ubic.gemma.core.loader.expression.arrayDesign

Class ArrayDesignProbeMapperServiceImpl

java.lang.Object

ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignProbeMapperServiceImpl

All Implemented Interfaces:

ArrayDesignProbeMapperService

@Component
public class ArrayDesignProbeMapperServiceImpl
extends Object
implements ArrayDesignProbeMapperService

For an array design, generate gene product mappings for the sequences.

Author:

pavlidis

Constructor Summary

Constructors

Constructor and Description

ArrayDesignProbeMapperServiceImpl(AnnotationAssociationService annotationAssociationService, ArrayDesignAnnotationService arrayDesignAnnotationService, ArrayDesignReportService arrayDesignReportService, ArrayDesignService arrayDesignService, ProbeMapper probeMapper, BioSequenceService bioSequenceService, BlatResultService blatResultService, CompositeSequenceService compositeSequenceService, ExpressionDataFileService expressionDataFileService, GeneProductService geneProductService, GeneService geneService, Persister persisterHelper, TaskExecutor taskExecutor)

Method Summary

Modifier and Type	Method and Description
void	deleteOldFiles(ArrayDesign arrayDesign) Delete outdated annotation and associated experiment files.
void	printResult(CompositeSequence compositeSequence, Collection<BlatAssociation> col) Print results to STDOUT
void	processArrayDesign(ArrayDesign arrayDesign) Do probe mapping, writing the results to the database and using default settings.
void	processArrayDesign(ArrayDesign arrayDesign, ProbeMapperConfig config, boolean useDB)
void	processArrayDesign(ArrayDesign arrayDesign, Taxon taxon, File source, ExternalDatabase sourceDB, boolean ncbiIds) Annotate an array design using a direct source file.
Map<String,Collection<BlatAssociation>>	processCompositeSequence(ProbeMapperConfig config, Taxon taxon, GoldenPathSequenceAnalysis goldenPathDb, CompositeSequence compositeSequence)

Methods inherited from class java.lang.Object

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

Constructor Detail

ArrayDesignProbeMapperServiceImpl

@Autowired
public ArrayDesignProbeMapperServiceImpl(AnnotationAssociationService annotationAssociationService,
                                                    ArrayDesignAnnotationService arrayDesignAnnotationService,
                                                    ArrayDesignReportService arrayDesignReportService,
                                                    ArrayDesignService arrayDesignService,
                                                    ProbeMapper probeMapper,
                                                    BioSequenceService bioSequenceService,
                                                    BlatResultService blatResultService,
                                                    CompositeSequenceService compositeSequenceService,
                                                    ExpressionDataFileService expressionDataFileService,
                                                    GeneProductService geneProductService,
                                                    GeneService geneService,
                                                    Persister persisterHelper,
                                                    TaskExecutor taskExecutor)

Method Detail

printResult

public void printResult(CompositeSequence compositeSequence,
                        Collection<BlatAssociation> col)

Description copied from interface: ArrayDesignProbeMapperService

Print results to STDOUT

Specified by:

printResult in interface ArrayDesignProbeMapperService

Parameters:

compositeSequence - composite sequence

col - blat associations

processArrayDesign

public void processArrayDesign(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignProbeMapperService

Do probe mapping, writing the results to the database and using default settings.

Specified by:

processArrayDesign in interface ArrayDesignProbeMapperService

Parameters:

arrayDesign - AD

processArrayDesign

public void processArrayDesign(ArrayDesign arrayDesign,
                               ProbeMapperConfig config,
                               boolean useDB)

Specified by:

processArrayDesign in interface ArrayDesignProbeMapperService

Parameters:

arrayDesign - AD

config - config

useDB - if false, the results will not be written to the database, but printed to stdout instead.

processArrayDesign

public void processArrayDesign(ArrayDesign arrayDesign,
                               Taxon taxon,
                               File source,
                               ExternalDatabase sourceDB,
                               boolean ncbiIds)
                        throws IOException

Description copied from interface: ArrayDesignProbeMapperService

Annotate an array design using a direct source file. This should only be used if we can't run sequence analysis ourselves. The expected file format is tab-delimited with the following columns:

• Probe name which must match the probe names Gemma uses for the array design.
• Sequence name. If blank, it will be ignored but the probe will still be mapped if possible. The probe will be skipped if it isn't already associated with a sequence. If not blank, it will be checked against the sequence for the probe. If the probe has no sequence, it will be used to create one. If it does, it will be checked for a name match.
• Gene symbol. More than one gene can be specified, delimited by '|'. Genes will only be found if Gemma has a unambiguous match to the name. The gene must already exist in the system.

Comment lines begin with '#'; Note that all the RNA gene products of the gene will be associated with the sequence. This is necessary because 1) Gemma associates sequences with transcripts, not genes and 2) if all we get is a gene, we have to assume all gene products are relevant.

Specified by:

processArrayDesign in interface ArrayDesignProbeMapperService

Parameters:

arrayDesign - AD

taxon - We require this to ensure correct association of the sequences with the genes.

source - source

sourceDB - describes where the annotations came from. Can be null if you really don't know.

ncbiIds - true if the values provided are ncbi ids, not gene symbols (ncbi ids are more reliable)

Throws:

IOException - when IO problems occur.

processCompositeSequence

@Transactional
public Map<String,Collection<BlatAssociation>> processCompositeSequence(ProbeMapperConfig config,
                                                                                       Taxon taxon,
                                                                                       GoldenPathSequenceAnalysis goldenPathDb,
                                                                                       CompositeSequence compositeSequence)

Specified by:

processCompositeSequence in interface ArrayDesignProbeMapperService

deleteOldFiles

public void deleteOldFiles(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignProbeMapperService

Delete outdated annotation and associated experiment files.

Specified by:

deleteOldFiles in interface ArrayDesignProbeMapperService

Parameters:

arrayDesign - platform