| Package | Description |
|---|---|
| com.pacbio.secondary.vis.data.marker |
Marker 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.utils |
Drawing utilities
|
| com.pacbio.secondary.vis.gui.draw.views |
Genomic views
|
| com.pacbio.secondary.vis.gui.panels |
Specialized dockable genomic panels
|
| com.pacbio.secondary.vis.io.epipro |
Parser for epipro/unmapped reads data
|
| com.pacbio.secondary.vis.io.export |
GFF3 export support
|
| com.pacbio.secondary.vis.io.gff.variants |
GFF3 variants support
|
| Modifier and Type | Field and Description |
|---|---|
protected java.util.ArrayList<Marker> |
MarkerCollection.markers |
| Modifier and Type | Method and Description |
|---|---|
Marker |
MarkerCollection.findNearest(long bp)
Finds the marker lying nearest to the given bp position
|
Marker |
MarkerCollection.findNeighbour(Marker target,
boolean forward)
Find nearest marker, used to search next/previous markers
|
Marker |
MarkerCollection.getMarker(int marker_index) |
| Modifier and Type | Method and Description |
|---|---|
java.util.List<Marker> |
MarkerCollection.find(Interval interval)
Find all markers intercepting specific interval;
Used during drawing
|
java.util.List<Marker> |
MarkerCollection.findSlow(Interval interval) |
java.util.List<Marker> |
MarkerCollection.getMarkers() |
| Modifier and Type | Method and Description |
|---|---|
void |
MarkerCollection.add(Marker marker)
Adds a marker to the collection
|
int |
MarkerComparator.compare(Marker o1,
Marker o2)
Used for kinetics drawing code artifact removal
|
int |
MarkerComparator.compareForGenomicLocation(Marker o1,
Marker o2)
not used
|
int |
Marker.compareTo(Marker marker) |
Marker |
MarkerCollection.findNeighbour(Marker target,
boolean forward)
Find nearest marker, used to search next/previous markers
|
| Modifier and Type | Method and Description |
|---|---|
Marker |
DetailsStorage.findReadByPositionAndLane(long bp,
int lane) |
| Modifier and Type | Method and Description |
|---|---|
java.util.List<Marker> |
DetailsStorage.getMarkers() |
| Modifier and Type | Method and Description |
|---|---|
void |
DetailsStorage.add(Marker m) |
| Modifier and Type | Method and Description |
|---|---|
protected ReadInfo |
DetailsStorage.getReadInfoFromWsRead(java.util.List<Marker> list,
WsRead read) |
| Modifier and Type | Method and Description |
|---|---|
Marker |
TableModelAnnotations.getMarkerFromRowIndex(int row_index) |
Marker |
TableModelBase.getMarkerFromRowIndex(int row_index)
Override to return marker at this row
|
Marker |
TableModelGenomicInterval.getMarkerFromRowIndex(int row_index) |
| Modifier and Type | Method and Description |
|---|---|
protected static void |
InfoBuilder.addBaseModInfo(java.lang.StringBuffer buf,
Marker marker,
java.lang.String text,
int min_offset,
int max_offset) |
protected static void |
InfoBuilder.addGeneHtmlTooltip(GenomicViewEvents source,
java.lang.StringBuffer buf,
Marker gene,
java.text.NumberFormat nf,
boolean addImage)
gene tooltip
|
protected static void |
InfoBuilder.addMarkerHtmlTooltip(GenomicViewEvents source,
java.lang.StringBuffer buf,
Marker marker,
MarkerCollection track,
java.text.NumberFormat nf,
boolean addImage)
marker tooltip
|
protected static void |
InfoBuilder.addReadHtmlTooltip(GenomicViewDetails view,
java.lang.StringBuffer buf,
Marker read,
java.text.NumberFormat nf,
boolean addImage)
read tooltip
|
static void |
GraphUtil.drawAlleleShape(java.awt.Graphics2D g,
Marker marker,
int x,
int y,
int w,
int h)
Draw a variant using two colors scheme from allele results
|
static void |
InfoBuilder.getHtmlToolTipForTable(GenomicViewEvents source,
Marker marker,
MarkerCollection track,
java.lang.StringBuffer buf)
gets tooltip for table view
|
static void |
InfoBuilder.getIntersectedMarkers(java.lang.StringBuffer buf,
Marker selectedMarker,
Marker selectedGene,
GenomicViewEvents view) |
static java.lang.String |
InfoBuilder.getMarkerInfo(MarkerCollection track,
Marker marker,
GenomicViewEvents source) |
static void |
InfoBuilder.getSelectionInfoGenes(java.lang.StringBuffer buf,
Marker selectedMarker,
Marker selected_gene,
GenomicViewData view) |
| Modifier and Type | Field and Description |
|---|---|
protected Marker |
GenomicViewBase.selected_gene |
protected Marker |
GenomicViewBase.selectedMarker |
| Modifier and Type | Method and Description |
|---|---|
Marker |
GenomicViewDetailsData.findReadByPositionAndLane(long bp,
int lane) |
Marker |
GenomicViewEvents.findVariantByPositionAndYCoordinate(MarkerCollection track,
long bp,
int y) |
Marker |
GenomicViewEvents.getSelectedGene() |
Marker |
GenomicViewEvents.getSelectedMarker() |
| Modifier and Type | Method and Description |
|---|---|
protected java.util.List<Marker> |
GenomicViewDetails.getListOfReadsToDraw() |
| Modifier and Type | Method and Description |
|---|---|
protected void |
GenomicViewDetailsDraw.drawEpiProFoldedRead(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
protected void |
GenomicViewDetailsDraw.drawEpiProUnfoldedReadMappedCoord(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
protected void |
GenomicViewDetailsDraw.drawEpiProUnfoldedReadSubreadCoord(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
protected void |
GenomicViewDetailsDraw.drawEpiProUnfoldedReadSubreadCoordOrg(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width)
Deprecated.
