@Test public void testFindGSE3193() throws Exception { GeoFamilyParser parser = new GeoFamilyParser(); try (InputStream is = new GZIPInputStream( this.getClass() .getResourceAsStream( "/data/loader/expression/geo/GSE3193Short/GSE3193_family.soft.gz" ) )) { parser.parse( is ); } GeoParseResult parseResult = ( ( GeoParseResult ) parser.getResults().iterator().next() ); GeoSeries gse = parseResult.getSeries().values().iterator().next(); DatasetCombiner datasetCombiner = new DatasetCombiner(); GeoSampleCorrespondence result = datasetCombiner.findGSECorrespondence( gse ); DatasetCombinerTest.log.debug( result ); Iterator<Set<String>> it = result.iterator(); int numBioMaterials = 0; while ( it.hasNext() ) { it.next(); numBioMaterials++; } assertEquals( 57, numBioMaterials ); }
public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) { if ( dataSets == null ) return null; if ( dataSets.size() == 0 ) { throw new IllegalArgumentException( "No datasets!" ); } this.checkPlatformsMatchSeries( dataSets ); this.fillAccessionMaps( dataSets ); int numDatasets = dataSets.size(); return this.findCorrespondence( numDatasets ); }
DatasetCombiner { public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) { if ( dataSets == null ) return null; if ( dataSets.size() == 0 ) { throw new IllegalArgumentException( "No datasets!" ); } this.checkPlatformsMatchSeries( dataSets ); this.fillAccessionMaps( dataSets ); int numDatasets = dataSets.size(); return this.findCorrespondence( numDatasets ); } }
DatasetCombiner { public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) { if ( dataSets == null ) return null; if ( dataSets.size() == 0 ) { throw new IllegalArgumentException( "No datasets!" ); } this.checkPlatformsMatchSeries( dataSets ); this.fillAccessionMaps( dataSets ); int numDatasets = dataSets.size(); return this.findCorrespondence( numDatasets ); } DatasetCombiner();  DatasetCombiner( boolean doSampleMatching ); }
DatasetCombiner { public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) { if ( dataSets == null ) return null; if ( dataSets.size() == 0 ) { throw new IllegalArgumentException( "No datasets!" ); } this.checkPlatformsMatchSeries( dataSets ); this.fillAccessionMaps( dataSets ); int numDatasets = dataSets.size(); return this.findCorrespondence( numDatasets ); } DatasetCombiner();  DatasetCombiner( boolean doSampleMatching ); static Collection<String> findGDSforGSE( Collection<String> seriesAccessions ); static Collection<String> findGDSforGSE( String seriesAccession ); static Collection<String> findGSEforGDS( String datasetAccession ); static Map<GeoPlatform, List<GeoSample>> getPlatformSampleMap( GeoSeries geoSeries ); Collection<String> findGDSforGDS( String datasetAccession ); GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ); GeoSampleCorrespondence findGSECorrespondence( GeoSeries series ); }
DatasetCombiner { public GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ) { if ( dataSets == null ) return null; if ( dataSets.size() == 0 ) { throw new IllegalArgumentException( "No datasets!" ); } this.checkPlatformsMatchSeries( dataSets ); this.fillAccessionMaps( dataSets ); int numDatasets = dataSets.size(); return this.findCorrespondence( numDatasets ); } DatasetCombiner();  DatasetCombiner( boolean doSampleMatching ); static Collection<String> findGDSforGSE( Collection<String> seriesAccessions ); static Collection<String> findGDSforGSE( String seriesAccession ); static Collection<String> findGSEforGDS( String datasetAccession ); static Map<GeoPlatform, List<GeoSample>> getPlatformSampleMap( GeoSeries geoSeries ); Collection<String> findGDSforGDS( String datasetAccession ); GeoSampleCorrespondence findGSECorrespondence( Collection<GeoDataset> dataSets ); GeoSampleCorrespondence findGSECorrespondence( GeoSeries series );  }