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apollo.gui.drawable
Class DrawableSeqFeature  

java.lang.Object
  apollo.gui.drawable.DrawableSeqFeature

All Implemented Interfaces:

apollo.datamodel.Comparable, Drawable, apollo.datamodel.RangeI, apollo.gui.SelectableI, apollo.datamodel.SeqFeatureI, java.io.Serializable

Direct Known Subclasses:

DrawableAnnotatedSeqFeature, DrawableEnsemblSeqFeature, DrawableFeatureSet, DrawableGeneSeqFeature, DrawableResultSeqFeature, SiteCodon

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public class DrawableSeqFeature

extends java.lang.Object

implements apollo.datamodel.Comparable, Drawable, apollo.gui.SelectableI, apollo.datamodel.SeqFeatureI

A drawable for drawing basic sequence features.

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Field Summary
protected  java.awt.Rectangle	boxBounds
protected static byte	DECORATED
protected  apollo.datamodel.SeqFeatureI	feature
protected  byte	flags
protected  apollo.gui.schemes.FeatureProperty	groupProperty
protected static byte	HIGHLIGHTED
protected static byte	LABELED
private static java.awt.Rectangle	labStaticBounds
protected static byte	LEFTEDGE
protected  apollo.datamodel.SeqFeatureI	refFeature
protected static byte	RIGHTEDGE
protected static byte	SELECTED
protected static java.lang.String[]	startCodons
protected static java.lang.String[]	stopCodons
protected static byte	VISIBLE
private  int	yindex           yindex is the tier number - could be renamed tierIndex? yindex -1 says i havent been assigned a tier yet

 

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

 

Constructor Summary

DrawableSeqFeature()

DrawableSeqFeature(apollo.datamodel.SeqFeatureI feature)

 

