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A
acceptButtonHandler()
- Method in class
PTCControls
Defines how to handle the action of the Ok button in Seeting window clicking event.
actionPerformed(ActionEvent)
- Method in class
FM
Defines how to handle the actions of the OK buttons for the question and the answer windows in the FM algorithm.
actionPerformed(ActionEvent)
- Method in class
MP
Defines how to handle the actions of the OK buttons for the question and the answer windows in the MP algorithm.
actionPerformed(ActionEvent)
- Method in class
NJ
Defines how to handle the actions of the OK buttons for the question and the answer windows in the NJ algorithm.
actionPerformed(ActionEvent)
- Method in class
PTCControls
Defines how to handle the actions of the button clicking events.
actionPerformed(ActionEvent)
- Method in class
PTCFrame
Defines how to handle the actions of the File and Help menu selections.
actionPerformed(ActionEvent)
- Method in class
UPGMA
Defines how to handle the actions of the OK buttons for the question and the answer windows in the UPGMA algorithm.
Algorithm
- class
Algorithm
.
This class is an abstract class and defines the methods common to all algorithms.
Algorithm(PTCControls)
- Constructor for class
Algorithm
Initializes the GUI components used in all algorithms and constructs the question and the answer windows.
ansField
- Variable in class
Algorithm
The answer area for the users to type
ansFrame
- Variable in class
Algorithm
The answer window
ansLabel
- Variable in class
Algorithm
The field to hold answers
answer
- Variable in class
Algorithm
The answer of the question
B
BestTreeFM
- class
BestTreeFM
.
This class keeps the best tree information in the FM algorithm.
BestTreeFM()
- Constructor for class
BestTreeFM
Constructs a default best tree object in the FM algorithm
BestTreeMP
- class
BestTreeMP
.
This class keeps the best tree information in the MP algorithm.
BestTreeMP()
- Constructor for class
BestTreeMP
Constructs a default best tree object in the MP algorithm
buildAns1()
- Method in class
MP
Generates the answers for the type 1 questions in the MP algorithm.
buildAnswer()
- Method in class
UPGMA
Generates the answers for the questions in the UPGMA algorithm.
buildAnswer1()
- Method in class
FM
Generates the answers for the type 1 questions in the FM algorithm.
buildAnswer1()
- Method in class
NJ
Generates the answers for the type 1 questions in the NJ algorithm.
buildAnswer2()
- Method in class
FM
Generates the answers for the type 2 questions in the FM algorithm.
buildAnswer2()
- Method in class
MP
Generates the answers for the type 2 questions in the MP algorithm.
buildAnswer2()
- Method in class
NJ
Generates the answers for the type 2 questions in the NJ algorithm.
C
calculateDistanceToOthers(int, int)
- Method in class
FM
Calculates the distance to the other nodes.
calculateNewDistance()
- Method in class
Algorithm
The abstract method of the algorithm.
calculateNewDistance()
- Method in class
FM
Implements the method in the Algorithm calss and defines how to calculate new distance matrix in the FM algorithm.
calculateNewDistance()
- Method in class
MP
This method does nothing in the MP algorithm
calculateNewDistance()
- Method in class
NJ
Implements the method in the Algorithm calss and defines how to calculate new distance matrix in the NJ algorithm.
calculateNewDistance()
- Method in class
UPGMA
Implements the method in the Algorithm calss and defines how to calculate new distance matrix in the UPGMA algorithm.
calculateNumOfSubstitutions()
- Method in class
MP
Defines how to calculate the number of substitutions table in the MP algorithm
calculateOutputDistance()
- Method in class
FM
Calculates the computed distance matrix.
calculateSumAndR()
- Method in class
NJ
Defines how to calculate sum and r values in the NJ algorithm.
calculateTotalNumOfSubstitutions(int, int[][])
- Method in class
MP
Defines how to calculate the total number of substitutions for a given column in a given table
calculateTransformDistance()
- Method in class
NJ
Defines how to calculate transform distance table in the NJ algorithm.
checkInput()
- Method in class
PTCControls
Checks the input.
checkInput(JFrame)
- Method in class
InputCharacterModel
Checks users' input data in the MP algorithm.
checkInput(JFrame)
- Method in class
InputDistanceModel
Checks users' input data in the distance based algorithms
checkInput(JFrame)
- Method in class
InputModel
Each input table model should implements the method to define how the input data should be checked.
closeBestTrees(Vector)
- Method in class
FM
Closes all best tree windows in the FM algorithm.
ColorQuestionCellRenderer
- class
ColorQuestionCellRenderer
.
This class sets the colors of all tables involved in pop up questions.
ColorQuestionCellRenderer()
- Constructor for class
ColorQuestionCellRenderer
ColorTableCellRenderer
- class
ColorTableCellRenderer
.
This class sets the colors of all the other tables except those described in ColorQuestionCellRenderer.
ColorTableCellRenderer()
- Constructor for class
ColorTableCellRenderer
compute()
- Method in class
TreeDisplay
Defines how to compute the positions of all the nodes.
compute(Node, int, int, int, int)
- Method in class
TreeDisplay
Defines how to compute the positions of a node.
computeAllNonLeafDistance(Node, Node, double)
- Method in class
FM
Computes the distances among the nodes in two trees.
computeAllSitesSubstitutions(Vector, String[][], int[][])
- Method in class
MP
Defines how to calculate the total number of substitutions table for all sites in the MP algorithm
ComputedDistanceModel
- class
ComputedDistanceModel
.
This class is used to set the computed distance table data in the FM algorithm.
