Uses of Class
com.pacbio.secondary.vis.data.interval.Interval

Packages that use Interval

Package	Description
com.pacbio.secondary.vis.common.utils.constants	Client/Server common constants
com.pacbio.secondary.vis.data.interval	Support for genomic interval
com.pacbio.secondary.vis.data.locus	Support for genomic locus
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.data.table.model	Genomic tables data models
com.pacbio.secondary.vis.gui.draw.views	Genomic views
com.pacbio.secondary.vis.io.export	GFF3 export support

Uses of Interval in com.pacbio.secondary.vis.common.utils.constants

Methods in com.pacbio.secondary.vis.common.utils.constants that return Interval

Modifier and Type	Method and Description
static Interval	ProgramConstants.getInspectionIntervalAt(long center_location)

Uses of Interval in com.pacbio.secondary.vis.data.interval

Fields in com.pacbio.secondary.vis.data.interval declared as Interval

Modifier and Type	Field and Description
Interval	IntervalTreeNode.interval

Methods in com.pacbio.secondary.vis.data.interval that return Interval

Modifier and Type	Method and Description
Interval	IntervalTreeNode.getInterval()
Interval	IntervalTree.getRange()
Interval	Interval.intersection(Interval interval)
Interval	Interval.union(Interval interval)

Methods in com.pacbio.secondary.vis.data.interval with parameters of type Interval

Modifier and Type	Method and Description
int	Interval.compareTo(Interval interval)
boolean	Interval.contains(Interval I)
long	Interval.epiprodistance(Interval interval)
boolean	Interval.equals(Interval obj)
IntervalTreeNode	IntervalTree.insert(Interval interval) Inserts a new interval into the tree so that each children will be contained in its parent interval.
protected IntervalTreeNode	IntervalTree.internalInsert(IntervalTreeNode node, Interval interval)
Interval	Interval.intersection(Interval interval)
boolean	Interval.intersects(Interval I)
java.util.ArrayList<IntervalTreeNode>	IntervalTreeQuery.Query(Interval interval, byte minLevel, byte maxLevel) Finds all node intersecting the given Interval interval and with a level between minLevel and maxLevel.
Interval	Interval.union(Interval interval)

Constructors in com.pacbio.secondary.vis.data.interval with parameters of type Interval

Constructor and Description
Interval(Interval interval)
IntervalTreeNode(Interval interval)

Uses of Interval in com.pacbio.secondary.vis.data.locus

Fields in com.pacbio.secondary.vis.data.locus declared as Interval

Modifier and Type	Field and Description
Interval	Locus.interval

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

Fields in com.pacbio.secondary.vis.data.marker declared as Interval

Modifier and Type	Field and Description
Interval	Marker.interval Basepair range.

Methods in com.pacbio.secondary.vis.data.marker with parameters of type Interval

Modifier and Type	Method and Description
java.util.List<Marker>	MarkerCollection.find(Interval interval) Find all markers intercepting specific interval; Used during drawing
protected int[]	MarkerCollection.findBin(Interval interval) returns a bin to use for fast searching intercepting markers
java.util.List<Marker>	MarkerCollection.findSlow(Interval interval)

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

Constructor and Description
Marker(Interval interval, float[] results)
Marker(Interval interval, GeneInfo info)

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

Methods in com.pacbio.secondary.vis.data.read that return Interval

Modifier and Type	Method and Description
Interval	EpiProReadInfo.EpiProInfo.getInterval()

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

Fields in com.pacbio.secondary.vis.data.session declared as Interval

Modifier and Type	Field and Description
protected Interval	SessionDataHelper.details_interval
protected Interval	SessionDataHelper.region_interval

Fields in com.pacbio.secondary.vis.data.session with type parameters of type Interval

Modifier and Type	Field and Description
protected java.util.ArrayList<Interval>	SessionDataHelper.view_intervals

