A B C D F G H I L M N O P R S T

A

actionPerformed(ActionEvent) - Method in class phylosort.ui.TreeWindow

add(File, TreeNode) - Method in class phylosort.TreeCluster

Adds a tree to cluster

add(File) - Method in class phylosort.TreeCluster

Adds a file to cluster

add(String) - Method in class phylosort.ui.MutableList

addChild(TreeNode) - Method in class phylosort.TreeNode

Adds a child to the tree

addObject(Object) - Method in class phylosort.ui.TreeWindow

Adds child to the currently selected node.

addObject(DefaultMutableTreeNode, Object) - Method in class phylosort.ui.TreeWindow

Adds child to parent node.

addObject(DefaultMutableTreeNode, Object, boolean) - Method in class phylosort.ui.TreeWindow

Adds child to parent node.

addSelectionListener(SelectionListener) - Method in class phylosort.ui.TreeWindow

Adds SelectionListener

addTreeSelectionListener(TreeSelectionListener) - Method in class phylosort.ui.TreeWindow

Adds a tree selection listener

B

belongs(TreeNode, Set<String>) - Static method in class phylosort.TreeNodeUtil

Checks whether the set of all OTUs is a subset of taxa

C

clear() - Method in class phylosort.ui.TreeWindow

Remove all nodes except the root node.

close() - Method in class phylosort.ui.logging.DocumentHandler

cluster(String, String) - Static method in class phylosort.PhyloCluster

Clusters trees from an input folder

cluster(String, String, int) - Static method in class phylosort.PhyloCluster

Clusters trees from an input folder

COLON - Static variable in class phylosort.util.NewickConstants

Colon

COMMA - Static variable in class phylosort.util.NewickConstants

Comma

COMMENT_STARTER - Static variable in class phylosort.util.Commons

Comment starter

Commons - Class in phylosort.util

Global constants/variables/settings and utility methods

Commons() - Constructor for class phylosort.util.Commons

compare(TreeNode, TreeNode) - Method in class phylosort.TreeNodeComparator

Compares between two subtrees based on their branch lengths.

Config - Class in phylosort.util

A singleton PhyloSort set of configurations

contains(String) - Method in class phylosort.TreeCluster

Returns true if cluster contains a specific taxon

contains(Iterable<String>) - Method in class phylosort.TreeCluster

Returns true if cluster contains at least one taxon from a list of taxa

contains(Iterable<String>, int) - Method in class phylosort.TreeCluster

Returns true if cluster contains at least one taxon from a list of taxa

contains(TreeNode) - Method in class phylosort.TreeCluster

Returns true if cluster contains at least one taxon from a tree

contains(TreeNode, int) - Method in class phylosort.TreeCluster

Returns true if cluster contains at least one taxon from a tree

contains(File) - Method in class phylosort.TreeCluster

Returns true if cluster contains at least one taxon from a tree file

contains(File, int) - Method in class phylosort.TreeCluster

Returns true if cluster contains at least one taxon from a tree file

contains(TreeNode, Set<String>) - Static method in class phylosort.TreeNodeUtil

Checks whether each group of taxa is represented at least by one OTU

copy(TreeNode, TreeNode) - Static method in class phylosort.TreeNodeUtil

Returns a copy of a TreeNode

copy(File, File) - Static method in class phylosort.util.Commons

Copies a file from a source to a destination

copy(InputStream, OutputStream) - Static method in class phylosort.util.Commons

Copies a file from a source to a destination

D

DEFAULT_BRANCH_LENGTH - Static variable in class phylosort.TreeNode

Default branch length

DEFAULT_MAXIMUM_AVERAGE_NUMBER_OF_COPIES - Static variable in class phylosort.util.Config

Default maximum average number of copies

DEFAULT_MAXIMUM_NUMBER_OF_TAXA - Static variable in class phylosort.util.Config

Default maximum number of taxa

DEFAULT_MINIMUM_BOOTSTRAP_SUPPORT - Static variable in class phylosort.util.Config

