Uses of Class
com.pacbio.secondary.vis.svc.server.data.WsResults

Packages that use WsResults

Package	Description
com.pacbio.secondary.vis.data.session	Client side user session data models
com.pacbio.secondary.vis.gui.app	Main application classes, support local, remote, webstart based deployment
com.pacbio.secondary.vis.gui.draw.views	Genomic views
com.pacbio.secondary.vis.svc.hdf.client	HDFService client support
com.pacbio.secondary.vis.svc.server.hdf	HDFService utils

Uses of WsResults in com.pacbio.secondary.vis.data.session

Methods in com.pacbio.secondary.vis.data.session with parameters of type WsResults

Modifier and Type	Method and Description
boolean	DetailsStorage.acceptNewDataAndClear(GenomicViewDetailsData view, Interval view_visible_range, WsResults results, java.lang.String track_name)
void	DetailsStorage.setResultsInfo(GenomicViewDetailsData view, WsResults data)
boolean	DetailsStorage.updateDataDoNotClear(GenomicViewDetailsData view, Interval view_visible_range, WsResults results, Locus data_locus)

Uses of WsResults in com.pacbio.secondary.vis.gui.app

Methods in com.pacbio.secondary.vis.gui.app with parameters of type WsResults

Modifier and Type	Method and Description
boolean	VioletApp.importGZippedHDFResults(WsResults data, TrackDataInfo clientData)

Uses of WsResults in com.pacbio.secondary.vis.gui.draw.views

Methods in com.pacbio.secondary.vis.gui.draw.views with parameters of type WsResults

Modifier and Type	Method and Description
boolean	GenomicViewDetailsData.setDetailsViewData(WsResults results, TrackDataInfo clientData)

Uses of WsResults in com.pacbio.secondary.vis.svc.hdf.client

Methods in com.pacbio.secondary.vis.svc.hdf.client that return WsResults

Modifier and Type	Method and Description
static WsResults	HDFServiceCallbackImpl.getWSResultsFromDataHandler(javax.activation.DataHandler data)

Uses of WsResults in com.pacbio.secondary.vis.svc.server.hdf

Methods in com.pacbio.secondary.vis.svc.server.hdf that return WsResults

Modifier and Type	Method and Description
protected WsResults	GenomicDataBuilder.assembleReads(WsResults results, int mode, java.util.List<WsRead> alignedReads, boolean isStrobe, boolean isV12, long start_time, int client_contig_index, long start, long end, long total_bases) analyze and pile-up reads, create structure info and results metadata
protected WsResults	GenomicDataBuilder.copyResults(WsResults results, java.util.List<WsRead> alignedReads)
protected WsResults	GenomicDataBuilder.copyResults(WsResults results, java.util.List<WsRead> alignedReads, java.util.List<RawRead> raw_reads, float metrics_factor, int mode) copy as basic array from arraylist
protected WsResults	GenomicDataBuilder.getReadsDataFromFile(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end, int mode) getAlignedReadsFromFile
protected WsResults	GenomicDataBuilder.getReadsDataWithInsertionsFromFile(java.lang.String url, java.lang.String contig_id, int client_contig_index, long start, long end, int mode)
protected WsResults	GenomicDataBuilder.prepareResults(WsResults results, int mode, java.util.ArrayList<WsRead> alignedReads, boolean isStrobe, boolean isV12, long start_time, int client_contig_index, long start, long end, long total_bases)

Methods in com.pacbio.secondary.vis.svc.server.hdf with parameters of type WsResults

Modifier and Type	Method and Description
protected WsResults	GenomicDataBuilder.assembleReads(WsResults results, int mode, java.util.List<WsRead> alignedReads, boolean isStrobe, boolean isV12, long start_time, int client_contig_index, long start, long end, long total_bases) analyze and pile-up reads, create structure info and results metadata
protected void	GenomicDataAssembler.assembleResultsWithoutStructures(WsResults results, java.util.List<WsRead> alignedReads, int mode)
protected void	GenomicDataAssembler.assembleResultsWithStructures(WsResults results, java.util.List<WsRead> alignedReads, int mode) Full assembly of results with graphic structures
protected WsResults	GenomicDataBuilder.copyResults(WsResults results, java.util.List<WsRead> alignedReads)
protected WsResults	GenomicDataBuilder.copyResults(WsResults results, java.util.List<WsRead> alignedReads, java.util.List<RawRead> raw_reads, float metrics_factor, int mode) copy as basic array from arraylist
protected GraphStructure	GenomicDataAssembler.createGraphStructure(WsResults results, GenomicDataStructures.WsReadStructure[] structures, int total_structures, int mode) Creates annotated graph structure from data
protected void	GenomicDataAssembler.PileUpResultsWithoutStructure(WsResults results, java.util.List<WsRead> alignedReads)
protected void	GenomicDataAssembler.PileUpResultsWithoutStructureForBaseMods(WsResults results, java.util.List<WsRead> alignedReads)
protected void	GenomicDataAssembler.PileUpResultsWithStructures(GenomicDataStructures.WsReadStructure[] structures, WsResults results, int total_reads, int mode) Pileup of results with graphics structures Supports CCS and strobe reads
protected WsResults	GenomicDataBuilder.prepareResults(WsResults results, int mode, java.util.ArrayList<WsRead> alignedReads, boolean isStrobe, boolean isV12, long start_time, int client_contig_index, long start, long end, long total_bases)
protected void	GenomicDataBuilder.removeDataAboveThreshold(WsResults results, java.util.List<WsRead> alignedReads, int mode) eventually remove reads and structures with lane above max coverage threshold
protected void	GenomicDataBuilder.updateIOTimeStats(WsResults results, long start_time)