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
RenderableDomainArchitecture
public RenderableDomainArchitecture(DomainArchitecture domain_structure)
asSimpleText
public StringBuffer asSimpleText()
- Specified by:
asSimpleText
in interface PhylogenyData
- Overrides:
asSimpleText
in class DomainArchitecture
asText
public 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 SortedMap<Double,ProteinDomain> getDomains()
- Overrides:
getDomains
in class DomainArchitecture
getNumberOfDomains
public int getNumberOfDomains()
- Overrides:
getNumberOfDomains
in class DomainArchitecture
getOriginalSize
public Dimension getOriginalSize()
- Specified by:
getOriginalSize
in interface RenderablePhylogenyData
getParameter
public Object getParameter()
- Specified by:
getParameter
in interface RenderablePhylogenyData
getRenderingFactorWidth
public double getRenderingFactorWidth()
getRenderingSize
public Dimension getRenderingSize()
- Specified by:
getRenderingSize
in interface RenderablePhylogenyData
getTotalLength
public int getTotalLength()
- Overrides:
getTotalLength
in class DomainArchitecture
isDisplayDomainNames
public boolean isDisplayDomainNames()
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,
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
setDisplayDomainNames
public void setDisplayDomainNames(boolean display_domain_names)
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 StringBuffer toNHX()
- Specified by:
toNHX
in interface PhylogenyData
- Overrides:
toNHX
in class DomainArchitecture
toPhyloXML
public void toPhyloXML(Writer writer,
int level,
String indentation)
throws 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:
IOException
setColorMap
public static void setColorMap(Map<String,Color> domain_colors)