Changeset 620


Ignore:
Timestamp:
Mar 7, 2008, 8:40:42 AM (13 years ago)
Author:
Martin Svensson
Message:

Fixes #93 Added some more javadoc and improved the code format in a few places.

File:
1 edited

Legend:

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

    r591 r620  
    4848
    4949/**
    50  * @author Martin
    51  * @version 2.6
     50  This is a validator and meta data extractor for
     51  Illumina SNP manifest files.
     52  To pass the validation the manifest file needs to have
     53  at least the columns 'IlmnID' and 'AddressA_ID' in the
     54  '[Assay]' section.
     55 
     56  The extraction of meta data takes the value for 'SNP Count'
     57  column and set this number to the array design's
     58  numFileFileFeatures-property.
     59  @author Martin
     60  @version 2.6
    5261 */
    5362public class SnpCvsFileHandler
     
    6574
    6675  // Required column names
    67   private String[] requiredColumns =
    68   { "IlmnID,", ",AddressA_ID," };
     76  private String[] requiredColumns = { "IlmnID,", ",AddressA_ID," };
    6977
    7078  public SnpCvsFileHandler()
     
    7684  @Override
    7785  public void validate(DbControl dc)
    78       throws InvalidDataException,
    79       InvalidRelationException
     86      throws InvalidDataException, InvalidRelationException
    8087  {
    8188    ArrayDesign design = (ArrayDesign) getItem();
    82     if (design.getPlatform() == null
    83         || !(Illumina.PLATFORM_ID.equals(design.getPlatform()
    84             .getExternalId())))
     89    if (design.getPlatform() == null ||
     90        !(Illumina.PLATFORM_ID.equals(design.getPlatform().getExternalId())))
    8591    {
    8692      throw new InvalidDataException("Array design '" + design.getName()
     
    106112      if (manifestMember != null)
    107113      {
    108         parsedHeadings = parseHeadings(manifestMember.getFile(),
    109             linesToParse);
     114        parsedHeadings = parseHeadings(manifestMember.getFile(), linesToParse);
    110115      }
    111116    }
     
    190195          {
    191196            numFeatures = Integer.parseInt(num.trim());
    192           } catch (NumberFormatException nex)
     197          }
     198          catch (NumberFormatException nex)
    193199          {
    194200            throw new InvalidDataException(nex);
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