Interface ArrayDesignSequenceAlignmentService
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- All Known Implementing Classes:
ArrayDesignSequenceAlignmentServiceImpl
public interface ArrayDesignSequenceAlignmentService
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Method Summary
All Methods Instance Methods Abstract Methods 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.
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Method Detail
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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
- adsensitive
- if true, blat will be run in a more sensitive mode, if available.- Returns:
- blat results
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processArrayDesign
Collection<BlatResult> processArrayDesign(ArrayDesign ad, Taxon taxon, Collection<BlatResult> rawBlatResults)
- Parameters:
ad
- adtaxon
- (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.
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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 processtaxon
- Taxon supplied- Returns:
- taxon
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processArrayDesign
Collection<BlatResult> processArrayDesign(ArrayDesign design)
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processArrayDesign
Collection<BlatResult> processArrayDesign(ArrayDesign ad, Blat blat)
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