|
FORESTER 1.7 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--forester.tree.Tree
Field Summary | |
(package private) static int |
MAX_LENGTH
|
(package private) static long |
serialVersionUID
|
Constructor Summary | |
Tree()
Default Tree constructor. |
|
Tree(java.lang.String nh_string)
Tree constructor which constructs a Tree from the nh_string. |
Method Summary | |
(package private) void |
addNodeAndConnect(java.lang.String s1,
java.lang.String s2)
Used for building Trees. |
void |
adjustNodeCount()
(Re)counts the number of children for each Node of this Tree. |
void |
allowMoreThanBinaryNodesInNHoutput(boolean b)
Sets whether to allow more than binary Nodes in New Hampshire (NH) output. |
boolean |
areBranchLenghtsBootstraps()
Checks whether the branch length values actually are bootstrap values All external Nodes must have the same, >0, divisible by 10 branch length. |
double |
calculateRealHeight()
Calculates the real height of this (rooted) Tree -- the longest distance from root to external node. |
void |
copyBranchLengthValuesFrom(Tree t)
Modifies this Tree with the branch lenghts of Tree t. |
Tree |
copyTree()
Returns a deep copy of this Tree. |
void |
delete()
Deletes this Tree. |
void |
findExtremeLnL()
Finds the highest of all log likelihood value associated with branches of this Tree. |
java.lang.String[] |
getAllExternalSeqNames()
Returns the sequence names of all external Nodes of this Tree as array of Strings. |
Node |
getExtNode0()
Returns the first external Node. |
double |
getHighestLnL()
Returns the highest log likelihood value associated with branches of this Tree (double). |
Node |
getLastCommonAncestor(int id1,
int id2)
Finds the last common ancestor Node of two Nodes specified by their IDs id1 and id2. |
Node |
getLastCommonAncestor(java.lang.String seqname1,
java.lang.String seqname2)
Finds the last common ancestor Node of two Nodes specified by their sequence names seqname1 and seqname2. |
double |
getLowestLnL()
Returns the lowest log likelihood value associated with branches of this Tree (double). |
java.lang.String |
getName()
Returns the name of this Tree. |
Node |
getNode(int id)
Finds the Node of this Tree which has a matching ID number. |
Node |
getNode(java.lang.String seqname)
Returns a Node of this Tree which has a matching sequence name seqname. |
java.util.Vector |
getNodes(java.lang.String seqname)
Returns a Vector with references to all Nodes of this Tree which have a matching sequence name. |
java.util.Vector |
getNodesWithMatchingSpecies(java.lang.String specname)
Returns a Vector with references to all Nodes of this Tree which have a matching species name. |
int |
getNumberOfDuplications()
Returns the number of duplications of this Tree (int). |
int |
getNumberOfExtNodes()
Returns the sum of external Nodes of this Tree (int). |
java.util.Vector |
getOrthologs(Node n)
Returns all orthologs of the external Node n of this Tree. |
java.util.Vector |
getPath(Node node1,
Node node2,
boolean ret_pseudo_nodes)
Returns a Vector containing the Node IDs of all Nodes which are between two external Nodes (node2 and node1). |
double |
getRealHeight()
Returns the real height of this Tree - the longest distance from root to external node. |
Node |
getRoot()
Returns the root Node of this Tree. |
java.util.Vector |
getSiblings(Node n)
Returns a Vector of references to all external siblings and nieces of a external Node n. |
java.util.Vector |
getStrictlySrelatedNodes(Node n)
Returns all Nodes which are connected to external Node n of this Tree by a path containing only speciation events. |
void |
hashIDs()
Hashes the ID number of each Node of this Tree to its corresonding Node, in order to make method getNode( id ) run in constant time. |
boolean |
isCompletelyBinary()
Returns whether this is a completely binary tree (i.e. |
boolean |
isEmpty()
Checks whether a Tree object is deleted (or empty). |
boolean |
isRooted()
Returns true is this Tree is rooted. |
void |
levelOrderReID(int i)
Resets the ID numbers of the Nodes of this Tree in level order, starting with i (for the root). |
void |
moveBranchLenghtsToBootstrap()
Moves the values in the branch length field to the bootstrap field, for each Node of this Tree. |
int |
preorderReID(int i)
Resets the ID numbers of the Nodes of this Tree in preorder, starting with i. |
void |
printAllNodes()
Prints descriptions of all Nodes of this Tree to the console. |
void |
printExtNodes()
Prints descriptions of all external Nodes of this Tree to the console. |
void |
recalculateAndReset()
Recalculates and resets parameters of this Tree: highest and lowest lnL, real height, sum of ext Nodes. |
void |
removeExtNode(Node n)
Removes external Node from this Tree. |
void |
reRoot(int id)
Places the root of this Tree on the parent branch of the Node with a corresponding ID. |
void |
reRoot(int id,
java.lang.String s)
Places the root of this Tree on the parent branch of the Node with a corresponding ID. |
void |
reRoot(Node n)
Places the root of this Tree on the parent branch Node n. |
void |
reRoot(Node n,
java.lang.String s)
Places the root of this Tree on the parent branch Node n. |
void |
setExtNodes(int i)
Sets the sum of external Nodes of this Tree (int). |
void |
setIndicatorsToZero()
