com.pacbio.secondary.vis.gui.draw.utils

Class InfoBuilder

java.lang.Object

com.pacbio.secondary.vis.gui.draw.utils.InfoBuilder

public class InfoBuilder
extends java.lang.Object

Creates summary information for genes, markers, reads, contigs, etc. Used for selection panel, tooltips and headers

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected static int	MAX_LIST_INTERSECT_ITEMS_PER_TRACK
protected static java.lang.String	tag_gene_id
protected static int	TOOLTIP_IMAGE_SIZE

Constructor Summary

Constructors

Constructor and Description
InfoBuilder()

Method Summary

Methods

Modifier and Type	Method and Description
protected static void	addBaseModInfo(java.lang.StringBuffer buf, Marker marker, java.lang.String text, int min_offset, int max_offset)
protected static void	addGeneHtmlTooltip(GenomicViewEvents source, java.lang.StringBuffer buf, Marker gene, java.text.NumberFormat nf, boolean addImage) gene tooltip
protected static void	addGenesTrackInfo(GenomicViewEvents source, java.lang.StringBuffer buf, java.text.NumberFormat nf)
protected static void	addMarkerCollectionHtmlTooltip(GenomicViewEvents source, java.lang.StringBuffer html, MarkerCollection track, java.text.NumberFormat nf, boolean b) track tooltip
protected static void	addMarkerHtmlTooltip(GenomicViewEvents source, java.lang.StringBuffer buf, Marker marker, MarkerCollection track, java.text.NumberFormat nf, boolean addImage) marker tooltip
protected static void	addReadHtmlTooltip(GenomicViewDetails view, java.lang.StringBuffer buf, Marker read, java.text.NumberFormat nf, boolean addImage) read tooltip
protected static void	addReadsInfo(GenomicViewEvents source, java.lang.StringBuffer buf, java.text.NumberFormat nf)
protected static void	addReferenceKinetogramInfo(GenomicViewEvents view, java.lang.StringBuffer buf, java.text.NumberFormat nf)
protected static void	appendImageInfo(GenomicViewEvents source, java.lang.StringBuffer buf, java.lang.String imagename, int img_width, int img_height, java.lang.String stype)
protected static java.lang.String	getHeaderLevel() get header level
static void	getHtmlToolTipForTable(GenomicViewEvents source, Marker marker, MarkerCollection track, java.lang.StringBuffer buf) gets tooltip for table view
static void	getHtmlToolTipText(GenomicViewEvents source, java.lang.StringBuffer buf, java.awt.Point mouse_pos)
static void	getIntersectedMarkers(java.lang.StringBuffer buf, Marker selectedMarker, Marker selectedGene, GenomicViewEvents view)
static java.lang.String	getMarkerInfo(MarkerCollection track, Marker marker, GenomicViewEvents source)
protected static java.lang.String	getReadFontStyle() get font style for read info in table
static void	getSelectionInfoChromosomes(GenomicViewEvents source, java.lang.StringBuffer buf)
static void	getSelectionInfoGenes(java.lang.StringBuffer buf, Marker selectedMarker, Marker selected_gene, GenomicViewData view)
static void	getSelectionInfoMarkers(GenomicViewEvents source, java.lang.StringBuffer buf)
static void	getSelectionInfoReads(GenomicViewEvents source, java.lang.StringBuffer buf)
static void	getSelectionInfoTracks(GenomicViewEvents source, java.lang.StringBuffer buf)
static java.lang.String	getSessionProperties(VioletApp app) creates html info of all loaded data
protected static java.lang.String	getTableFontStyle() get font style for tables
protected static java.lang.String	getTextFontSize() get font size for body in table
protected static boolean	haveBaseModsSummary(GenomicViewEvents source)
protected static boolean	haveVariantsSummary(GenomicViewEvents source)

Methods inherited from class java.lang.Object

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

Field Detail

tag_gene_id

protected static final java.lang.String tag_gene_id

See Also:

Constant Field Values

TOOLTIP_IMAGE_SIZE

protected static final int TOOLTIP_IMAGE_SIZE

See Also:

Constant Field Values

MAX_LIST_INTERSECT_ITEMS_PER_TRACK

protected static final int MAX_LIST_INTERSECT_ITEMS_PER_TRACK

See Also:

Constant Field Values

Constructor Detail

InfoBuilder

public InfoBuilder()

Method Detail

getSelectionInfoTracks

public static void getSelectionInfoTracks(GenomicViewEvents source,
                          java.lang.StringBuffer buf)