Method Summary
protected  void	_draw(java.awt.Graphics g, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager, java.awt.Rectangle boxBounds)
void	accept(apollo.util.Visitor visitor)           General implementation of Visitor pattern.
void	addDecorations(java.awt.Graphics g, java.awt.Rectangle boxBounds, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)           draw in label and codons
void	addHighlights(java.awt.Graphics g, java.awt.Rectangle boxBounds, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)           highlights edges and box around if isHighlighted
void	addProperty(java.lang.String name, java.lang.String value)
void	addScore(double score)
void	addScore(apollo.datamodel.Score s)
void	addScore(java.lang.String name, double score)
void	addScore(java.lang.String name, java.lang.String score)
private  boolean	checkCodon(apollo.datamodel.FeatureSetI trans, int position, java.lang.String[] allowedCodons)
int	compareTo(java.lang.Object sfObj)
boolean	contains(int position)
boolean	contains(java.awt.Point point, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
boolean	contains(apollo.datamodel.RangeI sf)
boolean	descendsFrom(apollo.datamodel.SeqFeatureI sf)           from SeqFeatureI
boolean	draw(java.awt.Graphics g, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)           This method draws the feature on the Graphics using a Transformer for coordinate transformations.
boolean	draw(java.awt.Graphics g, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager, apollo.gui.genomemap.PixelMaskI mask)
private  void	drawCodon(apollo.datamodel.FeatureSetI trans, int position, java.awt.Graphics g, apollo.gui.Transformer transformer, int ycoord, int ysize, java.lang.String[] allowedCodons, java.awt.Color colour)
void	drawSelected(java.awt.Graphics g, java.awt.Rectangle boxBounds, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
void	drawStartAndStopCodons(java.awt.Graphics g, apollo.gui.Transformer transformer, int ycoord, int ysize)
void	drawUnselected(java.awt.Graphics g, java.awt.Rectangle boxBounds, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
Drawable	findDrawable(apollo.datamodel.SeqFeatureI sf)
private  boolean	flagValue(int mask)
void	flipFlop()           This is used simply to move the feature directly to the opposite strand, without complementation of the Reference Sequence
java.awt.Color	fontColorForBackground(java.awt.Color bgColor)
java.lang.String	get_cDNA()
java.lang.String	getBioType()
java.awt.Rectangle	getBoxBounds(apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
protected  int	getCharY(java.awt.FontMetrics fm, java.awt.Rectangle box)           Return y value for writing characters in the box passed in,
java.util.Vector	getChildren()           If hasChildren() is true, returns FeatureSetI.getFeatures()
java.lang.String	getCodingDNA()           Returns a String of sequence from start to end of translation, in the case where a feature does not have a start and stop the cDNA is returned
protected  java.awt.Point	getCodonStartPoint(apollo.gui.Transformer transformer, int x_position, int y_position)
java.awt.Color	getColour()           Gets the colour to draw the Drawable in.
java.lang.String	getDatabase()
java.lang.String	getDisplayLabel()
int	getEnd()
int	getEndPhase()
apollo.datamodel.SeqFeatureI	getFeature()
int	getFeaturePosition(int genomic_pos)
apollo.gui.schemes.FeatureProperty	getFeatureProperty()
apollo.datamodel.SequenceI	getFeatureSequence()           Retrieve the SequenceI defined by this feature itself.
private  java.awt.Font	getFont(apollo.datamodel.SeqFeatureI g)
int	getFrame()
int	getGenomicPosition(int feature_pos)
int	getHigh()
java.lang.String	getId()
private  java.awt.Rectangle	getLabeledBounds(apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager, java.awt.Graphics g, java.awt.Rectangle boxBounds)
int	getLeft(apollo.gui.Transformer transformer)
int	getLeftOverlap(apollo.datamodel.RangeI sf)
int	getLow()
java.awt.Rectangle	getMaxBounds(apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
java.lang.String	getName()           In the case where the range is chromosomal the name is the chromosome name
int	getPhase()
java.lang.String	getProgramName()
java.util.Hashtable	getProperties()
java.lang.String	getProperty(java.lang.String name)
apollo.datamodel.SeqFeatureI	getRefFeature()           I believe the RefFeature that is often stored is actually a DrawableFeatureSet as DrawableFeatureSet is a SeqFeatureI so to get your Drawable parent one would cast (DrawableFeatureSet)getRefFeature() My qualm here is drawables and seqFeatureI/models being muddled.
java.lang.String	getRefId()
apollo.datamodel.SequenceI	getRefSequence()           Retrieve the SequenceI that this feature annotates.
java.lang.String	getResidues()
int	getRight(apollo.gui.Transformer transformer)
int	getRightOverlap(apollo.datamodel.RangeI sf)
double	getScore()           Do all SeqFeatures have scores.
double	getScore(java.lang.String name)
java.util.Hashtable	getScores()
int	getSize(apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
int	getStart()
int	getStrand()
protected  int	getTierIndex(apollo.gui.genomemap.FeatureTierManager manager)           This returns the variable called yindex, which is actually its tier value so i renamed to getTierIndex - hope thats ok.
java.lang.String	getType()
int	getYCentre(apollo.gui.genomemap.FeatureTierManager manager)
int	getYindex()           Get the tier on which this Drawable resides
int	getYSpace(apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
boolean	hasChildren()           If SeqFeatureI is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then return true.
boolean	hasType()           convenience method returns !getType()==NO_TYPE
boolean	intersects(java.awt.Rectangle pixrect, apollo.gui.Transformer transformer, apollo.gui.genomemap.FeatureTierManager manager)
boolean	isAncestorOf(apollo.datamodel.SeqFeatureI sf)           from SeqFeatureI - this should be called on model not drawable
boolean	isDecorated()
boolean	isExactOverlap(apollo.datamodel.RangeI sf)
boolean	isForwardStrand()
boolean	isHighlighted()
boolean	isLabeled()
boolean	isLeftEdge()
boolean	isReverseStrand()
boolean	isRightEdge()
boolean	isSelected()           Determine if this Drawable is currently selected.
boolean	isSequenceAvailable(int position)
boolean	isVisible()           Determine if this Drawable is to be drawn.
int	length()
apollo.datamodel.SeqFeatureI	merge(apollo.datamodel.SeqFeatureI sf)
boolean	overlaps(apollo.datamodel.RangeI sf)
void	reverseComplement()           This is used if the Reference Sequence is being reverse complemented to move this feature onto the coordinates counting from the 3' end rather than the 5' end
protected  boolean	sameFeature(apollo.datamodel.SeqFeatureI one, apollo.datamodel.SeqFeatureI two)
void	setBioType(java.lang.String type)
void	setColour(java.awt.Color newColour)           Sets the colour of the Drawable.
void	setDatabase(java.lang.String name)
void	setEdgeHighlights(int[] edges, boolean state, apollo.gui.Transformer transformer)
void	setEnd(int end)
void	setFeature(apollo.datamodel.SeqFeatureI feature)
void	setFeatureProperty(apollo.gui.schemes.FeatureProperty fp)
private  void	setFlag(boolean state, byte mask)
void	setHigh(int high)
void	setHighlighted(boolean state)
void	setId(java.lang.String id)
void	setLabeled(boolean state)
void	setLow(int low)
void	setName(java.lang.String name)
void	setPhase(int phase)
void	setProgramName(java.lang.String name)
void	setRefFeature(apollo.datamodel.SeqFeatureI f)           Set the parent SeqFeatureI.
void	setRefSequence(apollo.datamodel.SequenceI refSeq)           Set the SequenceI that this feature annotates.
void	setScore(double score)
void	setSelected(boolean state)           Set whether this Drawable is currently selected or not.
void	setStart(int start)
void	setStrand(int strand)
void	setType(java.lang.String type)
void	setVisible(boolean state)           Set whether this Drawable is to be drawn or not.
void	setYindex(int index)           Set the tier on which this Drawable resides
java.lang.String	translate()
protected  boolean	wantToDraw(java.awt.Graphics g, apollo.gui.genomemap.FeatureTierManager manager, apollo.gui.Transformer transformer, java.awt.Rectangle boxBounds)

