org.forester.phylogeny
Class Phylogeny

java.lang.Object
  org.forester.phylogeny.Phylogeny

public class Phylogeny
extends java.lang.Object

Field Summary

static boolean

ALLOW_MULTIPLE_PARENTS_DEFAULT

Constructor Summary

Phylogeny()
Default Phylogeny constructor.

Method Summary

void	addAsChild(PhylogenyNode parent) Adds this Phylogeny to the list of child nodes of PhylogenyNode parent and sets the parent of this to parent.
void	addAsSibling(PhylogenyNode sibling)
double	calculateSubtreeHeight(PhylogenyNode n) This calculates the height of the subtree emanating at n for rooted, tree-shaped phylogenies
void	clearHashIdToNodeMap()
Phylogeny	copy() Returns a deep copy of this Phylogeny.
Phylogeny	copy(PhylogenyNode source) Returns a deep copy of this Phylogeny.
Phylogeny	copyShallow() Returns a shallow copy of this Phylogeny.
Phylogeny	copyShallow(PhylogenyNode source)
void	deleteSubtree(PhylogenyNode remove_us, boolean collapse_resulting_node_with_one_desc) Need to call clearHashIdToNodeMap() afterwards (not done automatically to allow client multiple deletions in linear time).
void	externalNodesHaveChanged()
java.lang.String[]	getAllExternalNodeNames()
Confidence	getConfidence()
java.lang.String	getDescription()
java.lang.String	getDistanceUnit()
java.util.List<PhylogenyNode>	getExternalNodes() Warning.
PhylogenyNode	getFirstExternalNode() Returns the first external PhylogenyNode.
double	getHeight() This calculates the height for rooted, tree-shaped phylogenies.
Identifier	getIdentifier()
java.lang.String	getName() Returns the name of this Phylogeny.
PhylogenyNode	getNode(int id) Finds the PhylogenyNode of this Phylogeny which has a matching ID number.
PhylogenyNode	getNode(java.lang.String name) Returns a PhylogenyNode of this Phylogeny which has a matching name.
int	getNodeCount() This is time-inefficient since it runs a iterator each time it is called.
java.util.List<PhylogenyNode>	getNodes(java.lang.String name) Returns a List with references to all Nodes of this Phylogeny which have a matching name.
java.util.List<PhylogenyNode>	getNodesViaSequenceName(java.lang.String seq_name)
java.util.List<PhylogenyNode>	getNodesViaTaxonomyCode(java.lang.String taxonomy_code)
java.util.List<PhylogenyNode>	getNodesWithMatchingSpecies(java.lang.String specname) Returns a Vector with references to all Nodes of this Phylogeny which have a matching species name.
PhylogenyNode	getNodeViaSequenceName(java.lang.String seq_name)
PhylogenyNode	getNodeViaTaxonomyCode(java.lang.String taxonomy_code)
int	getNumberOfBranches()
int	getNumberOfExternalNodes() Returns the sum of external Nodes of this Phylogeny (int).
java.util.List<PhylogenyNode>	getParalogousNodes(PhylogenyNode n, java.lang.String[] taxonomyCodeRange) Returns all paralogs of the external PhylogenyNode n of this Phylogeny.
java.util.Collection<SequenceRelation.SEQUENCE_RELATION_TYPE>	getRelevantSequenceRelationTypes()
PhylogenyNode	getRoot() Returns the root PhylogenyNode of this Phylogeny.
java.util.Collection<Sequence>	getSequenceRelationQueries()
java.lang.String	getType()
void	init() Deletes this Phylogeny.
boolean	isCompletelyBinary() Returns whether this is a completely binary tree (i.e.
boolean	isEmpty() Checks whether a Phylogeny object is deleted (or empty).
boolean	isRerootable()
boolean	isRooted() Returns true is this Phylogeny is rooted.
boolean	isTree()
PhylogenyNodeIterator	iteratorExternalForward()
PhylogenyNodeIterator	iteratorLevelOrder()
PhylogenyNodeIterator	iteratorPostorder()
PhylogenyNodeIterator	iteratorPreorder()
void	levelOrderReID() Resets the ID numbers of the nodes of this Phylogeny in level order, starting with start_label (for the root).
void	preOrderReId()
void	printExtNodes() Prints descriptions of all external Nodes of this Phylogeny to System.out.
void	recalculateNumberOfExternalDescendants(boolean consider_collapsed_nodes) (Re)counts the number of children for each PhylogenyNode of this Phylogeny.
void	reRoot(int id) Places the root of this Phylogeny on the parent branch of the PhylogenyNode with a corresponding ID.
void	reRoot(PhylogenyBranch b) Places the root of this Phylogeny on Branch b.
void	reRoot(PhylogenyNode n) Places the root of this Phylogeny on the parent branch PhylogenyNode n.
void	reRoot(PhylogenyNode n, double distance_n_to_parent)
void	setAllNodesToNotCollapse() Sets all Nodes of this Phylogeny to not-collapsed.
void	setConfidence(Confidence confidence)
void	setDescription(java.lang.String description)
void	setDistanceUnit(java.lang.String _distance_unit)
void	setIdentifier(Identifier identifier)
void	setIndicatorsToZero() Sets the indicators of all Nodes of this Phylogeny to 0.
void	setName(java.lang.String s) Sets the name of this Phylogeny to s.
void	setRelevantSequenceRelationTypes(java.util.Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> types)
void	setRerootable(boolean rerootable)
void	setRoot(PhylogenyNode n)
void	setRooted(boolean b) Sets whether this Phylogeny is rooted or not.
void	setSequenceRelationQueries(java.util.Collection<Sequence> sequencesByName)
void	setType(java.lang.String type)
java.lang.String	toNewHampshire()
java.lang.String	toNewHampshire(boolean simple_nh, PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style)
java.lang.String	toNewHampshireX()
java.lang.String	toNexus()
java.lang.String	toNexus(PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)
java.lang.String	toPhyloXML(int phyloxml_level)
java.lang.String	toString() Converts this Phylogeny to a New Hampshire X (String) representation.
void	unRoot() Removes the root PhylogenyNode this Phylogeny.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

