com.pacbio.secondary.vis.svc.server.hdf

Class GenomicDataAssembler

java.lang.Object

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

com.pacbio.secondary.vis.svc.server.hdf.GenomicDataAssembler

Direct Known Subclasses:

GenomicDataBuilder

public class GenomicDataAssembler
extends GenomicDataStructures

Author:

mmilletti

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

GenomicDataStructures.WsReadStructure

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	CHIMERIC_STANDARD_THRESHOLD
protected static int	CHIMERIC_STROBE_THRESHOLD
protected static int	LANE_EXTRA_DISTANCE
protected static int	MAX_ORDINATE_PILEUP

Fields inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

BASE_DELETION, BASE_LEFT_INSERTION, BASE_MATCH, BASE_POS_INSERTION, BASE_RIGHT_INSERTION, BASE_SVN

Constructor Summary

Constructors

Constructor and Description
GenomicDataAssembler()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	assembleResultsWithoutStructures(WsResults results, java.util.List<WsRead> alignedReads, int mode)
protected void	assembleResultsWithStructures(WsResults results, java.util.List<WsRead> alignedReads, int mode) Full assembly of results with graphic structures
protected GraphStructure	createGraphLinesStructure(GenomicDataStructures.WsReadStructure[] structures, int total_structures) Strobe reads as graphic lines
protected GraphStructure	createGraphLinksStructure(GenomicDataStructures.WsReadStructure[] structures, int total_structures) CCS reads as graphic links
protected GraphStructure	createGraphNodesStructure(GenomicDataStructures.WsReadStructure[] structures, int total_structures) Strobe reads as graphic nodes
protected GraphStructure	createGraphStructure(WsResults results, GenomicDataStructures.WsReadStructure[] structures, int total_structures, int mode) Creates annotated graph structure from data
protected void	PileUpResultsWithoutStructure(WsResults results, java.util.List<WsRead> alignedReads)
protected void	PileUpResultsWithoutStructureForBaseMods(WsResults results, java.util.List<WsRead> alignedReads)
protected void	PileUpResultsWithStructures(GenomicDataStructures.WsReadStructure[] structures, WsResults results, int total_reads, int mode) Pileup of results with graphics structures Supports CCS and strobe reads

Methods inherited from class com.pacbio.secondary.vis.svc.server.hdf.GenomicDataStructures

buildStats, createFromRawRead, createFromRawReadWithInsertions, reverse, reverse, reverse, reverseRawRead, setQVValue, updateMetricsFromRawRead

Methods inherited from class java.lang.Object

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

Field Detail

MAX_ORDINATE_PILEUP

protected static final int MAX_ORDINATE_PILEUP

See Also:

Constant Field Values

LANE_EXTRA_DISTANCE

protected static final int LANE_EXTRA_DISTANCE

See Also:

Constant Field Values

CHIMERIC_STROBE_THRESHOLD

protected static final int CHIMERIC_STROBE_THRESHOLD

See Also:

Constant Field Values

CHIMERIC_STANDARD_THRESHOLD

protected static final int CHIMERIC_STANDARD_THRESHOLD

See Also:

Constant Field Values

Constructor Detail

GenomicDataAssembler

public GenomicDataAssembler()

Method Detail

assembleResultsWithStructures

protected void assembleResultsWithStructures(WsResults results,
                                 java.util.List<WsRead> alignedReads,
                                 int mode)

Full assembly of results with graphic structures

Parameters:

results -

alignedReads -

mode -

PileUpResultsWithStructures

protected void PileUpResultsWithStructures(GenomicDataStructures.WsReadStructure[] structures,
                               WsResults results,
                               int total_reads,
                               int mode)

Pileup of results with graphics structures Supports CCS and strobe reads

Parameters:

structures -

results -

total_reads -

mode -

createGraphStructure

protected GraphStructure createGraphStructure(WsResults results,
                                  GenomicDataStructures.WsReadStructure[] structures,
                                  int total_structures,
                                  int mode)

Creates annotated graph structure from data

Parameters:

results -

structures -

total_structures -

mode -

Returns:

createGraphLinesStructure

protected GraphStructure createGraphLinesStructure(GenomicDataStructures.WsReadStructure[] structures,
                                       int total_structures)

Strobe reads as graphic lines

Parameters:

structures -

total_structures -

Returns:

createGraphNodesStructure

protected GraphStructure createGraphNodesStructure(GenomicDataStructures.WsReadStructure[] structures,
                                       int total_structures)

Strobe reads as graphic nodes

Parameters:

structures -

total_structures -

Returns:

createGraphLinksStructure

protected GraphStructure createGraphLinksStructure(GenomicDataStructures.WsReadStructure[] structures,
                                       int total_structures)

CCS reads as graphic links

Parameters:

structures -

total_structures -

Returns:

assembleResultsWithoutStructures

protected void assembleResultsWithoutStructures(WsResults results,
                                    java.util.List<WsRead> alignedReads,
                                    int mode)

PileUpResultsWithoutStructure

protected void PileUpResultsWithoutStructure(WsResults results,
                                 java.util.List<WsRead> alignedReads)

PileUpResultsWithoutStructureForBaseMods

protected void PileUpResultsWithoutStructureForBaseMods(WsResults results,
                                            java.util.List<WsRead> alignedReads)