ComputedDistanceModel(int, String[], double[][])
- Constructor for class
ComputedDistanceModel
Construct the object with the specified values.
computeMaxName()
- Method in class
Algorithm
Computes the longest name of the species.
computeMaxSeqWidth(FontMetrics, Node)
- Method in class
TreeDisplay
Defines how to compute the pixels needed to draw the longest sequence.
computeMinMaxLength()
- Method in class
Algorithm
Computes the longest and shortest branch lengths.
computeNJRight(Node, int, int, int, int)
- Method in class
TreeDisplay
Defines how to compute the positions of a node in the last step of the NJ and the FM algorithms.
computeNumOfTrees(int)
- Method in class
FM
Computes the number of different trees for the given number of species.
computeNumOfTrees(int)
- Method in class
MP
Computes the number of different trees for the given number of species.
computeSumOfSquares()
- Method in class
FM
Computes the Sum Of Squares.
constrcutRadioMenu(String, String[])
- Method in class
PTCFrame
Constructs the menu of radio buttons for the PTC package.
constructAnsFrame()
- Method in class
Algorithm
Constructs the answer window.
constructBestTreeFrame(int, int)
- Method in class
FM
Constructs the best tree window used in the FM algorithm.
constructBestTreeFrame(int, int)
- Method in class
MP
Constructs the best tree window used in the MP algorithm.
constructButton(String)
- Method in class
Algorithm
Constructs the buttons used in the window.
constructButton(String)
- Method in class
PTCControls
Constructs the button.
constructComputeDistanceFrame()
- Method in class
FM
Constructs the computed distance table window.
constructDistPanel(String, MyJTable)
- Method in class
PreviousFrame
Constructs the panel containing tables.
constructLeftPanel()
- Method in class
PTCControls
Constructs the left Panel.
constructMenuBar()
- Method in class
PTCFrame
Constructs the menu bar for the PTC package.
constructQuesFrame()
- Method in class
Algorithm
Constructs the question window.
constructRightPanel()
- Method in class
PTCControls
Constructs the right Panel.
constructTransFrame()
- Method in class
NJ
Constructs the tranform distance table window.
copy()
- Method in class
Node
Gets a deep copy of a node.
count
- Variable in class
Algorithm
The number of species
count
- Variable in class
InputModel
The number of species
D
deleteNodes()
- Method in class
Algorithm
Kills the nodes joined together in the each step of the algorithms.
display
- Variable in class
Algorithm
The value indicates whether the last step of MP and FM
displayOneBestTree(Vector, String[][], int[][], TreeDisplay, JFrame)
- Method in class
MP
Defines how to display one tree in the MP algorithm.
displayTransformDistance()
- Method in class
NJ
Defines how to display transform distance table in the NJ algorithm.
distance
- Variable in class
InterDistanceModel
The distance matrix in the distance based algorithms
draw(Graphics, int, int, int, int, int)
- Method in class
Node
Defines how to draw a node in distance based algorithms.
draw(Graphics, Node, int)
- Method in class
TreeDisplay
Defines how to draw a tree.
drawMP(Graphics, int, int, int, int)
- Method in class
Node
Defines how to draw a node in the MP algorithms.
drawMPRight(Graphics, int, int, int, int)
- Method in class
Node
Defines how to draw a node in the last step of the MP algorithm by rotating one rooted tree to the right.
drawMPRight(Graphics, Node)
- Method in class
TreeDisplay
Defines how to draw the right tree in the last step of the MP algorithm.
drawNJRight(Graphics, int, int, int, int, int)
- Method in class
Node
Defines how to draw a node in the last step of the FM and NJ algorithms by rotating one rooted tree to the right.
drawNJRight(Graphics, Node, int)
- Method in class
TreeDisplay
Defines how to draw the right tree in the last step of the NJ and the FM algorithms.
F
find()
- Method in class
MP
Defines how to find the nodes to join in the MP algorithm.
findAndCalculate()
- Method in class
FM
Defines how to find the nodes to join and calculates branch lengths in the FM algorithm.
findAndCalculate()
- Method in class
NJ
Defines how to find the nodes to join and calculate branch lengths in the NJ algorithm.
findAndCalculate()
- Method in class
UPGMA
Defines how to find the nodes to join and calculate branch lengths in the UPGMA algorithm.
findInformativeSites()
- Method in class
MP
Finds the informative sites for a given input
findMin(double[][])
- Method in class
Algorithm
Finds the smallest value for a matrix.
findMiniMinj()
- Method in class
FM
Finds the next two nodes to be joined in the FM algorithm.
findMiniMinj()
- Method in class
MP
Finds the next two nodes to be joined in the MP algorithm.
findOne()
- Method in class
Algorithm
The abstract method of the algorithm.
findOne()
- Method in class
FM
Implements the method in the Algorithm class and indicates if one tree is found in the FM algorithm.
findOne()
- Method in class
MP
Implements the method in the Algorithm class and indicates if one tree is found in the MP algorithm.
findOne()
- Method in class
NJ
Implements the method in the Algorithm class and indicates if one tree is found.
findOne()
- Method in class
UPGMA
Implements the method in the Algorithm class and indicates if one tree is found.
finishStepTwo()
- Method in class
MP
Indicates if the algorithm has finished the second step of the MP algorithm.
FM
- class
FM
.
This class implements the Fitch Margoliash algorithm described in the package.
FM
- Static variable in class
PTC
The algorithm type used with FM
FM(PTCControls)
- Constructor for class
FM
Initializes specific GUI components used in the FM algorithm.
