forester v1.4
A B C D E F G H I L M N O 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.
add(Component, GridBagLayout, GridBagConstraints, int, int, int, int) - Method in class forester.atv_awt.PopupProtected
 
adjustNodeCount() - Method in class forester.tree.Tree
(Re)counts the number of children for each Node of this Tree.
allowMoreThanBinaryNodesInNHoutput(boolean) - Method in class forester.tree.Tree
Sets whether to allow more than binary Nodes in New Hampshire (NH) output.
apply - Variable in class forester.atv_awt.PopupProtected
 
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.
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
 
ATVappletWjs - class forester.atv_awt.ATVappletWjs.
 
ATVappletWjs() - Constructor for class forester.atv_awt.ATVappletWjs
 
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

BasketDataStructure - class forester.datastructures.BasketDataStructure.
 
BasketDataStructure(int) - Constructor for class forester.datastructures.BasketDataStructure
Constructs a BasketDataStructure of size s.
BOOTSTRAP_DEFAULT - Static variable in class forester.tree.Node
Value of -99 is used as default value.

C

calculateRealHeight() - Method in class forester.tree.Tree
Calculates the real height of this Tree (=sum of real branch lenghts).
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 "/", "_", "-", "\", ";", ".".
close - Variable in class forester.atv_awt.PopupProtected
 
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.
computeMappingCost() - Method in class forester.tools.SDI
Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree.
computeMappingCost() - Method in class forester.tools.SDIoe
Computes the cost of mapping the gene tree gene_tree onto the species tree species_tree.
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.
createATVFrame(ATVapplet) - Method in class forester.atv_awt.ATVapplet
Will be overwritten by subclasses.
createATVFrame(ATVapplet) - Method in class forester.atv_awt.ATVapplet
Will be overwritten by subclasses.
createATVFrame(ATVapplet) - Method in class forester.atv_awt.ATVappletWjs
 
createBalancedTree(int) - Static method in class forester.tree.TreeHelper
Creates a completely balanced Tree with 2^i external nodes.
createBasket(int, int) - Method in class forester.datastructures.BasketDataStructure
Creates a basket( s ), which is affiliated with the Node s of the species Tree and which contains the Node g of the gene Tree.
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

DEFAULT - Static variable in class forester.tools.DistanceCalculator
 
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_MATRIX_FILE_SUFFIX - Static variable in class forester.tools.RIO
 
DISTANCE_NULL - Static variable in class forester.tree.Node
Value of -100 is used to indicate that the branch does not exist.
DistanceCalculator - class forester.tools.DistanceCalculator.
 
DistanceCalculator() - Constructor for class forester.tools.DistanceCalculator
Default constructor.
DistanceCalculator(Tree) - Constructor for class forester.tools.DistanceCalculator
Constructor.
DistanceCalculator(Tree, Vector) - Constructor for class forester.tools.DistanceCalculator
Constructor.
DoRIO - class forester.tools.DoRIO.
 
DoRIO() - Constructor for class forester.tools.DoRIO
 

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

findBasket(int) - Method in class forester.datastructures.BasketDataStructure
Finds the basket containing the Node g of the gene Tree.
findExtremeLnL() - Method in class forester.tree.Tree
Finds the highest of all log likelihood value associated with branches of this 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.datastructures - package forester.datastructures
 
forester.tools - package forester.tools
 
forester.tree - package forester.tree
 
fuseToAllBranches(Tree) - Method in class forester.tree.Tree
Returns a Array of references to Trees which are the result of fusing Tree t2 to all possible branches of this Tree.
fuseTrees(int, 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(int, 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(int, double, Tree) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.
fuseTrees(int, 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(int, Tree) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.
fuseTrees(int, Tree, Node) - Method in class forester.tree.Tree
Returns a Tree which is the result of fusing a rooted Tree to this Tree.

