info.bioinfweb.libralign.pherogram

Class PherogramFormats

java.lang.Object

info.bioinfweb.libralign.pherogram.PherogramFormats

public class PherogramFormats
extends java.lang.Object

Class that stores colors and fonts and settings used to display a pherogram from Sanger sequencing. It is used by implementations of PherogramComponent and PherogramHeadingView to format their output.

Changes to all properties can be tracked using PropertyChangeListeners during runtime. Note that separate listeners could be added to the nested ZoomableFont objects, but their events are also forwarded to listeners registered with this objects. The forwarded events then have the font property name as a prefix (e.g. "baseCallFont.name" if the "name" property of getBaseCallFont() was changed).

Since:

0.1.0

Author:

Ben Stöver

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PherogramFormats.QualityOutputType Enumeration that determines the way quality scores are displays in an

Field Summary

Fields

Modifier and Type	Field and Description
static float	BASE_CALL_LINE_COLOR_FACTOR Used to calculate the default base call line color.
static float	CUT_COLOR_FACTOR Used to calculate the default background color for the cut off areas.
static double	FONT_HEIGHT_FACTOR Used to determine the line spacing around base calls, indices or probabilities.

Constructor Summary

Constructors

Constructor and Description
PherogramFormats(PherogramComponent owner) Creates a new instance of this class with default values.

Method Summary

Modifier and Type	Method and Description
void	addPropertyChangeListener(java.beans.PropertyChangeListener listener)
void	addPropertyChangeListener(java.lang.String propertyName, java.beans.PropertyChangeListener listener)
double	calculateFontZoomFactor() Calculates the factor to multiply font heights with to fit to the current size of the owning component.
void	changeQualityOutputType() Changes the current quality output type to the next value in the order defined by PherogramFormats.QualityOutputType.
ZoomableFont	getAnnotationFont() Returns the font used to print the base call quality scores and probability values.
java.awt.Color	getBackgroundColor() Returns the background color for displaying the central part of the pherogram (the positions that have not been cut off).
ZoomableFont	getBaseCallFont() Returns the font used to print the characters of the base call sequence.
java.awt.Color	getBaseCallLineColor() Returns the color used to paint the vertical lines at each base call position in the background of the trace curve output in the center area that has not been cut off by the user.
java.awt.Color	getCutBackgroundColor() Returns the background color for displaying the parts of the pherogram on the left and right end that have been cut off by the user.
java.awt.Color	getCutBaseCallLineColor() Returns the color used to paint the vertical lines at each base call position in the background of the trace curve output at the left and right areas that have been cut off by the user.
java.awt.Color	getHeadingBackgroundColor() Returns the background color for the heading of the pherogram (displaying the base call sequence and nucleotide indices).
ZoomableFont	getIndexFont() Returns the font used to print the nucleotide indices.
java.awt.Color	getNucleotideColor(char nucleotide) Returns the color associated with the specified token representation.
PherogramComponent	getOwner() Returns the owning trace curve view or pherogram data area using this instance.
java.awt.Color	getProbabilityColor() Returns the font color for displaying probability values.
PherogramFormats.QualityOutputType	getQualityOutputType() Determines the way quality scores shall be displayed.
boolean	isShowBaseCallLines() Determines if base call lines (vertical lines at each base call position in the background of the trace curve output) shall be painted.
boolean	isShowProbabilityValues() Determines whether probability values (substitution, overcall and undercall) should be displayed in the pherogram heading.
double	qualityOutputHeight() Returns the height of the quality score output depending on the current output type for the current zoom factor.
void	removePropertyChangeListener(java.beans.PropertyChangeListener listener)
void	removePropertyChangeListener(java.lang.String propertyName, java.beans.PropertyChangeListener listener)
void	setBackgroundColor(java.awt.Color backgroundColor) Sets a new background color for displaying the central part of the pherogram (the positions that have not been cut off).
void	setBaseCallLineColor(java.awt.Color baseCallLineColor) Sets a new color used to paint the vertical lines at each base call position in the background of the trace curve output in the center area that has not been cut off by the user.
void	setCutBackgroundColor(java.awt.Color cutBackgroundColor) Sets a new background color for displaying the parts of the pherogram on the left and right end that have been cut off by the user.
void	setCutBaseCallLineColor(java.awt.Color cutBaseCallLineColor) Sets a new color used to paint the vertical lines at each base call position in the background of the trace curve output at the left and right areas that have been cut off by the user.
void	setHeadingBackgroundColor(java.awt.Color headingBackgroundColor) Sets a new background color for the heading of the pherogram (displaying the base call sequence and nucleotide indices).
void	setNucleotideColor(char nucleotide, java.awt.Color color) Sets a new color for a nucleotide representation in the internal color map of this instance.
void	setProbabilityColor(java.awt.Color probabilityColor) Sets a new font font color for displaying probability values.
void	setQualityOutputType(PherogramFormats.QualityOutputType qualityOutputType)
void	setShowBaseCallLines(boolean showBaseCallLines) Allows to define if base call lines (vertical lines at each base call position in the background of the trace curve output) shall be painted.
void	setShowProbabilityValues(boolean showProbabilityValues) Allows to specify whether probability values (substitution, overcall and undercall) should be displayed in the pherogram heading.
void	toggleShowBaseCallLines() Toggles whether base call lines (vertical lines at each base call position in the background of the trace curve output) shall be painted.
void	toggleShowProbabilityValues() Toggles whether probability values (substitution, overcall and undercall) should be displayed in the pherogram heading.