|
protected abstract void |
GenomicViewBase.drawGene(java.awt.Graphics g,
Marker M,
boolean show_band,
java.awt.Color color) |
protected void |
GenomicViewDraw.drawGene(java.awt.Graphics g,
Marker M,
boolean is_selected,
java.awt.Color color)
Draws a gene into the graphic context
|
protected void |
GenomicViewHorizontal.drawGene(java.awt.Graphics g,
Marker marker,
boolean is_selected,
java.awt.Color selected_color)
Draws a gene into the graphic context
|
protected abstract void |
GenomicViewBase.drawMarker(java.awt.Graphics g,
Marker marker,
int column,
java.awt.Rectangle rect,
java.awt.Color color,
boolean show_band,
java.awt.Color band_color) |
protected void |
GenomicViewDraw.drawMarker(java.awt.Graphics g,
Marker marker,
int column,
java.awt.Rectangle rect,
java.awt.Color color,
boolean is_selected,
java.awt.Color selected_color)
Draws a single marker.
|
protected void |
GenomicViewHorizontal.drawMarkerHorizontal(java.awt.Graphics g,
Marker marker,
java.util.ArrayList<java.lang.Integer> track_indexes,
java.awt.Rectangle rect,
java.awt.Color color,
boolean is_selected,
java.awt.Color selected_color)
Draws a single marker.
|
protected void |
GenomicViewDraw.drawMarkerInterval(java.awt.Graphics g,
Marker marker,
int column,
java.awt.Rectangle rect,
boolean is_selected,
java.awt.Color selected_color) |
protected void |
GenomicViewHorizontal.drawMarkerInterval(java.awt.Graphics g,
Marker marker,
int track,
java.awt.Rectangle rect,
boolean is_selected,
java.awt.Color selected_color) |
protected void |
GenomicViewHorizontal.drawModification(java.awt.Graphics g,
Marker marker,
java.util.ArrayList<java.lang.Integer> track_indexes,
java.awt.Rectangle rect,
VariableResolutionDataSetValues min_max_values) |
protected void |
GenomicViewDraw.drawModification(java.awt.Graphics g,
Marker marker,
int column,
java.awt.Rectangle rect) |
protected void |
GenomicViewDraw.drawModificationInterval(java.awt.Graphics2D g,
Marker marker,
int column,
java.awt.Rectangle rect,
VariableResolutionDataSetValues min_max_values) |
protected void |
GenomicViewHorizontal.drawModificationInterval(java.awt.Graphics2D g,
Marker marker,
int track_index,
java.awt.Rectangle rect,
VariableResolutionDataSetValues min_max_values) |
protected void |
GenomicViewHorizontal.drawModificationSummaryHeatmap(java.awt.Graphics2D g2d,
Marker marker,
int visible_track_index,
int num_metrics,
int x1,
int x2,
VariableResolutionDataSetValues minmaxValues) |
protected void |
GenomicViewHorizontal.drawModificationSummaryHistogram(java.awt.Graphics2D g2d,
Marker marker,
int visible_track_index,
int num_metrics,
int x1,
int x2,
VariableResolutionDataSetValues minmaxValues) |
protected void |
GenomicViewDetails.drawReadFiltered(java.awt.Graphics g,
java.util.List<Marker> variants,
Marker marker,
int y_start,
boolean bDrawDNABases,
boolean bDrawQV) |
protected void |
GenomicViewDetails.drawReadKinetic(java.awt.Graphics g,
Marker marker,
int y_start,
boolean bDrawDNABases,
int mode) |
protected void |
GenomicViewInspect.drawReadKinetic(java.awt.Graphics g,
Marker marker,
int y_start,
boolean bDrawDNABases,
int mode) |
protected void |
GenomicViewDetailsDraw.drawReadShape(java.awt.Graphics g,
Marker marker,
int x,
int y,
int width) |
protected void |
GenomicViewDetails.drawReadUnfiltered(java.awt.Graphics g,
Marker marker,
int y_start,
boolean bDrawDNABases,
boolean bDrawQV) |
protected void |
GenomicViewInspect.drawReadUnfiltered(java.awt.Graphics g,
Marker marker,
int y_start,
boolean bDrawDNABases,
boolean bDrawQV) |
protected void |
GenomicViewDraw.drawSummary(java.awt.Graphics g,
Marker marker,
int column,
java.awt.Color color,
double max_coverage,
int max_variants)
Draws coverage info for one coverage slot (marker)
|
protected void |
GenomicViewDraw.drawSummaryInterval(java.awt.Graphics g,