ALLOW_MULTIPLE_PARENTS_DEFAULT

public static final boolean ALLOW_MULTIPLE_PARENTS_DEFAULT

See Also:

Constant Field Values

Constructor Detail

Phylogeny

public Phylogeny()

Default Phylogeny constructor. Constructs an empty Phylogeny.

Method Detail

addAsChild

public void addAsChild(PhylogenyNode parent)

Adds this Phylogeny to the list of child nodes of PhylogenyNode parent and sets the parent of this to parent.

Parameters:

n - the PhylogenyNode to add

addAsSibling

public void addAsSibling(PhylogenyNode sibling)

calculateSubtreeHeight

public double calculateSubtreeHeight(PhylogenyNode n)

This calculates the height of the subtree emanating at n for rooted, tree-shaped phylogenies

Parameters:

n - the root-node of a subtree

Returns:

the height of the subtree emanating at n

copy

public Phylogeny copy()

Returns a deep copy of this Phylogeny.

(The resulting Phylogeny has its references in the external nodes corrected, if they are lacking/obsolete in this.)

copyShallow

public Phylogeny copyShallow()

Returns a shallow copy of this Phylogeny.

(The resulting Phylogeny has its references in the external nodes corrected, if they are lacking/obsolete in this.)

copyShallow

public Phylogeny copyShallow(PhylogenyNode source)

copy

public Phylogeny copy(PhylogenyNode source)

Returns a deep copy of this Phylogeny.

(The resulting Phylogeny has its references in the external nodes corrected, if they are lacking/obsolete in this.)

deleteSubtree

public void deleteSubtree(PhylogenyNode remove_us,
                          boolean collapse_resulting_node_with_one_desc)

Need to call clearHashIdToNodeMap() afterwards (not done automatically to allow client multiple deletions in linear time). Need to call 'recalculateNumberOfExternalDescendants(boolean)' after this if tree is to be displayed.

Parameters:

remove_us - the parent node of the subtree to be deleted

externalNodesHaveChanged

public void externalNodesHaveChanged()

getAllExternalNodeNames

public java.lang.String[] getAllExternalNodeNames()

getConfidence

public Confidence getConfidence()

getDescription

public java.lang.String getDescription()

getDistanceUnit

public java.lang.String getDistanceUnit()

getExternalNodes

public java.util.List<PhylogenyNode> getExternalNodes()

Warning. The order of the returned nodes is random -- and hence cannot be relied on.

