PhyloSort
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
PhyloSort

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