Default minimum bootstrap support

DEFAULT_MINIMUM_NUMBER_OF_TAXA - Static variable in class phylosort.util.Config

Default minimum number of taxa

DEFAULT_MINIMUM_OVERLAP - Static variable in class phylosort.TreeCluster

Default minimum overlap

DEFAULT_MODE - Static variable in class phylosort.util.Config

Default mode of operation

DEFAULT_ON_MATCH_ACTION - Static variable in class phylosort.util.Config

Default on match action

DEFAULT_PHYLOSORT_FILE_NAME - Static variable in class phylosort.util.Config

Default PhyloSort config file name

DEFAULT_REGEXP - Static variable in class phylosort.util.Config

Default pattern for taxa extraction

DEFAULT_ROOT - Static variable in class phylosort.util.Config

Default tree rerooting (midpoint)

DEFAULT_ROOT_ID - Static variable in class phylosort.TreeNode

Default root node id

DEFAULT_ROOT_LEVEL - Static variable in class phylosort.TreeNode

Default root node level

DELIMITERS - Static variable in class phylosort.util.Commons

Delimiters

depthFirstSearch() - Method in class phylosort.TreeNode

Performs a depth-first search (DFS) starting at the current node

DocumentHandler - Class in phylosort.ui.logging

Logging handler of JTextPane.

DocumentHandler(JTextPane) - Constructor for class phylosort.ui.logging.DocumentHandler

Constructor

F

find(TreeNode, String) - Static method in class phylosort.TreeNode

Finds a node with a specific label

findOutgroup(TreeNode, List<Set<String>>) - Static method in class phylosort.TreeNodeUtil

Finds a leaf node with a taxon not included within a list of taxa

findOutgroup(TreeNode, Set<String>) - Static method in class phylosort.TreeNodeUtil

Finds a leaf node with a taxon not included within a list of taxa

flush() - Method in class phylosort.ui.logging.DocumentHandler

format(LogRecord) - Method in class phylosort.ui.logging.RecordFormatter

This method is called for every log records

G

get(int) - Method in class phylosort.ui.MutableList

Returns a String item specified by int position

getAllMonophyleticNodes(TreeNode, List<List<String>>) - Static method in class phylosort.TreeNodeUtil

Checks whether a tree has a common branch holding groups of taxa

getAllMonophyleticNodes(TreeNode, List<List<String>>, boolean) - Static method in class phylosort.TreeNodeUtil

Checks whether a tree has a common branch holding groups of taxa

getAverageNumberOfCopies(TreeNode) - Static method in class phylosort.TreeNodeUtil

Returns the average number of copies per species

getBuildTimestamp() - Static method in class phylosort.util.Commons

Returns current version from the jar manifest

getChildren() - Method in class phylosort.TreeNode

Returns an iterator to the children

getChildrenCount() - Method in class phylosort.TreeNode

Returns the number of children

getCount() - Method in class phylosort.ui.MutableList

getCurrentVersion() - Static method in class phylosort.util.Commons

Returns build teimstamp from the jar manifest

getDescription(int) - Method in class phylosort.ui.TaxaRegexpExamples

Returns the description of an expression at specific position in the list of examples

getDescription(String) - Method in class phylosort.ui.TaxaRegexpExamples

Returns a description for an expression

getExpression(int) - Method in class phylosort.ui.TaxaRegexpExamples

Returns expression at specific position in the list of examples

getExpressions() - Method in class phylosort.ui.TaxaRegexpExamples

Returns avaliable of expression examples

getFiles() - Method in class phylosort.TreeCluster

Returns a list of the tree files in the cluster

getFileSeparator() - Static method in class phylosort.util.Commons

Returns system file separator.

getHead(Handler) - Method in class phylosort.ui.logging.RecordFormatter

This method is called just after the handler using this formatter is created

getId() - Method in class phylosort.TreeNode

Returns the node id

getInstance() - Static method in class phylosort.ui.TaxaRegexpExamples

Returns an instance of TaxaRegexpExamples

getInstance() - Static method in class phylosort.util.Config

Returns an instance of Config

getLabel() - Method in class phylosort.TreeNode

Returns the label of the node

getLeaves() - Method in class phylosort.TreeNode

Returns all leaves under this node

getLength() - Method in class phylosort.TreeNode

Returns the length of the node branch

getLevel() - Method in class phylosort.TreeNode

Returns the node level

getLineSeparator() - Static method in class phylosort.util.Commons

Returns system line separator.