G

gb - Variable in class forester.atv_awt.PopupProtected
 
gbc - Variable in class forester.atv_awt.PopupProtected
 
get_newHampshire() - Method in class forester.atv_awt.ATVappletWjs
 
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.
getAllExternalSeqNames() - Method in class forester.tree.Tree
Returns the sequence names of all external Nodes of this Tree as array of Strings.
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.
getCount() - Method in class forester.tools.SDIunrooted
Returns the number of differently rooted trees with minimal number of duplications, as determined by method "infer".
getDistance(String, String) - Method in class forester.tools.RIO
Returns the distance between two sequences/taxa after a distance matrix file has been read in with readDistanceMatrix(File).
getDistanceToLCA(String) - Method in class forester.tools.DistanceCalculator
Calculates the distance of the Node with seq name seq_name to the LCA of ext_nodes, which has been set either with constructor DistanceCalculator(Tree,Vector) or method setTreeAndExtNodes(Tree,Vector).
getDistanceToNode(Node, Node) - Method in class forester.tools.DistanceCalculator
Calculates the distance of Node outer to Node inner.
getDistanceToNode(String, Node) - Method in class forester.tools.DistanceCalculator
Calculates the distance of the Node with seq name seq_name to Node inner.
getDistanceToParent() - Method in class forester.tree.Node
Returns the length of the branch leading to the parent of this Node (double).
getDistanceToRoot(Node) - Method in class forester.tools.DistanceCalculator
Calculates the distance of Node n to the root of Tree t which has been set either with a constructor, setTree(Tree), or setTreeAndExtNodes(Tree,Vector).
getDistanceToRoot(String) - Method in class forester.tools.DistanceCalculator
Calculates the distance of the Node with seq name seq_name to the root of Tree t, which has been set either with a constructor, setTree(Tree), or setTreeAndExtNodes(Tree,Vector).
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 (int) of this Node.
getIndicator() - Method in class forester.tree.Node
Returns the indicator value of this Node (int).
getInferredOrthologs(String) - Method in class forester.tools.RIO
Returns a HashMap containing the inferred orthologs of the external gene tree node with the sequence name seq_name.
getInferredSuperOrthologs(String) - Method in class forester.tools.RIO
Returns a HashMap containing the inferred "super orthologs" of the external gene tree node with the sequence name seq_name.
getLastCommonAncestor(int, int) - 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 (float).
getLowestLnL() - Method in class forester.tree.Tree
Returns the lowest log likelihood value associated with branches of this Tree (double).
getMean() - Method in class forester.tools.DistanceCalculator
Returns the mean distance.
getMinimalDuplications() - Method in class forester.tools.SDIunrooted
Returns the minimal number of duplications, as determined by method "infer".
getMinimalMappingCost() - Method in class forester.tools.SDIunrooted
Returns the minimal mapping cost "L", as determined by method "infer".
getN() - Method in class forester.tools.DistanceCalculator
Returns the sum of all Nodes used to calculate the mean.
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(int) - Method in class forester.tree.Tree
Finds the Node of this Tree which has a matching ID number.
getNode(String) - Method in class forester.tree.Tree
Returns a Node of this Tree which has a matching sequence name seqname.
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.
getNumberOfDuplications() - Method in class forester.tree.Tree
Returns the number of duplications of this Tree (int).
getNumberOfExtNodes() - Method in class forester.tree.Tree
Returns the sum of external Nodes of this Tree (int).
getOrder(int) - Method in class forester.tools.RIO
Returns the order in which ortholog (o), "super ortholog" (s) and distance (d) are returned and sorted (priority of sort always goes from left to right), given sort.
getOrthologous() - Method in class forester.tree.Node
Returns how many times this Node is orthologous to another one.
getOrthologs(Node) - Method in class forester.tree.Tree
Returns all orthologs of the external Node n of this Tree.
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.
getRealHeight() - Method in class forester.tree.Tree
Returns the real height of this Tree (=sum of real branch lenghts).
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).
getStandardDeviation() - Method in class forester.tools.DistanceCalculator
Returns the standard deviation.
getStrictlySrelatedNodes(Node) - Method in class forester.tree.Tree
Returns all Nodes which are connected to external Node n of this Tree by a path containing only speciation events.
getSumExtNodes() - Method in class forester.tree.Node
Returns the total number of external Nodes originating from this Node (int).
getSuperOrthologous() - Method in class forester.tree.Node
Returns how many times this Node is super orthologous to another one.
getTaxonomyID() - Method in class forester.tree.Node
Returns the NCBI Taxonomy ID (int) of this Node.
getTime() - Method in class forester.tools.RIO
Returns the time (in ms) needed to run "inferOrthologs".
getTimeSumSDI() - Method in class forester.tools.SDIunrooted
Returns the sum of times (in ms) needed to run method infer of class SDI.
getVariance() - Method in class forester.tools.DistanceCalculator
Returns the variance.
getVector() - Method in class forester.tree.Node
Returns a refernce to the Vector associated with 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.

H

handleEvent(Event) - Method in class forester.atv_awt.PopupProtected
 
handleEvent(Event) - Method in class forester.atv_awt.OutputFileRemotePopup
 
hashIDs() - Method in class forester.tree.Tree
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.

