Class RenderableDomainArchitecture
- java.lang.Object
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- org.forester.phylogeny.data.DomainArchitecture
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- org.forester.archaeopteryx.phylogeny.data.RenderableDomainArchitecture
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- All Implemented Interfaces:
RenderablePhylogenyData
,PhylogenyData
public final class RenderableDomainArchitecture extends DomainArchitecture implements RenderablePhylogenyData
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Field Summary
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Fields inherited from class org.forester.phylogeny.data.DomainArchitecture
NHX_SEPARATOR
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Constructor Summary
Constructors Constructor Description RenderableDomainArchitecture(DomainArchitecture domain_structure)
RenderableDomainArchitecture(DomainArchitecture domain_structure, java.lang.String node_name)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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()
float
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(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).static void
setColorMap(java.util.Map<java.lang.String,java.awt.Color> domain_colors)
void
setParameter(double e_value_threshold_exp)
void
setRenderingFactorWidth(float rendering_factor_width)
void
setRenderingHeight(float 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
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Constructor Detail
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RenderableDomainArchitecture
public RenderableDomainArchitecture(DomainArchitecture domain_structure)
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RenderableDomainArchitecture
public RenderableDomainArchitecture(DomainArchitecture domain_structure, java.lang.String node_name)
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Method Detail
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setColorMap
public static void setColorMap(java.util.Map<java.lang.String,java.awt.Color> domain_colors)
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
- Overrides:
asSimpleText
in classDomainArchitecture
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
- Overrides:
asText
in classDomainArchitecture
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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 interfacePhylogenyData
- Overrides:
copy
in classDomainArchitecture
- Returns:
- a ~deep~ copy of this PhylogenyData
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getDomain
public ProteinDomain getDomain(int i)
- Overrides:
getDomain
in classDomainArchitecture
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getDomains
public java.util.SortedMap<java.math.BigDecimal,ProteinDomain> getDomains()
- Overrides:
getDomains
in classDomainArchitecture
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getNumberOfDomains
public int getNumberOfDomains()
- Overrides:
getNumberOfDomains
in classDomainArchitecture
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getOriginalSize
public java.awt.Dimension getOriginalSize()
- Specified by:
getOriginalSize
in interfaceRenderablePhylogenyData
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getParameter
public java.lang.Object getParameter()
- Specified by:
getParameter
in interfaceRenderablePhylogenyData
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getRenderingFactorWidth
public float getRenderingFactorWidth()
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getRenderingSize
public java.awt.Dimension getRenderingSize()
- Specified by:
getRenderingSize
in interfaceRenderablePhylogenyData
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getTotalLength
public int getTotalLength()
- Overrides:
getTotalLength
in classDomainArchitecture
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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 interfacePhylogenyData
- Overrides:
isEqual
in classDomainArchitecture
- Returns:
- in general, true if and only if all fiels are exactly identical, false otherwise
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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 interfaceRenderablePhylogenyData
g
- the Graphics to render to
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setParameter
public void setParameter(double e_value_threshold_exp)
- Specified by:
setParameter
in interfaceRenderablePhylogenyData
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setRenderingFactorWidth
public void setRenderingFactorWidth(float rendering_factor_width)
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setRenderingHeight
public void setRenderingHeight(float rendering_height)
- Specified by:
setRenderingHeight
in interfaceRenderablePhylogenyData
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
- Overrides:
toNHX
in classDomainArchitecture
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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 interfacePhylogenyData
- Overrides:
toPhyloXML
in classDomainArchitecture
- Throws:
java.io.IOException
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