getList() - Method in class phylosort.ui.TabbedList

Returns the MutableList in the JTabbedPane

getLogger() - Static method in class phylosort.ui.logging.SingleLogger

Returns Logger

getMaximumAverageNumberOfCopies() - Method in class phylosort.util.Config

Returns the maximum average number of copies

getMaximumId() - Method in class phylosort.TreeNode

Returns the maximum node id under this node

getMaximumNumberOfTaxa() - Method in class phylosort.util.Config

Returns the maximum number of taxa

getMinimumBootstrapSupport() - Method in class phylosort.util.Config

Returns the minimum bootstrap support

getMinimumNumberOfTaxa() - Method in class phylosort.util.Config

Returns the minimum number of taxa

getMode() - Method in class phylosort.util.Config

Returns mode

getMonophyleticNode(TreeNode, List<List<String>>) - Static method in class phylosort.TreeNodeUtil

Checks whether a tree has a common branch holding groups of taxa

getMonophyleticNode(TreeNode, List<List<String>>, boolean) - Static method in class phylosort.TreeNodeUtil

Checks whether a tree has a common branch holding groups of taxa

getNode(int) - Method in class phylosort.TreeNode

Retrieve a node using its id

getNodesByTaxa(TreeNode, Set<String>) - Static method in class phylosort.TreeNodeUtil

Returns all OTU nodes with labels matching the set of taxa

getNodesByTaxa(TreeNode, Set<String>, boolean) - Static method in class phylosort.TreeNodeUtil

Returns all OTU nodes with labels matching the set of taxa

getOnMatchAction() - Method in class phylosort.util.Config

Returns on match action

getParent() - Method in class phylosort.TreeNode

Returns the parent of the node

getPathFromRoot() - Method in class phylosort.TreeNode

Returns an ordered list representing the path from the root to this node.

getRegexp() - Method in class phylosort.util.Config

Returns the taxa extraction regular expression

getRoot() - Method in class phylosort.TreeNode

Returns the root of the tree of a node

getRoot() - Method in class phylosort.util.Config

Returns rooting method

getSortedChildren() - Method in class phylosort.TreeNode

Returns an iterorator to the sorted children

getTail(Handler) - Method in class phylosort.ui.logging.RecordFormatter

This method is called just after the handler using this formatter is closed

getTaxa() - Method in class phylosort.TreeCluster

Returns a list of the taxa in the cluster

getTaxa(TreeNode) - Static method in class phylosort.TreeNodeUtil

Returns a Set of String of taxa in a TreeNode

getTaxa(File) - Static method in class phylosort.TreeNodeUtil

Returns a Set of String of all taxa in a file

getTaxon() - Method in class phylosort.TreeNode

Extracts a taxon string from the node label

getTaxon(boolean) - Method in class phylosort.TreeNode

Extracts a taxon string from the node label

getUserDirectory() - Static method in class phylosort.util.Commons

Returns user's current directory.

H

hasMonophyly(TreeNode, Set<String>, List<Set<String>>, Set<Integer>) - Static method in class phylosort.TreeNodeUtil

Returns node id if the node is valid, otherwise returns -1

I

INVALID_NODE_ID - Static variable in class phylosort.TreeNode

Invalid node id (for example, node not found)

isExclusive() - Method in class phylosort.util.Config

Returns true if the mode is set to "exclusive"

isLeaf() - Method in class phylosort.TreeNode

Returns true if the nodes does not have any children

isMaximumAverageNumberOfCopiesOn() - Method in class phylosort.util.Config

Returns true if the maximum number of copies is negative, otherwise false

isMaximumNumberOfTaxaOn() - Method in class phylosort.util.Config

Returns true if the maximum bootstrap support is negative, otherwise false

isMinimumBootstrapSupportOn() - Method in class phylosort.util.Config

Returns true if the minimum bootstrap support is negative, otherwise false

isMinimumNumberOfTaxaOn() - Method in class phylosort.util.Config

Returns true if the minimum number of taxa is negative, otherwise false

isOutgroup() - Method in class phylosort.util.Config

Returns the root boolean flag

isRoot() - Method in class phylosort.TreeNode

Returns true if this the root node of the tree (i.e.

