PhylogenyNode (Forester 1.038 API)

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

All Implemented Interfaces:

Comparable<PhylogenyNode>
```
public final class PhylogenyNode
extends Object
implements 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
Modifier and Type Class and Description

static class PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE

Nested Classes
Modifier and Type	Class and Description
`static class`	`PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE`

Constructor Summary

Constructors
Constructor and Description

PhylogenyNode()
Default constructor for PhylogenyNode.

PhylogenyNode(String node_name)

Constructors
Constructor and Description
`PhylogenyNode()` Default constructor for PhylogenyNode.
`PhylogenyNode(String node_name)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAsChild(PhylogenyNode node)` Adds PhylogenyNode n to the list of child nodes and sets the _parent of n to this.
`int`	`calculateDepth()`
`double`	`calculateDistanceToRoot()`
`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(String nhx)`
`static PhylogenyNode`	`createInstanceFromNhxString(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction)`
`static PhylogenyNode`	`createInstanceFromNhxString(String nhx, NHXParser.TAXONOMY_EXTRACTION taxonomy_extraction, boolean replace_underscores)`
`boolean`	`equals(Object o)`
`List<PhylogenyNode>`	`getAllDescendants()`
`List<PhylogenyNode>`	`getAllExternalDescendants()` Returns a List containing references to all external children of this PhylogenyNode.
`List<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
`List<PhylogenyNode>`	`getDescendants()`
`double`	`getDistanceToParent()` Returns the length of the branch leading to the _parent of this PhylogenyNode (double).
`PhylogenyNode`	`getFirstChildNode()` Convenience method.
`long`	`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.
`String`	`getName()`
`PhylogenyNode`	`getNextExternalNode()` Returns a refernce to the next external PhylogenyNode of this PhylogenyNode.
`PhylogenyNode`	`getNextExternalNodeWhileTakingIntoAccountCollapsedNodes()`
`static long`	`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`	`isEmpty()`
`boolean`	`isExternal()` Checks whether this PhylogenyNode is external (tip).
`boolean`	`isFirstChildNode()`
`boolean`	`isFirstExternalNode()`
`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()`
`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(long 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(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.
`String`	`toNewHampshire(boolean write_distance_to_parent, PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)`
`String`	`toNewHampshireX()` Converts this PhylogenyNode to a New Hampshire X (NHX) String representation.
`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.
  - PhylogenyNode
```
public PhylogenyNode(String node_name)
```
- Method Detail
  - 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)

Class PhylogenyNode

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PhylogenyNode

PhylogenyNode

Method Detail

addAsChild

calculateDepth

calculateDistanceToRoot

compareTo

copyNodeData

copyNodeDataShallow

equals

getAllDescendants

getAllExternalDescendants

getAllExternalDescendantsNames

getBranchData

getChildNode

getChildNode1

getChildNode2

getChildNodeIndex

getChildNodeIndex

getDescendants

getDistanceToParent

getFirstChildNode

getId

getIndicator

getLastChildNode

getLink

getName

getNextExternalNode

getNextExternalNodeWhileTakingIntoAccountCollapsedNodes

getNodeData

getNumberOfDescendants

getNumberOfExternalNodes

getNumberOfParents

getParent

getPreviousExternalNode

getXcoord

getXSecondary

getYcoord

getYSecondary

hashCode

isCollapse

isDuplication

isEmpty

isExternal

isFirstChildNode

isFirstExternalNode

isHasAssignedEvent

isInternal

isLastChildNode

isLastExternalNode

isRoot

isSpeciation

preorderPrint

removeChildNode

removeChildNode

removeConnections

setBranchData

setChild1

setChild2

setChildNode

setCollapse

setDistanceToParent

setIndicator

setLink

setName

setParent

setSumExtNodes

setXcoord

setXSecondary

setYcoord

setYSecondary

swapChildren

toNewHampshire

toNewHampshireX