 

Methods inherited from class java.lang.Object

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

 

Field Detail

VISIBLE

protected static byte VISIBLE

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SELECTED

protected static byte SELECTED

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HIGHLIGHTED

protected static byte HIGHLIGHTED

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LEFTEDGE

protected static byte LEFTEDGE

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RIGHTEDGE

protected static byte RIGHTEDGE

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LABELED

protected static byte LABELED

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DECORATED

protected static byte DECORATED

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stopCodons

protected static java.lang.String[] stopCodons

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startCodons

protected static java.lang.String[] startCodons

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feature

protected apollo.datamodel.SeqFeatureI feature

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refFeature

protected apollo.datamodel.SeqFeatureI refFeature

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flags

protected byte flags

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groupProperty

protected apollo.gui.schemes.FeatureProperty groupProperty

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yindex

private int yindex

yindex is the tier number - could be renamed tierIndex? yindex -1 says i havent been assigned a tier yet

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boxBounds

protected java.awt.Rectangle boxBounds

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labStaticBounds

private static java.awt.Rectangle labStaticBounds

Constructor Detail

DrawableSeqFeature

public DrawableSeqFeature()

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DrawableSeqFeature

public DrawableSeqFeature(apollo.datamodel.SeqFeatureI feature)

Method Detail

getFeature

public apollo.datamodel.SeqFeatureI getFeature()

Specified by:

getFeature in interface Drawable

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getLeft

public int getLeft(apollo.gui.Transformer transformer)

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getRight

public int getRight(apollo.gui.Transformer transformer)

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getTierIndex

protected int getTierIndex(apollo.gui.genomemap.FeatureTierManager manager)

This returns the variable called yindex, which is actually its tier value so i renamed to getTierIndex - hope thats ok. if yindex==-1 then hasnt got a tier yet. synchDrawablesWithTiers assigns all tiers this happens when doing a find on a feature that has never been in view

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getYCentre

public int getYCentre(apollo.gui.genomemap.FeatureTierManager manager)

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getMaxBounds

public java.awt.Rectangle getMaxBounds(apollo.gui.Transformer transformer,
                                       apollo.gui.genomemap.FeatureTierManager manager)

