Changeset 751


Ignore:
Timestamp:
Sep 2, 2008, 4:38:53 PM (13 years ago)
Author:
Martin Svensson
Message:

References #119 Bug-fixing

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

Legend:

Unmodified
Added
Removed
  • plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/AbstractSpotData.java

    r750 r751  
    4040    StringBuilder sb = new StringBuilder();
    4141    sb.append(this.getPosition()).append("\t");
    42     sb.append(this.getNormalizableData()).append("\t");
    4342    for (float intensity : this.getChannelData())
    4443    {
  • plugins/base2/net.sf.basedb.normalizers/trunk/src/net/sf/basedb/plugins/RankInvariantNormalization.java

    r750 r751  
    281281        parameters.add(normalizationSection);
    282282        parameters.add(minIntensityParameter);
     283       
     284        String description = "Set min intensity for each channel and properties for the child";
     285       
     286        configureJob = new RequestInformation
     287        (
     288          Request.COMMAND_CONFIGURE_JOB,
     289          "Configure job",
     290          description,
     291          parameters
     292        );
    283293      }
    284294    }
     
    345355      {
    346356        // Create temp-file to store the spot's original values and position.
    347         File tempFile = File.createTempFile(null, ".tmp");
     357        File tempFile = File.createTempFile("Rank", null);
    348358        FileWriter fw = new FileWriter(tempFile);
    349359        // Write spot information to a file and summarize the rows.
     
    351361        {
    352362          AbstractSpotData spot = data.get(i);
    353           double newRowValue = assays.indexOf(assay) < 0 ?
     363          double newRowValue = assays.indexOf(assay) > 0 ?
    354364              (rowSummaries[i] + spot.getNormalizableData()) :
    355365              spot.getNormalizableData();
    356366          rowSummaries[i] = newRowValue;
    357367         
    358           if (i < 0)fw.write("\n");
     368          if (i > 0)fw.write("\n");
    359369          fw.write(spot.toString());
    360370        }
     
    399409        BufferedReader input =  new BufferedReader(new FileReader(assayFile));
    400410       
    401         String line = input.readLine();
     411        String line;
    402412        int rowIndex = 0;
    403413        while ((line = input.readLine()) != null)
     
    408418          batcher.insert(columnNo, spot.getPosition(), spot.getChannelData());
    409419          normalizedSpots++;
     420          rowIndex++;
    410421        }
    411422       
     
    414425          normalizedSpots + " spots normalized");
    415426      }
     427      return child;
    416428    }
    417429    catch (IOException e)
    418430    {
    419431      throw new BaseException(e);
    420     }
    421     return null;
     432    }   
    422433  }
    423434 
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