Constructor Detail

• CladeSystem

  public CladeSystem​(IdGroup idGroup,
                     int size)

  Parameters:

  idGroup - sequence labels

  size - number of clades

Method Detail

• getCladeCount

  public int getCladeCount()

  get number of clades

• getLabelCount

  public int getLabelCount()

  get number of labels

• getCladeArray

  public boolean[][] getCladeArray()

  get clade array

• getClade

  public boolean[] getClade​(int i)

  get clade

• getIdGroup

  public IdGroup getIdGroup()

  get idGroup

• hasClade

  public boolean hasClade​(boolean[] clade)

  + test whether a clade is contained in this clade system (assuming the same leaf order)

  Parameters:

  clade - clade

• toString

  public java.lang.String toString()

  print clade system

  Overrides:

  toString in class java.lang.Object

• getCladeSystems

  public static CladeSystem[] getCladeSystems​(Tree[] trees)

  Returns:

  all clade systems for a group of trees.

• calculateCladeProbabilities

  public static void calculateCladeProbabilities​(Tree tree,
                                                 CladeSystem[] cladeSystems)

• getClades

  public static CladeSystem getClades​(IdGroup idGroup,
                                      Tree tree)

  creates a clade system from a tree (using a pre-specified order of sequences)

  Parameters:

  idGroup - sequence order for the matrix

  tree -

• getClades

  public static CladeSystem getClades​(Tree tree)

  creates a clade system from a tree (using tree-induced order of sequences)

  Parameters:

  tree -

• getClade

  public static void getClade​(IdGroup idGroup,
                              Node internalNode,
                              boolean[] clade)

  get clade for internal node

  Parameters:

  idGroup - order of labels

  internalNode - Node

  boolean - [] clade

• isSame

  public static boolean isSame​(boolean[] s1,
                               boolean[] s2)

  checks whether two clades are identical (assuming they are of the same length and use the same leaf order)

  Parameters:

  s1 - clade 1

  s2 - clade 2