fixed bug 'Follow up analysis pepXML export fails #24'

compomics · May 13, 2019 · 3f79a14 · 3f79a14
1 parent 23a0335
commit 3f79a14
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/src/main/java/eu/isas/peptideshaker/followup/PepXmlExport.java b/src/main/java/eu/isas/peptideshaker/followup/PepXmlExport.java
@@ -460,12 +460,13 @@ private String getModLine(Modification modification, boolean variable) {
      */
     private void writeSpectrumQueries(SimpleXmlWriter sw, Identification identification, IdentificationParameters identificationParameters, String spectrumFile, WaitingHandler waitingHandler) throws IOException {
 
-        SpectrumMatchesIterator psmIterator = identification.getSpectrumMatchesIterator(waitingHandler, "spectrumFile == '" + spectrumFile + "'");
+        SpectrumMatchesIterator psmIterator = identification.getSpectrumMatchesIterator(waitingHandler);
         SpectrumMatch spectrumMatch;
 
         while ((spectrumMatch = psmIterator.next()) != null) {
-
             String spectrumKey = spectrumMatch.getSpectrumKey();
+            if (!Spectrum.getSpectrumFile(spectrumKey).equals(spectrumFile)) continue;
+
             String spectrumTitle = Spectrum.getSpectrumTitle(spectrumKey);
             StringBuilder spectrumQueryStart = new StringBuilder();
             spectrumQueryStart.append("<spectrum_query unique_search_id=\"").append(StringEscapeUtils.escapeHtml4(spectrumTitle)).append("\">");

diff --git a/src/main/java/eu/isas/peptideshaker/recalibration/RunMzDeviation.java b/src/main/java/eu/isas/peptideshaker/recalibration/RunMzDeviation.java
@@ -281,16 +281,17 @@ public RunMzDeviation(String spectrumFileName, Identification identification, Se
             waitingHandler.setMaxSecondaryProgressCounter(spectrumFactory.getSpectrumTitles(spectrumFileName).size());
         }
 
-        SpectrumMatchesIterator psmIterator = identification.getSpectrumMatchesIterator(waitingHandler, "spectrumFile == '" + spectrumFileName + "'");
+        SpectrumMatchesIterator psmIterator = identification.getSpectrumMatchesIterator(waitingHandler);
         SpectrumMatch spectrumMatch;
 
         while ((spectrumMatch = psmIterator.next()) != null) {
-
             if (waitingHandler != null && waitingHandler.isRunCanceled()) {
                 break;
             }
-
+            
             String spectrumKey = spectrumMatch.getSpectrumKey();
+            if (!Spectrum.getSpectrumFile(spectrumKey).equals(spectrumFileName)) continue;
+
 
             psParameter = (PSParameter) spectrumMatch.getUrParam(psParameter);