Package ubic.gemma.core.loader.expression.arrayDesign

Interface ArrayDesignSequenceAlignmentService

All Known Implementing Classes:
ArrayDesignSequenceAlignmentServiceImpl
public interface ArrayDesignSequenceAlignmentService

  • Method Details

    • processArrayDesign

      Collection<BlatResult> processArrayDesign(ArrayDesign ad, boolean sensitive)
      Run blat on all sequences on the array design. For arrays with sequences from multiple taxa, BLAT is run appropriately assuming sequences are available for all the represented taxa.
      Parameters:
      ad - ad
      sensitive - if true, blat will be run in a more sensitive mode, if available.
      Returns:
      blat results

    • processArrayDesign

      Collection<BlatResult> processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
      Parameters:
      ad - ad
      taxon - (to allow for the possibility of multiple taxa for the array) - if not given, attempt to infer from ad.
      rawBlatResults - , assumed to be from alignments to correct taxon Typically these would have been read in from a file.
      Returns:
      persisted BlatResults.

    • validateTaxaForBlatFile

      Taxon validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)
      If no taxon is supplied then infer it from array. If more than one taxa is on array then stop processing as blat file details should relate to one taxon
      Parameters:
      arrayDesign - Array design to process
      taxon - Taxon supplied
      Returns:
      taxon

    • processArrayDesign

      Collection<BlatResult> processArrayDesign(ArrayDesign design)

    • processArrayDesign

      Collection<BlatResult> processArrayDesign(ArrayDesign ad, Blat blat)