSignature: " + signsign);
+						signCount++;
+					}
 				}
 				else{
 					throw new DSException("File: " + filepath + " line " 
@@ -212,7 +215,7 @@ protected List<? extends ITestResult> doRunTest( ICDKMolecule cdkmol,
         .getJavaSignaturesManager();
 
 		logger.debug("Generating AtomSignatures and comparing with stored.");
-		Map<Integer, List<String>> matches=new HashMap<Integer, List<String>>();
+//		Map<Integer, List<String>> matches=new HashMap<Integer, List<String>>();
 
         try {