G
generateRandom_ij()
- Method in class
FM
Generates random numbers for pop up questions in the FM algorithm.
generateRandom_ij()
- Method in class
MP
Generates random numbers for pop up questions in the MP algorithm.
generateRandom_ij()
- Method in class
NJ
Generates random numbers for pop up questions involved the new distance table in the NJ algorithm.
generateRandom_ij()
- Method in class
UPGMA
Generates random numbers for pop up questions involved the new distance table in the UPGMA algorithm.
generateRandom_mn()
- Method in class
NJ
Generates random numbers for pop up questions involved the transform distance table in the NJ algorithm.
generateRandomCharacters(InputCharacterModel)
- Method in class
PTCControls
Genertaes a random input for the character based algorithms.
generateRandomDistance(InputDistanceModel)
- Method in class
PTCControls
Genertaes a random input for the distance based algorithms.
getAllLeaves(Node, Vector)
- Method in class
FM
Gets the leaves of a node.
getAllNumOfSubs()
- Method in class
BestTreeMP
Gets the number of substitutions table in all sites in the MP algorithm.
getAllSitesSubs()
- Method in class
BestTreeMP
Gets the total number of substitutions in all sites in the MP algorithm.
getAllSitesSubs()
- Method in class
MP
Gets the total number of substituions for all sites used in the MP algorithm.
getBegin_x()
- Method in class
Node
Gets the begin x axis value to draw a node.
getBegin_y()
- Method in class
Node
Gets the begin y axis value to draw a node.
getBestCharacters()
- Method in class
BestTreeMP
Gets the character sequences for all nodes in the best tree in the MP algorithm.
getBestComputeDisTable()
- Method in class
BestTreeFM
Gets the computed distance table in the best tree in the FM algorithm.
getBestInterNodes()
- Method in class
BestTreeMP
Gets the interior nodes in the best tree in the MP algorithm.
getBestTotalNumOfSubstitutions()
- Method in class
MP
Gets the best minimum total number of substituions for informative sites used in the MP algorithm.
getBestTreeDisplay()
- Method in class
BestTreeFM
Gets the tree drawing object in the best tree in the FM algorithm.
getBestTreeDisplay()
- Method in class
BestTreeMP
Gets the tree drawing object in the best tree in the MP algorithm.
getBestTreeFrame()
- Method in class
BestTreeFM
Gets the best tree window in the FM algorithm.
getBestTreeFrame()
- Method in class
BestTreeMP
Gets the best tree window in the MP algorithm.
getCharacters()
- Method in class
InputCharacterModel
Converts the users input to characters array.
getCharacters()
- Method in class
MP
Gets the characters table used in the MP algorithm.
getColumnClass(int)
- Method in class
ComputedDistanceModel
Overrides the method in the TableModel class and returns the class for each table column.
getColumnClass(int)
- Method in class
NumOfSubModel
Overrides the method in the TableModel class and returns the class for each table column.
getColumnClass(int)
- Method in class
PreviousDistanceModel
Overrides the method in the TableModel class and returns the class for each table column.
getColumnCount()
- Method in class
ComputedDistanceModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnCount()
- Method in class
InputCharacterModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnCount()
- Method in class
InputDistanceModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnCount()
- Method in class
InterCharacterModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnCount()
- Method in class
InterDistanceModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnCount()
- Method in class
NumOfSubModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnCount()
- Method in class
ResetModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnCount()
- Method in class
TransDistanceModel
Overrides the method in the TableModel class and returns the column count of the table.
getColumnName(int)
- Method in class
ComputedDistanceModel
Overrides the method in the TableModel class and returns the column names of the table.
getColumnName(int)
- Method in class
InputCharacterModel
Overrides the method in the TableModel class and returns the column names of the table.
getColumnName(int)
- Method in class
InputDistanceModel
Overrides the method in the TableModel class and returns the column names of the table.
getColumnName(int)
- Method in class
InterCharacterModel
Overrides the method in the TableModel class and returns the column names of the table.
getColumnName(int)
- Method in class
InterDistanceModel
Overrides the method in the TableModel class and returns the column names of the table.
getColumnName(int)
- Method in class
NumOfSubModel
Overrides the method in the TableModel class and returns the column names of the table.
getColumnName(int)
- Method in class
TransDistanceModel
Overrides the method in the TableModel class and returns the column names of the table.
getCount()
- Method in class
Algorithm
Gets the number of species.
getCount()
- Method in class
InputModel
Gets the number of the species.
getCount()
- Method in class
InterDistanceModel
Gets the number of the species.
getCount()
- Method in class
Node
Gets the number of nodes in a node.
getDataFromFile(String)
- Method in class
PTCFrame
Reads the input from a file and displays in the input data area.
getDir()
- Method in class
PTCFrame
Gets the root of the current working directory.
getDisplay()
- Method in class
Algorithm
The method indicates whether the last step of MP and FM.
getDistance()
- Method in class
FM
Returns the distance matrix in the FM algorithm.
getDistance()
- Method in class
InputDistanceModel
Converts the users input to double array
getDistance()
- Method in class
NJ
Gets the distance matrix used in the NJ algorithm.
getDistance()
- Method in class
UPGMA
Gets the distance matrix used in the UPGMA algorithm.
getEnd_x()
- Method in class
Node
Gets the end x axis value to draw a node.
getEnd_y()
- Method in class
Node
Gets the end y axis value to draw a node.
getFind()
- Method in class
MP
Gets the status if the one tree has finished to compute the number of substitutions table.
getFlagString()
- Method in class
FM
Returns the string corresponding to the negative branch length flag.
getFormattedName()
- Method in class
Node
Gets the name of the node in html formatted style.
getHeight()
- Method in class
Node
Gets the height of a node.
getIndex()
- Method in class
Node
Gets the index of a node in the nodes array.
getInfoArea()
- Method in class
PTCControls
Gets the object to display instructions.
getInfoSites()
- Method in class
MP
Gets the informative sites found in the MP algorithm.
getInputTable()
- Method in class
PTCControls
Gets the object to display input table.
getInterNode()
- Method in class
Algorithm
Gets the interior node name.
getInterNodes()
- Method in class
MP
Gets the names of the inter nodes used in the MP algorithm.
getInterSection(String, String)
- Method in class
MP
Defines the set intersection operation
getInterTable()
- Method in class
PTCControls
Gets the object to display intermediate result table.
getLeftNode()
- Method in class
Node
Gets the left node of a node.
getLength()
- Method in class
Node
Gets the branch length of a node.