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getBoxBounds

public java.awt.Rectangle getBoxBounds(apollo.gui.Transformer transformer,
                                       apollo.gui.genomemap.FeatureTierManager manager)

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draw

public boolean draw(java.awt.Graphics g,
                    apollo.gui.Transformer transformer,
                    apollo.gui.genomemap.FeatureTierManager manager,
                    apollo.gui.genomemap.PixelMaskI mask)

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wantToDraw

protected boolean wantToDraw(java.awt.Graphics g,
                             apollo.gui.genomemap.FeatureTierManager manager,
                             apollo.gui.Transformer transformer,
                             java.awt.Rectangle boxBounds)

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getLabeledBounds

private java.awt.Rectangle getLabeledBounds(apollo.gui.Transformer transformer,
                                            apollo.gui.genomemap.FeatureTierManager manager,
                                            java.awt.Graphics g,
                                            java.awt.Rectangle boxBounds)

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draw

public boolean draw(java.awt.Graphics g,
                    apollo.gui.Transformer transformer,
                    apollo.gui.genomemap.FeatureTierManager manager)

This method draws the feature on the Graphics using a Transformer for coordinate transformations. There are minimum size limits set the displayed feature so that it is not too small to be seen (3 pixels X and Y).

Specified by:

draw in interface Drawable

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_draw

protected void _draw(java.awt.Graphics g,
                     apollo.gui.Transformer transformer,
                     apollo.gui.genomemap.FeatureTierManager manager,
                     java.awt.Rectangle boxBounds)

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addHighlights

public void addHighlights(java.awt.Graphics g,
                          java.awt.Rectangle boxBounds,
                          apollo.gui.Transformer transformer,
                          apollo.gui.genomemap.FeatureTierManager manager)

highlights edges and box around if isHighlighted

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addDecorations

public void addDecorations(java.awt.Graphics g,
                           java.awt.Rectangle boxBounds,
                           apollo.gui.Transformer transformer,
                           apollo.gui.genomemap.FeatureTierManager manager)

draw in label and codons

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getFont

private java.awt.Font getFont(apollo.datamodel.SeqFeatureI g)

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drawStartAndStopCodons

public void drawStartAndStopCodons(java.awt.Graphics g,
                                   apollo.gui.Transformer transformer,
                                   int ycoord,
                                   int ysize)

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getCodonStartPoint

protected java.awt.Point getCodonStartPoint(apollo.gui.Transformer transformer,
                                            int x_position,
                                            int y_position)

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drawCodon

private void drawCodon(apollo.datamodel.FeatureSetI trans,
                       int position,
                       java.awt.Graphics g,
                       apollo.gui.Transformer transformer,
                       int ycoord,
                       int ysize,
                       java.lang.String[] allowedCodons,
                       java.awt.Color colour)

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checkCodon

private boolean checkCodon(apollo.datamodel.FeatureSetI trans,
                           int position,
                           java.lang.String[] allowedCodons)

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drawSelected

public void drawSelected(java.awt.Graphics g,
                         java.awt.Rectangle boxBounds,
                         apollo.gui.Transformer transformer,
                         apollo.gui.genomemap.FeatureTierManager manager)

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drawUnselected

public void drawUnselected(java.awt.Graphics g,
                           java.awt.Rectangle boxBounds,
                           apollo.gui.Transformer transformer,
                           apollo.gui.genomemap.FeatureTierManager manager)

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getYSpace

public int getYSpace(apollo.gui.Transformer transformer,
                     apollo.gui.genomemap.FeatureTierManager manager)

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getSize

public int getSize(apollo.gui.Transformer transformer,
                   apollo.gui.genomemap.FeatureTierManager manager)

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setYindex

public void setYindex(int index)

Description copied from interface: Drawable

Set the tier on which this Drawable resides

Specified by:

setYindex in interface Drawable

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getYindex

public int getYindex()

Description copied from interface: Drawable

Get the tier on which this Drawable resides

Specified by:

getYindex in interface Drawable

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setColour

public void setColour(java.awt.Color newColour)

Description copied from interface: Drawable

Sets the colour of the Drawable. Some Drawables may be drawn in more than one colour.

Specified by:

setColour in interface Drawable

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getColour

public java.awt.Color getColour()

Description copied from interface: Drawable

Gets the colour to draw the Drawable in.

Specified by:

getColour in interface Drawable

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setSelected

public void setSelected(boolean state)

Description copied from interface: apollo.gui.SelectableI

Set whether this Drawable is currently selected or not.

Specified by:

setSelected in interface apollo.gui.SelectableI

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isSelected

public boolean isSelected()

Description copied from interface: apollo.gui.SelectableI

Determine if this Drawable is currently selected.

Specified by:

isSelected in interface apollo.gui.SelectableI

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setVisible

public void setVisible(boolean state)

Description copied from interface: Drawable

Set whether this Drawable is to be drawn or not.

Specified by:

setVisible in interface Drawable

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isVisible

public boolean isVisible()

Description copied from interface: Drawable

Determine if this Drawable is to be drawn.

Specified by:

isVisible in interface Drawable

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setFlag

private void setFlag(boolean state,
                     byte mask)

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flagValue

private boolean flagValue(int mask)

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setStart

public void setStart(int start)

Specified by:

setStart in interface apollo.datamodel.RangeI

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getStart

public int getStart()

Specified by:

getStart in interface apollo.datamodel.RangeI

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setEnd

public void setEnd(int end)

Specified by:

setEnd in interface apollo.datamodel.RangeI

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getEnd

public int getEnd()

Specified by:

getEnd in interface apollo.datamodel.RangeI

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setStrand

public void setStrand(int strand)

Specified by:

setStrand in interface apollo.datamodel.RangeI

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getStrand

public int getStrand()

Specified by:

getStrand in interface apollo.datamodel.RangeI

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isForwardStrand

public boolean isForwardStrand()

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isReverseStrand

public boolean isReverseStrand()

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setName

public void setName(java.lang.String name)

Specified by:

setName in interface apollo.datamodel.RangeI

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getName

public java.lang.String getName()

Description copied from interface: apollo.datamodel.RangeI

In the case where the range is chromosomal the name is the chromosome name

Specified by:

getName in interface apollo.datamodel.RangeI

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setId

public void setId(java.lang.String id)

Specified by:

setId in interface apollo.datamodel.SeqFeatureI

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getId

public java.lang.String getId()

Specified by:

getId in interface apollo.datamodel.SeqFeatureI

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getScore

public double getScore()

Description copied from interface: apollo.datamodel.SeqFeatureI

Do all SeqFeatures have scores. Should this be a separate sub interface?

Specified by:

getScore in interface apollo.datamodel.SeqFeatureI

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getScore

public double getScore(java.lang.String name)

Specified by:

getScore in interface apollo.datamodel.SeqFeatureI

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getScores

public java.util.Hashtable getScores()

Specified by:

getScores in interface apollo.datamodel.SeqFeatureI

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setScore

public void setScore(double score)

Specified by:

setScore in interface apollo.datamodel.SeqFeatureI

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addScore

public void addScore(apollo.datamodel.Score s)

Specified by:

addScore in interface apollo.datamodel.SeqFeatureI

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addScore

public void addScore(double score)

Specified by:

addScore in interface apollo.datamodel.SeqFeatureI

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addScore

public void addScore(java.lang.String name,
                     double score)

Specified by:

addScore in interface apollo.datamodel.SeqFeatureI

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addScore

public void addScore(java.lang.String name,
                     java.lang.String score)

Specified by:

addScore in interface apollo.datamodel.SeqFeatureI

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setType

public void setType(java.lang.String type)

Specified by:

setType in interface apollo.datamodel.RangeI

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getType

public java.lang.String getType()

Specified by:

getType in interface apollo.datamodel.RangeI

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hasType

public boolean hasType()

Description copied from interface: apollo.datamodel.RangeI

convenience method returns !getType()==NO_TYPE

Specified by:

hasType in interface apollo.datamodel.RangeI

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getBioType

public java.lang.String getBioType()

Specified by:

getBioType in interface apollo.datamodel.SeqFeatureI

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setBioType

public void setBioType(java.lang.String type)

