Changeset 4537


Ignore:
Timestamp:
Dec 17, 2013, 1:46:16 PM (9 years ago)
Author:
Fredrik Levander
Message:

Fixes #820. Peptide level filtering

Location:
trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/client/servlet/src/org/proteios/action/hit/PrideExport.java

    r4500 r4537  
    9797    instruction += " One PRIDE XML file is created for each peak list file in mzData format.";
    9898    instruction += " For gels, only proteins with a combined FDR (False Discovery Rate) below a set upper cutoff will be used.";
    99     instruction += " For non gel export (local sample ID selected), all Proteios Protein entries generated by the Protein Assembly report will be exported, and all peptides from that protein found in the hits report will be reported, regardless of combined FDR for the peptides.";
     99    instruction += " For non gel export (local sample ID selected), all Proteios Protein entries generated by the Protein Assembly report will be exported, and all peptides from that protein with a combined FDR below the cutoff will be reported.";
    100100    instruction += " Please enter additional data needed for the PRIDE XML export.";
    101101    instructionArea.setContent(instruction);
  • trunk/plugin/src/org/proteios/plugins/PrideExportPlugin.java

    r4514 r4537  
    12151215      Expressions.parameter("protein")));
    12161216    hitQuery.setParameter("protein", false, null);
     1217    if (localSampleIdStr != null)
     1218    {
     1219      // Filter peptides on combined FDR
     1220      hitQuery.restrict(Restrictions.lteq(Hql.property("combinedFDR"),
     1221        Expressions.aFloat((float) cutoff)));
     1222    }
    12171223    //
    12181224    // Restrict query to hits marked as not being of score type
     
    12631269      else
    12641270      {
    1265         log.info("Peptide E-Value upper cutoff = " + cutoff);
    1266         hitQuery.restrict(Restrictions.lt(
    1267           Hql.property("expectationValue"),
     1271        log.info("Peptide combined FDR upper cutoff = " + cutoff);
     1272        hitQuery.restrict(Restrictions.lteq(
     1273          Hql.property("combinedFDR"),
    12681274          Expressions.aFloat((float) cutoff)));
    12691275      }
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