From d0d73d57e169103b162d25f0244543445ee1fdbc Mon Sep 17 00:00:00 2001
From: Chih-Chiang Tsou <tsouc@umich.edu>
Date: Fri, 13 Nov 2015 16:57:10 -0500
Subject: [PATCH] v1.4272

---
 .../src/MSUmpire/SearchResultParser/PepXMLParseHandler.java | 6 ++++--
 .../src/MSUmpire/SearchResultParser/PepXMLParser.java       | 2 ++
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java b/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java
index 1dcffd8..da2570f 100644
--- a/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java
+++ b/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParseHandler.java
@@ -293,8 +293,10 @@ private void ParseSpectrumNode(Element spectrum) throws XmlPullParserException,
     private void GetModificationInfo(PSM psmid, Node node) throws XmlPullParserException, XmlPullParserException, XmlPullParserException, XmlPullParserException, XmlPullParserException, IOException {
         String PepSeq = psmid.Sequence;
         String modseq = psmid.Sequence;
-        String TPPmodseq = node.getAttributes().getNamedItem("modified_peptide").getNodeValue();
-
+        String TPPmodseq = modseq;
+        if (node.getAttributes().getNamedItem("modified_peptide") != null) {
+            TPPmodseq = node.getAttributes().getNamedItem("modified_peptide").getNodeValue();
+        }
         if (node.getAttributes().getNamedItem("mod_nterm_mass") != null) {
             float mass = Float.parseFloat(node.getAttributes().getNamedItem("mod_nterm_mass").getNodeValue());
             String site = "N-term";
diff --git a/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParser.java b/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParser.java
index 871e88f..5c1151c 100644
--- a/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParser.java
+++ b/DIA-Umpire/src/MSUmpire/SearchResultParser/PepXMLParser.java
@@ -30,6 +30,7 @@
 import java.io.InputStreamReader;
 import java.io.PrintWriter;
 import javax.xml.parsers.ParserConfigurationException;
+import org.apache.commons.lang.exception.ExceptionUtils;
 import org.apache.log4j.Logger;
 import org.xml.sax.SAXException;
 import org.xmlpull.v1.XmlPullParserException;
@@ -68,6 +69,7 @@ public PepXMLParser(LCMSID singleLCMSID, String FileName, float threshold, boole
         try {
             ParseSAX();
         } catch (Exception e) {
+            Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e));
             Logger.getRootLogger().info("Parsing pepXML: " + FileName + " failed. Trying to fix the file...");
             insert_msms_run_summary(new File(FileName));
             ParseSAX();