forester v1.2
A B C D E F G I M N P R S T U W

A

actionPerformed(ActionEvent) - Method in class forester.atv.ATVjframe
Called automatically.
actionPerformed(ActionEvent) - Method in class forester.atv_awt.ATVframe
Called automatically.
addsLvaluesToTree - class forester.tools.addsLvaluesToTree.
 
addsLvaluesToTree() - Constructor for class forester.tools.addsLvaluesToTree
 
allowMoreThanBinaryNodesInNHoutput(boolean) - Method in class forester.tree.Tree
Sets whether to allow more than binary Nodes in New Hampshire (NH) output.
areBranchLenghtsBootstraps() - Method in class forester.tree.Tree
Checks whether the branch length values actually are bootstrap values All external Nodes must have the same, >0, divisible by 10 branch length.
assign(Tree, Tree) - Static method in class forester.tools.SDI
Determines for each Node of a gene Tree (gene_tree) whether it represents a speciation or duplication event.
ATVapplet - class forester.atv_awt.ATVapplet.
 
ATVapplet - class forester.atv_awt.ATVapplet.
 
ATVapplet() - Constructor for class forester.atv_awt.ATVapplet
 
ATVapplet() - Constructor for class forester.atv_awt.ATVapplet
 
ATVframe - class forester.atv_awt.ATVframe.
 
ATVframe(Tree) - Constructor for class forester.atv_awt.ATVframe
This constructor creates and displays a Frame containing the image of a Tree t plus all the necessary controls.
ATVjapplet - class forester.atv.ATVjapplet.
 
ATVjapplet - class forester.atv.ATVjapplet.
 
ATVjapplet() - Constructor for class forester.atv.ATVjapplet
 
ATVjapplet() - Constructor for class forester.atv.ATVjapplet
 
ATVjframe - class forester.atv.ATVjframe.
 
ATVjframe(Tree) - Constructor for class forester.atv.ATVjframe
This constructor creates and displays a JFrame containing the image of a Tree t plus all the necessary controls.

B

BOOTSTRAP_DEFAULT - Static variable in class forester.tree.Node
Value of -99 is used as default value.

C

calculateNumberOfBranches() - Method in class forester.tree.Tree
Calculates to number of branches of this Tree.
checkCommas(String) - Static method in class forester.tree.TreeHelper
Checks the commas of a String nh_string potentially representing a Tree in NH or NHX format.
checkForUnnessaryParentheses(String, int) - Static method in class forester.tree.TreeHelper
Checks for unnessary parentheses in a String nh_string potentially representing a Tree in NH or NHX format.
checkNHformat(String) - Static method in class forester.tree.TreeHelper
Checks a String s potentially representing a Tree in NH or NHX format.
cleanSpeciesNamesInExtNodes(Tree) - Static method in class forester.tree.TreeHelper
For each external node of Tree tree: Cleans up SWISS-PROT species names: It removes everything (including ) after a potential "/", "_", "-", "\", ";", ".".
collapse() - Method in class forester.tree.Node
Returns whether this Node should be drawn as collapsed.
compareArraysOfNodes(Node[], Node[]) - Static method in class forester.tree.Node
Returns true if Node arrays nodes1 and nodes2 are equal, false otherwise.
compareSeqNamesInArraysOfNodes(Node[], Node[]) - Static method in class forester.tree.Node
Returns true if Node arrays nodes1 and nodes2 are equal, false otherwise.
copyAllExtChildren() - Method in class forester.tree.Node
Returns a array containing copies all external children of this Node.
copyBranchLengthValuesFrom(Tree) - Method in class forester.tree.Tree
Returns a Tree which is a copy of this Tree, except it has the branch lenghts of tree2.
copyNodeData() - Method in class forester.tree.Node
Returns a new Node which has its data copied from this Node.
copyTree() - Method in class forester.tree.Tree
Returns a deep copy of this Tree.
countAndCheckParantheses(String) - Static method in class forester.tree.TreeHelper
Checks whether number of "(" equals number of ")" in String nh_string potentially representing a Tree in NH or NHX format.
createBalancedTree(int) - Static method in class forester.tree.TreeHelper
Creates a completely balanced Tree with 2^i external nodes.
createUnbalancedTree(int) - Static method in class forester.tree.TreeHelper
Creates a completely unbalanced Tree with i external nodes.
currentNode() - Method in class forester.tree.PostorderTreeIterator
Returns the current Node, unless all Nodes have been visited (isDone() returns true), in which case it returns null.
currentNode() - Method in class forester.tree.PreorderTreeIterator
Returns the current Node, unless all Nodes have been visited (isDone() returns true), in which case it returns null.