I

increaseNodeCount() - Static method in class forester.tree.Node
Increases the total number of all Nodes created so far by one.
infer(boolean) - Method in class forester.tools.SDI
Abstract method.
infer(boolean) - Method in class forester.tools.SDIoe
Infers for each Node of gene_tree whether it represents a speciation or duplication event.
infer(boolean) - Method in class forester.tools.SDIse
Infers for each Node of gene_tree whether it represents a speciation or duplication event.
infer(File, File, File, File, String, boolean, boolean, boolean, boolean) - Static method in class forester.tools.SDIdirectory
Runs method "infer" of class SDIunrooted on all gene trees in directory indir.
infer(Tree, Tree, boolean, boolean, boolean, int, boolean) - Method in class forester.tools.SDIunrooted
Infers gene duplications on a unrooted gene Tree.
inferAllOrthologs(File, File, File, String, String, int, double, double) - Static method in class forester.tools.RIOdirectory
Counts all orthologs for all multiple gene trees files in directory indir.
inferOrthologs(File, Tree) - Method in class forester.tools.RIO
Infers the orthologs (and "super orthologs") for each external node of the gene Trees in multiple tree File gene_trees_file (=output of PHYLIP).
inferOrthologs(Tree[], Tree) - Method in class forester.tools.RIO
Infers the orthologs (and "super orthologs") for each external node in Tree array gene_trees.
inferredOrthologsToArrayList(String, double, double) - Method in class forester.tools.RIO
Returns an ArrayList containg the names of orthologs of the Node with seq name seq_name.
inferredOrthologsToFile(File, int, double, double) - Method in class forester.tools.RIO
Writes the orthologs as well as the "super orthologs" for each external nodes of the gene trees to outfile.
inferredOrthologsToString(String, int, double, double) - Method in class forester.tools.RIO
Returns a String containg the names of orthologs of the Node with seq name seq_name.
inferredOrthologTableToFile(File) - Method in class forester.tools.RIO
Writes the orthologs for each external nodes of the gene trees to outfile in the form of a table.
inferredSuperOrthologTableToFile(File) - Method in class forester.tools.RIO
Writes the "super orthologs" for each external nodes of the gene trees to outfile in the form of a table.
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.
init() - Method in class forester.atv_awt.ATVappletWjs
 
insertIntoBasket(int, int) - Method in class forester.datastructures.BasketDataStructure
Inserts gene Tree Node g into basket( s ).
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.

L

levelOrderReID(int) - Method in class forester.tree.Tree
Resets the ID numbers of the Nodes of this Tree in level order, starting with i (for the root).

M

main(String[]) - Static method in class forester.tools.RIOdirectory
Main method for this class.
main(String[]) - Static method in class forester.tools.SDI
A "main method" for SDI (Speciation versus Duplication Inference).
main(String[]) - Static method in class forester.tools.RIO
Main method for this class.
main(String[]) - Static method in class forester.tools.DistanceCalculator
 
main(String[]) - Static method in class forester.tools.SDIdirectory
Main method for this class.
main(String[]) - Static method in class forester.tools.SDIunrooted
Main method for this class.
main(String[]) - Static method in class forester.tools.DoRIO
Main method to call RIO.inferOrthologs(Tree,Tree), followed by RIO.inferredOrthologsToString(String,boolean).
mergeBasket(int, int) - Method in class forester.datastructures.BasketDataStructure
Adds the elements of basket( s1 ) to the elements of basket( s2 ) and deletes basket( s1 ) (Corresponds to method link of DisjointSet.)
moveBasket(int, int) - Method in class forester.datastructures.BasketDataStructure
Changes the affiliation of basket( s1 ) from s1 to s2.
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.
MULTIPLE_TREES_FILE_SUFFIX - Static variable in class forester.tools.RIO
 

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.

O

ORTHOLOG_OUTFILE_TABLE_SUFFIX - Static variable in class forester.tools.RIO
 
ORTHOLOGOUS_DEFAULT - Static variable in class forester.tree.Node
 
OUTFILE_LIST_SUFFIX - Static variable in class forester.tools.RIO
 
OutputFileRemotePopup - class forester.atv_awt.OutputFileRemotePopup.
 
OutputFileRemotePopup(Frame, String, String, JSObject, String, String) - Constructor for class forester.atv_awt.OutputFileRemotePopup
 

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.
PopupProtected - class forester.atv_awt.PopupProtected.
 
