Changeset 1120


Ignore:
Timestamp:
Jun 10, 2009, 10:42:02 PM (12 years ago)
Author:
Jari Häkkinen
Message:

Fixes #232.

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

Legend:

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

    • Property svn:eol-style set to native
    • Property svn:keywords set to Id
    r941 r1120  
    22  $Id$
    33
    4   Copyright (C) 2008 Jari Häkkinen
     4  Copyright (C) 2008, 2009 Jari Häkkinen
    55
    66  This file is part of Illumina plug-in package for BASE.
     
    391391      DynamicSpotQuery query = source.getSpotData();
    392392      query.selectPermanent(Dynamic.select(VirtualColumn.POSITION));
    393       Expression ch1=Dynamic.column(VirtualColumn.channel(1));
     393      Expression ch1=Dynamic.column(VirtualColumn.channelIntensity(1));
    394394      query.selectPermanent(Selects.expression(ch1,null));
    395395      query.restrictPermanent(bioAssayRestriction);
     
    415415          query.setParameter("bioAssayColumn", (int)bioassayColumn, Type.INT);
    416416          DynamicResultIterator dri = query.iterate(dc);
    417           int ch1Index = dri.getIndex(VirtualColumn.channel(1).getName());
     417          int ch1Index = dri.getIndex(VirtualColumn.channelIntensity(1).getName());
    418418          backgroundCh1[assayNo]=
    419419            ( method.equals("Illumina BeadStudio median") ?
     
    440440          DynamicResultIterator dri = query.iterate(dc);
    441441          int positionIndex = dri.getIndex(VirtualColumn.POSITION.getName());
    442           int ch1Index = dri.getIndex(VirtualColumn.channel(1).getName());
     442          int ch1Index = dri.getIndex(VirtualColumn.channelIntensity(1).getName());
    443443          float background=backgroundCh1[assayNo++];
    444444          while (dri.hasNext())
  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java

    r1114 r1120  
    467467          controlQuery.setParameter("bioAssayColumn", (int)bioassayColumn, Type.INT);
    468468          DynamicResultIterator dri = controlQuery.iterate(dc);
    469           int ch1Index = dri.getIndex(VirtualColumn.channel(1).getName());
     469          int ch1Index = dri.getIndex(VirtualColumn.channelIntensity(1).getName());
    470470          float[] sortedControlIntensity=new float[(int)dri.getTotalCount()];
    471471          int beadNo=0;
     
    504504          int positionIndex = dri.getIndex(VirtualColumn.POSITION.getName());
    505505          int columnIndex = dri.getIndex(VirtualColumn.COLUMN.getName());
    506           ch1Index = dri.getIndex(VirtualColumn.channel(1).getName());
     506          ch1Index = dri.getIndex(VirtualColumn.channelIntensity(1).getName());
    507507          while (dri.hasNext())
    508508          {
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