D

delete() - Method in class forester.tree.Tree
Deletes this Tree.
deleteData() - Method in class forester.tree.Node
Deletes data of this Node.
destroy() - Method in class forester.atv_awt.ATVapplet
Closes the JFrame containg the Tree display.
destroy() - Method in class forester.atv.ATVjapplet
Closes the JFrame containg the Tree display.
destroy() - Method in class forester.atv.ATVjapplet
Closes the JFrame containg the Tree display.
destroy() - Method in class forester.atv_awt.ATVapplet
Closes the JFrame containg the Tree display.
DISTANCE_DEFAULT - Static variable in class forester.tree.Node
Value of -99.0 is used as default value.
DISTANCE_NULL - Static variable in class forester.tree.Node
Value of -100 is used to indicate that the branch does not exist.

E

equals(Node) - Method in class forester.tree.Node
Compares this Node with Node node.
extractSpeciesNameFromSPseqName(Tree) - Static method in class forester.tree.TreeHelper
For each node of Tree tree: Extracts the species name (as SWISS-PROT abbreviation) from the sequence name (if SWISS-PROT names are used) and writes it to the species name field if this is empty.

F

findHighestLnL() - Method in class forester.tree.Tree
Finds the highest of all log likelihood value associated with branches of this Tree.
findLowestLnL() - Method in class forester.tree.Tree
Finds the lowest of all log likelihood value associated with branches of this Tree.
findRoot(Tree, Tree) - Static method in class forester.tools.Root
The purpose of this method is to root a gene tree by minimizing the number of duplications when compared to a species tree.
first() - Method in class forester.tree.PostorderTreeIterator
Resets the Iterator.
first() - Method in class forester.tree.PreorderTreeIterator
Resets the Iterator.
forester.atv - package forester.atv
 
forester.atv_awt - package forester.atv_awt
 
forester.tools - package forester.tools
 
forester.tree - package forester.tree
 
fuseToAllBranches(Tree) - Method in class forester.tree.Tree
Returns an array of references to Trees which are the result of fusing Tree t2 to all possible branches of this Tree.
fuseTrees(long, double, double, Tree) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.
fuseTrees(long, double, double, Tree, Node) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.
fuseTrees(long, double, Tree) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.
fuseTrees(long, double, Tree, Node) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.
fuseTrees(long, Tree) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.
fuseTrees(long, Tree, Node) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.

