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FORESTER 1.92 | |||||||
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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--forester.tree.Node
Field Summary | |
static int |
BOOTSTRAP_DEFAULT
Value of -99 is used as default value. |
static double |
DISTANCE_DEFAULT
Value of -99.0 is used as default value. |
static double |
DISTANCE_NULL
Value of -100 is used to indicate that the branch does not exist. |
static int |
ORTHOLOGOUS_DEFAULT
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static int |
SEQ_X
Value of getOrthologous == -11 is used to indicate that this Node is sequence X in the context of orthologous relationships. |
(package private) static long |
serialVersionUID
|
static int |
TAXO_ID_DEFAULT
Value of -99 is used as default value. |
Constructor Summary | |
Node()
Default constructor for Node. |
|
Node(java.lang.String s)
Constructor for Node. |
Method Summary | |
(package private) void |
addExtNode(java.lang.String s)
For building Trees. |
boolean |
collapse()
Returns whether this Node should be drawn as collapsed. |
static boolean |
compareArraysOfNodes(Node[] nodes1,
Node[] nodes2)
Returns true if Node arrays nodes1 and nodes2 are equal, false otherwise. |
(package private) void |
connect(java.lang.String s)
For building Trees. |
Node[] |
copyAllExtChildren()
Returns a array containing copies all external children of this Node. |
Node |
copyNodeData()
Returns a new Node which has its data copied from this Node. |
(package private) static Node |
copyTree(Node source)
Deep copies the Tree originating from this Node. |
(package private) static void |
decreaseNodeCount()
Decreases the total number of all Nodes created so far by one. |
void |
deleteData()
Deletes data of this Node. |
boolean |
equals(Node node)
Compares this Node with Node node. |
java.util.Vector |
getAllChildren()
Returns a Vector containing references to all (both internal and external) children of this Node. |
java.util.Vector |
getAllExternalChildren()
Returns a Vector containing references to all external children of this Node. |
int |
getBootstrap()
Returns the bootstrap value (int) of this Node. |
Node |
getChild1()
Returns a refernce to the first child Node of this Node. |
Node |
getChild2()
Returns a refernce to the second child Node of this Node. |
double |
getDistanceToParent()
Returns the length of the branch leading to the parent of this Node (double). |
java.lang.String |
getECnumber()
Returns the EC number associated with this Node (as String). |
int |
getID()
Returns the ID (int) of this Node. |
int |
getIndicator()
Returns the indicator value of this Node (int). |
(package private) Node |
getLastExtNode()
Returns the last external Node. |
Node |
getLink()
Returns a refernce to the linked Node of this Node. |
float |
getLnLonParentBranch()
Returns the log likelihood value associated with the branch leading to the parent of this Node (float). |
Node |
getNextExtNode()
Returns a refernce to the next external Node of this Node. |
static int |
getNodeCount()
Returns the total number of all Nodes created so far. |
int |
getOrthologous()
Returns how many times this Node is orthologous to another one. |
Node |
getParent()
Returns a refernce to the parent Node of this Node. |
Node |
getPrevExtNode()
Returns a refernce to the previous external Node of this Node. |
(package private) Node |
getRoot()
Returns the root Node of the tree of which this Node is member. |
java.lang.String |
getSeqName()
Returns the name of the sequence associated with this Node (String). |
java.lang.String |
getSpecies()
Returns the name of the species associated with this Node (String). |
int |
getSubtreeNeighborings()
Returns how many times this Node is a subtree-neighbor to another one. |
int |
getSumExtNodes()
Returns the total number of external Nodes originating from this Node (int). |
int |
getSuperOrthologous()
Returns how many times this Node is super orthologous to another one. |
int |
getTaxonomyID()
Returns the NCBI Taxonomy ID (int) of this Node. |
java.util.Vector |
getVector()
Returns a refernce to the Vector associated with this Node. |
int |
getXcoord()
Used for drawing of Trees. |
int |
getYcoord()
Used for drawing of Trees. |
static void |
increaseNodeCount()
Increases the total number of all Nodes created so far by one. |
boolean |
isChild1()
Returns true if this Node is the first child of its parent Node. |
boolean |
isDuplication()
Returns true if this Node represents a duplication event, false otherwise. |
boolean |
isDuplicationOrSpecAssigned()
Returns whether a duplication or speciation event has been assigned for this Node. |
boolean |
isExternal()
Checks whether this Node is external (tip). |
boolean |
isLnLonParentBranchAssigned()
Returns whether a log likelihood value associated with the branch leading to the parent of this Node has been assigned. |
boolean |
isPseudoNode()
Checks whether this Node is a pseudo Node, i.e. |
boolean |
isRoot()
Checks whether this Node is a root. |
void |
preorderPrint()
Prints to the console the subtree originating from this Node in preorder. |
void |
setBootstrap(int i)
Sets the bootstrap value of this Node to i (int). |
void |
setChild1(Node n)
Sets the first child Node of this Node to n. |
void |
setChild2(Node n)
Sets the second child Node of this Node to n. |
void |
setCollapse(boolean b)
Sets whether this Node should be drawn as collapsed. |
void |
setDistanceToParent(double d)
Sets the length of the branch leading to the parent of this Node to double d. |
void |
setDuplication(boolean b)
Sets whether this Node represents a duplication event or not. |
void |
setDuplicationOrSpecAssigned(boolean b)
Sets whether a duplication or speciation event has been assigned for this Node. |
void |
setECnumber(java.lang.String s)
Sets the EC number associated with this Node to String s. |
void |
setID(int i)
Sets the ID of this Node to i (int). |
void |
setIndicator(int i)
Sets the indicator value of this Node to i (int). |
