Changeset 698


Ignore:
Timestamp:
May 21, 2008, 11:57:29 PM (13 years ago)
Author:
Jari Häkkinen
Message:

Fixes #110.

File:
1 edited

Legend:

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

    r689 r698  
    114114     is added, or a corresponding list for 2-channel types must be
    115115     added.
    116 
    117      Note, changing the string in the list will affect the behaviour
    118      of the plug-in and most certaintly unexpected results will be
    119      generated. As an example, changing 'Whole Genome BeadChip'
    120      will break the median method.
    121116  */
    122117  private static final
    123   PluginParameter<String> arrayType1Parameter = new PluginParameter<String>
    124     ( "method",
    125       "Correction method",
    126       "These methods are implemented:\n\n" +
    127       "Detection P-value calculation for Illumine Whole Genome BeadChips\n" +
    128       "Detection P-value calculation for Illumine Focused Arrays",
     118  PluginParameter<String> arrayTypeParameter = new PluginParameter<String>
     119    ( "arraytype",
     120      "Array type",
     121      "Detection P-value calculation for array types:\n\n" +
     122      "Illumina Whole Genome BeadChips\n" +
     123      "Illumina Focused Arrays (not yet implemented)",
    129124      new StringParameterType(255, "Whole Genome BeadChip", true, 1, 0, 0,
    130125                              Arrays.asList(
     
    185180
    186181        // Plug-in options
    187         storeValue(job, request, arrayType1Parameter);
     182        storeValue(job, request, arrayTypeParameter);
    188183        storeValue(job, request, outlierParameter);
    189184
     
    241236
    242237        // background correction method
    243         parameters.add(arrayType1Parameter);
     238        parameters.add(arrayTypeParameter);
    244239        parameters.add(outlierParameter);
    245240 
     
    382377    try
    383378    {
    384       String arrayType = (String)job.getValue(arrayType1Parameter.getName());
     379      String arrayType = (String)job.getValue(arrayTypeParameter.getName());
    385380      dc = sc.newDbControl();
    386381      BioAssaySet source = getSourceBioAssaySet(dc);
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