Uses of Class
com.pacbio.secondary.vis.data.marker.MarkerCollection

Packages that use MarkerCollection

Package	Description
com.pacbio.secondary.vis.data.base	Base genomic data model
com.pacbio.secondary.vis.data.db	Ideogram and genes collections support
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.data.variableresolution.model	Variable resolution data models
com.pacbio.secondary.vis.gui.draw.utils	Drawing utilities
com.pacbio.secondary.vis.gui.draw.views	Genomic views
com.pacbio.secondary.vis.io.export	GFF3 export support

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

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

Modifier and Type	Field and Description
protected MarkerCollection[]	BaseDataModel.mc

Methods in com.pacbio.secondary.vis.data.base that return MarkerCollection

Modifier and Type	Method and Description
MarkerCollection	BaseDataModel.getMarkersForContig(int contig)

Uses of MarkerCollection in com.pacbio.secondary.vis.data.db

Fields in com.pacbio.secondary.vis.data.db declared as MarkerCollection

Modifier and Type	Field and Description
protected MarkerCollection[]	GeneDB.genes

Methods in com.pacbio.secondary.vis.data.db that return MarkerCollection

Modifier and Type	Method and Description
MarkerCollection[]	GeneDB.getGenes()

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

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

Modifier and Type	Method and Description
MarkerCollection	DetailsStorage.getMarkerCollection()

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

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

Modifier and Type	Method and Description
MarkerCollection	TableModelAnnotations.getMarkerCollectionFromRowIndex(int row_index)
MarkerCollection	TableModelBase.getMarkerCollectionFromRowIndex(int row_index) Override to return marker collection at this row
MarkerCollection	TableModelGenomicInterval.getMarkerCollectionFromRowIndex(int row_index)

Uses of MarkerCollection in com.pacbio.secondary.vis.data.variableresolution.model

Methods in com.pacbio.secondary.vis.data.variableresolution.model that return MarkerCollection

Modifier and Type	Method and Description
MarkerCollection[]	IVariableResolutionDataModelServer.copyAsMarkerCollectionArray()
MarkerCollection[]	VariableResolutionDataModel.copyAsMarkerCollectionArray() Creates copy of a variableresolution model as a MarkerCollection array.

Uses of MarkerCollection in com.pacbio.secondary.vis.gui.draw.utils

Methods in com.pacbio.secondary.vis.gui.draw.utils with parameters of type MarkerCollection

Modifier and Type	Method and Description
protected static void	InfoBuilder.addMarkerCollectionHtmlTooltip(GenomicViewEvents source, java.lang.StringBuffer html, MarkerCollection track, java.text.NumberFormat nf, boolean b) track tooltip
protected static void	InfoBuilder.addMarkerHtmlTooltip(GenomicViewEvents source, java.lang.StringBuffer buf, Marker marker, MarkerCollection track, java.text.NumberFormat nf, boolean addImage) marker tooltip
static void	InfoBuilder.getHtmlToolTipForTable(GenomicViewEvents source, Marker marker, MarkerCollection track, java.lang.StringBuffer buf) gets tooltip for table view
static java.lang.String	InfoBuilder.getMarkerInfo(MarkerCollection track, Marker marker, GenomicViewEvents source)

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

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

Modifier and Type	Field and Description
protected java.util.ArrayList<MarkerCollection>	GenomicViewBase.markers

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

Modifier and Type	Method and Description
MarkerCollection	GenomicViewData.getGenesOfCurrentContig()
MarkerCollection	GenomicViewData.getMarkerCollection(int i)

Methods in com.pacbio.secondary.vis.gui.draw.views that return types with arguments of type MarkerCollection

Modifier and Type	Method and Description
protected java.util.ArrayList<MarkerCollection>	GenomicViewData.getMarkers()

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

Modifier and Type	Method and Description
void	GenomicViewData.addTrackDataToViewAndUpdateLayout(MarkerCollection M, boolean bUpdateLayout) Adds a marker set to a track MarkerCollection.
protected void	GenomicViewHorizontal.drawFilteredTrack(java.awt.Graphics g, java.util.List<Marker> list, MarkerCollection track, java.util.ArrayList<java.lang.Integer> track_indexes, VariableResolutionDataSet slot)
Marker	GenomicViewEvents.findVariantByPositionAndYCoordinate(MarkerCollection track, long bp, int y)

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

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

Modifier and Type	Method and Description
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