org.forester.phylogeny
Class PhylogenyNode

java.lang.Object
  org.forester.phylogeny.PhylogenyNode

All Implemented Interfaces:

java.lang.Comparable<PhylogenyNode>, PhylogenyNodeI

public final class PhylogenyNode
extends java.lang.Object
implements PhylogenyNodeI, java.lang.Comparable<PhylogenyNode>

Warning. Implementation of method 'compareTo' only looks at node name. Thus, use of this class in SortedSets might lead to unexpected behavior.

Nested Class Summary

Nested classes/interfaces inherited from interface org.forester.phylogeny.PhylogenyNodeI

PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE

Constructor Summary

PhylogenyNode()
Default constructor for PhylogenyNode.

Method Summary

void	addAsChild(PhylogenyNodeI node) Adds PhylogenyNode n to the list of child nodes and sets the _parent of n to this.
int	compareTo(PhylogenyNode o)
PhylogenyNode	copyNodeData() Returns a new PhylogenyNode which has its data copied from this PhylogenyNode.
PhylogenyNode	copyNodeDataShallow() Returns a new PhylogenyNode which has the same data as this PhylogenyNode.
static PhylogenyNode	createInstanceFromNhxString(java.lang.String nhx)
static PhylogenyNode	createInstanceFromNhxString(java.lang.String nhx, PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction)
static PhylogenyNode	createInstanceFromNhxString(java.lang.String nhx, PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores)
boolean	equals(java.lang.Object o)
java.util.List<PhylogenyNode>	getAllDescendants()
java.util.List<PhylogenyNode>	getAllExternalDescendants() Returns a List containing references to all external children of this PhylogenyNode.
java.util.List<java.lang.String>	getAllExternalDescendantsNames() Returns a List containing references to all names of the external children of this PhylogenyNode.
BranchData	getBranchData()
PhylogenyNode	getChildNode(int i) This return child node n of this node.
PhylogenyNode	getChildNode1() Convenience method.
PhylogenyNode	getChildNode2() Convenience method.
int	getChildNodeIndex() This gets the child node index of this node.
int	getChildNodeIndex(PhylogenyNode parent) This gets the child node index of this node, given that parent is its parent
java.util.List<PhylogenyNode>	getDescendants()
double	getDistanceToParent() Returns the length of the branch leading to the _parent of this PhylogenyNode (double).
PhylogenyNode	getFirstChildNode() Convenience method.
int	getId() Returns the ID (int) of this PhylogenyNode.
byte	getIndicator() Returns the _indicator value of this PhylogenyNode.
PhylogenyNode	getLastChildNode() Convenience method.
PhylogenyNode	getLink() Returns a refernce to the linked PhylogenyNode of this PhylogenyNode.
java.lang.String	getName() Returns the name of this node.
PhylogenyNode	getNextExternalNode() Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.
PhylogenyNode	getNextExternalNodeWhileTakingIntoAccountCollapsedNodes()
static int	getNodeCount() Returns the total number of all Nodes created so far.
NodeData	getNodeData()
int	getNumberOfDescendants()
int	getNumberOfExternalNodes() Returns the total number of external Nodes originating from this PhylogenyNode (int).
int	getNumberOfParents()
PhylogenyNode	getParent() Returns a refernce to the parent PhylogenyNode of this PhylogenyNode.
PhylogenyNode	getPreviousExternalNode() Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.
float	getXcoord() Used for drawing of Trees.
float	getXSecondary()
float	getYcoord() Used for drawing of Trees.
float	getYSecondary()
int	hashCode()
boolean	isCollapse() Returns whether this PhylogenyNode should be drawn as collapsed.
boolean	isDuplication() Returns true if this PhylogenyNode represents a _duplication event, false otherwise.
boolean	isExternal() Checks whether this PhylogenyNode is external (tip).
boolean	isFirstChildNode() DOCUMENT ME!
boolean	isFirstExternalNode() DOCUMENT ME!
boolean	isHasAssignedEvent() Returns whether a _duplication or speciation event has been assigned for this PhylogenyNode.
boolean	isInternal() Checks whether this PhylogenyNode is internal (tip).
boolean	isLastChildNode() Returns true if this node is the last child node of its _parent.
boolean	isLastExternalNode() DOCUMENT ME!
boolean	isRoot() Checks whether this PhylogenyNode is a root.
boolean	isSpeciation()
void	preorderPrint() Prints to the console the subtree originating from this PhylogenyNode in preorder.
void	removeChildNode(int i)
void	removeChildNode(PhylogenyNode remove_me)
void	removeConnections()
void	setBranchData(BranchData branch_data)
void	setChild1(PhylogenyNode n) Sets the first child PhylogenyNode of this PhylogenyNode to n.
void	setChild2(PhylogenyNode n) Sets the second child PhylogenyNode of this PhylogenyNode to n.
void	setChildNode(int i, PhylogenyNode node) Inserts PhylogenyNode n at the specified position i into the list of child nodes.
void	setCollapse(boolean b) Sets whether this PhylogenyNode should be drawn as collapsed.
void	setDistanceToParent(double d) Sets the length of the branch leading to the _parent of this PhylogenyNode to double d.
protected void	setId(int i) Sets the Id of this PhylogenyNode to i.
void	setIndicator(byte i) Sets the _indicator value of this PhylogenyNode to i.
void	setLink(PhylogenyNode n) Sets the linked PhylogenyNode of this PhylogenyNode to n.
void	setName(java.lang.String node_name) Sets the name of this node.
void	setParent(PhylogenyNode n) Sets the _parent PhylogenyNode of this PhylogenyNode to n.
void	setSumExtNodes(int i) Sets the total number of external Nodes originating from this PhylogenyNode to i (int).
void	setXcoord(float x) Used for drawing of Trees.
void	setXSecondary(float x_secondary)
void	setYcoord(float y) Used for drawing of Trees.
void	setYSecondary(float y_secondary)
void	swapChildren() Swaps the the two childern of a PhylogenyNode node of this Phylogeny.
java.lang.String	toNewHampshire(boolean simple_nh, boolean write_distance_to_parent, PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
java.lang.String	toNewHampshireX() Converts this PhylogenyNode to a New Hampshire X (NHX) String representation.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