iterator() - Method in class phylosort.TreeNode

Returns depth first search Iterable

L

lca(Iterable<TreeNode>) - Static method in class phylosort.TreeNodeUtil

Returns the lowest common ancestor (LCA) for a list of nodes

LEFT_PARENTHESIS - Static variable in class phylosort.util.NewickConstants

Left parenthesis

load(File) - Static method in class phylosort.TreeNodeUtil

Loads a tree from a text file

load(String) - Static method in class phylosort.util.Config

Loads configuration settings from a file

loadGroups(String) - Static method in class phylosort.PhyloSort

Loads groups of taxa from a text file

loadTaxaFromTree() - Method in class phylosort.ui.PhyloSortWindow

loadTaxaFromTree(File) - Method in class phylosort.ui.PhyloSortWindow

M

main(String[]) - Static method in class phylosort.PhyloCluster

main(String[]) - Static method in class phylosort.ui.PhyloSortCommandLine

main(String[]) - Static method in class phylosort.ui.PhyloSortWindow

makeButton(String, String, String, String) - Method in class phylosort.ui.TreeWindow

Creates a new button

merge(TreeCluster) - Method in class phylosort.TreeCluster

Merges two clusters into one cluster

mouseClicked(MouseEvent) - Method in class phylosort.ui.MutableList

mouseClicked(MouseEvent) - Method in class phylosort.ui.TreeWindow

mouseEntered(MouseEvent) - Method in class phylosort.ui.MutableList

mouseEntered(MouseEvent) - Method in class phylosort.ui.TreeWindow

mouseExited(MouseEvent) - Method in class phylosort.ui.MutableList

mouseExited(MouseEvent) - Method in class phylosort.ui.TreeWindow

mousePressed(MouseEvent) - Method in class phylosort.ui.MutableList

mousePressed(MouseEvent) - Method in class phylosort.ui.TreeWindow

mouseReleased(MouseEvent) - Method in class phylosort.ui.MutableList

mouseReleased(MouseEvent) - Method in class phylosort.ui.TreeWindow

move(File, File) - Static method in class phylosort.util.Commons

Moves a file from a source to a destination

MutableList - Class in phylosort.ui

Mutable JList

MutableList() - Constructor for class phylosort.ui.MutableList

MutableList(MutableList) - Constructor for class phylosort.ui.MutableList

N

NewickConstants - Class in phylosort.util

Common constant (Newick format characters).

NewickConstants() - Constructor for class phylosort.util.NewickConstants

NewickParser - Class in phylosort

A parser to Newick (8:45) tree standard format.

NewickParser() - Constructor for class phylosort.NewickParser

nextFocusAction - Variable in class phylosort.ui.PhyloSortWindow

O

overlaps(TreeCluster) - Method in class phylosort.TreeCluster

Checks if two clusters overlap with at least one taxon

overlaps(TreeCluster, int) - Method in class phylosort.TreeCluster

Checks if two clusters overlap with a minimum number of overlapping taxa

P

parse(String) - Static method in class phylosort.NewickParser

Parses a tree string into a TreeNode

parse(String, TreeNode) - Static method in class phylosort.NewickParser

Parses a tree string into a TreeNode

Path - Class in phylosort

Path from the root of a tree to some other node in the tree.

Path() - Constructor for class phylosort.Path

PhyloCluster - Class in phylosort

Phylogenetic trees clustering tool

PhyloCluster() - Constructor for class phylosort.PhyloCluster

phylosort - package phylosort

PhyloSort core package.

