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

Class ArrayDesignSequenceAlignmentServiceImpl

java.lang.Object

ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentServiceImpl

All Implemented Interfaces:

ArrayDesignSequenceAlignmentService

@Component
public class ArrayDesignSequenceAlignmentServiceImpl
extends Object
implements ArrayDesignSequenceAlignmentService

Aligns sequences from array designs to the genome, using blat, and persists the blat results. Note: to avoid having very long transactions, this does not run transactionally at the level of a platform. Thus it is possible for it to die with a platform half-processed. But if we don't do this the transactions are too big and cause various deadlocking problems.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
ArrayDesignSequenceAlignmentServiceImpl(ArrayDesignReportService arrayDesignReportService, ArrayDesignService arrayDesignService, BioSequenceService bioSequenceService, Persister persisterHelper)

Method Summary

Modifier and Type	Method	Description
static Collection<BioSequence>	getSequences(ArrayDesign ad)
static Collection<BioSequence>	getSequences(ArrayDesign ad, Taxon taxon)
Collection<BlatResult>	processArrayDesign(ArrayDesign design)
Collection<BlatResult>	processArrayDesign(ArrayDesign design, boolean sensitive)	Run blat on all sequences on the array design.
Collection<BlatResult>	processArrayDesign(ArrayDesign design, 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ArrayDesignSequenceAlignmentServiceImpl

@Autowired
public ArrayDesignSequenceAlignmentServiceImpl(ArrayDesignReportService arrayDesignReportService,
                                               ArrayDesignService arrayDesignService,
                                               BioSequenceService bioSequenceService,
                                               Persister persisterHelper)

Method Detail

getSequences

public static Collection<BioSequence> getSequences(ArrayDesign ad)

Parameters:

ad - platform

Returns:

all sequences, across all taxa that might be represented on the array design

getSequences

public static Collection<BioSequence> getSequences(ArrayDesign ad,
                                                   Taxon taxon)

Parameters:

ad - platform

taxon - (specified in case array has multiple taxa)

Returns:

bio sequences

processArrayDesign

public Collection<BlatResult> processArrayDesign(ArrayDesign design,
                                                 boolean sensitive)

Description copied from interface: ArrayDesignSequenceAlignmentService

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.

Specified by:

processArrayDesign in interface ArrayDesignSequenceAlignmentService

Parameters:

design - ad

sensitive - if true, blat will be run in a more sensitive mode, if available.

Returns:

blat results

processArrayDesign

public Collection<BlatResult> processArrayDesign(ArrayDesign ad,
                                                 Taxon taxon,
                                                 Collection<BlatResult> rawBlatResults)

Specified by:

processArrayDesign in interface ArrayDesignSequenceAlignmentService

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

public Taxon validateTaxaForBlatFile(ArrayDesign arrayDesign,
                                     Taxon taxon)

Description copied from interface: ArrayDesignSequenceAlignmentService

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

Specified by:

validateTaxaForBlatFile in interface ArrayDesignSequenceAlignmentService

Parameters:

arrayDesign - Array design to process

taxon - Taxon supplied

Returns:

taxon

processArrayDesign

public Collection<BlatResult> processArrayDesign(ArrayDesign design)

Specified by:

processArrayDesign in interface ArrayDesignSequenceAlignmentService

processArrayDesign

public Collection<BlatResult> processArrayDesign(ArrayDesign design,
                                                 Blat blat)

Specified by:

processArrayDesign in interface ArrayDesignSequenceAlignmentService