Class Phylogeny

Method Details

• 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

• clearHashIdToNodeMap

  public void clearHashIdToNodeMap()

• 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.)

• 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.)

• 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)

• 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 String[] getAllExternalNodeNames()

• getConfidence

  public Confidence getConfidence()

• getDescription

  public String getDescription()

• getDistanceUnit

  public String getDistanceUnit()

• createInstanceFromNhxString

  public static final Phylogeny createInstanceFromNhxString(String nhx) throws IOException

  Throws:

  IOException

• getExternalNodes

  public 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 String getName()

  Returns the name of this Phylogeny.

• getNode

  public PhylogenyNode getNode(long id) throws NoSuchElementException

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

  Returns:

  PhylogenyNode with matching ID, null if not found

  Throws:

  NoSuchElementException

• getNode

  public PhylogenyNode getNode(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

• getNodeCount

  public int getNodeCount()

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

• getNodes

  public List<PhylogenyNode> getNodes(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 List<PhylogenyNode> getNodesViaSequenceName(String seq_name)

• getNodesViaSequenceSymbol

  public List<PhylogenyNode> getNodesViaSequenceSymbol(String seq_name)

• getNodesViaGeneName

  public List<PhylogenyNode> getNodesViaGeneName(String seq_name)

• getNodesViaTaxonomyCode

  public List<PhylogenyNode> getNodesViaTaxonomyCode(String taxonomy_code)

• getNodesWithMatchingSpecies

  public List<PhylogenyNode> getNodesWithMatchingSpecies(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(String seq_name)

• getNodeViaTaxonomyCode

  public PhylogenyNode getNodeViaTaxonomyCode(String taxonomy_code)

• getNumberOfBranches

  public int getNumberOfBranches()

• getNumberOfInternalNodes

  public int getNumberOfInternalNodes()

• getNumberOfExternalNodes

  public int getNumberOfExternalNodes()

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

• getParalogousNodes

  public List<PhylogenyNode> getParalogousNodes(PhylogenyNode n, 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 Collection<SequenceRelation.SEQUENCE_RELATION_TYPE> getRelevantSequenceRelationTypes()

• getRoot

  public PhylogenyNode getRoot()

  Returns the root PhylogenyNode of this Phylogeny.

• getSequenceRelationQueries

  public Collection<Sequence> getSequenceRelationQueries()

• getType

  public String getType()

• 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.

• 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(long 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(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(String description)

• setDistanceUnit

  public void setDistanceUnit(String _distance_unit)

• setIdentifier

  public void setIdentifier(Identifier identifier)

• setIdToNodeMap

  public void setIdToNodeMap(HashMap<Long,PhylogenyNode> idhash)

• setIndicatorsToZero

  public void setIndicatorsToZero()

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

• setName

  public void setName(String s)

  Sets the name of this Phylogeny to s.

• setRelevantSequenceRelationTypes

  public void setRelevantSequenceRelationTypes(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(Collection<Sequence> sequencesByName)

• setType

  public void setType(String type)

• toNewHampshire

  public String toNewHampshire()

• toNewHampshire

  public String toNewHampshire(PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style)

• toNewHampshireX

  public String toNewHampshireX()

• toNexus

  public String toNexus()

• toNexus

  public String toNexus(PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE svs)

• toPhyloXML

  public String toPhyloXML(int phyloxml_level)

• toString

  public String toString()

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

  Overrides:

  toString in class Object

  Returns:

  New Hampshire X (String) representation of this

  See Also:

  • toNewHampshireX()

• unRoot

  public void unRoot() throws RuntimeException

  Removes the root PhylogenyNode this Phylogeny.

  Throws:

  RuntimeException