From c2083b3723841b016413fde4a0598f332ba2c1b1 Mon Sep 17 00:00:00 2001
From: Dan Polasky <dpolasky@umich.edu>
Date: Tue, 24 Sep 2024 10:40:46 -0400
Subject: [PATCH] fix a bug in parsing glycan spectra for library

---
 src/edu/umich/andykong/ptmshepherd/glyco/GlycoAnalysis.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/edu/umich/andykong/ptmshepherd/glyco/GlycoAnalysis.java b/src/edu/umich/andykong/ptmshepherd/glyco/GlycoAnalysis.java
index b9765ef..129df7d 100644
--- a/src/edu/umich/andykong/ptmshepherd/glyco/GlycoAnalysis.java
+++ b/src/edu/umich/andykong/ptmshepherd/glyco/GlycoAnalysis.java
@@ -188,10 +188,10 @@ public HashMap<String, GlycanSpectrumCandidate> generateConsensusSpectra(GlycoPa
                 boolean skip = Double.parseDouble(splits[qValCol]) >= glycoParams.speclibMaxQ;
                 String[] fragmentInfo = splits.length >= fragmentStartCol ? Arrays.copyOfRange(splits, fragmentStartCol, splits.length) : new String[]{};
 
-                GlycanCandidate fragmentInfoContainer = new GlycanCandidate(glycanString, fragmentInfo, glycoParams);
-                String glycanHash = fragmentInfoContainer.toString();
                 // only include targets in fragment info
                 if (!skip) {
+                    GlycanCandidate fragmentInfoContainer = new GlycanCandidate(glycanString, fragmentInfo, glycoParams);
+                    String glycanHash = fragmentInfoContainer.toString();
                     if (glycanInputMap.containsKey(glycanHash)) {
                         glycanInputMap.get(glycanHash).add(fragmentInfoContainer);
                     } else {