Class GeoFamilyParser

java.lang.Object
ubic.gemma.core.loader.expression.geo.GeoFamilyParser
All Implemented Interfaces:
Parser<GeoParseResult>
public class GeoFamilyParser extends Object implements Parser<GeoParseResult>
Class for parsing GSE and GDS files from NCBI GEO. See ncbi geo for format information.
Author:
keshav, pavlidis

  • Constructor Details

    • GeoFamilyParser

      public GeoFamilyParser()

  • Method Details

    • getResults

      public Collection<GeoParseResult> getResults()
      Specified by:
      getResults in interface Parser<GeoParseResult>
      Returns:
      the results of the parse.

    • parse

      public void parse(File f) throws IOException
      Description copied from interface: Parser
      Parse a File
      Specified by:
      parse in interface Parser<GeoParseResult>
      Parameters:
      f - file
      Throws:
      IOException - if there is a problem while manipulating the file

    • parse

      public void parse(InputStream is) throws IOException
      Description copied from interface: Parser
      Parse a InputStream.
      Specified by:
      parse in interface Parser<GeoParseResult>
      Parameters:
      is - input stream
      Throws:
      IOException - if there is a problem while manipulating the file

    • parse

      public void parse(String fileName) throws IOException
      Description copied from interface: Parser
      Parse a file identified by its path.
      Specified by:
      parse in interface Parser<GeoParseResult>
      Parameters:
      fileName - Absolute path to the file
      Throws:
      IOException - if there is a problem while manipulating the file

    • sampleTypeSet

      public void sampleTypeSet(String accession, String string)

    • setProcessPlatformsOnly

      public void setProcessPlatformsOnly(boolean b)

    • setMetadataOnly

      public void setMetadataOnly(boolean b)
      Parse records that carry no data and no platform, as GEO's view=brief series and sample records do.

      Only the data-table bookkeeping is skipped, because there is nothing for it to describe: a sample's quantitation types are keyed by its platform, and a platform is only attached to a sample when a ^PLATFORM record was parsed. Without one, initializing them walks off the end of an empty collection.

    • convertStringToSeriesType

      public static GeoSeriesType convertStringToSeriesType(String string)
      See also GeoDataset.convertStringToExperimentType
      Parameters:
      string - series type string
      Returns:
      series type object