PhyloSort - Class in phylosort

Phylogenetic trees sorting tool

PhyloSort() - Constructor for class phylosort.PhyloSort

phylosort.ui - package phylosort.ui

Command line and graphical user interface.

phylosort.ui.logging - package phylosort.ui.logging

Logging package.

phylosort.util - package phylosort.util

Utility and helper classes

PhyloSortCommandLine - Class in phylosort.ui

Command line interface for PhyloSort.

PhyloSortCommandLine() - Constructor for class phylosort.ui.PhyloSortCommandLine

PhyloSortWindow - Class in phylosort.ui

Graphical user inteface for PhyloSort.

PhyloSortWindow() - Constructor for class phylosort.ui.PhyloSortWindow

Constructor

populate(List<String>) - Method in class phylosort.ui.MutableList

populateRegexpExamples() - Method in class phylosort.ui.PhyloSortWindow

populateTree(TreeNode) - Method in class phylosort.ui.TreeWindow

Populates DefaultMutableTreeNode from TreeNode

preprocess() - Method in class phylosort.TreeNode

Processes the tree and sets the id and level for each in the tree

preprocess(int, int) - Method in class phylosort.TreeNode

Processes the tree and sets the id and level for each in the tree

prevFocusAction - Variable in class phylosort.ui.PhyloSortWindow

PROPERTY_MAXIMUM_AVERAGE_NUMBER_OF_COPIES - Static variable in class phylosort.util.Config

Property maximum average number of copies

PROPERTY_MAXIMUM_NUMBER_OF_TAXA - Static variable in class phylosort.util.Config

Property maximum number of taxa

PROPERTY_MINIMUM_BOOTSTRAP_SUPPORT - Static variable in class phylosort.util.Config

Property minimum bootstrap support

PROPERTY_MINIMUM_NUMBER_OF_TAXA - Static variable in class phylosort.util.Config

Property minimum number of taxa

PROPERTY_MODE - Static variable in class phylosort.util.Config

System property mode of operation

PROPERTY_MODE_EXCLUSIVE - Static variable in class phylosort.util.Config

Exclusive mode of searching

PROPERTY_MODE_INCLUSIVE - Static variable in class phylosort.util.Config

Inclusive mode of searching

PROPERTY_ON_MATCH_ACTION - Static variable in class phylosort.util.Config

Property on match action

PROPERTY_ON_MATCH_ACTION_COPY - Static variable in class phylosort.util.Config

On match action copy

PROPERTY_ON_MATCH_ACTION_COUNT - Static variable in class phylosort.util.Config

On match action count

PROPERTY_ON_MATCH_ACTION_MOVE - Static variable in class phylosort.util.Config

On match action copy

PROPERTY_REGEXP - Static variable in class phylosort.util.Config

Property pattern for taxa extraction

PROPERTY_ROOT - Static variable in class phylosort.util.Config

System property tree rooting

PROPERTY_ROOT_OUTGROUP_NO - Static variable in class phylosort.util.Config

Tree rooting using an outgroup NO

PROPERTY_ROOT_OUTGROUP_YES - Static variable in class phylosort.util.Config

Tree rooting using an outgroup YES

publish(LogRecord) - Method in class phylosort.ui.logging.DocumentHandler

R

RecordFormatter - Class in phylosort.ui.logging

Logging record formatter

RecordFormatter() - Constructor for class phylosort.ui.logging.RecordFormatter

remove(int) - Method in class phylosort.ui.MutableList

Removes a item at a specified position

removeAll() - Method in class phylosort.ui.MutableList

Removes all items from the list

removeChild(TreeNode) - Method in class phylosort.TreeNode

Removes a child

removeChild(int) - Method in class phylosort.TreeNode

Removes a child

removeCurrentNode() - Method in class phylosort.ui.TreeWindow

Removes the currently selected node.

removeSelectionListener(SelectionListener) - Method in class phylosort.ui.TreeWindow

Removes SelectionListener

reroot(TreeNode) - Static method in class phylosort.TreeNodeUtil

Reroots a tree based on an outgroup node.

