Interface ProbeMapper

  • All Known Implementing Classes:
    ProbeMapperImpl

    public interface ProbeMapper
    • Method Detail

      • 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:
        ProbeMapperConfig
      • 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
        config - config
        blatResults - blat results
        Returns:
        A map of sequence names to collections of blat associations for each sequence.
      • 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:
        sequence - sequence
        goldenPath - golden path analysis
        Returns:
        blat associations