getMaxLength()
- Method in class
Algorithm
Gets the longest branch length in the trees.
getMaxName()
- Method in class
Algorithm
Gets the longest name of the species.
getMinLength()
- Method in class
Algorithm
Gets the shortest branch length in the trees.
getName()
- Method in class
Node
Gets the name of a node.
getNames()
- Method in class
Algorithm
Gets the name of the species.
getNames()
- Method in class
InputModel
Gets the names of the species.
getNegativeFlag()
- Method in class
FM
Returns the negative branch length flag in the FM algorithm.
getNode(int)
- Method in class
Algorithm
Gets the node at specified index.
getNodes()
- Method in class
Algorithm
Gets the nodes created so far.
getNoInfoSites()
- Method in class
MP
Gets the status if any informative sites are found in the MP algorithm.
getNumOfLeaves()
- Method in class
Node
Gets the number of leaf nodes rooted at a node.
getNumOfNodes()
- Method in class
Algorithm
Gets the number of nodes created so far.
getNumOfNodesLeft()
- Method in class
Algorithm
Gets the number of nodes left to join in the trees.
getNumOfSites()
- Method in class
InputCharacterModel
Gets the number of the sites in the MP algorithm.
getNumOfSubstitutions()
- Method in class
MP
Gets the number of substituions table used in the MP algorithm.
getPathLength()
- Method in class
Node
Gets the path length from a node to the leaf node.
getPTransDistanceModel()
- Method in class
NJ
Gets the transform distance model used in the transform distance table in the NJ algorithm.
getRightNode()
- Method in class
Node
Gets the right node of a node.
getRoots()
- Method in class
Algorithm
Gets the roots of the trees.
getRoots()
- Method in class
TreeDisplay
Gets the roots of a tree.
getRowCount()
- Method in class
ComputedDistanceModel
Overrides the method in the TableModel class and returns the row count of the table.
getRowCount()
- Method in class
InputCharacterModel
Overrides the method in the TableModel class and returns the row count of the table.
getRowCount()
- Method in class
InputDistanceModel
Overrides the method in the TableModel class and returns the row count of the table.
getRowCount()
- Method in class
InterCharacterModel
Overrides the method in the TableModel class and returns the row count of the table.
getRowCount()
- Method in class
InterDistanceModel
Overrides the method in the TableModel class and returns the row count of the table.
getRowCount()
- Method in class
NumOfSubModel
Overrides the method in the TableModel class and returns the row count of the table.
getRowCount()
- Method in class
ResetModel
Overrides the method in the TableModel class and returns the row count of the table.
getRowCount()
- Method in class
TransDistanceModel
Overrides the method in the TableModel class and returns the row count of the table.
getSeq()
- Method in class
Node
Gets the character sequence of this node.
getSumOfSquares()
- Method in class
FM
Returns the Sum Of Squares in the FM algorithm.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int)
- Method in class
ColorQuestionCellRenderer
The method overrids the one in the DefaultTableCellRenderer class and used to set the table cell renderer in the PTC package.
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int)
- Method in class
ColorTableCellRenderer
The method overrids the one in the DefaultTableCellRenderer class and used to set the table cell renderer in the PTC package.
getTotal()
- Method in class
InterCharacterModel
Gets the total number of substitutions in the MP algorithm.
getTotalNumOfSubstitutions()
- Method in class
MP
Gets the total number of substituions for informative sites used in the MP algorithm.
getTransDistance()
- Method in class
NJ
Gets the transform distance matrix used in the NJ algorithm.
getTreeDisplay()
- Method in class
PTCControls
Gets the object to draw the tree.
getUnion(String, String)
- Method in class
MP
Defines the set union operation
getValueAt(int, int)
- Method in class
ComputedDistanceModel
Overrides the method in the TableModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
InputCharacterModel
Overrides the method in the TableModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
InputDistanceModel
Overrides the method in the TableModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
InterCharacterModel
Overrides the method in the TableModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
InterDistanceModel
Overrides the method in the TableModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
NumOfSubModel
Overrides the method in the TableModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
PreviousDistanceModel
Overrides the method in the InterDistanceModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
ResetModel
Overrides the method in the TableModel class and returns the value of each table cell.
getValueAt(int, int)
- Method in class
TransDistanceModel
Overrides the method in the TableModel class and returns the value of each table cell.
H
HTMLViewer
- class
HTMLViewer
.
This class is used to display the HELP info with the HTML files
HTMLViewer(String, String)
- Constructor for class
HTMLViewer
Constructs a new instance of HTMLViewer
hyperlinkUpdate(HyperlinkEvent)
- Method in class
HTMLViewer
Notification of a change relative to a hyperlink.
I
infoArea
- Variable in class
Algorithm
The instruction area to display information
init()
- Method in class
Algorithm
Initalizes the components used in the algorithms.
init()
- Method in class
FM
Overrides the method in the Algorithm class and initializes specific data components used in the FM algorithm.
init()
- Method in class
MP
Overrides the method in the Algorithm class and initializes specific data components used in the MP algorithm.
init()
- Method in class
NJ
Overrides the method in the Algorithm class and initializes specific data components used in the NJ algorithm.
init()
- Method in class
UPGMA
Overrides the method in the Algorithm class and initializes specific data components used in the UPGMA algorithm.
initialize_init_x(Graphics)
- Method in class
TreeDisplay
Defines how to compute the initial x position to draw a tree.
initialize_init_y(Graphics)
- Method in class
TreeDisplay
Defines how to compute the initial y position to draw a tree.
initialize_unit_x()
- Method in class
TreeDisplay
Defines how to initialize the x axis scaling factor.
initialize_unit_y()
- Method in class
TreeDisplay
Defines how to initialize the y axis scaling factor.
initializeOTUNames(int)
- Method in class
PTCControls
Initializes the names of the species.
InputCharacterModel
- class
InputCharacterModel
.
