Absent zero bin bug fix

Nesvilab · Jul 21, 2021 · 13b88c4 · 13b88c4
1 parent ea60cfb
commit 13b88c4
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Showing 2 changed files with 20 additions and 7 deletions.
diff --git a/src/edu/umich/andykong/ptmshepherd/peakpicker/ModSummary.java b/src/edu/umich/andykong/ptmshepherd/peakpicker/ModSummary.java
@@ -67,9 +67,10 @@ public ModSummary(File inPeaks, Set<String> dsets) throws Exception{
             }
             for(int j = 1; j < inFile.size(); j++){
                 String line [] = inFile.get(j);
-                if(line.length == mod1i){
+                if(line.length == mod1i) {
                     psmCounts.get(ds).put("None", Double.parseDouble(line[headis.get(ds + "_PSMs")]));
                     psmCountsNorm.get(ds).put("None", Double.parseDouble(line[headis.get(ds + "_percent_PSMs")]));
+                    mods.add("None");
                 }
             }
         }
@@ -94,11 +95,23 @@ public ModSummary(File inPeaks, Set<String> dsets) throws Exception{
     public void toFile(File modOut) throws Exception{
         //sort modifications by psm count for table
         LinkedHashMap<String, Integer> modsCount = new LinkedHashMap<>();
-        mods.add("None"); //allow mods to be searched for
+        //mods.add("None"); //allow mods to be searched for
         for (String mod : mods) { //sum PSMs across DSs
             int nPsms = 0;
-            for (String ds : datasets){
-                nPsms += psmCounts.get(ds).get(mod);
+            for (String ds : datasets) {
+                try {
+                    nPsms += psmCounts.get(ds).get(mod);
+                } catch (Exception e)  {
+                    System.out.println(ds);
+                    System.out.println(mod);
+                    System.out.println(psmCounts.size());
+                    System.out.println(psmCounts.get(ds).size());
+                    for(String s : psmCounts.get(ds).keySet()) {
+                        System.out.println(s);
+                    }
+                    System.out.println(e);
+                    System.exit(1);
+                }
             }
             modsCount.put(mod, nPsms);
         }

diff --git a/src/edu/umich/andykong/ptmshepherd/peakpicker/PeakAnnotator.java b/src/edu/umich/andykong/ptmshepherd/peakpicker/PeakAnnotator.java
@@ -387,7 +387,7 @@ else if (cdiff < lowerBound)
 			DeltaMassAnnotation dma = new DeltaMassAnnotation();
 			for (int j = 0; j < cUnimodIs.size(); j++) {
 				dma.UnimodMasses.add(mdasUnimod.get(cUnimodIs.get(j)).diff);
-				dma.UnimodAnnos.add(mdasUnimod.get(cUnimodIs.get(j)).annotation);
+				dma.UnimodAnnos.add("Mod1: " + mdasUnimod.get(cUnimodIs.get(j)).annotation);
 			}
 			for (int j = 0; j < cPtmsIs.size(); j++) {
 				dma.PtmsMasses.add(this.peaks[0][cPtmsIs.get(j)]);
@@ -485,9 +485,9 @@ private String formatMultiplePtmsMods (String[] massAnnos) {
 			if (massAnnos[i].equals(""))
 				continue;
 			if (cMods.length() > 0)
-				cMods.append(String.format(", %s", massAnnos[i]));
+				cMods.append(String.format(", Mod2: %s", massAnnos[i]));
 			else
-				cMods.append(String.format("%s", massAnnos[i]));
+				cMods.append(String.format("Mod1: %s", massAnnos[i]));
 		}
 		return cMods.toString();
 	}