Package org.forester.archaeopteryx.phylogeny.data

Class RenderableMsaSequence

java.lang.Object

org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence

All Implemented Interfaces:

RenderablePhylogenyData, PhylogenyData

public final class RenderableMsaSequence
extends java.lang.Object
implements RenderablePhylogenyData

Field Summary

Fields

Modifier and Type	Field	Description
static int	DEFAULT_WIDTH

Method Summary

Modifier and Type	Method	Description
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
java.lang.Object	clone()
PhylogenyData	copy()	Creates a new PhylogenyData object with identical values as this PhylogenyData.
static RenderableMsaSequence	createInstance(java.lang.String seq, java.lang.String type, Configuration configuration)
java.awt.Dimension	getOriginalSize()
java.lang.Object	getParameter()
double	getRenderingFactorWidth()
java.awt.Dimension	getRenderingSize()
int	getTotalLength()
boolean	isEqual(PhylogenyData data)	Compares this PhylogenyData to PhylogenyData data.
void	render(float x1, float y1, java.awt.Graphics2D g, TreePanel tree_panel, boolean to_pdf)	This can be used to render phylogeny data as graphics (for example, display of the domain structure).
void	setParameter(double parameter)
void	setRenderingFactorWidth(double rendering_factor_width)
void	setRenderingHeight(float height)
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation)	Writes a phyloXML representation of this phylogeny data.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_WIDTH

public static final int DEFAULT_WIDTH

See Also:

Constant Field Values

Method Detail

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

asText

public java.lang.StringBuffer asText()

Specified by:

asText in interface PhylogenyData

clone

public java.lang.Object clone()

Overrides:

clone in class java.lang.Object

copy

public PhylogenyData copy()

Description copied from interface: PhylogenyData

Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.

Specified by:

copy in interface PhylogenyData

Returns:

a ~deep~ copy of this PhylogenyData

getOriginalSize

public java.awt.Dimension getOriginalSize()

Specified by:

getOriginalSize in interface RenderablePhylogenyData

getParameter

public java.lang.Object getParameter()

Specified by:

getParameter in interface RenderablePhylogenyData

getRenderingFactorWidth

public double getRenderingFactorWidth()

getRenderingSize

public java.awt.Dimension getRenderingSize()

Specified by:

getRenderingSize in interface RenderablePhylogenyData

getTotalLength

public int getTotalLength()

isEqual

public boolean isEqual(PhylogenyData data)

Description copied from interface: PhylogenyData

Compares this PhylogenyData to PhylogenyData data. In general, this should return true if and only if all fiels are exactly identical.

Specified by:

isEqual in interface PhylogenyData

Returns:

in general, true if and only if all fiels are exactly identical, false otherwise

render

public void render(float x1,
                   float y1,
                   java.awt.Graphics2D g,
                   TreePanel tree_panel,
                   boolean to_pdf)

Description copied from interface: RenderablePhylogenyData

This can be used to render phylogeny data as graphics (for example, display of the domain structure). In most Renderable implementations this will do nothing (i.e. just return).

Specified by:

render in interface RenderablePhylogenyData

g - the Graphics to render to

setParameter

public void setParameter(double parameter)

Specified by:

setParameter in interface RenderablePhylogenyData

setRenderingFactorWidth

public void setRenderingFactorWidth(double rendering_factor_width)

setRenderingHeight

public void setRenderingHeight(float height)

Specified by:

setRenderingHeight in interface RenderablePhylogenyData

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

toPhyloXML

public void toPhyloXML(java.io.Writer writer,
                       int level,
                       java.lang.String indentation)
                throws java.io.IOException

Description copied from interface: PhylogenyData

Writes a phyloXML representation of this phylogeny data.

Specified by:

toPhyloXML in interface PhylogenyData

Throws:

java.io.IOException

createInstance

public static RenderableMsaSequence createInstance(java.lang.String seq,
                                                   java.lang.String type,
                                                   Configuration configuration)