Package ubic.gemma.core.analysis.sequence

Interface ProbeMapper

All Known Implementing Classes:

ProbeMapperImpl

public interface ProbeMapper

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.

Method Detail

processBlatResults

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. Default settings (ProbeMapperConfig) are used. This is a major entry point for this API.

Parameters:

goldenPathDb - golden path db

blatResults - blat results

Returns:

map

See Also:

ProbeMapperConfig

processBlatResults

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. This is a major entry point for this API.

Parameters:

goldenPathDb - golden path db

config - config

blatResults - blat results

Returns:

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

processGbId

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

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

Parameters:

goldenPathDb - Gp analysis

genbankId - gene bank id

Returns:

map

processGbIds

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

processSequence

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

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

Parameters:

sequence - sequence

goldenPath - golden path analysis

Returns:

blat associations

processSequences

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

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

Parameters:

goldenpath - for the genome to be used.

sequences - sequences

config - config

Returns:

map