public final class RenderableDomainArchitecture extends DomainArchitecture implements RenderablePhylogenyData
NHX_SEPARATOR
Constructor and Description |
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RenderableDomainArchitecture(DomainArchitecture domain_structure,
Configuration configuration) |
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.
|
addDomain, setTotalLength, toString
public RenderableDomainArchitecture(DomainArchitecture domain_structure, Configuration configuration)
public java.lang.StringBuffer asSimpleText()
asSimpleText
in interface PhylogenyData
asSimpleText
in class DomainArchitecture
public java.lang.StringBuffer asText()
asText
in interface PhylogenyData
asText
in class DomainArchitecture
public PhylogenyData copy()
PhylogenyData
copy
in interface PhylogenyData
copy
in class DomainArchitecture
public ProteinDomain getDomain(int i)
getDomain
in class DomainArchitecture
public java.util.SortedMap<java.math.BigDecimal,ProteinDomain> getDomains()
getDomains
in class DomainArchitecture
public int getNumberOfDomains()
getNumberOfDomains
in class DomainArchitecture
public java.awt.Dimension getOriginalSize()
getOriginalSize
in interface RenderablePhylogenyData
public java.lang.Object getParameter()
getParameter
in interface RenderablePhylogenyData
public double getRenderingFactorWidth()
public java.awt.Dimension getRenderingSize()
getRenderingSize
in interface RenderablePhylogenyData
public int getTotalLength()
getTotalLength
in class DomainArchitecture
public boolean isEqual(PhylogenyData data)
DomainArchitecture
isEqual
in interface PhylogenyData
isEqual
in class DomainArchitecture
public void render(double x1, double y1, java.awt.Graphics2D g, TreePanel tree_panel, boolean to_pdf)
RenderablePhylogenyData
render
in interface RenderablePhylogenyData
g
- the Graphics to render topublic void setParameter(double e_value_threshold_exp)
setParameter
in interface RenderablePhylogenyData
public void setRenderingFactorWidth(double rendering_factor_width)
public void setRenderingHeight(double rendering_height)
setRenderingHeight
in interface RenderablePhylogenyData
public java.lang.StringBuffer toNHX()
toNHX
in interface PhylogenyData
toNHX
in class DomainArchitecture
public void toPhyloXML(java.io.Writer writer, int level, java.lang.String indentation) throws java.io.IOException
PhylogenyData
toPhyloXML
in interface PhylogenyData
toPhyloXML
in class DomainArchitecture
java.io.IOException
public static void setColorMap(java.util.Map<java.lang.String,java.awt.Color> domain_colors)