G

getAllChildren() - Method in class forester.tree.Node
Returns a Vector containing references to all (both internal and external) children of this Node.
getAllExternalChildren() - Method in class forester.tree.Node
Returns a Vector containing references to all external children of this Node.
getBlOfSeqOnParentBranch() - Method in class forester.tree.Node
Returns the resulting (ML) branch length of a Node placed on the parent branch of this Node (double).
getBootstrap() - Method in class forester.tree.Node
Returns the bootstrap value (int) of this Node.
getChild1() - Method in class forester.tree.Node
Returns a refernce to the first child Node of this Node.
getChild2() - Method in class forester.tree.Node
Returns a refernce to the second child Node of this Node.
getDistanceToParent() - Method in class forester.tree.Node
Returns the length of the branch leading to the parent of this Node (double).
getECnumber() - Method in class forester.tree.Node
Returns the EC number associated with this Node (as String).
getExtNode0() - Method in class forester.tree.Tree
Returns the first external Node.
getHighestLnL() - Method in class forester.tree.Tree
Returns the highest log likelihood value associated with branches of this Tree (double).
getID() - Method in class forester.tree.Node
Returns the ID (long) of this Node.
getIndicator() - Method in class forester.tree.Node
Returns the indicator value of this Node (int).
getLastCommonAncestor(long, long) - Method in class forester.tree.Tree
Finds the last common ancestor Node of two Nodes specified by their IDs id1 and id2.
getLastCommonAncestor(String, String) - Method in class forester.tree.Tree
Finds the last common ancestor Node of two Nodes specified by their sequence names seqname1 and seqname2.
getLink() - Method in class forester.tree.Node
Returns a refernce to the linked Node of this Node.
getLnLonParentBranch() - Method in class forester.tree.Node
Returns the log likelihood value associated with the branch leading to the parent of this Node (double).
getLongestDistance() - Method in class forester.tree.Tree
Returns the longest distance of this Tree (double).
getLowestLnL() - Method in class forester.tree.Tree
Returns the lowest log likelihood value associated with branches of this Tree (double).
getMostBranchesPerExtNode() - Method in class forester.tree.Tree
Returns the maximum number of branches per external Node (int).
getName() - Method in class forester.tree.Tree
Returns the name of this Tree.
getNextExtNode() - Method in class forester.tree.Node
Returns a refernce to the next external Node of this Node.
getNode(long) - Method in class forester.tree.Tree
Finds the Node of this Tree which has a matching ID number.
getNodeCount() - Static method in class forester.tree.Node
Returns the total number of all Nodes created so far.
getNodes(String) - Method in class forester.tree.Tree
Returns a Vector with references to all Nodes of this Tree which have a matching sequence name.
getNodesWithMatchingSpecies(String) - Method in class forester.tree.Tree
Returns a Vector with references to all Nodes of this Tree which have a matching species name.
getNumberOfBranches() - Method in class forester.tree.Tree
Returns the total number of branches of this Tree (int).
getNumberOfExtNodes() - Method in class forester.tree.Tree
Returns the sum of external Nodes of this Tree (int).
getOrigSeqName() - Method in class forester.tree.Node
Returns the original (unchanged) name of the sequence associated with this Node (String).
getParent() - Method in class forester.tree.Node
Returns a refernce to the parent Node of this Node.
getPath(Node, Node, boolean) - Method in class forester.tree.Tree
Returns a Vector containing the Node IDs of all Nodes which are between two external Nodes (node2 and node1).
getPrevExtNode() - Method in class forester.tree.Node
Returns a refernce to the previous external Node of this Node.
getRoot() - Method in class forester.tree.Tree
Returns the root Node of this Tree.
getSeqName() - Method in class forester.tree.Node
Returns the name of the sequence associated with this Node (String).
getSiblings(Node) - Method in class forester.tree.Tree
Returns a Vector of references to all external siblings and nieces of a external Node n.
getSpecies() - Method in class forester.tree.Node
Returns the name of the species associated with this Node (String).
getSumExtNodes() - Method in class forester.tree.Node
Returns the total number of external Nodes originating from this Node (int).
getTaxonomyID() - Method in class forester.tree.Node
Returns the NCBI Taxonomy ID (int) of this Node.
getXcoord() - Method in class forester.tree.Node
Used for drawing of Trees.
getYcoord() - Method in class forester.tree.Node
Used for drawing of Trees.

