Uses of Class
ubic.gemma.core.analysis.sequence.ProbeMapperConfig
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Packages that use ProbeMapperConfig Package Description ubic.gemma.core.analysis.sequence ubic.gemma.core.goldenpath ubic.gemma.core.loader.expression.arrayDesign -
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Uses of ProbeMapperConfig in ubic.gemma.core.analysis.sequence
Methods in ubic.gemma.core.analysis.sequence with parameters of type ProbeMapperConfig Modifier and Type Method Description Map<String,Collection<BlatAssociation>>ProbeMapper. 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>>ProbeMapperImpl. processBlatResults(GoldenPathSequenceAnalysis goldenPathDb, Collection<BlatResult> blatResults, ProbeMapperConfig config)Map<String,Collection<BlatAssociation>>ProbeMapper. processSequences(GoldenPathSequenceAnalysis goldenpath, Collection<BioSequence> sequences, ProbeMapperConfig config)Given a collection of sequences, blat them against the selected genome.Map<String,Collection<BlatAssociation>>ProbeMapperImpl. processSequences(GoldenPathSequenceAnalysis goldenpath, Collection<BioSequence> sequences, ProbeMapperConfig config) -
Uses of ProbeMapperConfig in ubic.gemma.core.goldenpath
Methods in ubic.gemma.core.goldenpath with parameters of type ProbeMapperConfig Modifier and Type Method Description Collection<BlatAssociation>GoldenPathSequenceAnalysis. findAssociations(String chromosome, Long queryStart, Long queryEnd, String starts, String sizes, String strand, ThreePrimeDistanceMethod method, ProbeMapperConfig config)Given a physical location, identify overlapping genes or predicted genes. -
Uses of ProbeMapperConfig in ubic.gemma.core.loader.expression.arrayDesign
Methods in ubic.gemma.core.loader.expression.arrayDesign with parameters of type ProbeMapperConfig Modifier and Type Method Description voidArrayDesignProbeMapperService. processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB)voidArrayDesignProbeMapperServiceImpl. processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB)Map<String,Collection<BlatAssociation>>ArrayDesignProbeMapperService. processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence)Map<String,Collection<BlatAssociation>>ArrayDesignProbeMapperServiceImpl. processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence)
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