Changeset 4547

Timestamp:

Feb 28, 2014, 11:58:27 AM (9 years ago)

Author:

Fredrik Levander

Message:

Corrected formatting of peaks and added protein ids in msp library export.

File:

• trunk/contrib/SpectrumLibraryExport/src/satoshi/LibraryExportPlugin.java (modified) (8 diffs)

trunk/contrib/SpectrumLibraryExport/src/satoshi/LibraryExportPlugin.java

@@ -358 +358 @@
       outCoreFile2.setName(coreFilename2);
       fileNameAssigned2 = true;
+      outCoreFile2.setMimeType("text/plain");
       /*
        * Save core file item before getting uploadstream
@@ -590 +591 @@
       List<String> requestSpectraSEQ = new ArrayList<String>();
       List<String> requestSpectraModification = new ArrayList<String>();
+      List<String> requestSpectraProtein = new ArrayList<String>();
       List<Float> requestSpectraEXP = new ArrayList<Float>();
       List<List<String>> requestSpectraExternalID = new ArrayList<List<String>>();
@@ -610 +612 @@
             .contains(phit.getSpectrumStringId())) {
           requestSpectraStringID.add(phit.getSpectrumStringId());
+          String externalID = phit.getExternalId();
           String[] s1 = phit.getDescription().split(" ", 2);
           if (s1.length == 2 && s1[1].contains(">"))
@@ -622 +625 @@
                 int pos = Integer.parseInt(s2.substring(s2.indexOf('@')+2,s2.indexOf('('))); 
                 char newchar = s2.charAt(s2.indexOf('>')+1);
+                externalID += " " + s2.substring(s2.indexOf('>')-1,s2.indexOf('>')+2) + "@" + pos;
                 if (pos>0) --pos;
                 String newSeq = s1[0].substring(0,pos)+newchar+s1[0].substring(pos+1);
@@ -635 +639 @@
             s1[1]=newString;
           }
-          
+          requestSpectraProtein.add(externalID);
           requestSpectraSEQ.add(s1[0]); // sequence
           if (s1.length == 2) {
@@ -1032 +1036 @@
           // output2.write(" Pep=Tryptic");
           // output2.write(" Fullname= ");
+          output2.write(" Protein=\""+requestSpectraProtein.get(i)+"\"");
           if (mods == null) {
             output2.write(" Mods=0 \n");
@@ -1042 +1047 @@
           // output2.write(" Mz_exact= ");
           // output2.write(" Mz_az= ");
-          // output2.write(" Protein= ");
+          
           // output2.write(" /gene= ");
           // output2.write(" /function= ");
@@ -1089 +1094 @@
           // print out masses and intensities
           for (int l = 0; l < mzs.size(); l++) {
-            output2.write(fourDecimals.format(mzs.get(l)) + "\t"
-                + ints.get(l) + "\t\"");
             List<Ion<PeptideFragment>> matchedIons = PeptideUtil.matchingIons(ions, mzs.get(l), mzTolerance);
             if (!matchedIons.isEmpty())