Interface ArrayDesignSequenceAlignmentService

    • Method Detail

      • 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