Sets the indicators of all Nodes of this Tree to 0. |
void |
setName(java.lang.String s)
Sets the name of this Tree to s. |
void |
setNumberOfDuplications(int i)
Sets the number of duplications of this Tree (int). |
void |
setRealHeight(double d)
Sets the real height of this Tree - the longest distance from root to external node. |
(package private) void |
setRoot(Node n)
|
void |
setRooted(boolean b)
Sets whether this Tree is rooted or not. |
Tree |
subTree(int id)
Returns the subtree of this Tree which has the Node with ID id as its root Node. |
void |
swapChildren(int id)
Swaps the the two childern of a Node with ID id of this Tree. |
void |
swapChildren(Node node)
Swaps the the two childern of a Node node of this Tree. |
java.lang.String |
toNewHampshire(boolean clean_nh)
Converts this Tree to a New Hampshire (String) representation. |
java.lang.String |
toNewHampshireX()
Converts this Tree to a New Hampshire X (String) representation. |
java.lang.String |
toString()
Converts this Tree to a New Hampshire X (String) representation. |
void |
unRoot()
Removes the root Node this Tree. |
void |
unRootAndTrifurcate()
Removes the root Node of this Tree and makes at least a trifurcation at its basal node. |
Methods inherited from class java.lang.Object |
|
Field Detail |
static final int MAX_LENGTH
static final long serialVersionUID
Constructor Detail |
public Tree()
public Tree(java.lang.String nh_string) throws java.lang.Exception
nh_string
- String in New Hampshire (NH) or New Hampshire X (NHX) formatMethod Detail |
public boolean isEmpty()
public void delete()
public java.util.Vector getOrthologs(Node n)
n
- external Node whose orthologs are to be returnedpublic java.util.Vector getStrictlySrelatedNodes(Node n)
n
- external Node whose strictly speciation related Nodes are to be
returnedpublic java.lang.String[] getAllExternalSeqNames()
public void removeExtNode(Node n)
n
- Node to removepublic java.util.Vector getNodes(java.lang.String seqname) throws java.lang.Exception
seqname
- Sequence name (String) of Nodes to findgetNodesWithMatchingSpecies(String)
public Node getNode(java.lang.String seqname) throws java.lang.Exception
seqname
- Sequence name (String) of Node to findpublic java.util.Vector getNodesWithMatchingSpecies(java.lang.String specname) throws java.lang.Exception
specname
- species name (String) of Nodes to findgetNodes(String)
public Node getNode(int id)
id
- ID number (int) of the Node to findpublic void swapChildren(int id)
id
- ID (int) of Nodepublic void swapChildren(Node node)
node
- a Node of this Treepublic Tree subTree(int id) throws java.lang.Exception
id
- ID (int) of Nodepublic void reRoot(int id) throws java.lang.Exception
id
- ID (int) of Node of this Treepublic void reRoot(Node n) throws java.lang.Exception
n
- Node of this Treepublic void reRoot(int id, java.lang.String s) throws java.lang.Exception
id
- ID (int) of Node of this Trees
- String describing new Nodepublic void reRoot(Node n, java.lang.String s) throws java.lang.Exception
n
- Node of this Trees
- String describing new Nodepublic void copyBranchLengthValuesFrom(Tree t) throws java.lang.Exception
t
- the Tree to copy the branch lenghts frompublic void recalculateAndReset()
public Tree copyTree()
public void unRootAndTrifurcate()
public void unRoot()
public Node getRoot()
void setRoot(Node n)
public boolean isRooted()
public void setRooted(boolean b)
public double getHighestLnL()
findExtremeLnL()
public double getLowestLnL()
findExtremeLnL()
public double getRealHeight()
calculateRealHeight()
,
setRealHeight(double)
public void setRealHeight(double d)
the
- real height of this TreecalculateRealHeight()
public int getNumberOfDuplications()
public void setNumberOfDuplications(int i)
clean_nh
- set to true for clean NH formatpublic Node getExtNode0()
public int getNumberOfExtNodes()
public void setExtNodes(int i)
public void allowMoreThanBinaryNodesInNHoutput(boolean b)
public java.lang.String getName()
public void setName(java.lang.String s)
public void printExtNodes()
public void printAllNodes()
public void setIndicatorsToZero()
public double calculateRealHeight()
Takes into account collapsed Nodes.
(Last modified: 01/18/01)
public void findExtremeLnL()
getHighestLnL()
public boolean isCompletelyBinary()
public void moveBranchLenghtsToBootstrap()
public boolean areBranchLenghtsBootstraps()
public java.lang.String toString()
toString
in class java.lang.Object
toNewHampshireX()
public java.lang.String toNewHampshire(boolean clean_nh)
clean_nh
- set to true for clean NH formatpublic java.lang.String toNewHampshireX()
public java.util.Vector getPath(Node node1, Node node2, boolean ret_pseudo_nodes) throws java.lang.Exception
public java.util.Vector getSiblings(Node n) throws java.lang.Exception
public Node getLastCommonAncestor(java.lang.String seqname1, java.lang.String seqname2) throws java.lang.Exception
public Node getLastCommonAncestor(int id1, int id2) throws java.lang.Exception
public void adjustNodeCount()
void addNodeAndConnect(java.lang.String s1, java.lang.String s2) throws java.lang.Exception
public void levelOrderReID(int i)
i
- the starting value (int)public int preorderReID(int i)
i
- the starting value (int)public void hashIDs()
|
FORESTER 1.7 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |