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forester v1.3 | |||||||
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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 |
TAXO_ID_DEFAULT
Value of -99 is used as default value. |
Constructor Summary | |
Node()
Default constructor for Node. |
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Node(java.lang.String s)
Constructor for Node. |
Method Summary | |
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. |
static boolean |
compareSeqNamesInArraysOfNodes(Node[] nodes1,
Node[] nodes2)
Returns true if Node arrays nodes1 and nodes2 are equal, false otherwise. |
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. |
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. |
double |
getBlOfSeqOnParentBranch()
Returns the resulting (ML) branch length of a Node placed on the parent branch of this Node (double). |
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). |
Node |
getLink()
Returns a refernce to the linked Node of this Node. |
double |
getLnLonParentBranch()
Returns the log likelihood value associated with the branch leading to the parent of this Node (double). |
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. |
java.lang.String |
getOrigSeqName()
Returns the original (unchanged) name of the sequence associated with this Node (String). |
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. |
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 |
getSumExtNodes()
Returns the total number of external Nodes originating from this Node (int). |
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 |
setBlOfSeqOnParentBranch(double d)
Sets the resulting (ML) branch length of a Node placed on the parent branch of this Node to double d. |
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). |
void |
setLink(Node n)
Sets the linked Node of this Node to n. |
void |
setLnLonParentBranch(double d)
Sets the log likelihood value associated with the branch leading to the parent of this Node to double d. |
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 |
setOrigSeqName(java.lang.String s)
Sets the original (unchanged) name of the sequence associated with this Node to String s. |
void |
setParent(Node n)
Sets the parent Node of this Node to n. |
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 |
setSumExtNodes(int i)
Sets the total number of external Nodes originating from this Node to i (int). |
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. |
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 |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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
Constructor Detail |
public Node()
public Node(java.lang.String s) throws java.lang.Exception
s
- String representing one Node in New Hampshire (NH)
or New Hampshire X (NHX) format.Method Detail |
public static int getNodeCount()
public static void setNodeCount(int i)
public static void increaseNodeCount()
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 void setOrigSeqName(java.lang.String s)
public java.lang.String getOrigSeqName()
public double getDistanceToParent()
public void setDistanceToParent(double d)
public double getLnLonParentBranch()
public void setLnLonParentBranch(double d)
public boolean significantlyWorse()
public void setSignificantlyWorse(boolean b)
public boolean isLnLonParentBranchAssigned()
public void setLnLonParentBranchAssigned(boolean b)
public double getBlOfSeqOnParentBranch()
public void setBlOfSeqOnParentBranch(double d)
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 boolean isChild1()
public void deleteData()
getLink()
public Node copyNodeData()
getLink()
public void preorderPrint()
public java.util.Vector getAllExternalChildren()
public java.util.Vector getAllChildren()
public Node[] copyAllExtChildren() throws java.lang.Exception
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 static boolean compareSeqNamesInArraysOfNodes(Node[] nodes1, Node[] nodes2) throws java.lang.Exception
|
forester v1.3 | |||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||
SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |