v1.4273

Author: cctsou

DIA-Umpire/src/MSUmpire/PSMDataStructure/PTMManager.java

@@ -123,7 +123,7 @@ public PTM GetPTM(String AA, float massdiff) {
             }
             if (sitecorrect) {
                 double diff = Math.abs(ptm.getMass() - massdiff);
-                if (diff < 1f) {
+                if (diff < 0.5f) {
                     if (diff < smallmassdiff) {
                         smallmassdiff = diff;
                         smallestdiffptm = ptm;

DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java

@@ -269,7 +269,7 @@ public boolean IsDecoy(String decoytag) {
         if (IsDecoy == -1) {
             IsDecoy = 1;
             for (String pro : ParentProtID_PepXML) {
-                if (!pro.startsWith(decoytag)) {
+                if (!(pro.startsWith(decoytag) | pro.endsWith(decoytag))) {
                     IsDecoy = 0;
                     break;
                 }

DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java

@@ -238,7 +238,7 @@ public String GetGeneName() {
     }
 
     public boolean IsDecoy(String decoytag) {
-        if (getAccNo().startsWith(decoytag)) {
+        if (getAccNo().startsWith(decoytag) | getAccNo().endsWith(decoytag)) {
             return true;
         }
         return false;

DIA-Umpire/src/MSUmpire/SearchResultParser/ProtXMLParseHandler.java

@@ -57,7 +57,15 @@ public void handle(Element node) throws Exception {
     private void ParseProteinGroupNode(Element protgroupnode) throws XmlPullParserException, IOException, ClassNotFoundException, InterruptedException {
 
         int groupindex = Integer.parseInt(protgroupnode.getAttributes().getNamedItem("group_number").getNodeValue());
-        float groupprob = Float.parseFloat(protgroupnode.getAttributes().getNamedItem("probability").getNodeValue());
+        
+        float groupprob=0f;
+        if (protgroupnode.getAttributes().getNamedItem("probability") != null) {
+            groupprob = Float.parseFloat(protgroupnode.getAttributes().getNamedItem("probability").getNodeValue());
+        }
+        else if (protgroupnode.getAttributes().getNamedItem("probability") != null) {
+            groupprob = Float.parseFloat(protgroupnode.getAttributes().getNamedItem("group_probability").getNodeValue());
+        }
+        
         int alphabet = 1;
 
         for (int j = 0; j < protgroupnode.getChildNodes().getLength(); j++) {
@@ -154,9 +162,16 @@ private void ParseProteinGroupNode(Element protgroupnode) throws XmlPullParserEx
                             } else {                               
                                 PepIonID pepIonID = new PepIonID();
                                 pepIonID.Sequence = child.getAttributes().getNamedItem("peptide_sequence").getNodeValue();
-                                pepIonID.MaxProbability = Float.parseFloat(child.getAttributes().getNamedItem("initial_probability").getNodeValue());
-                                pepIonID.Is_NonDegenerate = "Y".equals(child.getAttributes().getNamedItem("is_nondegenerate_evidence").getNodeValue());
-                                pepIonID.Weight = Float.parseFloat(child.getAttributes().getNamedItem("weight").getNodeValue());
+                                
+                                if (child.getAttributes().getNamedItem("initial_probability") != null) {
+                                    pepIonID.MaxProbability = Float.parseFloat(child.getAttributes().getNamedItem("initial_probability").getNodeValue());
+                                }
+                                if (child.getAttributes().getNamedItem("is_nondegenerate_evidence") != null) {
+                                    pepIonID.Is_NonDegenerate = "Y".equals(child.getAttributes().getNamedItem("is_nondegenerate_evidence").getNodeValue());
+                                }
+                                if (child.getAttributes().getNamedItem("weight") != null) {
+                                    pepIonID.Weight = Float.parseFloat(child.getAttributes().getNamedItem("weight").getNodeValue());
+                                }
                                 if (child.getAttributes().getNamedItem("group_weight") != null) {
                                     pepIonID.GroupWeight = Float.parseFloat(child.getAttributes().getNamedItem("group_weight").getNodeValue());
                                 }

DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/FileThread.java

@@ -110,7 +110,7 @@ private void ChangeScanTitlePepXML() throws FileNotFoundException, IOException{
                         writer.write(line.replaceAll(basename+"_Q",basename+".ForLibQ")+"\n");
                     }
                     writer.close();
-                }                
+                }
             }
         }
     }