org.forester.archaeopteryx.phylogeny.data

Class RenderableDomainArchitecture

java.lang.Object

org.forester.phylogeny.data.DomainArchitecture

org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture

All Implemented Interfaces:

RenderablePhylogenyData, PhylogenyData

public final class RenderableDomainArchitecture
extends DomainArchitecture
implements RenderablePhylogenyData

Field Summary

Fields inherited from class org.forester.phylogeny.data.DomainArchitecture

NHX_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
RenderableDomainArchitecture(DomainArchitecture domain_structure, Configuration configuration)

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.
ProteinDomain	getDomain(int i)
java.util.SortedMap<java.math.BigDecimal,ProteinDomain>	getDomains()
int	getNumberOfDomains()
java.awt.Dimension	getOriginalSize()
java.lang.Object	getParameter()
double	getRenderingFactorWidth()
java.awt.Dimension	getRenderingSize()
int	getTotalLength()
boolean	isEqual(PhylogenyData data) Returns true if the names and the order of the domains match (domain and linker lengths are ignored).
void	render(double x1, double 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).
static void	setColorMap(java.util.Map<java.lang.String,java.awt.Color> domain_colors)
void	setParameter(double e_value_threshold_exp)
void	setRenderingFactorWidth(double rendering_factor_width)
void	setRenderingHeight(double rendering_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 org.forester.phylogeny.data.DomainArchitecture

addDomain, setTotalLength, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

RenderableDomainArchitecture

public RenderableDomainArchitecture(DomainArchitecture domain_structure,
                            Configuration configuration)

Method Detail

asSimpleText

public java.lang.StringBuffer asSimpleText()

Specified by:

asSimpleText in interface PhylogenyData

Overrides:

asSimpleText in class DomainArchitecture

asText

public java.lang.StringBuffer asText()

Specified by:

asText in interface PhylogenyData

Overrides:

asText in class DomainArchitecture

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

Overrides:

copy in class DomainArchitecture

Returns:

a ~deep~ copy of this PhylogenyData

getDomain

public ProteinDomain getDomain(int i)

Overrides:

getDomain in class DomainArchitecture

getDomains

public java.util.SortedMap<java.math.BigDecimal,ProteinDomain> getDomains()

Overrides:

getDomains in class DomainArchitecture

getNumberOfDomains

public int getNumberOfDomains()

Overrides:

getNumberOfDomains in class DomainArchitecture

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()

Overrides:

getTotalLength in class DomainArchitecture

isEqual

public boolean isEqual(PhylogenyData data)

Description copied from class: DomainArchitecture

Returns true if the names and the order of the domains match (domain and linker lengths are ignored).

Specified by:

isEqual in interface PhylogenyData

Overrides:

isEqual in class DomainArchitecture

Returns:

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

render

public void render(double x1,
          double 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 e_value_threshold_exp)

Specified by:

setParameter in interface RenderablePhylogenyData

setRenderingFactorWidth

public void setRenderingFactorWidth(double rendering_factor_width)

setRenderingHeight

public void setRenderingHeight(double rendering_height)

Specified by:

setRenderingHeight in interface RenderablePhylogenyData

toNHX

public java.lang.StringBuffer toNHX()

Specified by:

toNHX in interface PhylogenyData

Overrides:

toNHX in class DomainArchitecture

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

Overrides:

toPhyloXML in class DomainArchitecture

Throws:

java.io.IOException

setColorMap

public static void setColorMap(java.util.Map<java.lang.String,java.awt.Color> domain_colors)