int column,
Marker marker,
boolean bLeft,
java.awt.Color color,
double max_coverage,
int max_variants) |
protected void |
GenomicViewHorizontal.drawVariant(java.awt.Graphics g,
Marker marker,
java.util.ArrayList<java.lang.Integer> track_indexes,
java.awt.Rectangle rect,
VariableResolutionDataSetValues min_max_values) |
protected void |
GenomicViewDraw.drawVariant(java.awt.Graphics g,
Marker marker,
int track,
java.awt.Rectangle rect) |
protected void |
GenomicViewDraw.drawVariantInterval(java.awt.Graphics2D g,
Marker marker,
int track,
java.awt.Rectangle rect,
VariableResolutionDataSetValues min_max_values) |
protected void |
GenomicViewHorizontal.drawVariantInterval(java.awt.Graphics2D g,
Marker marker,
int track,
java.awt.Rectangle rect,
VariableResolutionDataSetValues min_max_values) |
protected void |
GenomicViewHorizontal.drawVariantIntervalOrg(java.awt.Graphics2D g,
Marker marker,
int track,
java.awt.Rectangle rect,
VariableResolutionDataSetValues min_max_values) |
protected boolean |
GenomicViewDraw.prepareDrawVariant(java.awt.Graphics g,
Marker marker) |
protected boolean |
GenomicViewEvents.setSelectedGeneAndTrack(Marker m,
int trackIndex,
boolean bFireEvent)
Sets the currently selected gene to m.
|
protected boolean |
GenomicViewEvents.setSelectedMarkerAndSlot(Marker marker,
int slotIndex,
boolean bFireEvent)
Selects a marker/sample
|
| Modifier and Type | Method and Description |
|---|---|
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) |
protected void |
GenomicViewDetails.drawReadFiltered(java.awt.Graphics g,
java.util.List<Marker> variants,
Marker marker,
int y_start,
boolean bDrawDNABases,
boolean bDrawQV) |
protected void |
GenomicViewHorizontal.drawSummaryTracks(java.awt.Graphics2D g2d,
java.util.List<Marker> markers,
java.util.ArrayList<java.lang.Integer> track_indexes,
java.awt.Color color,
VariableResolutionDataSetValues minmaxValues) |
double |
GenomicViewHorizontal.getMaxCoverageInInterval(java.util.List<Marker> markers) |
| Modifier and Type | Field and Description |
|---|---|
protected Marker |
SelectionInfoPanel.lastMarker |
| Modifier and Type | Method and Description |
|---|---|
protected Marker |
EpiProReadsReader.processReadRecord(VioletApp app,
java.lang.String[] ar,
int contig_idx) |
protected Marker |
EpiProReadsReader.processSplitReadRecord(java.util.TreeMap<java.lang.Integer,java.lang.Integer> contigs_map,
java.util.ArrayList<Marker> markers,
java.lang.String[] ar,
int contig_idx) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
EpiProReadsReader.assembleResultsWithoutStructures(java.util.ArrayList<Marker> alignedReads,
int num_contigs) |
protected int |
EpiProReadsReader.PileUpContigResultsWithoutStructure(java.util.List<Marker> alignedReads) |
protected Marker |
EpiProReadsReader.processSplitReadRecord(java.util.TreeMap<java.lang.Integer,java.lang.Integer> contigs_map,
java.util.ArrayList<Marker> markers,
java.lang.String[] ar,
int contig_idx) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
ExportDataUtils.exportGenericMarker(Marker marker,
java.io.FileWriter writer,
java.lang.String contig_name,
int track_index) |
protected void |
ExportDataUtils.exportModification(Marker marker,
java.io.FileWriter writer,
java.lang.String contig_name,
int track_index) |
protected void |
ExportDataUtils.exportRead(Marker marker,
java.io.FileWriter writer,
java.lang.String contig_name,
int track_index) |
protected void |
ExportDataUtils.exportVariant(Marker marker,
java.io.FileWriter writer,
java.lang.String contig_name,
int track_index) |
| Modifier and Type | Method and Description |
|---|---|
static java.lang.String |
GFFVariantsReader.getVariantLabel(Marker marker)
returns a variant string from type
|
Copyright © 2010-2014 Pacific Biosciences. All Rights Reserved.