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

Packages that use WsRead

Package	Description
com.pacbio.secondary.vis.data.marker	Marker data model
com.pacbio.secondary.vis.data.read	Genomic read data model
com.pacbio.secondary.vis.data.session	Client side user session data models
com.pacbio.secondary.vis.svc.server.data	Server side data models
com.pacbio.secondary.vis.svc.server.hdf	HDFService utils

Uses of WsRead in com.pacbio.secondary.vis.data.marker

Constructors in com.pacbio.secondary.vis.data.marker with parameters of type WsRead

Constructor and Description
Marker(WsRead read)

Uses of WsRead in com.pacbio.secondary.vis.data.read

Constructors in com.pacbio.secondary.vis.data.read with parameters of type WsRead

Constructor and Description
ReadInfo(WsRead read)

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

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

Modifier and Type	Method and Description
protected ReadInfo	DetailsStorage.getReadInfoFromWsRead(java.util.List<Marker> list, WsRead read)

Uses of WsRead in com.pacbio.secondary.vis.svc.server.data

Subclasses of WsRead in com.pacbio.secondary.vis.svc.server.data

Modifier and Type	Class and Description
class	WsReadEx

Fields in com.pacbio.secondary.vis.svc.server.data declared as WsRead

Modifier and Type	Field and Description
protected WsRead[]	WsResults.reads

Methods in com.pacbio.secondary.vis.svc.server.data that return WsRead

Modifier and Type	Method and Description
WsRead[]	WsResults.getReads()

Methods in com.pacbio.secondary.vis.svc.server.data with parameters of type WsRead

Modifier and Type	Method and Description
int	KineticsComparator.compare(WsRead o1, WsRead o2)
int	RStartComparator.compare(WsRead o1, WsRead o2)
int	StrandComparator.compare(WsRead o2, WsRead o1)
int	StrandComparator.compareold(WsRead o1, WsRead o2)
int	WsRead.compareTo(WsRead obj)
void	WsResults.setReads(WsRead[] data)

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

Methods in com.pacbio.secondary.vis.svc.server.hdf that return types with arguments of type WsRead

Modifier and Type	Method and Description
java.util.ArrayList<WsRead>	GenomicDataStructures.WsReadStructure.getSub_reads()

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

Modifier and Type	Method and Description
void	GenomicDataStructures.WsReadStructure.addSubRead(WsRead read) add more sub-reads
protected void	GenomicDataStructures.createFromRawRead(WsRead aligned_read, RawRead read_data, float metrics_factor, int mode) must report right or left insertion...
protected void	GenomicDataStructures.createFromRawReadWithInsertions(WsRead aligned_read, RawRead read_data, float metrics_factor, int mode, long start_from) report insertion at position...
protected void	GenomicDataStructures.setQVValue(WsRead aligned_read, RawRead read_data, int raw_base_index, int annotated_base_index, float metrics_factor)
protected void	GenomicDataStructures.updateMetricsFromRawRead(WsRead aligned_read, RawRead read_data, float metrics_factor) must report right or left insertion...

Method parameters in com.pacbio.secondary.vis.svc.server.hdf with type arguments of type WsRead

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 java.util.ArrayList<RawRead>	GenomicDataBuilder.gatherBasesData(CMPH5File cmp_h5_file, java.util.ArrayList<WsRead> alignedReads, AlignmentIndexTable table, long start, long end, int mode)
protected float	GenomicDataBuilder.gatherMetricsData(CMPH5File cmp_h5_file, java.util.ArrayList<WsRead> alignedReads, java.util.ArrayList<RawRead> raw_reads, AlignmentIndexTable table, long start, long end, int mode)
protected void	GenomicDataAssembler.PileUpResultsWithoutStructure(WsResults results, java.util.List<WsRead> alignedReads)
protected void	GenomicDataAssembler.PileUpResultsWithoutStructureForBaseMods(WsResults results, java.util.List<WsRead> alignedReads)
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
void	GenomicDataStructures.WsReadStructure.setSub_reads(java.util.ArrayList<WsRead> sub_reads)

Constructors in com.pacbio.secondary.vis.svc.server.hdf with parameters of type WsRead

Constructor and Description
GenomicDataStructures.WsReadStructure(WsRead read)