corrected CliqueID annotation
@@ -116,6 +116,7 @@ public class CliqueMSTask extends AbstractTask {
parameters.getParameter(CliqueMSParameters.FILTER).getEmbeddedParameters()
.getParameter(SimilarFeatureParameters.IN_DIFF).getValue(),
parameters.getParameter(CliqueMSParameters.TOL).getValue());
+ System.out.println("Size of peakData List 1"+anClique.getPeakDataList().size());
// Check if not canceled
if (isCanceled()) {
return;
@@ -146,6 +147,7 @@ public class CliqueMSTask extends AbstractTask {
if (isCanceled()) {
return;
}
+
ComputeAdduct computeAdduct = new ComputeAdduct(anClique, this, this.progress);
PolarityType polarity =
@@ -198,13 +200,17 @@ public class CliqueMSTask extends AbstractTask {
numberOfDigitsInMaxPeakID++;
maxID/=10;
}
-
+ numberOfDigitsInMaxPeakID++;
for (PeakData pd : pdList) {
- String cqID = null;
- if(pd.getCliqueID() != null)
+ String cqID;
+ if(nodeToPeakID.get(pd.getCliqueID()) != null)
cqID = String.format("%0"+numberOfDigitsInMaxPeakID+"d",nodeToPeakID.get(pd.getCliqueID()));
- if(cqID.equals("null"))
+ else if(pd.getCliqueID() != null){
+ cqID = String.format("%0"+numberOfDigitsInMaxPeakID+"d",pd.getCliqueID());
+ }
+ else{
cqID= "NA";
+ }
CliqueMSTabularPeakIdentity annotation = new CliqueMSTabularPeakIdentity("CliqueID "+cqID);
annotation.addSingularProperty(PeakIdentity.PROPERTY_METHOD,"CliqueMS Algorithm");
annotation.addSingularProperty("Isotope Annotation",pd.getIsotopeAnnotation());