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

Modifier and Type	Method and Description
boolean	DetailsStorage.acceptNewDataAndClear(GenomicViewDetailsData view, Interval view_visible_range, WsResults results, java.lang.String track_name)
boolean	IPDConsensusStorage.acceptNewDataAndClear(GenomicViewDetailsData view, int view_contig, Interval view_visible_range, java.lang.String data)
boolean	ReferenceSequenceStorage.acceptNewDataAndClear(GenomicViewDetailsData view, int view_contig, Interval view_visible_range, java.lang.String data)
boolean	IPDConsensusStorage.contains(Interval int_visible_range) custom method to check if requested visible interval is available takes into account that visible range can start from 0, while coordinates are 1-based
char[]	ReferenceSequenceStorage.getDNASequence(Interval int_visible_range)
double	IPDConsensusStorage.getMaxIPDInInterval(Interval interval)
boolean	IPDConsensusStorage.intersects(int viewContig, Interval int_visible_range)
boolean	ReferenceSequenceStorage.intersects(int viewContig, Interval int_visible_range)
boolean	DetailsStorage.updateDataDoNotClear(GenomicViewDetailsData view, Interval view_visible_range, WsResults results, Locus data_locus)

Uses of Interval in com.pacbio.secondary.vis.data.table.model

Methods in com.pacbio.secondary.vis.data.table.model that return Interval

Modifier and Type	Method and Description
Interval	TableModelAnnotations.getRowInterval(int row_index) Returns the interval associated with this row
Interval	TableModelBase.getRowInterval(int row_index) Override to return the interval associated with this row
Interval	TableModelGenomicInterval.getRowInterval(int row_index) Return the interval associated with this row
Interval	TableModelTrack.getRowInterval(int row_index) Return the interval associated with this row

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

Fields in com.pacbio.secondary.vis.gui.draw.views declared as Interval

Modifier and Type	Field and Description
protected Interval	GenomicViewBase.int_visible_range
protected Interval	GenomicViewBase.rangeSelection

Fields in com.pacbio.secondary.vis.gui.draw.views with type parameters of type Interval

Modifier and Type	Field and Description
protected java.util.LinkedList<Interval>	GenomicViewBase.viewHistory

Methods in com.pacbio.secondary.vis.gui.draw.views that return Interval

Modifier and Type	Method and Description
protected Interval	GenomicViewDetails.getDefaultVisibleRange()
Interval	GenomicViewDraw.getRangeSelection()
Interval	GenomicViewDraw.getVisibleGenomicRange()
Interval	GenomicViewEvents.popView()

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

Modifier and Type	Method and Description
void	GenomicViewDetailsData.addGenomicRangeToDetailsViewDataRequestsQueue(Interval interval, boolean updateGenomicRange)
void	GenomicViewEvents.addGenomicRangeToDetailsViewDataRequestsQueue(Interval interval, boolean updateGenomicRange)
protected void	GenomicViewDetailsData.addGenomicRangeToDetailsViewIPDConsensusRequestQueue(Interval interval)
protected void	GenomicViewDetailsData.addGenomicRangeToDetailsViewReferenceRequestQueue(Interval interval)
void	GenomicViewEvents.setRangeSelection(Interval selection)
void	GenomicViewEvents.setViewWithOrWithoutUpdate(Interval interval, boolean bredraw) Sets the current genomic range for this view
void	GenomicViewInspect.setViewWithOrWithoutUpdate(Interval interval, boolean bredraw)
void	GenomicViewEvents.setVisibleGenomicRange(Interval interval, boolean firechangeevent) Sets the genomic range for this view

Uses of Interval in com.pacbio.secondary.vis.io.export

Methods in com.pacbio.secondary.vis.io.export with parameters of type Interval

Modifier and Type	Method and Description
protected void	ExportDataUtils.exportCMPH5DataToGFF(DetailsStorage data, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
protected void	ExportRegionAsGFF.exportCMPH5DataToGFF(DetailsStorage data, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
protected void	ExportDataUtils.exportGenericMarkerTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
protected void	ExportRegionAsGFF.exportGenericMarkerTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
protected void	ExportDataUtils.exportModificationsTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index)
protected void	ExportDataUtils.exportVariantsTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index) coverage=4;length=1;reference=T
protected void	ExportRegionAsGFF.exportVariantsTrack(MarkerCollection markers, java.io.FileWriter writer, java.lang.String contig_name, Interval curr_interval, int track_index) coverage=4;length=1;reference=T