changed annotations display
@@ -44,8 +44,8 @@ public class CliqueMSTask extends AbstractTask {
private static final Logger logger = Logger.getLogger(CliqueMSTask.class.getName());
//progress constants
- public final double EIC_PROGRESS = 0.5; // EIC calculation takes about 50% time
- public final double MATRIX_PROGRESS = 0.3; // Cosine matrix calculation takes about 30% time
+ public final double EIC_PROGRESS = 0.3; // EIC calculation takes about 50% time
+ public final double MATRIX_PROGRESS = 0.5; // Cosine matrix calculation takes about 30% time
public final double NET_PROGRESS = 0.1; // Network calculations takes 10% time
public final double ISO_PROGRESS = 0.01; // Isotope calculation takes 1% time
public final double ANNOTATE_PROGRESS = 0.09; // Adduct annotation takes 9% time
@@ -178,14 +178,18 @@ public class CliqueMSTask extends AbstractTask {
}
for (AdductInfo adInfo : addInfos) {
PeakData pd = pdHash.get(adInfo.feature);
+ SimplePeakIdentity adductAnnotation = new SimplePeakIdentity("Annotations");
+ int counter = 1;
for (int i = 0; i < ComputeAdduct.numofAnnotation; i++) {
- SimplePeakIdentity adductAnnotation = new SimplePeakIdentity("Annotation " + (i + 1));
- adductAnnotation.setPropertyValue("Mass", String.valueOf(adInfo.masses.get(i)));
- adductAnnotation.setPropertyValue("Score", String.valueOf(adInfo.scores.get(i)));
- adductAnnotation.setPropertyValue("Annotation", adInfo.annotations.get(i));
+ if(adInfo.annotations.get(i).equals("NA"))
+ continue;
+ adductAnnotation.setPropertyValue("Mass:"+counter, String.valueOf(adInfo.masses.get(i)));
+ adductAnnotation.setPropertyValue("Score:"+counter, String.valueOf(adInfo.scores.get(i)));
+ adductAnnotation.setPropertyValue("Annotation:"+counter, adInfo.annotations.get(i));
if (this.peakList.findRowByID(pd.getPeakListRowID()) != null) {
this.peakList.findRowByID(pd.getPeakListRowID()).addPeakIdentity(adductAnnotation, true);
}
+ counter++;
}
}
}