This class is used to set the inpute character table data in the MP algorithm
InputCharacterModel(int, int, String[])
- Constructor for class
InputCharacterModel
Constructs the empty table for users' input in the MP algorithm.
InputCharacterModel(int, int, String[], Object[][])
- Constructor for class
InputCharacterModel
Constructs the data with specified values in the MP algorithm.
InputDistanceModel
- class
InputDistanceModel
.
This class is used to set the inpute distance table data in the distance based algorithms
InputDistanceModel(int, String[])
- Constructor for class
InputDistanceModel
Constructs the empty table for users' input in the distance based algorithms.
InputDistanceModel(int, String[], Object[][])
- Constructor for class
InputDistanceModel
Constructs the data with specified values in the distance based algorithms.
InputModel
- class
InputModel
.
This class is used to defines the common methods used in the input tables.
InputModel()
- Constructor for class
InputModel
inputTable
- Variable in class
Algorithm
The input table in the algorithms
InterCharacterModel
- class
InterCharacterModel
.
This class is used to set the intermediate result table data in the MP algorithm
InterCharacterModel(MP)
- Constructor for class
InterCharacterModel
Constructs the data with the MP algorithm.
InterCharacterModel(MP, int)
- Constructor for class
InterCharacterModel
Constructs the data with the MP algorithm.
InterDistanceModel
- class
InterDistanceModel
.
This class is used to set the intermediate result table data in the MP algorithm
InterDistanceModel(FM)
- Constructor for class
InterDistanceModel
Constructs the data with the FM algorithm.
InterDistanceModel(FM, int, int)
- Constructor for class
InterDistanceModel
Constructs the data with the FM algorithm.
InterDistanceModel(NJ)
- Constructor for class
InterDistanceModel
Constructs the data with the NJ algorithm.
InterDistanceModel(NJ, int, int)
- Constructor for class
InterDistanceModel
Constructs the data with the NJ algorithm.
InterDistanceModel(UPGMA)
- Constructor for class
InterDistanceModel
Constructs the data with the UPGMA algorithm.
InterDistanceModel(UPGMA, int, int)
- Constructor for class
InterDistanceModel
Constructs the data with the UPGMA algorithm.
interNode
- Variable in class
Algorithm
The interior node name
interSection(String, String)
- Method in class
MP
Indicates if the intersection of two sets are empty
interTable
- Variable in class
Algorithm
The intermediate result table in the algorithms
isCellEditable(int, int)
- Method in class
InputDistanceModel
Overrides the method in the InputModel class and sets if the cell can be edited.
isCellEditable(int, int)
- Method in class
InputModel
Overrides the method in the TableModel class and sets if the cell can be edited.
isEnd()
- Method in class
Algorithm
The abstract method of the algorithm.
isEnd()
- Method in class
FM
Implements the method in the Algorithm class and indicates if the algorithm terminates in the FM algorithm.
isEnd()
- Method in class
MP
Implements the method in the Algorithm class and indicates if the algorithm terminates in the MP algorithm.
isEnd()
- Method in class
NJ
Implements the method in the Algorithm class and indicates if the algorithm terminates in the NJ algorithm.
isEnd()
- Method in class
UPGMA
Implements the method in the Algorithm class and indicates if the algorithm terminates in the UPGMA algorithm.
isLeaf()
- Method in class
Node
Indicates if a node is a leaf node.
isLive()
- Method in class
Node
Indicates if a node is live.
itemStateChanged(ItemEvent)
- Method in class
PTCFrame
Defines how to handle the actions of the Algorithm, Option, Zoom In and Zoom Out menu selections.
J
join()
- Method in class
NJ
Defines how to join the two nodes when there are more than two nodes left in the NJ algorithm.
join(double)
- Method in class
FM
Defines how to join the two nodes when there are more than two nodes left in the FM algorithm.
join(double)
- Method in class
UPGMA
Defines how to join nodes in the UPGMA algorithm.
joinAndCalculate()
- Method in class
MP
Defines how to join nodes and calculates the characters in the MP algorithm.
joinLastTwoNodes()
- Method in class
FM
Defines how to join the last two nodes in the FM algorithm.
joinLastTwoNodes()
- Method in class
MP
Defines how to join the last two nodes in the MP algorithm.
joinLastTwoNodes()
- Method in class
NJ
Defines how to joins the last two nodes in the NJ algorithm.
K
kill()
- Method in class
Node
Defines how to kill a node when the node is joined to the other node.
L
linkActivated(URL)
- Method in class
HTMLViewer
Follows the reference in an link.
M
main(String[])
- Static method in class
PTC
The main method of java program.
maxLength
- Variable in class
Algorithm
The maximum branch length in the final trees
maxName
- Variable in class
Algorithm
The longest name of species
mini
- Variable in class
Algorithm
The row index of the node to be joined
minj
- Variable in class
Algorithm
The column index of the node to be joined
minLength
- Variable in class
Algorithm
The minimum branch length in the final trees
MP
- class
MP
.
This class implements the Maximum Parsimony algorithm described in the package.
MP
- Static variable in class
PTC
The algorithm type used with MP
MP(PTCControls)
- Constructor for class
MP
Initializes specific GUI components used in the MP algorithm.
MyJTable
- class
MyJTable
.
This class defines the common methods used in all the tables.
MyJTable()
- Constructor for class
MyJTable
Constructs the table object with the default table model.
MyJTable(TableModel)
- Constructor for class
MyJTable
Constructs the table object with the specified table model.
N
names
- Variable in class
Algorithm
The names of species
names
- Variable in class
InputModel
The names of the species
names
- Variable in class
InterDistanceModel
The the names of the species
NJ
- class
NJ
.
This class implements the Neighbor Joining algorithm described in the package.
NJ
- Static variable in class
PTC
The algorithm type used with NJ
NJ(PTCControls)
- Constructor for class
NJ
Initializes specific GUI components used in the NJ algorithm.