Returns:

Unordered set of PhylogenyNode

getFirstExternalNode

public PhylogenyNode getFirstExternalNode()

Returns the first external PhylogenyNode.

getHeight

public double getHeight()

This calculates the height for rooted, tree-shaped phylogenies. The height is the longest distance from the root to an external node. Please note. Child nodes of collapsed nodes are ignored -- which is useful for display purposes but might be misleading for other applications.

Returns:

the height for rooted, tree-shaped phylogenies

getIdentifier

public Identifier getIdentifier()

getName

public java.lang.String getName()

Returns the name of this Phylogeny.

getNode

public PhylogenyNode getNode(int id)
                      throws java.util.NoSuchElementException

Finds the PhylogenyNode of this Phylogeny which has a matching ID number.

Returns:

PhylogenyNode with matching ID, null if not found

Throws:

java.util.NoSuchElementException

getNode

public PhylogenyNode getNode(java.lang.String name)

Returns a PhylogenyNode of this Phylogeny which has a matching name. Throws an Exception if seqname is not present in this or not unique.

Parameters:

name - name (String) of PhylogenyNode to find

Returns:

PhylogenyNode with matchin name

getNodes

public java.util.List<PhylogenyNode> getNodes(java.lang.String name)

Returns a List with references to all Nodes of this Phylogeny which have a matching name.

Parameters:

name - name (String) of Nodes to find

Returns:

Vector of references to Nodes of this Phylogeny with matching names

See Also:

getNodesWithMatchingSpecies(String)

getNodesViaSequenceName

public java.util.List<PhylogenyNode> getNodesViaSequenceName(java.lang.String seq_name)

getNodesViaTaxonomyCode

public java.util.List<PhylogenyNode> getNodesViaTaxonomyCode(java.lang.String taxonomy_code)

getNodesWithMatchingSpecies

public java.util.List<PhylogenyNode> getNodesWithMatchingSpecies(java.lang.String specname)

Returns a Vector with references to all Nodes of this Phylogeny which have a matching species name.

Parameters:

specname - species name (String) of Nodes to find

Returns:

Vector of references to Nodes of this Phylogeny with matching species names.

See Also:

getNodes(String)

getNodeViaSequenceName

public PhylogenyNode getNodeViaSequenceName(java.lang.String seq_name)

getNodeViaTaxonomyCode

public PhylogenyNode getNodeViaTaxonomyCode(java.lang.String taxonomy_code)

getNodeCount

public int getNodeCount()

This is time-inefficient since it runs a iterator each time it is called.

getNumberOfBranches

public int getNumberOfBranches()

getNumberOfExternalNodes

public int getNumberOfExternalNodes()

Returns the sum of external Nodes of this Phylogeny (int).

getParalogousNodes

public java.util.List<PhylogenyNode> getParalogousNodes(PhylogenyNode n,
                                                        java.lang.String[] taxonomyCodeRange)

Returns all paralogs of the external PhylogenyNode n of this Phylogeny. paralog are returned as List of node references.

PRECONDITION: This tree must be binary and rooted, and speciation - duplication need to be assigned for each of its internal Nodes.

Returns null if this Phylogeny is empty or if n is internal.

(Last modified: 11/22/00) Olivier CHABROL : olivier.chabrol@univ-provence.fr

Parameters:

n - external PhylogenyNode whose orthologs are to be returned

Returns:

Vector of references to all orthologous Nodes of PhylogenyNode n of this Phylogeny, null if this Phylogeny is empty or if n is internal

getRelevantSequenceRelationTypes

public java.util.Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> getRelevantSequenceRelationTypes()

getRoot

public PhylogenyNode getRoot()

Returns the root PhylogenyNode of this Phylogeny.

getSequenceRelationQueries

public java.util.Collection<Sequence> getSequenceRelationQueries()

getType

public java.lang.String getType()

clearHashIdToNodeMap

public void clearHashIdToNodeMap()

init

public void init()

Deletes this Phylogeny.

isCompletelyBinary

public boolean isCompletelyBinary()

Returns whether this is a completely binary tree (i.e. all internal nodes are bifurcations).

isEmpty

public boolean isEmpty()

Checks whether a Phylogeny object is deleted (or empty).