I

increaseNodeCount() - Static method in class forester.tree.Node
Increases the total number of all Nodes created so far by one.
init() - Method in class forester.atv_awt.ATVapplet
Initializes the Applet.
init() - Method in class forester.atv.ATVjapplet
Initializes the JApplet.
init() - Method in class forester.atv.ATVjapplet
Initializes the JApplet.
init() - Method in class forester.atv_awt.ATVapplet
Initializes the Applet.
intervalNumberSpecies(Tree, int) - Static method in class forester.tree.TreeHelper
Sets the species name of the external Nodes of Tree t to 1, 1+i, 2, 2+i, 3, 3+i, ....
isChild1() - Method in class forester.tree.Node
Returns true if this Node is the first child of its parent Node.
isDone() - Method in class forester.tree.PostorderTreeIterator
Returns true if all Nodes have been visited.
isDone() - Method in class forester.tree.PreorderTreeIterator
Returns true if all Nodes have been visited.
isDuplication() - Method in class forester.tree.Node
Returns true if this Node represents a duplication event, false otherwise.
isDuplicationOrSpecAssigned() - Method in class forester.tree.Node
Returns whether a duplication or speciation event has been assigned for this Node.
isEmpty() - Method in class forester.tree.Tree
Checks whether a Tree object is deleted (or empty).
isEmpty(StringBuffer) - Static method in class forester.tree.TreeHelper
Checks whether StringBuffer sb is empty.
isExternal() - Method in class forester.tree.Node
Checks whether this Node is external (tip).
isLnLonParentBranchAssigned() - Method in class forester.tree.Node
Returns whether a log likelihood value associated with the branch leading to the parent of this Node has been assigned.
isPseudoNode() - Method in class forester.tree.Node
Checks whether this Node is a pseudo Node, i.e.
isRoot() - Method in class forester.tree.Node
Checks whether this Node is a root.
isRooted() - Method in class forester.tree.Tree
Returns true is this Tree is rooted.

M

main(String[]) - Static method in class forester.tools.transfersBranchLenghts
Transfers branch length values from one Tree to another.
main(String[]) - Static method in class forester.tools.placesOneNodeOnAllBranches
Places one Node on all branches of a Tree.
main(String[]) - Static method in class forester.tools.SDIx
A "main method" for SDI (Speciation versus Duplication Inference).
main(String[]) - Static method in class forester.tools.SDIxx
 
main(String[]) - Static method in class forester.tools.addsLvaluesToTree
Adds log L values to a Tree.
modify(File) - Method in class forester.tree.Tree
Rerootes and assignes sequence names to internal nodes.
modify(String) - Method in class forester.tree.Tree
Rerootes and assignes sequence names to internal Nodes.
modify(URL) - Method in class forester.tree.Tree
Rerootes and assignes sequence names to internal nodes.
moveBranchLenghtsToBootstrap() - Method in class forester.tree.Tree
Moves the values in the branch length field to the bootstrap field, for each Node of this Tree.

N

next() - Method in class forester.tree.PostorderTreeIterator
Advances the Iterator by one.
next() - Method in class forester.tree.PreorderTreeIterator
Advances the Iterator by one.
Node - class forester.tree.Node.
 
Node() - Constructor for class forester.tree.Node
Default constructor for Node.
Node(String) - Constructor for class forester.tree.Node
Constructor for Node.
numberSpeciesInDescOrder(Tree) - Static method in class forester.tree.TreeHelper
Sets the species namea of the external Nodes of Tree t to descending integers, ending with 1.
numberSpeciesInOrder(Tree) - Static method in class forester.tree.TreeHelper
Sets the species namea of the external Nodes of Tree t to ascending integers, starting with 1.

P

paint(Graphics) - Method in class forester.atv_awt.ATVapplet
Prints message when initialization is finished.
paint(Graphics) - Method in class forester.atv.ATVjapplet
Prints message when initialization is finished.
paint(Graphics) - Method in class forester.atv.ATVjapplet
Prints message when initialization is finished.
paint(Graphics) - Method in class forester.atv_awt.ATVapplet
Prints message when initialization is finished.
placesOneNodeOnAllBranches - class forester.tools.placesOneNodeOnAllBranches.
 
placesOneNodeOnAllBranches() - Constructor for class forester.tools.placesOneNodeOnAllBranches
 
PostorderTreeIterator - class forester.tree.PostorderTreeIterator.
 
PostorderTreeIterator(Tree) - Constructor for class forester.tree.PostorderTreeIterator
Constructor which creates a postorder Iterator for Tree t.
preorderPrint() - Method in class forester.tree.Node
Prints to the console the subtree originating from this Node in preorder.
preorderReID(long) - Method in class forester.tree.Tree
Resets the ID values of the Nodes of this Tree in preorder, starting with l.
PreorderTreeIterator - class forester.tree.PreorderTreeIterator.
 