(package private) void |
setIndicatorsToZero()
Sets the indicators of all the children of this Node to zero. |
void |
setLink(Node n)
Sets the linked Node of this Node to n. |
void |
setLnLonParentBranch(float f)
Sets the log likelihood value associated with the branch leading to the parent of this Node to float f. |
void |
setLnLonParentBranchAssigned(boolean b)
Sets whether a log likelihood value associated with the branch leading to the parent of this Node has been assigned. |
void |
setNextExtNode(Node n)
Sets the next external Node of this Node to n. |
static void |
setNodeCount(int i)
Sets the total number of all Nodes created so far to i (int). |
void |
setOrthologous(int i)
Sets how many times this Node is orthologous to another one. |
void |
setParent(Node n)
Sets the parent Node of this Node to n. |
(package private) void |
setParents()
Resets the parents of all Nodes of the subtree originating from this Node, given that child1 and child2 are correctly set. |
void |
setPrevExtNode(Node n)
Sets the previous external Node of this Node to n. |
void |
setSeqName(java.lang.String s)
Sets the name of the sequence associated with this Node to String s. |
void |
setSignificantlyWorse(boolean b)
Sets a boolean which could represent whether placement of an additional Node on the parent branch of this Node makes the likelihood of the resulting tree significantly worse. |
void |
setSpecies(java.lang.String s)
Sets the name of the species associated with this Node to String s. |
void |
setSubtreeNeighborings(int i)
Sets how many times this Node is a subtree-neighbor to another one. |
void |
setSumExtNodes(int i)
Sets the total number of external Nodes originating from this Node to i (int). |
void |
setSuperOrthologous(int i)
Sets how many times this Node is super orthologous to another one. |
void |
setTaxonomyID(int i)
Sets the NCBI Taxonomy ID of this Node to i (int). |
void |
setVector(java.util.Vector v)
Sets the Vector associated with this Node to v. |
void |
setXcoord(int i)
Used for drawing of Trees. |
void |
setYcoord(int i)
Used for drawing of Trees. |
boolean |
significantlyWorse()
Returns a boolean which could represent whether placement of an additional Node on the parent branch of this Node makes the likelihood of the resulting tree significantly worse. |
(package private) java.lang.String |
toNewHampshireX()
Converts this Node to a New Hampshire X (NHX) String representation. |
java.lang.String |
toString()
Converts this Node to a String, which looks "pretty" when printed to the console. |
Methods inherited from class java.lang.Object |
|
Field Detail |
static final long serialVersionUID
public static final double DISTANCE_DEFAULT
public static final int BOOTSTRAP_DEFAULT
public static final int TAXO_ID_DEFAULT
public static final double DISTANCE_NULL
public static final int SEQ_X
public static final int ORTHOLOGOUS_DEFAULT
Constructor Detail |
public Node(java.lang.String s) throws java.lang.Exception
(Last modified: 06/12/01)
s
- String representing one Node in New Hampshire (NH)
or New Hampshire X (NHX) format.public Node()
(Last modified: 06/12/01)
Method Detail |
public Node copyNodeData()
getLink()
public void deleteData()
getLink()
static Node copyTree(Node source)
public static int getNodeCount()
public static void setNodeCount(int i)
public static void increaseNodeCount()
static void decreaseNodeCount()
public int getID()
public void setID(int i)
public int getBootstrap()
public void setBootstrap(int i)
public void setTaxonomyID(int i)
public int getTaxonomyID()
public boolean isPseudoNode()
public boolean isExternal()
public boolean isRoot()
public int getSumExtNodes()
public void setSumExtNodes(int i)
public int getIndicator()
public void setIndicator(int i)
public int getXcoord()
public void setXcoord(int i)
public int getYcoord()
public void setYcoord(int i)
public boolean isDuplication()
public void setDuplication(boolean b)
public void setSeqName(java.lang.String s)
public java.lang.String getSeqName()
public void setECnumber(java.lang.String s)
public java.lang.String getECnumber()
public void setSpecies(java.lang.String s)
public java.lang.String getSpecies()
public double getDistanceToParent()
public void setDistanceToParent(double d)
public float getLnLonParentBranch()
public void setLnLonParentBranch(float f)
public boolean significantlyWorse()
public void setSignificantlyWorse(boolean b)
public boolean isLnLonParentBranchAssigned()
public void setLnLonParentBranchAssigned(boolean b)
public boolean isDuplicationOrSpecAssigned()
public void setDuplicationOrSpecAssigned(boolean b)
public void setCollapse(boolean b)
public boolean collapse()
public Node getNextExtNode()
public void setNextExtNode(Node n)
public Node getPrevExtNode()
public void setPrevExtNode(Node n)
public Node getChild1()
public void setChild1(Node n)
public Node getChild2()
public void setChild2(Node n)
public Node getParent()
public void setParent(Node n)
public void setLink(Node n)
public Node getLink()
public void setVector(java.util.Vector v)
public java.util.Vector getVector()
public int getOrthologous()
public void setOrthologous(int i)
public int getSuperOrthologous()
public void setSuperOrthologous(int i)
public int getSubtreeNeighborings()
public void setSubtreeNeighborings(int i)
public boolean isChild1()
public java.util.Vector getAllExternalChildren()
public java.util.Vector getAllChildren()
public Node[] copyAllExtChildren() throws java.lang.Exception
java.lang.String toNewHampshireX()
public java.lang.String toString()
toString
in class java.lang.Object
public boolean equals(Node node)
public static boolean compareArraysOfNodes(Node[] nodes1, Node[] nodes2) throws java.lang.Exception
public void preorderPrint()
void setIndicatorsToZero()
void setParents()
void addExtNode(java.lang.String s) throws java.lang.Exception
void connect(java.lang.String s) throws java.lang.Exception
Node getRoot()
Node getLastExtNode()
|
FORESTER 1.92 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |