Uses of Class
com.pacbio.secondary.vis.data.locus.Locus

Packages that use Locus

Package	Description
com.pacbio.secondary.vis.data.base	Base genomic data model
com.pacbio.secondary.vis.data.locus	Support for genomic locus
com.pacbio.secondary.vis.data.queue	Client/Server data requests utilities
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.gui.app	Main application classes, support local, remote, webstart based deployment
com.pacbio.secondary.vis.gui.draw.views	Genomic views
com.pacbio.secondary.vis.io.indexer.gff.metadata	GFF3 metadata info

Uses of Locus in com.pacbio.secondary.vis.data.base

Fields in com.pacbio.secondary.vis.data.base declared as Locus

Modifier and Type	Field and Description
Locus	BaseDataRecord.locus

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

Methods in com.pacbio.secondary.vis.data.locus with parameters of type Locus

Modifier and Type	Method and Description
int	Locus.compareTo(Locus other)
boolean	Locus.contains(Locus locus)
boolean	Locus.intersects(Locus locus)

Constructors in com.pacbio.secondary.vis.data.locus with parameters of type Locus

Constructor and Description
Locus(Locus locus)

Uses of Locus in com.pacbio.secondary.vis.data.queue

Methods in com.pacbio.secondary.vis.data.queue that return Locus

Modifier and Type	Method and Description
Locus	DetailsDataRequest.getLocus()

Methods in com.pacbio.secondary.vis.data.queue with parameters of type Locus

Modifier and Type	Method and Description
void	DetailsDataRequestsQueue.removeElementByLocus(Locus locus)
void	DetailsDataRequest.setLocus(Locus locus)

Constructors in com.pacbio.secondary.vis.data.queue with parameters of type Locus

Constructor and Description
DetailsDataRequest(Locus l)

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

Fields in com.pacbio.secondary.vis.data.read declared as Locus

Modifier and Type	Field and Description
protected Locus	EpiProReadInfo.EpiProInfo.locus

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

Modifier and Type	Method and Description
Locus	EpiProReadInfo.EpiProInfo.getLocus()

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

Methods in com.pacbio.secondary.vis.data.session that return Locus

Modifier and Type	Method and Description
Locus	IPDConsensusStorage.getIPDConsensus_locus()
Locus	DetailsStorage.getLocus()
Locus	ReferenceSequenceStorage.getReference_locus()

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

Modifier and Type	Method and Description
void	DetailsStorage.setLocus(Locus locus)
void	IPDConsensusStorage.setReference_locus(Locus ipd_consensus_locus)
void	ReferenceSequenceStorage.setReference_locus(Locus reference_locus)
boolean	DetailsStorage.updateDataDoNotClear(GenomicViewDetailsData view, Interval view_visible_range, WsResults results, Locus data_locus)

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

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

Modifier and Type	Method and Description
void	VioletApp.setVisibleLocusDetailsPanel(Locus locus, boolean updateTablePanel) selects a new locus in details panel
void	VioletApp.setVisibleLocusGenomePanel(Locus locus, boolean updateTablePanel, boolean isGoTo) selects a new locus in genome panel, eventually updates region and details
void	VioletApp.setVisibleLocusRegionPanel(Locus locus, boolean updateTablePanel) selects a new locus in region panel, eventually updates details

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

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

Modifier and Type	Field and Description
protected Locus	GenomicViewDetailsData.data_on_demand_queue
protected Locus	GenomicViewDetailsData.data_request_queue
protected Locus	GenomicViewDetailsData.ipd_consensus_request_queue
protected Locus	GenomicViewDetailsData.reference_request_queue

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

Modifier and Type	Method and Description
Locus	GenomicViewDetailsData.getDetailsDataLocus()
Locus	GenomicViewDetailsData.getIPDConsensusDataLocus()
Locus	GenomicViewDetailsData.getReferenceDataLocus()

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

Modifier and Type	Method and Description
void	GenomicViewEvents.setVisibleGenomicRegion(Locus locus, GenomicViewData contig_data, boolean firechangeevent, boolean updateTablePanel)

Uses of Locus in com.pacbio.secondary.vis.io.indexer.gff.metadata

Methods in com.pacbio.secondary.vis.io.indexer.gff.metadata that return types with arguments of type Locus

Modifier and Type	Method and Description
java.util.TreeMap<java.lang.Integer,Locus>	GFFMetadataInfo.getContigsMap() Get map containing list of all contigs in file and start/end for each contig