PopupProtected(Frame, String) - Constructor for class forester.atv_awt.PopupProtected
 
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(int) - Method in class forester.tree.Tree
Resets the ID numbers of the Nodes of this Tree in preorder, starting with i.
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.
readDistanceMatrix(File) - Method in class forester.tools.RIO
Reads in the distance matrix file matrix_file.
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: highest and lowest lnL, real height, sum of ext Nodes.
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(int) - Method in class forester.tree.Tree
Places the root of this Tree on the parent branch of the Node with a corresponding ID.
reRoot(int, 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(Node) - Method in class forester.tree.Tree
Places the root of this Tree on the parent branch Node n.
reRoot(Node, String) - Method in class forester.tree.Tree
Places the root of this Tree on the parent branch Node n.
RIO - class forester.tools.RIO.
 
RIO() - Constructor for class forester.tools.RIO
Default constructor.
RIOdirectory - class forester.tools.RIOdirectory.
 
RIOdirectory() - Constructor for class forester.tools.RIOdirectory
 

S

S_ORTHOLOG_OUTFILE_TABLE_SUFFIX - Static variable in class forester.tools.RIO
 
SDI - class forester.tools.SDI.
 
SDI(Tree, Tree) - Constructor for class forester.tools.SDI
Constructor.
SDIdirectory - class forester.tools.SDIdirectory.
 
SDIdirectory() - Constructor for class forester.tools.SDIdirectory
 
SDIoe - class forester.tools.SDIoe.
 
SDIoe(Tree, Tree) - Constructor for class forester.tools.SDIoe
Constructor.
SDIse - class forester.tools.SDIse.
 
SDIse(Tree, Tree) - Constructor for class forester.tools.SDIse
Constructor.
SDIunrooted - class forester.tools.SDIunrooted.
 
SDIunrooted() - Constructor for class forester.tools.SDIunrooted
Default constructor.
SEQ_X - Static variable in class forester.tree.Node
Value of getOrthologous == -11 is used to indicate that this Node is sequence X in the context of orthologous relationships.
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.
setExtNodes(int) - Method in class forester.tree.Tree
Sets the sum of external Nodes of this Tree (int).
setID(int) - Method in class forester.tree.Node
Sets the ID of this Node to i (int).
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(float) - Method in class forester.tree.Node
Sets the log likelihood value associated with the branch leading to the parent of this Node to float f.
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.
setMaxOrtho(int) - Method in class forester.atv.ATVjframe
Sets the maximal number a sequence is expected to be orthologous towards another, i.e.
setMaxOrtho(int) - Method in class forester.atv_awt.ATVframe
Sets the maximal number a sequence is expected to be orthologous towards another, i.e.
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.
setNodeCount(int) - Static method in class forester.tree.Node
Sets the total number of all Nodes created so far to i (int).
setNumberOfDuplications(int) - Method in class forester.tree.Tree
Sets the number of duplications of this Tree (int).
setOrthologous(int) - Method in class forester.tree.Node
Sets how many times this Node is orthologous to another one.
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).
setSuperOrthologous(int) - Method in class forester.tree.Node
Sets how many times this Node is super orthologous to another one.
setTaxonomyID(int) - Method in class forester.tree.Node
Sets the NCBI Taxonomy ID of this Node to i (int).
setTree(Tree) - Method in class forester.tools.DistanceCalculator
Sets the rooted Tree t for which the mean distance to the root and its variance and standard deviation are calculated.
setTreeAndExtNodes(Tree, ArrayList) - Method in class forester.tools.DistanceCalculator
Sets the rooted Tree t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated.
setTreeAndExtNodes(Tree, Vector) - Method in class forester.tools.DistanceCalculator
Sets the rooted Tree t and the external Nodes ext_nodes for which the mean distance to their lowest common ancestor and its variance and standard deviation are calculated.
setVector(Vector) - Method in class forester.tree.Node
Sets the Vector associated with this Node to v.
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.
status - Variable in class forester.atv_awt.PopupProtected
 
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(int) - Method in class forester.tree.Tree
Returns the subtree of this Tree which has the Node with ID id as its root Node.
swapChildren(int) - Method in class forester.tree.Tree
Swaps the the two childern of a Node with ID id of this Tree.
swapChildren(Node) - Method in class forester.tree.Tree
Swaps the the two childern of a Node node of this Tree.

T

TAXO_ID_DEFAULT - Static variable in class forester.tree.Node
Value of -99 is used as default value.
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.
toString() - Method in class forester.datastructures.BasketDataStructure
Transfers this to a String;
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 H I L M N O P R S T U W
forester v1.4