Class RenderableMsaSequence
- java.lang.Object
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- org.forester.archaeopteryx.phylogeny.data.RenderableMsaSequence
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- All Implemented Interfaces:
RenderablePhylogenyData
,PhylogenyData
public final class RenderableMsaSequence extends java.lang.Object implements RenderablePhylogenyData
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_WIDTH
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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()
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.
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Field Detail
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DEFAULT_WIDTH
public static final int DEFAULT_WIDTH
- See Also:
- Constant Field Values
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Method Detail
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asSimpleText
public java.lang.StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interfacePhylogenyData
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asText
public java.lang.StringBuffer asText()
- Specified by:
asText
in interfacePhylogenyData
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clone
public java.lang.Object clone()
- Overrides:
clone
in classjava.lang.Object
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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
- Returns:
- a ~deep~ copy of this PhylogenyData
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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 double getRenderingFactorWidth()
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getRenderingSize
public java.awt.Dimension getRenderingSize()
- Specified by:
getRenderingSize
in interfaceRenderablePhylogenyData
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getTotalLength
public int getTotalLength()
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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 interfacePhylogenyData
- 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 parameter)
- Specified by:
setParameter
in interfaceRenderablePhylogenyData
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setRenderingFactorWidth
public void setRenderingFactorWidth(double rendering_factor_width)
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setRenderingHeight
public void setRenderingHeight(float height)
- Specified by:
setRenderingHeight
in interfaceRenderablePhylogenyData
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toNHX
public java.lang.StringBuffer toNHX()
- Specified by:
toNHX
in interfacePhylogenyData
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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
- Throws:
java.io.IOException
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createInstance
public static RenderableMsaSequence createInstance(java.lang.String seq, java.lang.String type, Configuration configuration)
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