Class RenderableMsaSequence

Method Details

• asSimpleText

  public StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• asText

  public StringBuffer asText()

  Specified by:

  asText in interface PhylogenyData

• clone

  public Object clone()

  Overrides:

  clone in class Object

• 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

  Returns:

  a ~deep~ copy of this PhylogenyData

• 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()

• 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 interface PhylogenyData

  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 parameter)

  Specified by:

  setParameter in interface RenderablePhylogenyData

• setRenderingFactorWidth

  public void setRenderingFactorWidth(double rendering_factor_width)

• setRenderingHeight

  public void setRenderingHeight(float height)

  Specified by:

  setRenderingHeight in interface RenderablePhylogenyData

• toNHX

  public StringBuffer toNHX()

  Specified by:

  toNHX in interface PhylogenyData

• 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

  Throws:

  IOException

• createInstance

  public static RenderableMsaSequence createInstance(String seq, String type, Configuration configuration)