Package ubic.gemma.core.analysis.sequence

Class ProbeMapperImpl

java.lang.Object

ubic.gemma.core.analysis.sequence.ProbeMapperImpl

All Implemented Interfaces:

ProbeMapper

@Component
public class ProbeMapperImpl
extends Object
implements ProbeMapper

Provides methods for mapping sequences to genes and gene products. Some methods accept a configuration object that allows threshold etc. to be modified.

Author:

pavlidis

Constructor Summary

Constructors

Constructor	Description
ProbeMapperImpl()

Method Summary

Modifier and Type	Method	Description
Map<String,Collection<BlatAssociation>>	processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults)	Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associatd with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product.
Map<String,Collection<BlatAssociation>>	processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults, ProbeMapperConfig config)	Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associated with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product.
Map<String,Collection<BlatAssociation>>	processGbId(GoldenPathSequenceAnalysis goldenPathDb, String genbankId)	Given a genbank accession (for a mRNA or EST), find alignment data from GoldenPath.
Map<String,Collection<BlatAssociation>>	processGbIds(GoldenPathSequenceAnalysis goldenPathDb, Collection<String[]> genbankIds)
Collection<BlatAssociation>	processSequence(GoldenPathSequenceAnalysis goldenPath, BioSequence sequence)	Get BlatAssociation results for a single sequence.
Map<String,Collection<BlatAssociation>>	processSequences(GoldenPathSequenceAnalysis goldenpath, Collection<BioSequence> sequences, ProbeMapperConfig config)	Given a collection of sequences, blat them against the selected genome.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProbeMapperImpl

public ProbeMapperImpl()

Method Detail

processBlatResults

public Map<String,Collection<BlatAssociation>> processBlatResults(GoldenPathSequenceAnalysis goldenPathDb,
                                                                        Collection<BlatResult> blatResults)

Description copied from interface: ProbeMapper

Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associatd with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product. Default settings (ProbeMapperConfig) are used. This is a major entry point for this API.

Specified by:

processBlatResults in interface ProbeMapper

Parameters:

goldenPathDb - golden path db

blatResults - blat results

Returns:

map

See Also:

ProbeMapperConfig

processBlatResults

public Map<String,Collection<BlatAssociation>> processBlatResults(GoldenPathSequenceAnalysis goldenPathDb,
                                                                        Collection<BlatResult> blatResults,
                                                                        ProbeMapperConfig config)

Description copied from interface: ProbeMapper

Given some blat results (possibly for multiple sequences) determine which if any gene products they should be associated with; if there are multiple results for a single sequence, these are further analyzed for specificity and redundancy, so that there is a single BlatAssociation between any sequence andy andy gene product. This is a major entry point for this API.

Specified by:

processBlatResults in interface ProbeMapper

Parameters:

goldenPathDb - golden path db

blatResults - blat results

config - config

Returns:

A map of sequence names to collections of blat associations for each sequence.

processGbId

public Map<String,Collection<BlatAssociation>> processGbId(GoldenPathSequenceAnalysis goldenPathDb,
                                                                 String genbankId)

Description copied from interface: ProbeMapper

Given a genbank accession (for a mRNA or EST), find alignment data from GoldenPath.

Specified by:

processGbId in interface ProbeMapper

Parameters:

goldenPathDb - Gp analysis

genbankId - gene bank id

Returns:

map

processGbIds

public Map<String,Collection<BlatAssociation>> processGbIds(GoldenPathSequenceAnalysis goldenPathDb,
                                                                  Collection<String[]> genbankIds)

Specified by:

processGbIds in interface ProbeMapper

processSequence

public Collection<BlatAssociation> processSequence(GoldenPathSequenceAnalysis goldenPath,
                                                   BioSequence sequence)

Description copied from interface: ProbeMapper

Get BlatAssociation results for a single sequence. If you have multiple sequences to run it is always better to use processSequences();

Specified by:

processSequence in interface ProbeMapper

Parameters:

goldenPath - golden path analysis

sequence - sequence

Returns:

blat associations

processSequences

public Map<String,Collection<BlatAssociation>> processSequences(GoldenPathSequenceAnalysis goldenpath,
                                                                      Collection<BioSequence> sequences,
                                                                      ProbeMapperConfig config)

Description copied from interface: ProbeMapper

Given a collection of sequences, blat them against the selected genome.

Specified by:

processSequences in interface ProbeMapper

Parameters:

goldenpath - for the genome to be used.

sequences - sequences

config - config

Returns:

map