org.forester.phylogeny.data

Class NodeVisualization

java.lang.Object

org.forester.phylogeny.data.NodeVisualization

All Implemented Interfaces:

PhylogenyData

public class NodeVisualization
extends java.lang.Object
implements PhylogenyData

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NodeVisualization.NodeFill
static class	NodeVisualization.NodeShape

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	SIZE_REF
static java.lang.String	SIZE_TYPE

Constructor Summary

Constructors

Constructor and Description
NodeVisualization()
NodeVisualization(NodeVisualization.NodeShape shape, NodeVisualization.NodeFill fill_type, java.awt.Color border_color, java.awt.Color fill_color, double size, double transparancy)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.StringBuffer	asSimpleText()
java.lang.StringBuffer	asText()
PhylogenyData	copy() Creates a new PhylogenyData object with identical values as this PhylogenyData.
java.awt.Color	getBorderColor()
java.awt.Color	getFillColor()
NodeVisualization.NodeFill	getFillType()
NodeVisualization.NodeShape	getShape()
double	getSize()
double	getTransparancy()
boolean	isEqual(PhylogenyData data) Compares this PhylogenyData to PhylogenyData data.
void	setBorderColor(java.awt.Color border_color)
void	setFillColor(java.awt.Color fill_color)
void	setFillType(NodeVisualization.NodeFill fill_type)
void	setShape(NodeVisualization.NodeShape shape)
void	setSize(double size)
void	setTransparancy(double transparancy)
java.lang.StringBuffer	toNHX()
void	toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) Writes a phyloXML representation of this phylogeny data.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

SIZE_REF

public static final java.lang.String SIZE_REF

See Also:

Constant Field Values

SIZE_TYPE

public static final java.lang.String SIZE_TYPE

See Also:

Constant Field Values

Constructor Detail

NodeVisualization

public NodeVisualization()

NodeVisualization

public NodeVisualization(NodeVisualization.NodeShape shape,
                 NodeVisualization.NodeFill fill_type,
                 java.awt.Color border_color,
                 java.awt.Color fill_color,
                 double size,
                 double transparancy)

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

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

getBorderColor

public java.awt.Color getBorderColor()

getFillColor

public java.awt.Color getFillColor()

getFillType

public NodeVisualization.NodeFill getFillType()

getShape

public NodeVisualization.NodeShape getShape()

getSize

public double getSize()

getTransparancy

public double getTransparancy()

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

setBorderColor

public void setBorderColor(java.awt.Color border_color)

setFillColor

public void setFillColor(java.awt.Color fill_color)

setFillType

public void setFillType(NodeVisualization.NodeFill fill_type)

setShape

public void setShape(NodeVisualization.NodeShape shape)

setSize

public void setSize(double size)

setTransparancy

public void setTransparancy(double transparancy)

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object