PreorderTreeIterator(Tree) - Constructor for class forester.tree.PreorderTreeIterator
Constructor which creates a preorder Iterator for Tree t.
printAllNodes() - Method in class forester.tree.Tree
Prints descriptions of all Nodes of this Tree to the console.
printExtNodes() - Method in class forester.tree.Tree
Prints descriptions of all external Nodes of this Tree to the console.

R

randomizeSpecies(int, int, Tree) - Static method in class forester.tree.TreeHelper
Sets the species names of the external Nodes of Tree t to a random positive integer number between (and including) min and max.
readMultipleNHTrees(File) - Static method in class forester.tree.TreeHelper
Reads in multiple Trees from a File multipletreefile, containing Tree descriptions in New Hampshire (NH) or New Hampshire X (NHX) format separated by semicolons followed by a newline.
readNHtree(File, boolean) - Static method in class forester.tree.TreeHelper
Reads a Tree in NH or NHX format from a textfile f.
readNHtree(URL, boolean) - Static method in class forester.tree.TreeHelper
Reads a Tree in NH or NHX format from a URL url.
recalculateAndReset() - Method in class forester.tree.Tree
Recalculates and resets parameters of this Tree: most-branches-per-external-Node, highest and lowest lnL, longest distance, number of branches, deletes data of root Node if this Tree is unrooted.
removeCstyleComments(StringBuffer) - Static method in class forester.tree.TreeHelper
Removes C-style comments from StringBuffer sb.
removeExtNode(Node) - Method in class forester.tree.Tree
Removes external Node from this Tree.
removeWhiteSpace(StringBuffer) - Static method in class forester.tree.TreeHelper
Removes all white space from StringBuffer sb.
reRoot(long) - Method in class forester.tree.Tree
Places the root of this Tree on the parent branch of the Node with a corresponding ID.
reRoot(long, long, long) - Method in class forester.tree.Tree
Rerootes this Tree, given the IDs of three external nodes.
reRoot(long, String) - Method in class forester.tree.Tree
Places the root of this Tree on the parent branch of the Node with a corresponding ID.
reRoot(String, String, String) - Method in class forester.tree.Tree
Rerootes this Tree, given the sequence names of three external nodes.
Root - class forester.tools.Root.
 
Root() - Constructor for class forester.tools.Root
 

S

SDI - class forester.tools.SDI.
 
SDI() - Constructor for class forester.tools.SDI
 
SDIx - class forester.tools.SDIx.
 
SDIx() - Constructor for class forester.tools.SDIx
 
SDIxx - class forester.tools.SDIxx.
 