Methods inherited from class java.lang.Object

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

Field Detail

CUT_COLOR_FACTOR

public static final float CUT_COLOR_FACTOR

Used to calculate the default background color for the cut off areas.

See Also:

Constant Field Values

BASE_CALL_LINE_COLOR_FACTOR

public static final float BASE_CALL_LINE_COLOR_FACTOR

Used to calculate the default base call line color.

See Also:

Constant Field Values

FONT_HEIGHT_FACTOR

public static final double FONT_HEIGHT_FACTOR

Used to determine the line spacing around base calls, indices or probabilities.

See Also:

Constant Field Values

Constructor Detail

PherogramFormats

public PherogramFormats(PherogramComponent owner)

Creates a new instance of this class with default values.

Method Detail

getOwner

public PherogramComponent getOwner()

Returns the owning trace curve view or pherogram data area using this instance.

Returns:

the owning object

getBackgroundColor

public java.awt.Color getBackgroundColor()

Returns the background color for displaying the central part of the pherogram (the positions that have not been cut off).

Returns:

the current background color for the center positions

setBackgroundColor

public void setBackgroundColor(java.awt.Color backgroundColor)

Sets a new background color for displaying the central part of the pherogram (the positions that have not been cut off).

Parameters:

backgroundColor - the new background color for the center positions

getCutBackgroundColor

public java.awt.Color getCutBackgroundColor()

Returns the background color for displaying the parts of the pherogram on the left and right end that have been cut off by the user.

Returns:

the current background color for the cut off positions

setCutBackgroundColor

public void setCutBackgroundColor(java.awt.Color cutBackgroundColor)

Sets a new background color for displaying the parts of the pherogram on the left and right end that have been cut off by the user.

Parameters:

backgroundColor - the new background color for the cut off positions

getHeadingBackgroundColor

public java.awt.Color getHeadingBackgroundColor()

Returns the background color for the heading of the pherogram (displaying the base call sequence and nucleotide indices).

Returns:

the current background color for the header information area

setHeadingBackgroundColor

public void setHeadingBackgroundColor(java.awt.Color headingBackgroundColor)

Sets a new background color for the heading of the pherogram (displaying the base call sequence and nucleotide indices).

Parameters:

headingBackgroundColor - the new background color for the heading information area

getBaseCallLineColor

public java.awt.Color getBaseCallLineColor()

Returns the color used to paint the vertical lines at each base call position in the background of the trace curve output in the center area that has not been cut off by the user.

Returns:

the current base call line color

setBaseCallLineColor

public void setBaseCallLineColor(java.awt.Color baseCallLineColor)

Sets a new color used to paint the vertical lines at each base call position in the background of the trace curve output in the center area that has not been cut off by the user.

Parameters:

baseCallLineColor - the new base call line color for the center

getCutBaseCallLineColor

public java.awt.Color getCutBaseCallLineColor()

Returns the color used to paint the vertical lines at each base call position in the background of the trace curve output at the left and right areas that have been cut off by the user.

Returns:

the current base call line color for the cut off areas

setCutBaseCallLineColor

public void setCutBaseCallLineColor(java.awt.Color cutBaseCallLineColor)

Sets a new color used to paint the vertical lines at each base call position in the background of the trace curve output at the left and right areas that have been cut off by the user.

Parameters:

baseCallLineColor - the new base call line color for the cut off areas

getNucleotideColor

public java.awt.Color getNucleotideColor(char nucleotide)

Returns the color associated with the specified token representation.

If this instance is owned by a PherogramArea, this method will first try to determine the color from the associated token painter. If that produces no result, it will return a default color from its own nucleotide color map. If that map has no entry for the specified representation as well, getProbabilityColor() will be returned as the default color.

Parameters:

nucleotide - the token representation (nucleotide characters or the gap or unknown character are valid here)

Returns:

the color determined by the algorithm described above.

setNucleotideColor

public void setNucleotideColor(char nucleotide,
                               java.awt.Color color)

Sets a new color for a nucleotide representation in the internal color map of this instance.

Note that that color is only used if this instance is owned by a PherogramTraceCurveView or if the token painter associated with the owning PherogramArea does not specify an according color.

Parameters:

nucleotide - the nucleotide (or gap, ...) representation

color - the color to put in the map (Specify null here to remove the association for nucleotide from the map.)

isShowBaseCallLines

public boolean isShowBaseCallLines()

Determines if base call lines (vertical lines at each base call position in the background of the trace curve output) shall be painted.

Returns:

true if the lines are painted, false otherwise

setShowBaseCallLines

public void setShowBaseCallLines(boolean showBaseCallLines)

Allows to define if base call lines (vertical lines at each base call position in the background of the trace curve output) shall be painted. The pherogram will be repainted after setting the property.

Parameters:

showBaseCallLines - Specify true here if lines shall be painted or false if not.

See Also:

toggleShowBaseCallLines()

toggleShowBaseCallLines

public void toggleShowBaseCallLines()

Toggles whether base call lines (vertical lines at each base call position in the background of the trace curve output) shall be painted.

See Also:

setShowBaseCallLines(boolean)

getBaseCallFont

public ZoomableFont getBaseCallFont()

Returns the font used to print the characters of the base call sequence.

Returns:

the font object that is used

getIndexFont

public ZoomableFont getIndexFont()

Returns the font used to print the nucleotide indices.

Returns:

the font object that is used

getAnnotationFont

public ZoomableFont getAnnotationFont()

Returns the font used to print the base call quality scores and probability values.

Returns:

the font object that is used

getQualityOutputType

public PherogramFormats.QualityOutputType getQualityOutputType()

Determines the way quality scores shall be displayed.

Returns:

the output type for quality scores

setQualityOutputType

public void setQualityOutputType(PherogramFormats.QualityOutputType qualityOutputType)

changeQualityOutputType

public void changeQualityOutputType()

Changes the current quality output type to the next value in the order defined by PherogramFormats.QualityOutputType. If the end of the enum has been reached this method will start with the first value again.

See Also:

setQualityOutputType(QualityOutputType)

qualityOutputHeight

public double qualityOutputHeight()

Returns the height of the quality score output depending on the current output type for the current zoom factor.

Returns:

the height needed to display the quality output

isShowProbabilityValues

public boolean isShowProbabilityValues()

Determines whether probability values (substitution, overcall and undercall) should be displayed in the pherogram heading.

Returns:

true the values shall be displayed, false otherwise

setShowProbabilityValues

public void setShowProbabilityValues(boolean showProbabilityValues)

Allows to specify whether probability values (substitution, overcall and undercall) should be displayed in the pherogram heading.

Parameters:

showProbabilityValues - Specify true here if the values shall be displayed from now on or false otherwise.

See Also:

toggleShowProbabilityValues()

toggleShowProbabilityValues

public void toggleShowProbabilityValues()

Toggles whether probability values (substitution, overcall and undercall) should be displayed in the pherogram heading.

See Also:

setShowProbabilityValues(boolean)

getProbabilityColor

public java.awt.Color getProbabilityColor()

Returns the font color for displaying probability values.

Returns:

the current color for probability values

setProbabilityColor

public void setProbabilityColor(java.awt.Color probabilityColor)

Sets a new font font color for displaying probability values.

Parameters:

probabilityColor - the new color for probability values

calculateFontZoomFactor

public double calculateFontZoomFactor()

Calculates the factor to multiply font heights with to fit to the current size of the owning component.

Throws:

java.lang.IllegalStateException - if the owner is neither an instance of PherogramArea or PherogramTraceCurveView

addPropertyChangeListener

public void addPropertyChangeListener(java.beans.PropertyChangeListener listener)

addPropertyChangeListener

public void addPropertyChangeListener(java.lang.String propertyName,
                                      java.beans.PropertyChangeListener listener)

removePropertyChangeListener

public void removePropertyChangeListener(java.beans.PropertyChangeListener listener)

removePropertyChangeListener

public void removePropertyChangeListener(java.lang.String propertyName,
                                         java.beans.PropertyChangeListener listener)