Class PhylogenyNode

Method Details

• addAsChild

  public final void addAsChild(PhylogenyNode node)

  Adds PhylogenyNode n to the list of child nodes and sets the _parent of n to this.

  Parameters:

  n - the PhylogenyNode to add

• calculateDepth

  public final int calculateDepth()

• calculateDistanceToRoot

  public final double calculateDistanceToRoot()

• compareTo

  public final int compareTo(PhylogenyNode o)

  Specified by:

  compareTo in interface Comparable<PhylogenyNode>

• copyNodeData

  public final PhylogenyNode copyNodeData()

  Returns a new PhylogenyNode which has its data copied from this PhylogenyNode. Links to the other Nodes in the same Phylogeny are NOT copied (e.g. _link to _parent). Field "_link" IS copied.

  See Also:

  • getLink()

• copyNodeDataShallow

  public final PhylogenyNode copyNodeDataShallow()

  Returns a new PhylogenyNode which has the same data as this PhylogenyNode. Links to the other Nodes in the same Phylogeny are NOT copied (e.g. _link to _parent). Field "_link" IS copied.

  See Also:

  • getLink()

• equals

  public final boolean equals(Object o)

  Overrides:

  equals in class Object

• getAllDescendants

  public final List<PhylogenyNode> getAllDescendants()

• getAllExternalDescendants

  public final List<PhylogenyNode> getAllExternalDescendants()

  Returns a List containing references to all external children of this PhylogenyNode.

  Returns:

  List of references to external Nodes

• getAllExternalDescendantsNames

  public final List<String> getAllExternalDescendantsNames()

  Returns a List containing references to all names of the external children of this PhylogenyNode.

  Returns:

  List of references to names of external Nodes

• getBranchData

  public final BranchData getBranchData()

• getChildNode

  public final PhylogenyNode getChildNode(int i)

  This return child node n of this node.

  Parameters:

  n - the index of the child to get

  Returns:

  the child node with index n

  Throws:

  IllegalArgumentException - if n is out of bounds

• getChildNode1

  public final PhylogenyNode getChildNode1()

  Convenience method. Returns the first child PhylogenyNode of this PhylogenyNode.

• getChildNode2

  public final PhylogenyNode getChildNode2()

  Convenience method. Returns the second child PhylogenyNode of this PhylogenyNode.

  [last modified May 18, 2005 by CMZ]

• getChildNodeIndex

  public final int getChildNodeIndex()

  This gets the child node index of this node.

  Returns:

  the child node index of this node

  Throws:

  UnsupportedOperationException - if this node is a root node

• getChildNodeIndex

  public final int getChildNodeIndex(PhylogenyNode parent)

  This gets the child node index of this node, given that parent is its parent

  [last modified Aug 14, 2006 by CMZ]

  Returns:

  the child node index of this node

  Throws:

  UnsupportedOperationException - if this node is a root node

• getDescendants

  public final List<PhylogenyNode> getDescendants()

• getDistanceToParent

  public final double getDistanceToParent()

  Returns the length of the branch leading to the _parent of this PhylogenyNode (double).

• getFirstChildNode

  public final PhylogenyNode getFirstChildNode()

  Convenience method. Returns the first child node of this node.

  [last modified May 18, 2005 by CMZ]

  Returns:

  the first child node of this node

• getId

  public final long getId()

  Returns the ID (int) of this PhylogenyNode.

• getIndicator

  public final byte getIndicator()

  Returns the _indicator value of this PhylogenyNode.

• getLastChildNode

  public final PhylogenyNode getLastChildNode()

  Convenience method. Returns the last child node of this node.

  [last modified May 18, 2005 by CMZ]

  Returns:

  the last child node of this node

• getLink

  public final PhylogenyNode getLink()

  Returns a refernce to the linked PhylogenyNode of this PhylogenyNode. Currently, this method is only used for the speciation-_duplication assignment algorithms.

• getName

  public final String getName()

• getNextExternalNode

  public final PhylogenyNode getNextExternalNode()

  Returns a refernce to the next external PhylogenyNode of this PhylogenyNode. TODO should be in Phylogeny. Returns null if no next external node is available.

• getNextExternalNodeWhileTakingIntoAccountCollapsedNodes

  public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes()

• getNodeData

  public final NodeData getNodeData()

• getNumberOfDescendants

  public final int getNumberOfDescendants()

• getNumberOfExternalNodes

  public final int getNumberOfExternalNodes()

  Returns the total number of external Nodes originating from this PhylogenyNode (int).

• getNumberOfParents

  public final int getNumberOfParents()

• getParent

  public final PhylogenyNode getParent()

  Returns a refernce to the parent PhylogenyNode of this PhylogenyNode.

• getPreviousExternalNode

  public final PhylogenyNode getPreviousExternalNode()

  Returns a refernce to the next external PhylogenyNode of this PhylogenyNode. TODO should be in Phylogeny. Returns null if no next external node is available.

• getXcoord

  public final float getXcoord()

  Used for drawing of Trees.

• getXSecondary

  public final float getXSecondary()

• getYcoord

  public final float getYcoord()

  Used for drawing of Trees.