Specified by:

setBioType in interface apollo.datamodel.SeqFeatureI

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getFeatureProperty

public apollo.gui.schemes.FeatureProperty getFeatureProperty()

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setFeatureProperty

public void setFeatureProperty(apollo.gui.schemes.FeatureProperty fp)

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getRefFeature

public apollo.datamodel.SeqFeatureI getRefFeature()

I believe the RefFeature that is often stored is actually a DrawableFeatureSet as DrawableFeatureSet is a SeqFeatureI so to get your Drawable parent one would cast (DrawableFeatureSet)getRefFeature() My qualm here is drawables and seqFeatureI/models being muddled. It is not obvious that getRefFeature() actually returns a drawable, I figured it out by looking at other snips of code where the casting happens. Its more confused by the fact that getFeature actually returns the model/SeqFeatureI. I propose a refactor where the model and drawables(usually called view) are separated. - MG

Specified by:

getRefFeature in interface apollo.datamodel.SeqFeatureI

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setRefFeature

public void setRefFeature(apollo.datamodel.SeqFeatureI f)

Description copied from interface: apollo.datamodel.SeqFeatureI

Set the parent SeqFeatureI.

When building a part-whole hieracy of features, you must both add a feature to its parent, and then call child.setRefFeature(parent). It is possible for a feature to be added to multiple feature sets, but there is only one legitimate parent.

Specified by:

setRefFeature in interface apollo.datamodel.SeqFeatureI

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setPhase

public void setPhase(int phase)

Specified by:

setPhase in interface apollo.datamodel.SeqFeatureI

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getPhase

public int getPhase()

Specified by:

getPhase in interface apollo.datamodel.SeqFeatureI

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getEndPhase

public int getEndPhase()

Specified by:

getEndPhase in interface apollo.datamodel.SeqFeatureI

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getFrame

public int getFrame()

Specified by:

getFrame in interface apollo.datamodel.SeqFeatureI

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getRefId

public java.lang.String getRefId()

Specified by:

getRefId in interface apollo.datamodel.SeqFeatureI

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getLow

public int getLow()

Specified by:

getLow in interface apollo.datamodel.RangeI

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getHigh

public int getHigh()

Specified by:

getHigh in interface apollo.datamodel.RangeI

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setLow

public void setLow(int low)

Specified by:

setLow in interface apollo.datamodel.RangeI

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setHigh

public void setHigh(int high)

Specified by:

setHigh in interface apollo.datamodel.RangeI

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reverseComplement

public void reverseComplement()

Description copied from interface: apollo.datamodel.SeqFeatureI

This is used if the Reference Sequence is being reverse complemented to move this feature onto the coordinates counting from the 3' end rather than the 5' end

Specified by:

reverseComplement in interface apollo.datamodel.SeqFeatureI

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flipFlop

public void flipFlop()

Description copied from interface: apollo.datamodel.SeqFeatureI

This is used simply to move the feature directly to the opposite strand, without complementation of the Reference Sequence

Specified by:

flipFlop in interface apollo.datamodel.SeqFeatureI

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getRefSequence

public apollo.datamodel.SequenceI getRefSequence()

Description copied from interface: apollo.datamodel.RangeI

Retrieve the SequenceI that this feature annotates.

Specified by:

getRefSequence in interface apollo.datamodel.RangeI

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getFeatureSequence

public apollo.datamodel.SequenceI getFeatureSequence()

Description copied from interface: apollo.datamodel.SeqFeatureI

Retrieve the SequenceI defined by this feature itself.

Specified by:

getFeatureSequence in interface apollo.datamodel.SeqFeatureI

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setRefSequence

public void setRefSequence(apollo.datamodel.SequenceI refSeq)

Description copied from interface: apollo.datamodel.RangeI

Set the SequenceI that this feature annotates.