PhylogenyNode

public PhylogenyNode()

Default constructor for PhylogenyNode.

Method Detail

removeConnections

public void removeConnections()

addAsChild

public final void addAsChild(PhylogenyNodeI node)

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

Specified by:

addAsChild in interface PhylogenyNodeI

Parameters:

n - the PhylogenyNode to add

compareTo

public final int compareTo(PhylogenyNode o)

Specified by:

compareTo in interface java.lang.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(java.lang.Object o)

Overrides:

equals in class java.lang.Object

getAllExternalDescendants

public final java.util.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 java.util.List<java.lang.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.

Specified by:

getChildNode in interface PhylogenyNodeI

Parameters:

n - the index of the child to get

Returns:

the child node with index n

Throws:

java.lang.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:

java.lang.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:

java.lang.UnsupportedOperationException - if this node is a root node

getDescendants

public final java.util.List<PhylogenyNode> getDescendants()

getDistanceToParent

public final double getDistanceToParent()

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

Specified by:

getDistanceToParent in interface PhylogenyNodeI

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

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.

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()

getId

public final int getId()

Returns the ID (int) of this PhylogenyNode.

Specified by:

getId in interface PhylogenyNodeI

getName

public final java.lang.String getName()

Returns the name of this node.

Specified by:

getName in interface PhylogenyNodeI

getAllDescendants

public final java.util.List<PhylogenyNode> getAllDescendants()

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 java.lang.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.

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()

DOCUMENT ME!

Returns:

DOCUMENT ME!

isFirstExternalNode

public final boolean isFirstExternalNode()

DOCUMENT ME!

Returns:

DOCUMENT ME!

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()

DOCUMENT ME!

Returns:

DOCUMENT ME!

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)

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.

Specified by:

setDistanceToParent in interface PhylogenyNodeI

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(java.lang.String node_name)

Sets the name of this node.

Specified by:

setName in interface PhylogenyNodeI

setId

protected final void setId(int 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.

setParent

public final void setParent(PhylogenyNode n)

Sets the _parent PhylogenyNode of this PhylogenyNode to n.

Specified by:

setParent in interface PhylogenyNodeI

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)

toNewHampshire

public final java.lang.String toNewHampshire(boolean simple_nh,
                                             boolean write_distance_to_parent,
                                             PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)

swapChildren

public final void swapChildren()
                        throws java.lang.RuntimeException

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

Throws:

java.lang.RuntimeException

toNewHampshireX

public final java.lang.String toNewHampshireX()

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

toString

public final java.lang.String toString()

Overrides:

toString in class java.lang.Object

getNodeCount

public static final int getNodeCount()

Returns the total number of all Nodes created so far.

Returns:

total number of Nodes (int)

createInstanceFromNhxString

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

Throws:

NHXFormatException

PhyloXmlDataFormatException

createInstanceFromNhxString

public static PhylogenyNode createInstanceFromNhxString(java.lang.String nhx,
                                                        PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction)
                                                 throws NHXFormatException,
                                                        PhyloXmlDataFormatException

Throws:

NHXFormatException

PhyloXmlDataFormatException

createInstanceFromNhxString

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

Throws:

NHXFormatException

PhyloXmlDataFormatException