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

Interface ArrayDesignSequenceAlignmentService

All Known Implementing Classes:

ArrayDesignSequenceAlignmentServiceImpl

public interface ArrayDesignSequenceAlignmentService

Method Summary

Modifier and Type	Method	Description
Collection<BlatResult>	processArrayDesign(ArrayDesign design)
Collection<BlatResult>	processArrayDesign(ArrayDesign ad, boolean sensitive)	Run blat on all sequences on the array design.
Collection<BlatResult>	processArrayDesign(ArrayDesign ad, Blat blat)
Collection<BlatResult>	processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
Taxon	validateTaxaForBlatFile(ArrayDesign arrayDesign, Taxon taxon)	If no taxon is supplied then infer it from array.

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

processArrayDesign

Collection<BlatResult> processArrayDesign(ArrayDesign design)

processArrayDesign

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