Specified by:

setRefSequence in interface apollo.datamodel.RangeI

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isSequenceAvailable

public boolean isSequenceAvailable(int position)

Specified by:

isSequenceAvailable in interface apollo.datamodel.RangeI

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getResidues

public java.lang.String getResidues()

Specified by:

getResidues in interface apollo.datamodel.RangeI

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length

public int length()

Specified by:

length in interface apollo.datamodel.RangeI

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getProgramName

public java.lang.String getProgramName()

Specified by:

getProgramName in interface apollo.datamodel.SeqFeatureI

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setProgramName

public void setProgramName(java.lang.String name)

Specified by:

setProgramName in interface apollo.datamodel.SeqFeatureI

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getDatabase

public java.lang.String getDatabase()

Specified by:

getDatabase in interface apollo.datamodel.SeqFeatureI

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setDatabase

public void setDatabase(java.lang.String name)

Specified by:

setDatabase in interface apollo.datamodel.SeqFeatureI

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getLeftOverlap

public int getLeftOverlap(apollo.datamodel.RangeI sf)

Specified by:

getLeftOverlap in interface apollo.datamodel.RangeI

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getRightOverlap

public int getRightOverlap(apollo.datamodel.RangeI sf)

Specified by:

getRightOverlap in interface apollo.datamodel.RangeI

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isExactOverlap

public boolean isExactOverlap(apollo.datamodel.RangeI sf)

Specified by:

isExactOverlap in interface apollo.datamodel.RangeI

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contains

public boolean contains(apollo.datamodel.RangeI sf)

Specified by:

contains in interface apollo.datamodel.RangeI

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overlaps

public boolean overlaps(apollo.datamodel.RangeI sf)

Specified by:

overlaps in interface apollo.datamodel.RangeI

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merge

public apollo.datamodel.SeqFeatureI merge(apollo.datamodel.SeqFeatureI sf)

Specified by:

merge in interface apollo.datamodel.SeqFeatureI

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contains

public boolean contains(int position)

Specified by:

contains in interface apollo.datamodel.RangeI

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compareTo

public int compareTo(java.lang.Object sfObj)

Specified by:

compareTo in interface apollo.datamodel.Comparable

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setHighlighted

public void setHighlighted(boolean state)

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setLabeled

public void setLabeled(boolean state)

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isHighlighted

public boolean isHighlighted()

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isDecorated

public boolean isDecorated()

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isLabeled

public boolean isLabeled()

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isLeftEdge

public boolean isLeftEdge()

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isRightEdge

public boolean isRightEdge()

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setEdgeHighlights

public void setEdgeHighlights(int[] edges,
                              boolean state,
                              apollo.gui.Transformer transformer)

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addProperty

public void addProperty(java.lang.String name,
                        java.lang.String value)

Specified by:

addProperty in interface apollo.datamodel.SeqFeatureI

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getProperty

public java.lang.String getProperty(java.lang.String name)

Specified by:

getProperty in interface apollo.datamodel.SeqFeatureI

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getProperties

public java.util.Hashtable getProperties()

Specified by:

getProperties in interface apollo.datamodel.SeqFeatureI

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translate

public java.lang.String translate()

Specified by:

translate in interface apollo.datamodel.SeqFeatureI

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get_cDNA

public java.lang.String get_cDNA()

Specified by:

get_cDNA in interface apollo.datamodel.SeqFeatureI

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getCodingDNA

public java.lang.String getCodingDNA()

Description copied from interface: apollo.datamodel.SeqFeatureI

Returns a String of sequence from start to end of translation, in the case where a feature does not have a start and stop the cDNA is returned

Specified by:

getCodingDNA in interface apollo.datamodel.SeqFeatureI

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getGenomicPosition

public int getGenomicPosition(int feature_pos)

Specified by:

getGenomicPosition in interface apollo.datamodel.SeqFeatureI

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getFeaturePosition

public int getFeaturePosition(int genomic_pos)

Specified by:

getFeaturePosition in interface apollo.datamodel.SeqFeatureI

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contains

public boolean contains(java.awt.Point point,
                        apollo.gui.Transformer transformer,
                        apollo.gui.genomemap.FeatureTierManager manager)

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intersects

public boolean intersects(java.awt.Rectangle pixrect,
                          apollo.gui.Transformer transformer,
                          apollo.gui.genomemap.FeatureTierManager manager)

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setFeature

pub