Fix for cases when modified peptide seequence is not present in pepxml

chhh · Jun 25, 2019 · 3a90943 · 3a90943
1 parent df1ddf0
commit 3a90943
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/build.gradle b/build.gradle
@@ -9,7 +9,7 @@ plugins {
 }
 
 group = 'com.dmtavt'
-version = '1.2.1'
+version = '1.2.2'
 
 description = """DeltaMass - detection and visualization of common mass shifts in proteomic searches."""
 

diff --git a/src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java b/src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java
@@ -20,7 +20,7 @@ public final class DeltaMassInfo {
   private static final EventBus bus = EventBus.getDefault();
 
   public static final String Name = "DeltaMass";
-  public static final String Ver = "1.2.1";
+  public static final String Ver = "1.2.2";
 
   private static final String PROP_VER = "deltamass.version.current";
   private static final String PROP_DOWNLOAD_URL = "deltamass.download.url";

diff --git a/src/main/java/com/dmtavt/deltamass/parsers/PepxmlParser.java b/src/main/java/com/dmtavt/deltamass/parsers/PepxmlParser.java
@@ -169,7 +169,14 @@ public PepSearchFile parse(final Pattern decoyRegex) throws IOException {
           if (mi == null) {
             spm.seqModStateId = spm.seq;
           } else {
-            StringBuilder sb = new StringBuilder(mi.getModifiedPeptide());
+            StringBuilder sb = new StringBuilder();
+            if (mi.getModifiedPeptide() != null) {
+              sb.append(mi.getModifiedPeptide());
+            } else if (sh.getPeptide() != null) {
+              sb.append(sh.getPeptide());
+            } else {
+              throw new IOException("ModificationInfo->ModifiedPeptide and SearchHit->Peptide were both not present");
+            }
             StringBuilder sbMods = new StringBuilder();
             if (mi.getModNtermMass() != null) {
               sb.append(String.format("_%.2f@0", mi.getModNtermMass()));