From 3a90943e6b97039fbd14b3ea538f174dcc1b3d5f Mon Sep 17 00:00:00 2001
From: Dmitry Avtonomov <dmt.avt@gmail.com>
Date: Tue, 25 Jun 2019 12:50:10 +0200
Subject: [PATCH] Fix for cases when modified peptide seequence is not present
 in pepxml

---
 build.gradle                                             | 2 +-
 src/main/java/com/dmtavt/deltamass/DeltaMassInfo.java    | 2 +-
 .../java/com/dmtavt/deltamass/parsers/PepxmlParser.java  | 9 ++++++++-
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/build.gradle b/build.gradle
index 4ff1039..b2fad80 100644
--- 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
index 72c4956..0a85f22 100644
--- 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
index 6c82308..0921ef6 100644
--- 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()));