Changeset 590


Ignore:
Timestamp:
Feb 21, 2008, 11:36:31 AM (13 years ago)
Author:
Martin Svensson
Message:

References #93 You can now validate and extract meta-data from SNP-manifest files. The validator class and metadata extractor class is now being set when creating manifest data file-type in the installation plug-in.

Location:
trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina
Files:
1 added
2 edited

Legend:

Unmodified
Added
Removed
  • trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/Illumina.java

    r589 r590  
    9090 
    9191  /**
     92    Class name of the SNP manifest validator and meta data extractor
     93   */
     94  public static final String SNP_MANIFEST_VALIDATOR_METADATAREADER = "net.sf.basedb.illumina.filehandler.SnpCvsFileHandler";
     95 
     96  /**
    9297    The ID of the raw data type used to hold Illumina Bead Summary raw data.
    9398    Use {@link #getBeadSummaryType()} to get the raw data type object.
  • trunk/net/sf/basedb/illumina/src/net/sf/basedb/illumina/install/Install.java

    r589 r590  
    439439    DataFileType snpManifestType = createDataFileType(dc,
    440440        Illumina.SNP_MANIFEST_FILE_ID, "SNP manifest file", "Manifest file for Illumina SNP",
    441         Item.ARRAYDESIGN, SNP_MF_FILETYPE_EXTENSION, reporterMapType, null, null,
     441        Item.ARRAYDESIGN, SNP_MF_FILETYPE_EXTENSION, reporterMapType,
     442        Illumina.SNP_MANIFEST_VALIDATOR_METADATAREADER, Illumina.SNP_MANIFEST_VALIDATOR_METADATAREADER,
    442443        jarPath, ignoreExistingItems);
    443444    DataFileType snpSplitDataType = createDataFileType(dc,
    444445        Illumina.SNP_SPLITDATA_FILE_ID, "SNP split data file", "Data file for Illumina SNP. Contains data for only one sample",
    445446        Item.RAWBIOASSAY, SNP_SPLITDATA_FILETYPE_EXTENSION, rawDataType,
    446         null, null, jarPath, ignoreExistingItems);
     447        null, null, null, ignoreExistingItems);
    447448    DataFileType snpDataType = createDataFileType(dc,
    448449        Illumina.SNP_DATA_FILE_ID, "SNP original data file", "The original data file exported from Illumina BeadStudio",
    449450        Item.RAWBIOASSAY, null, rawDataType,
    450         null, null, jarPath, ignoreExistingItems);
     451        null, null, null, ignoreExistingItems);
    451452   
    452453    //Platform and variants
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