• getYSecondary

  public final float getYSecondary()

• hashCode

  public final int hashCode()

  Overrides:

  hashCode in class Object

• isCollapse

  public final boolean isCollapse()

  Returns whether this PhylogenyNode should be drawn as collapsed.

• isDuplication

  public final boolean isDuplication()

  Returns true if this PhylogenyNode represents a _duplication event, false otherwise.

• isEmpty

  public boolean isEmpty()

• isExternal

  public final boolean isExternal()

  Checks whether this PhylogenyNode is external (tip).

  Returns:

  true if this PhylogenyNode is external, false otherwise

• isFirstChildNode

  public final boolean isFirstChildNode()

• isFirstExternalNode

  public final boolean isFirstExternalNode()

• isHasAssignedEvent

  public final boolean isHasAssignedEvent()

  Returns whether a _duplication or speciation event has been assigned for this PhylogenyNode.

• isInternal

  public final boolean isInternal()

  Checks whether this PhylogenyNode is internal (tip).

  Returns:

  true if this PhylogenyNode is external, false otherwise

• isLastChildNode

  public final boolean isLastChildNode()

  Returns true if this node is the last child node of its _parent.

  [last modified June 01, 2005 by CMZ]

  Returns:

  true if this node is the last child node of its _parent, false otherwise

• isLastExternalNode

  public final boolean isLastExternalNode()

• isRoot

  public final boolean isRoot()

  Checks whether this PhylogenyNode is a root.

  Returns:

  true if this PhylogenyNode is the root, false otherwise

• isSpeciation

  public final boolean isSpeciation()

• preorderPrint

  public void preorderPrint()

  Prints to the console the subtree originating from this PhylogenyNode in preorder.

• removeChildNode

  public final void removeChildNode(int i)

• removeChildNode

  public final void removeChildNode(PhylogenyNode remove_me)

• removeConnections

  public void removeConnections()

• setBranchData

  public final void setBranchData(BranchData branch_data)

• setChild1

  public final void setChild1(PhylogenyNode n)

  Sets the first child PhylogenyNode of this PhylogenyNode to n.

• setChild2

  public final void setChild2(PhylogenyNode n)

  Sets the second child PhylogenyNode of this PhylogenyNode to n.

• setChildNode

  public final void setChildNode(int i, PhylogenyNode node)

  Inserts PhylogenyNode n at the specified position i into the list of child nodes. This does not allow null slots in the list of child nodes: If i is larger than the number of child nodes, n is just added to the list, not place at index i.

  Parameters:

  i - the index of position where to add the child

  n - the PhylogenyNode to add

• setCollapse

  public final void setCollapse(boolean b)

  Sets whether this PhylogenyNode should be drawn as collapsed.

• setDistanceToParent

  public final void setDistanceToParent(double d)

  Sets the length of the branch leading to the _parent of this PhylogenyNode to double d.

• setIndicator

  public final void setIndicator(byte i)

  Sets the _indicator value of this PhylogenyNode to i.

• setLink

  public final void setLink(PhylogenyNode n)

  Sets the linked PhylogenyNode of this PhylogenyNode to n. Currently, this method is only used for the speciation-_duplication assignment algorithms.

• setName

  public final void setName(String node_name)

  Sets the name of this node.

• setParent

  public final void setParent(PhylogenyNode n)

  Sets the _parent PhylogenyNode of this PhylogenyNode to n.

• setSumExtNodes

  public final void setSumExtNodes(int i)

  Sets the total number of external Nodes originating from this PhylogenyNode to i (int).

• setXcoord

  public final void setXcoord(float x)

  Used for drawing of Trees.

• setXSecondary

  public final void setXSecondary(float x_secondary)

• setYcoord

  public final void setYcoord(float y)

  Used for drawing of Trees.

• setYSecondary

  public final void setYSecondary(float y_secondary)

• swapChildren

  public final void swapChildren() throws RuntimeException

  Swaps the the two childern of a PhylogenyNode node of this Phylogeny.

  Throws:

  RuntimeException

• toNewHampshire

  public final String toNewHampshire(boolean write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)

• toNewHampshireX

  public final String toNewHampshireX()

  Converts this PhylogenyNode to a New Hampshire X (NHX) String representation.

• toString

  public final String toString()

  Overrides:

  toString in class Object

• setId

  protected final void setId(long i)

  Sets the Id of this PhylogenyNode to i. In most cases, this number should not be set to values lower than getNodeCount() -- which this method does not allow.

• createInstanceFromNhxString

  public static PhylogenyNode createInstanceFromNhxString(String nhx) throws NHXFormatException, PhyloXmlDataFormatException

  Throws:

  NHXFormatException

  PhyloXmlDataFormatException

• createInstanceFromNhxString

  public static PhylogenyNode createInstanceFromNhxString(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction) throws NHXFormatException, PhyloXmlDataFormatException

  Throws:

  NHXFormatException

  PhyloXmlDataFormatException

• createInstanceFromNhxString

  public static PhylogenyNode createInstanceFromNhxString(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores) throws NHXFormatException, PhyloXmlDataFormatException

  Throws:

  NHXFormatException

  PhyloXmlDataFormatException

• getNodeCount

  public static final long getNodeCount()

  Returns the total number of all Nodes created so far.

  Returns:

  total number of Nodes (long)