RIGHT_PARENTHESIS - Static variable in class phylosort.util.NewickConstants

Right parenthesis

rootNode - Variable in class phylosort.ui.TreeWindow

Root node

S

save(File) - Static method in class phylosort.util.Config

saveFile(String) - Static method in class phylosort.ui.PhyloSortWindow

Shows a dialog box to select and open a file

selected(List<String>) - Method in interface phylosort.ui.SelectionListener

Notify a listener that a item (node) has been selected

SelectionListener - Interface in phylosort.ui

Simple interface to listen to tree node selection events.

SEMI_COLON - Static variable in class phylosort.util.NewickConstants

Semicolon

setId(int) - Method in class phylosort.TreeNode

Sets the node id

setLabel(String) - Method in class phylosort.TreeNode

Sets the label of the node

setLength(float) - Method in class phylosort.TreeNode

Sets the length of the node branch

setLevel(int) - Method in class phylosort.TreeNode

Sets the node level

setMaximumAverageNumberOfCopies(float) - Method in class phylosort.util.Config

Sets the maximum average number of copies

setMaximumNumberOfTaxa(int) - Method in class phylosort.util.Config

Sets the maximum number of taxa

setMinimumBootstrapSupport(float) - Method in class phylosort.util.Config

Sets the minimum bootstrap support

setMinimumNumberOfTaxa(int) - Method in class phylosort.util.Config

Sets the minimum number of taxa

setMode(String) - Method in class phylosort.util.Config

Sets the mode

setOnMatchAction(String) - Method in class phylosort.util.Config

Sets the on match action

setOutgroup(boolean) - Method in class phylosort.util.Config

Sets the rooting boolean flag

setParent(TreeNode) - Method in class phylosort.TreeNode

Sets the parent of the node

setRegexp(String) - Method in class phylosort.util.Config

Sets the taxa extraction regular expression

setSelectedItems(List<String>) - Method in class phylosort.ui.MutableList

setTarget(MutableList) - Method in class phylosort.ui.MutableList

setUserDirectory(String) - Static method in class phylosort.util.Commons

Sets user's current directory.

SINGLE_QUOTE - Static variable in class phylosort.util.NewickConstants

Single quote

SingleLogger - Class in phylosort.ui.logging

One central logger (Logger)

SingleLogger() - Constructor for class phylosort.ui.logging.SingleLogger

size() - Method in class phylosort.TreeCluster

Returns the cluster size

size() - Method in class phylosort.TreeNode

Returns the number of terminal nodes in a tree

sort(String, String, List<List<String>>) - Static method in class phylosort.PhyloSort

Sorts trees from an input folder to an output folder based on a set of query taxa

SYSTEM_PROPERTY_PHYLOSORT_CONFIG - Static variable in class phylosort.util.Config

PhyloSort config system property

T

TAB - Static variable in class phylosort.util.Commons

Tab

TabbedList - Class in phylosort.ui

MutableList in a JTabbedPane

TabbedList(MutableList) - Constructor for class phylosort.ui.TabbedList

Constructor

TaxaRegexpExamples - Class in phylosort.ui

Examples of regular expression for taxa extraction

toString() - Method in class phylosort.TreeNode

Returns a string representation of the tree

TreeCluster - Class in phylosort

A cluster of overlapping phylogenetic trees.

TreeCluster() - Constructor for class phylosort.TreeCluster

TreeNode - Class in phylosort

A generic tree node that can be root, internal or leaf (operational taxonomic unit "OTU") node.

TreeNode() - Constructor for class phylosort.TreeNode

Default constructor

TreeNodeComparator - Class in phylosort

A comparator between between two nodes in a tree.

TreeNodeComparator() - Constructor for class phylosort.TreeNodeComparator

TreeNodeUtil - Class in phylosort

Utility methods for general TreeNode processing.

TreeNodeUtil() - Constructor for class phylosort.TreeNodeUtil

TreeWindow - Class in phylosort.ui

Modified from Dynamic Tree Demo Project - Using Swing Components: Examples.

TreeWindow() - Constructor for class phylosort.ui.TreeWindow

Constructor

A B C D F G H I L M N O P R S T