From e350d4f77af8c6c5f898f58f94d74bb5a3610cf6 Mon Sep 17 00:00:00 2001 From: danielgeiszler Date: Thu, 2 May 2024 11:28:59 +0300 Subject: [PATCH] Clean up some unnecessary 2-D Q-value code --- .../iterativelocalization/IterativeLocalizer.java | 1 + .../iterativelocalization/MatchedIonDistribution.java | 6 ------ 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java b/src/edu/umich/andykong/ptmshepherd/iterativelocalization/IterativeLocalizer.java index 138e06b..16a9820 100644 --- 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 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 index dc9c6d2..e563607 100644 --- 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); } }