Package ubic.gemma.core.analysis.sequence

Interface ProbeMapper

All Known Implementing Classes:
ProbeMapperImpl
public interface ProbeMapper

  • Method Details

    • processBlatResults

      Map<String,Collection<BlatAssociation>> processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults)
      Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associatd with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product. Default settings (ProbeMapperConfig) are used. This is a major entry point for this API.
      Parameters:
      goldenPathDb - golden path db
      blatResults - blat results
      Returns:
      map
      See Also:

    • processBlatResults

      Map<String,Collection<BlatAssociation>> processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults, ProbeMapperConfig config)
      Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associated with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product. This is a major entry point for this API.
      Parameters:
      goldenPathDb - golden path db
      blatResults - blat results
      config - config
      Returns:
      A map of sequence names to collections of blat associations for each sequence.

    • processGbId

      Map<String,Collection<BlatAssociation>> processGbId(GoldenPathSequenceAnalysis goldenPathDb, String genbankId)
      Given a genbank accession (for a mRNA or EST), find alignment data from GoldenPath.
      Parameters:
      goldenPathDb - Gp analysis
      genbankId - gene bank id
      Returns:
      map

    • processGbIds

      Map<String,Collection<BlatAssociation>> processGbIds(GoldenPathSequenceAnalysis goldenPathDb, Collection<String[]> genbankIds)

    • processSequence

      Collection<BlatAssociation> processSequence(GoldenPathSequenceAnalysis goldenPath, BioSequence sequence)
      Get BlatAssociation results for a single sequence. If you have multiple sequences to run it is always better to use processSequences();
      Parameters:
      goldenPath - golden path analysis
      sequence - sequence
      Returns:
      blat associations

    • processSequences

      Map<String,Collection<BlatAssociation>> processSequences(GoldenPathSequenceAnalysis goldenpath, Collection<BioSequence> sequences, ProbeMapperConfig config)
      Given a collection of sequences, blat them against the selected genome.
      Parameters:
      goldenpath - for the genome to be used.
      sequences - sequences
      config - config
      Returns:
      map