SDIxx() - Constructor for class forester.tools.SDIxx
 
setBlOfSeqOnParentBranch(double) - Method in class forester.tree.Node
Sets the resulting (ML) branch length of a Node placed on the parent branch of this Node to double d.
setBootstrap(int) - Method in class forester.tree.Node
Sets the bootstrap value of this Node to i (int).
setChild1(Node) - Method in class forester.tree.Node
Sets the first child Node of this Node to n.
setChild2(Node) - Method in class forester.tree.Node
Sets the second child Node of this Node to n.
setCollapse(boolean) - Method in class forester.tree.Node
Sets whether this Node should be drawn as collapsed.
setDistanceToParent(double) - Method in class forester.tree.Node
Sets the length of the branch leading to the parent of this Node to double d.
setDuplication(boolean) - Method in class forester.tree.Node
Sets whether this Node represents a duplication event or not.
setDuplicationOrSpecAssigned(boolean) - Method in class forester.tree.Node
Sets whether a duplication or speciation event has been assigned for this Node.
setECnumber(String) - Method in class forester.tree.Node
Sets the EC number associated with this Node to String s.
setID(long) - Method in class forester.tree.Node
Sets the ID of this Node to l (long).
setIndicator(int) - Method in class forester.tree.Node
Sets the indicator value of this Node to i (int).
setIndicatorsToZero() - Method in class forester.tree.Tree
Sets the indicators of all Nodes of this Tree to 0.
setLink(Node) - Method in class forester.tree.Node
Sets the linked Node of this Node to n.
setLnLonParentBranch(double) - Method in class forester.tree.Node
Sets the log likelihood value associated with the branch leading to the parent of this Node to double d.
setLnLonParentBranchAssigned(boolean) - Method in class forester.tree.Node
Sets whether a log likelihood value associated with the branch leading to the parent of this Node has been assigned.
setName(String) - Method in class forester.tree.Tree
Sets the name of this Tree to s.
setNextExtNode(Node) - Method in class forester.tree.Node
Sets the next external Node of this Node to n.
setOrigSeqName(String) - Method in class forester.tree.Node
Sets the original (unchanged) name of the sequence associated with this Node to String s.
setParent(Node) - Method in class forester.tree.Node
Sets the parent Node of this Node to n.
setPrevExtNode(Node) - Method in class forester.tree.Node
Sets the previous external Node of this Node to n.
setRooted(boolean) - Method in class forester.tree.Tree
Sets whether this Tree is rooted or not.
setSeqName(String) - Method in class forester.tree.Node
Sets the name of the sequence associated with this Node to String s.
setSignificantlyWorse(boolean) - Method in class forester.tree.Node
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.
setSpecies(String) - Method in class forester.tree.Node
Sets the name of the species associated with this Node to String s.
setSumExtNodes(int) - Method in class forester.tree.Node
Sets the total number of external Nodes originating from this Node to i (int).
setTaxonomyID(int) - Method in class forester.tree.Node
Sets the NCBI Taxonomy ID of this Node to i (int).
setXcoord(int) - Method in class forester.tree.Node
Used for drawing of Trees.
setYcoord(int) - Method in class forester.tree.Node
Used for drawing of Trees.
showWhole() - Method in class forester.atv.ATVjframe
Resizes the Tree, so that it is displayed in its entirety.
showWhole() - Method in class forester.atv_awt.ATVframe
Resizes the Tree, so that it is displayed in its entirety.
significantlyWorse() - Method in class forester.tree.Node
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.
stripTree(Tree, Tree) - Static method in class forester.tools.SDI
Removes from Tree to_be_stripped all external Nodes which are assocaited with a species not found in Tree reference.
subTree(long) - Method in class forester.tree.Tree
Returns the subtree of this Tree which has the Node with ID id as its root Node.
swapChildren(long) - Method in class forester.tree.Tree
Swaps the the two childern of a Node with ID id of this Tree.

T

toNewHampshire(boolean) - Method in class forester.tree.Tree
Converts this Tree to a New Hampshire (String) representation.
toNewHampshireX() - Method in class forester.tree.Tree
Converts this Tree to a New Hampshire X (String) representation.
toString() - Method in class forester.tree.Node
Converts this Node to a String, which looks pretty when printed to the console.
toString() - Method in class forester.tree.Tree
Converts this Tree to a New Hampshire X (String) representation.
transfersBranchLenghts - class forester.tools.transfersBranchLenghts.
 
transfersBranchLenghts() - Constructor for class forester.tools.transfersBranchLenghts
 
Tree - class forester.tree.Tree.
 
Tree() - Constructor for class forester.tree.Tree
Default Tree constructor.
Tree(String) - Constructor for class forester.tree.Tree
Tree constructor.
TreeHelper - class forester.tree.TreeHelper.
 
TreeHelper() - Constructor for class forester.tree.TreeHelper
 

U

unRoot() - Method in class forester.tree.Tree
Removes the root Node this Tree.
unRootAndTrifurcate() - Method in class forester.tree.Tree
Removes the root Node of this Tree and makes at least a trifurcation at its basal node.

W

writeNHtree(Tree, File, boolean, boolean, boolean) - Static method in class forester.tree.TreeHelper
Writes a Tree t to a textfile f.

A B C D E F G I M N P R S T U W
forester v1.2