Class RenderableDomainArchitecture

Method Details

• setColorMap

  public static void setColorMap(Map<String,Color> domain_colors)

• 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<BigDecimal,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 float getRenderingFactorWidth()

• getRenderingSize

  public 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(float x1, float 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

• setParameter

  public void setParameter(double e_value_threshold_exp)

  Specified by:

  setParameter in interface RenderablePhylogenyData

• setRenderingFactorWidth

  public void setRenderingFactorWidth(float rendering_factor_width)

• setRenderingHeight

  public void setRenderingHeight(float 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