From 3f79a14b56280b6d0bc57c9a85e62d6327c3519e Mon Sep 17 00:00:00 2001 From: "dominik.kopczynski" Date: Mon, 13 May 2019 09:48:53 +0200 Subject: [PATCH] fixed bug 'Follow up analysis pepXML export fails #24' --- .../java/eu/isas/peptideshaker/followup/PepXmlExport.java | 5 +++-- .../isas/peptideshaker/recalibration/RunMzDeviation.java | 7 ++++--- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/src/main/java/eu/isas/peptideshaker/followup/PepXmlExport.java b/src/main/java/eu/isas/peptideshaker/followup/PepXmlExport.java index 19add923a..ca88994e7 100644 --- 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(""); diff --git a/src/main/java/eu/isas/peptideshaker/recalibration/RunMzDeviation.java b/src/main/java/eu/isas/peptideshaker/recalibration/RunMzDeviation.java index e105217f8..aa08dff26 100644 --- 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);