Node
- class
Node
.
This class keeps track of all the information associated with each node.
Node(int, String, int, double, double, boolean)
- Constructor for class
Node
Constructs the node object with the specified values.
Node(String, int, int, double, Node, Node, String)
- Constructor for class
Node
Constructs the node object with the specified values.
nodes
- Variable in class
Algorithm
The nodes created in the trees
numOfNodes
- Variable in class
Algorithm
The number of nodes created so far
numOfNodesLeft
- Variable in class
Algorithm
The number of nodes left in the each step of the algorithms
NumOfSubModel
- class
NumOfSubModel
.
This class is used to display the table that includes the number of substitutions in the MP algorithm.
NumOfSubModel(int[][], int)
- Constructor for class
NumOfSubModel
Construct the object with the specified values.
O
okAnsButton
- Variable in class
Algorithm
The OK button used in answer window
okButtonHandler()
- Method in class
PTCControls
Defines how to handle the action of the OK button clicking event.
okQuesButton
- Variable in class
Algorithm
The OK buttion used in question window
P
paintComponent(Graphics)
- Method in class
TreeDisplay
Defines how a tree is redrawn every time.
phyTreesControls
- Variable in class
Algorithm
The control of PTC package
popUpQues
- Variable in class
Algorithm
The value indicates whether the pop up question is enabled
popUpQuestion()
- Method in class
UPGMA
Generates pop up questions in the UPGMA algorithm.
popUpQuestion1()
- Method in class
FM
Generates type 1 pop up questions in the FM algorithm.
popUpQuestion1()
- Method in class
NJ
Generates type 1 pop up questions in the NJ algorithm.
popUpQuestion1(int)
- Method in class
MP
Generates type 1 pop up questions in the MP algorithm.
popUpQuestion2()
- Method in class
FM
Generates type 2 pop up questions in the FM algorithm.
popUpQuestion2()
- Method in class
MP
Generates type 2 pop up questions in the MP algorithm.
popUpQuestion2()
- Method in class
NJ
Generates type 2 pop up questions in the NJ algorithm.
PreviousDistanceModel
- class
PreviousDistanceModel
.
This class is used to display the previous distance table in the previous state window.
PreviousDistanceModel(FM)
- Constructor for class
PreviousDistanceModel
Constructs the data with the FM algorithm.
PreviousDistanceModel(NJ)
- Constructor for class
PreviousDistanceModel
Constructs the data with the NJ algorithm.
PreviousDistanceModel(UPGMA)
- Constructor for class
PreviousDistanceModel
Constructs the data with the UPGMA algorithm.
PreviousFrame
- class
PreviousFrame
.
This class keeps track of and displays the previous state of every algorithm.
PreviousFrame()
- Constructor for class
PreviousFrame
Constructs the GUI components used in previouse state window.
process()
- Method in class
UPGMA
Defines how to process in the UPGMA algorithm.
processLastTwoNodes()
- Method in class
FM
Defines how to join last two nodes in the FM algorithm.
processLastTwoNodes()
- Method in class
MP
Defines how to join last two nodes in the MP algorithm.
processLastTwoNodes()
- Method in class
NJ
Defines how to join last two nodes in the NJ algorithm.
processMoreThanTwoNodes()
- Method in class
FM
Defines how to join more than two nodes in the FM algorithm.
processMoreThanTwoNodes()
- Method in class
MP
Defines how to join more than two nodes in the MP algorithm.
processMoreThanTwoNodes()
- Method in class
NJ
Defines how to join more than two nodes in the NJ algorithm.
processOneTree()
- Method in class
FM
Defines how to find one tree in the FM algorithm.
processOneTree()
- Method in class
MP
Defines how to find one tree in the MP algorithm.
PTC
- class
PTC
.
This class is the main program, which initializes all the components and pops up the main window.
PTC()
- Constructor for class
PTC
PTCControls
- class
PTCControls
.
This class is the main controller in the package.
PTCControls()
- Constructor for class
PTCControls
Constructs the GUI components for the PTC package.
PTCFrame
- class
PTCFrame
.
This class constructs the main user's interface and handles users menu selections.
PTCFrame()
- Constructor for class
PTCFrame
Constructs the main user interface for the PTC package.
Q
quesFrame
- Variable in class
Algorithm
The question window
quesLabel
- Variable in class
Algorithm
The field to hold pop up questions
question
- Variable in class
Algorithm
The question itself
R
random_i
- Variable in class
Algorithm
The random row value used in pop up questions
random_j
- Variable in class
Algorithm
The random column value used in pop up questions
randomButtonHandler()
- Method in class
PTCControls
Defines how to handle the action of the Random button clicking event.
randomInt(int)
- Method in class
Algorithm
Generates a random integer value.
reCalculate(Node, int, int)
- Method in class
TreeDisplay
Defines how to adjust the values to all nodes in the x axis and the y axis for a specified root.
reCalculateX(Node, int)
- Method in class
TreeDisplay
Defines how to adjust the values to all nodes in the x axis for a specified root.
reset()
- Method in class
Algorithm
Closes the question and answer windows.
reset()
- Method in class
FM
Overrides the method in the Algorithm class and resets all components in the FM algorithm.
reset()
- Method in class
MP
Overrides the method in the Algorithm class and resets all components in the MP algorithm.
reset()
- Method in class
NJ
Overrides the method in the Algorithm class and resets all components in the NJ algorithm.
reset()
- Method in class
PTCControls
Resets the data and the GUI components.
reset()
- Method in class
TreeDisplay
Defines how to clean a tree in the display areas.
resetButtonHandler()
- Method in class
PTCControls
Defines how to handle the action of the Reset button clicking event.
ResetModel
- class
ResetModel
.
This class is used to is used to reset all kinds of tables in the package.
