Changeset 1258


Ignore:
Timestamp:
Nov 2, 2010, 2:20:34 PM (13 years ago)
Author:
Nicklas Nordborg
Message:

Fix code using deprecated methods in BASE API due to ​http://base.thep.lu.se/ticket/1503

Location:
plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BackgroundCorrection.java

    r1217 r1258  
    581581        for (BioAssay assay : assays)
    582582        {
    583           checkInterrupted();
     583          ThreadSignalHandler.checkInterrupted();
    584584          // calculate background correction for this bioassay
    585585          short bioassayColumn = assay.getDataCubeColumnNo();
    … …  
    645645        for (BioAssay assay : assays)
    646646        {
    647           checkInterrupted();
     647          ThreadSignalHandler.checkInterrupted();
    648648          if (progress != null)
    649649          {

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/BeadSummaryImporter.java

    r1226 r1258  
    698698        {
    699699          // Check if user has aborted
    700           checkInterrupted();
     700          ThreadSignalHandler.checkInterrupted();
    701701         
    702702          // Progress reporting
    … …  
    777777       
    778778        // Check if user has aborted
    779         checkInterrupted();
     779        ThreadSignalHandler.checkInterrupted();
    780780       
    781781        // Progress reporting

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java

    r1235 r1258  
    531531        for (BioAssay assay : assays)
    532532        {
    533           checkInterrupted();
     533          ThreadSignalHandler.checkInterrupted();
    534534          if (progress != null)
    535535          {
    … …  
    578578          }
    579579
    580           checkInterrupted();
     580          ThreadSignalHandler.checkInterrupted();
    581581
    582582          // calculate detection P-value for all beadsets

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/SnpIntensityCalculator.java

    r1226 r1258  
    210210      int jobId = job.getId();
    211211      Job thisJob = Job.getById(dc, jobId);
    212       checkInterrupted();
     212      ThreadSignalHandler.checkInterrupted();
    213213     
    214214      // Create transformation and root bioassay set
    … …  
    553553      while (ffp.hasMoreData())
    554554      {         
    555         checkInterrupted();
     555        ThreadSignalHandler.checkInterrupted();
    556556        currentSpot++;
    557557        dataLine = ffp.nextData();
    … …  
    618618    while (ffp.hasMoreData())
    619619    {
    620       checkInterrupted();
     620      ThreadSignalHandler.checkInterrupted();
    621621      currentSpot++;
    622622      FlatFileParser.Data dataLine = ffp.nextData();
    … …  
    667667      if (proxy != null)
    668668      {
    669         checkInterrupted();
     669        ThreadSignalHandler.checkInterrupted();
    670670        currentSpot++;
    671671        proxy.setTheId(reporter.getInt(1));
    … …  
    710710    for (Map.Entry<String, ReporterProxy> entry : preloaded.entrySet())
    711711    {
    712       checkInterrupted();
     712      ThreadSignalHandler.checkInterrupted();
    713713      currentSpot++;
    714714      ReporterProxy proxy = entry.getValue();
    … …  
    738738      if (currentSpot % interval == 0 && progress != null)
    739739      {
    740         checkInterrupted();
     740        ThreadSignalHandler.checkInterrupted();
    741741        progress.displayAbsolute(baseProgress + currentSpot,
    742742          "Mapping reporters to positions: " +
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