Clean up some unnecessary 2-D Q-value code

Nesvilab · May 2, 2024 · e350d4f · e350d4f
1 parent 59c5fcc
commit e350d4f
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Showing 2 changed files with 1 addition and 6 deletions.
diff --git a/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java b/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java
@@ -599,6 +599,7 @@ public int compareTo(SpecProbQ o) {
                  i++;
              }
          }
+
         // Extract spectrum to q-val and probability mappings in matched order
         HashMap<String, Double> qValsMap = new HashMap<>();
         for (SpecProbQ spq : spqs)

diff --git a/src/edu/umich/andykong/ptmshepherd/iterativelocalization/MatchedIonDistribution.java b/src/edu/umich/andykong/ptmshepherd/iterativelocalization/MatchedIonDistribution.java
@@ -125,16 +125,10 @@ public void addIon(float intensity, float massError, boolean isDecoy) {
     public void addIon(float intensity, float massError, boolean isDecoy) {
         if (!isDecoy) {
             if (intensity > 0.0f) { // Only include matched ions, unmatched ions have negative intensity
-                int intIndx = (int) (intensity);
-                int massErrorIndx = (int) (massError * 100.0);
-                this.targetPMF.addVal(intIndx, massErrorIndx);
                 datapoints.addRow(massError, intensity, isDecoy);
             }
         } else {
             if (intensity > 0.0f) { // Only include matched ions, unmatched ions have negative intensity
-                int intIndx = (int) (intensity);
-                int massErrorIndx = (int) (massError * 100.0);
-                this.decoyPMF.addVal(intIndx, massErrorIndx);
                 datapoints.addRow(massError, intensity, isDecoy);
             }
         }