Parameters:

source -

buf -

getSelectionInfoGenes

public static void getSelectionInfoGenes(java.lang.StringBuffer buf,
                         Marker selectedMarker,
                         Marker selected_gene,
                         GenomicViewData view)

Parameters:

buf -

getIntersectedMarkers

public static void getIntersectedMarkers(java.lang.StringBuffer buf,
                         Marker selectedMarker,
                         Marker selectedGene,
                         GenomicViewEvents view)

Parameters:

buf -

getSelectionInfoMarkers

public static void getSelectionInfoMarkers(GenomicViewEvents source,
                           java.lang.StringBuffer buf)

getSelectionInfoReads

public static void getSelectionInfoReads(GenomicViewEvents source,
                         java.lang.StringBuffer buf)

getSelectionInfoChromosomes

public static void getSelectionInfoChromosomes(GenomicViewEvents source,
                               java.lang.StringBuffer buf)

addBaseModInfo

protected static void addBaseModInfo(java.lang.StringBuffer buf,
                  Marker marker,
                  java.lang.String text,
                  int min_offset,
                  int max_offset)

getMarkerInfo

public static java.lang.String getMarkerInfo(MarkerCollection track,
                             Marker marker,
                             GenomicViewEvents source)

getHtmlToolTipForTable

public static void getHtmlToolTipForTable(GenomicViewEvents source,
                          Marker marker,
                          MarkerCollection track,
                          java.lang.StringBuffer buf)

gets tooltip for table view

Parameters:

source -

marker -

track -

buf -

addGeneHtmlTooltip

protected static void addGeneHtmlTooltip(GenomicViewEvents source,
                      java.lang.StringBuffer buf,
                      Marker gene,
                      java.text.NumberFormat nf,
                      boolean addImage)

gene tooltip

Parameters:

source -

buf -

gene -

nf -

addReferenceKinetogramInfo

protected static void addReferenceKinetogramInfo(GenomicViewEvents view,
                              java.lang.StringBuffer buf,
                              java.text.NumberFormat nf)

addGenesTrackInfo

protected static void addGenesTrackInfo(GenomicViewEvents source,
                     java.lang.StringBuffer buf,
                     java.text.NumberFormat nf)

addReadsInfo

protected static void addReadsInfo(GenomicViewEvents source,
                java.lang.StringBuffer buf,
                java.text.NumberFormat nf)

addReadHtmlTooltip

protected static void addReadHtmlTooltip(GenomicViewDetails view,
                      java.lang.StringBuffer buf,
                      Marker read,
                      java.text.NumberFormat nf,
                      boolean addImage)

read tooltip

Parameters:

view -

buf -

read -

nf -

addMarkerHtmlTooltip

protected static void addMarkerHtmlTooltip(GenomicViewEvents source,
                        java.lang.StringBuffer buf,
                        Marker marker,
                        MarkerCollection track,
                        java.text.NumberFormat nf,
                        boolean addImage)

marker tooltip

Parameters:

source -

buf -

marker -

track -

nf -

addMarkerCollectionHtmlTooltip

protected static void addMarkerCollectionHtmlTooltip(GenomicViewEvents source,
                                  java.lang.StringBuffer html,
                                  MarkerCollection track,
                                  java.text.NumberFormat nf,
                                  boolean b)

track tooltip

Parameters:

source -

html -

track -

nf -

b -

getHtmlToolTipText

public static void getHtmlToolTipText(GenomicViewEvents source,
                      java.lang.StringBuffer buf,
                      java.awt.Point mouse_pos)

appendImageInfo

protected static void appendImageInfo(GenomicViewEvents source,
                   java.lang.StringBuffer buf,
                   java.lang.String imagename,
                   int img_width,
                   int img_height,
                   java.lang.String stype)

getSessionProperties

public static java.lang.String getSessionProperties(VioletApp app)

creates html info of all loaded data

Returns:

getTableFontStyle

protected static java.lang.String getTableFontStyle()

get font style for tables

Returns:

getReadFontStyle

protected static java.lang.String getReadFontStyle()

get font style for read info in table

Returns:

getTextFontSize

protected static java.lang.String getTextFontSize()

get font size for body in table

Returns:

getHeaderLevel

protected static java.lang.String getHeaderLevel()

get header level

Returns:

haveVariantsSummary

protected static boolean haveVariantsSummary(GenomicViewEvents source)

haveBaseModsSummary

protected static boolean haveBaseModsSummary(GenomicViewEvents source)