ResetModel()
- Constructor for class
ResetModel
roots
- Variable in class
Algorithm
The roots of the trees
RUN
- Static variable in class
PTC
The algorithm run mode with RUN
run()
- Method in class
Algorithm
The abstract method of the algorithm.
run()
- Method in class
FM
Implements the method in the Algorithm classs and defines how to run the FM algorithm.
run()
- Method in class
MP
Implements the method in the Algorithm classs and defines how to run the FM algorithm.
run()
- Method in class
NJ
Implements the method in the Algorithm classs and defines how to run the NJ algorithm.
run()
- Method in class
UPGMA
Implements the method in the Algorithm class and defines how to run the UPGMA algorithm.
runButtonHandler()
- Method in class
PTCControls
Defines how to handle the action of the Run button clicking event.
runType
- Variable in class
Algorithm
The algorithm run mode
S
saveInputToFile(String)
- Method in class
InputCharacterModel
Saves the input data to a file in the MP algorithm.
saveInputToFile(String)
- Method in class
InputDistanceModel
Saves the input data to a file in the distance based algorithms
saveInputToFile(String)
- Method in class
InputModel
Each input table model should implements the method to define how the input data can be saved.
scaleTree(int, int, int, int, Node)
- Method in class
TreeDisplay
Defines how to scale a node in the tree.
scaleTreeRight(int, int, int, int, Node)
- Method in class
TreeDisplay
Defines how to scale a node in the right part of a final tree in the NJ and the FM algorithms.
setAlgorithm(Algorithm)
- Method in class
TreeDisplay
Sets the algorithm with the drawing object.
setAlgorithmMenuDisabled()
- Method in class
PTCFrame
Disables the options in the Algorithm menu.
setAlgorithmMenuEnabled()
- Method in class
PTCFrame
Enables the options in the Algorithm menu.
setAlgorithmType(int)
- Method in class
PTCControls
Sets the algorithm type.
setAllNumOfSubs(int[][])
- Method in class
BestTreeMP
Sets the total number of substitutions in all sites in the MP algorithm.
setBegin_x(int)
- Method in class
Node
Sets the begin x axis value to draw a node.
setBegin_y(int)
- Method in class
Node
Sets the begin y axis value to draw a node.
setBestCharacters(String[][])
- Method in class
BestTreeMP
Sets the character sequences for all nodes in the best tree in the MP algorithm.
setBestComputeDisTable(MyJTable)
- Method in class
BestTreeFM
Sets the computed distance table in the best tree in the FM algorithm.
setBestInterNodes(Vector)
- Method in class
BestTreeMP
Sets the interior nodes in the best tree in the MP algorithm.
setBestTreeDisplay(TreeDisplay)
- Method in class
BestTreeFM
Sets the tree drawing object in the best tree in the FM algorithm.
setBestTreeDisplay(TreeDisplay)
- Method in class
BestTreeMP
Sets the tree drawing object in the best tree in the MP algorithm.
setBestTreeFrame(JFrame)
- Method in class
BestTreeFM
Sets the best tree window in the FM algorithm.
setBestTreeFrame(JFrame)
- Method in class
BestTreeMP
Sets the best tree window in the MP algorithm.
setCharacters(String[][])
- Method in class
InputCharacterModel
Sets the character data in the MP algorithm.
setColumnWidth(int)
- Method in class
MyJTable
Sets the width of all the table columns to a specified value.
setColumnWidth(int, int)
- Method in class
MyJTable
Sets the width of the table columns which begin at a specified index to a specified value.
setColumnWidth(int, int, int)
- Method in class
MyJTable
Sets the width of the table columns which begin at a specified index and end at a specified index to a specified value.
setDefault()
- Method in class
PTCFrame
Sets the default values for all the menus.
setDisabledItems()
- Method in class
PTCFrame
Disables the Open option and options in the Algorithm menu.
setDisplay(boolean)
- Method in class
TreeDisplay
Sets the display status.
setDistance(Object[][])
- Method in class
InputDistanceModel
Sets the distance data in the distance based algorithms
setDistData(Algorithm)
- Method in class
PreviousFrame
Sets and displays the table for the previous state window.
setEnd_x(int)
- Method in class
Node
Sets the end x axis value to draw a node.
setEnd_y(int)
- Method in class
Node
Sets the end y axis value to draw a node.
setFirst(boolean)
- Method in class
PTCControls
Sets the status of the algorithm.
setFlagString(String)
- Method in class
TreeDisplay
Sets the flag string used in the FM algorithm.
setLeftNode(Node)
- Method in class
Node
Sets the left node of a node.
setLength(double)
- Method in class
Node
Sets the branch length of a node.
setMaxName(String)
- Method in class
TreeDisplay
Sets the longest name of the species.
setNumOfLeaves(int)
- Method in class
Node
Sets the number of leaves rooted at a node.
setParameters(int, int, int)
- Method in class
TreeDisplay
Sets the parameters used in drawing.
setPathLength(double)
- Method in class
Node
Sets the path length of a node to a specified value
setPathLength(Node, double)
- Method in class
FM
Sets the branch length form the node to its child.
setPopUpQues(boolean)
- Method in class
Algorithm
Sets the pop up question flag.
setPopUpQuestion(boolean)
- Method in class
PTCControls
Sets the Pop Up Question option.
setPopUpQuestion(boolean)
- Method in class
PTCFrame
Sets the Pop Up Question option.
setPosition(int, int, int, int)
- Method in class
Node
Sets a node drawing postion form (
begin_x
,
begin_y
) to (
end_x
,
end_y
).
setRatio(double)
- Method in class
PTCControls
Sets the ratio of the tree scaling factor.
setRatio(double)
- Method in class
TreeDisplay
Sets the zoom in or the zoom out ratio of a tree.
setRightNode(Node)
- Method in class
Node
Sets the right node of a node.
setRoots(Vector)
- Method in class
Algorithm
Sets the roots of the trees.
setRunType(int)
- Method in class
Algorithm
Sets the algorithm run mode.