Returns:

true if the tree is deleted (or empty), false otherwise

isRerootable

public boolean isRerootable()

isRooted

public boolean isRooted()

Returns true is this Phylogeny is rooted.

isTree

public boolean isTree()

iteratorExternalForward

public PhylogenyNodeIterator iteratorExternalForward()

iteratorLevelOrder

public PhylogenyNodeIterator iteratorLevelOrder()

iteratorPostorder

public PhylogenyNodeIterator iteratorPostorder()

iteratorPreorder

public PhylogenyNodeIterator iteratorPreorder()

levelOrderReID

public void levelOrderReID()

Resets the ID numbers of the nodes of this Phylogeny in level order, starting with start_label (for the root).
WARNING. After this method has been called, node IDs are no longer unique.

preOrderReId

public void preOrderReId()

printExtNodes

public void printExtNodes()

Prints descriptions of all external Nodes of this Phylogeny to System.out.

recalculateNumberOfExternalDescendants

public void recalculateNumberOfExternalDescendants(boolean consider_collapsed_nodes)

(Re)counts the number of children for each PhylogenyNode of this Phylogeny. As an example, this method needs to be called after a Phylogeny has been reRooted and it is to be displayed.

Parameters:

consider_collapsed_nodes - set to true to take into account collapsed nodes (collapsed nodes have 1 child).

reRoot

public void reRoot(int id)

Places the root of this Phylogeny on the parent branch of the PhylogenyNode with a corresponding ID. The new root is always placed on the middle of the branch. If the resulting reRooted Phylogeny is to be used any further, in most cases the following methods have to be called on the resulting Phylogeny:

recalculateNumberOfExternalDescendants(boolean)

recalculateAndReset()

Parameters:

id - ID (int) of PhylogenyNode of this Phylogeny

reRoot

public void reRoot(PhylogenyBranch b)

Places the root of this Phylogeny on Branch b. The new root is always placed on the middle of the branch b.

reRoot

public void reRoot(PhylogenyNode n)

Places the root of this Phylogeny on the parent branch PhylogenyNode n. The new root is always placed on the middle of the branch.

If the resulting reRooted Phylogeny is to be used any further, in most cases the following three methods have to be called on the resulting Phylogeny:

• recalculateNumberOfExternalDescendants(boolean)
• recalculateAndReset()

(Last modified: 10/01/01)

Parameters:

n - PhylogenyNode of this Phylogeny\

reRoot

public void reRoot(PhylogenyNode n,
                   double distance_n_to_parent)

setAllNodesToNotCollapse

public void setAllNodesToNotCollapse()

Sets all Nodes of this Phylogeny to not-collapsed.

In most cases methods adjustNodeCount(false) and recalculateAndReset() need to be called after this method has been called.

setConfidence

public void setConfidence(Confidence confidence)

setDescription

public void setDescription(java.lang.String description)

setDistanceUnit

public void setDistanceUnit(java.lang.String _distance_unit)

setIdentifier

public void setIdentifier(Identifier identifier)

setIndicatorsToZero

public void setIndicatorsToZero()

Sets the indicators of all Nodes of this Phylogeny to 0.

setName

public void setName(java.lang.String s)

Sets the name of this Phylogeny to s.

setRelevantSequenceRelationTypes

public void setRelevantSequenceRelationTypes(java.util.Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> types)

setRerootable

public void setRerootable(boolean rerootable)

setRoot

public void setRoot(PhylogenyNode n)

setRooted

public void setRooted(boolean b)

Sets whether this Phylogeny is rooted or not.

setSequenceRelationQueries

public void setSequenceRelationQueries(java.util.Collection<Sequence> sequencesByName)

setType

public void setType(java.lang.String type)

toNewHampshire

public java.lang.String toNewHampshire()

toNewHampshire

public java.lang.String toNewHampshire(boolean simple_nh,
                                       PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style)

toNewHampshireX

public java.lang.String toNewHampshireX()

toNexus

public java.lang.String toNexus(PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)

toNexus

public java.lang.String toNexus()

toPhyloXML

public java.lang.String toPhyloXML(int phyloxml_level)

toString

public java.lang.String toString()

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

Overrides:

toString in class java.lang.Object

Returns:

New Hampshire X (String) representation of this

See Also:

toNewHampshireX()

unRoot

public void unRoot()
            throws java.lang.RuntimeException

Removes the root PhylogenyNode this Phylogeny.

Throws:

java.lang.RuntimeException