setSaveInput(boolean)
- Method in class
PTCControls
Sets the Save Input option.
setSaveInput(boolean)
- Method in class
PTCFrame
Sets the SaveInput option.
setSeq(String)
- Method in class
Node
Sets the character sequence of a node.
setTableData(int, int, String[], Object[][])
- Method in class
PTCControls
Displays the data read from a file in the input area for the character based algorithms.
setTableData(int, String[], Object[][])
- Method in class
PTCControls
Displays the data read from a file in the input area for the distance based algorithms.
setThreeFractionDigit(double)
- Method in class
Algorithm
Formats a double value with threee fraction digits.
settingButtonHandler()
- Method in class
PTCControls
Defines how to handle the action of the Setting button clicking event.
setTreeData(Algorithm)
- Method in class
PreviousFrame
Sets and displays the tree for the previous state window.
setType(int)
- Method in class
TreeDisplay
Sets the window drawing type, either a big one in the main phylogenetic tree or a small one in other windows.
setValueAt(Object, int, int)
- Method in class
InputCharacterModel
Overrides the method in the TableModel class and sets the table cell values.
setValueAt(Object, int, int)
- Method in class
InputDistanceModel
Overrides the method in the TableModel class and sets the table cell values.
setZoomInOut()
- Method in class
PTCFrame
Enables the Zomm In and Zoom Out options.
space(int)
- Method in class
InputModel
Generates the specified number of spaces.
start()
- Method in class
TreeDisplay
Defines how to begin to draw a tree.
T
TRACE
- Static variable in class
PTC
The algorithm run mode with TRACE
trace()
- Method in class
Algorithm
The abstract method of the algorithm.
trace()
- Method in class
FM
Implements the method in the Algorithm class and defines how to trace the FM algorithm.
trace()
- Method in class
MP
Implements the method in the Algorithm class and defines how to trace the MP algorithm.
trace()
- Method in class
NJ
Implements the method in the Algorithm class and defines how to trace the NJ algorithm.
trace()
- Method in class
UPGMA
Implements the method in the Algorithm class and defines how to trace the UPGMA algorithm.
traceButtonHandler()
- Method in class
PTCControls
Defines how to handle the action of the Trace button clicking event.
TransDistanceModel
- class
TransDistanceModel
.
This class is used to display the transform distance table in the NJ algorithm.
TransDistanceModel(int, Node[], double[][], int, int)
- Constructor for class
TransDistanceModel
Construct the object with the specified values.
treeDisplay
- Variable in class
Algorithm
The object to draw the trees
TreeDisplay
- class
TreeDisplay
.
This class is responsible for drawing different kinds of trees in different windows.
TreeDisplay()
- Constructor for class
TreeDisplay
Constructs a defalut tree display object.
TreeDisplay(boolean)
- Constructor for class
TreeDisplay
Constructs a tree display object with the value indicating whether the drawing begins.
U
update()
- Method in class
InterCharacterModel
Updates and resets the random site number.
update()
- Method in class
InterDistanceModel
Updates and resets the random question cell row and column.
update()
- Method in class
TransDistanceModel
Updates and resets the random question cell row and column.
updateAllNodes(Vector, String[][])
- Method in class
MP
Defines how to update all nodes information in the best tree window to display all sites in the MP algorithm
updateBestTree()
- Method in class
FM
Defines how to update the best tree window.
updateBestTree()
- Method in class
MP
Defines how to update the best tree window in the MP algorithm.
updateBestTree(double, Vector, BestTreeFM, String)
- Method in class
FM
Define how to update one best tree window.
updateBestTreeFrameUI(JFrame, int[][])
- Method in class
MP
Defines how to update the best tree window to add the number of substitutions table in the MP algorithm
updateMiniMinj()
- Method in class
FM
Updates the index of the nodes to be joined in the FM algorithm.
updateMiniMinj()
- Method in class
MP
Updates the index of the nodes to be joined in the MP algorithm.
updateNodeSeq(Node, String[][])
- Method in class
MP
Defines how to update one node information in the best tree window to display all sites in the MP algorithm
updateOneBestTree()
- Method in class
MP
Defines how to update one tree in the MP algorithm.
updateTable()
- Method in class
InterDistanceModel
Updates the table so that the value in the row i and the column j equals to the value in the row j and the column i.
updateTransformDistance()
- Method in class
NJ
Defines how to update transform distance table in the NJ algorithm.
updateTree()
- Method in class
Algorithm
Updates the tree status in the each step of the algorithm running.
updateUI()
- Method in class
FM
Defines how to update the tree and the intermediate distance table when there are more than two nodes left in the FM algorithm.
updateUI()
- Method in class
MP
Defines how to update the tree and the intermediate number of substitutions table in the MP algorithm.
updateUI()
- Method in class
NJ
Defines how to update the tree and the intermediate distance table when there are more than two nodes left in the NJ algorithm.
updateUI()
- Method in class
UPGMA
Defines how to update the tree and the intermediate distance table in the UPGMA algorithm.
updateUILastTwoNodes()
- Method in class
FM
Defines how to update the tree and the intermediate distance table when there are only two nodes left in the FM algorithm.
updateUILastTwoNodes()
- Method in class
MP
Defines how to update the tree and the intermediate distance table when there are only two nodes left in the MP algorithm.
updateUILastTwoNodes()
- Method in class
NJ
Defines how to update the tree and the intermediate distance table when there are only two nodes left in the NJ algorithm.
updateXY()
- Method in class
FM
Updates the position of the next best tree window.
updateXY()
- Method in class
MP
Updates the position of the next best tree window.
UPGMA
- class
UPGMA
.
This class implements UPGMA described in the package.
UPGMA
- Static variable in class
PTC
The algorithm type used with UPGMA
UPGMA(PTCControls)
- Constructor for class
UPGMA
Initializes specific GUI components used in the UPGMA algorithm.
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