All Packages  Class Hierarchy

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Index of all Fields and Methods

A

ABOUT_CMD. Static variable in class duploss.cmd.CommandReader
The about command type.
ABOUT_CMD_STR. Static variable in class duploss.cmd.CommandReader
The about command string.
ABOUT_STRING. Static variable in class duploss.cmd.CommandInterpreter
String describing version and copyright information.
actionPerformed(ActionEvent). Method in class duploss.gui.ControlListener
Processes action events generated by components on the control panel.
actionPerformed(ActionEvent). Method in class duploss.plus.DupLossApplet
Creates and shows the display window.
actionPerformed(ActionEvent). Method in class duploss.gui.EnterLabelDialog
Diposes the window.
actionPerformed(ActionEvent). Method in class duploss.gui.InputTreeFrame
Performs the corresponding action when a button is clicked.
actionPerformed(ActionEvent). Method in class duploss.gui.MessageDialog
Records the user's choice and disposes of the window.
actionPerformed(ActionEvent). Method in class duploss.gui.MessageFrame
Closes window when OK button is clicked.
addOption(Option). Method in class duploss.OptionsTable
Adds an option to the table.
addOptions(Option[]). Method in class duploss.OptionsTable
Adds options to the table.
APPLET_INFO. Static variable in class duploss.plus.DupLossApplet
String constant with info about applet such as title.

B

BASE_DUP_VERTICAL_SPACING. Static variable in class duploss.tree.GeneTree
Vertical spacing between a node and a duplication node.
BASE_GENE_ROOT_LENGTH. Static variable in class duploss.tree.GeneTree
Length of gene tree root.
BASE_H_TREE_MARGIN. Static variable in class duploss.tree.Tree
Top and bottom margin.
BASE_HEIGHT_SPACING. Static variable in class duploss.tree.Tree
Minimum vertical space between a node and any of its children.
BASE_LABEL_HEIGHT. Static variable in class duploss.tree.Tree
Height of label text.
BASE_LABEL_SPACE. Static variable in class duploss.tree.Tree
Vertical space between leaf nodes and leaf labels.
BASE_LEAF_WIDTH. Static variable in class duploss.tree.Tree
Horizontal space allocated for a leaf.
BASE_LOSS_BRANCH_LENGTH. Static variable in class duploss.tree.GeneTree
Length of branches representing a gene loss.
BASE_NODE_RADIUS. Static variable in class duploss.tree.Tree
Radius of a node.
BASE_ROOT_LENGTH. Static variable in class duploss.tree.SpeciesTree
Root length.
BASE_ROOT_RADIUS. Static variable in class duploss.tree.SpeciesTree
Radius of root.
BASE_ROOT_SPACING. Static variable in class duploss.tree.SpeciesTree
Additional vertical spacing before starting root branch edges.
BASE_W_TREE_MARGIN. Static variable in class duploss.tree.Tree
Left and right margin.
BASE_WIDTH_SPACING. Static variable in class duploss.tree.Tree
Horizontal space between two leaves.

C

CANCEL. Static variable in class duploss.gui.MessageDialog
Constant for CANCEL.
centerComponent(Component, Component). Static method in class duploss.Tools
Centers a GUI component relatively to some other component.
centerWindow(Window). Static method in class duploss.Tools
Centers a window on the screen.
clear(). Method in class duploss.gui.InputTreeFrame
Clears the current tree.
clear(). Method in class duploss.gui.ResultCanvas
Clears the canvas.
clear(). Method in class duploss.gui.TreeCanvas
Removes the tree.
CLEAR_CMD_STR. Static variable in class duploss.cmd.CommandReader
The clear command string.
clone(). Method in class duploss.geo.DPoint
Clones this object.
clone(). Method in class duploss.geo.Line
Clones this line.
clone(). Method in class duploss.tree.Node
Clones the tree rooted at this node.
clone(). Method in class duploss.tree.SpeciesNode
Clones the tree rooted at this node.
clone(). Method in class duploss.tree.Tree
Clones the entire tree.
close(). Method in class duploss.gui.TextAreaWriter
Closes the stream.
close(). Method in class duploss.tree.TreeReader
Closes the input stream.
CommandArgException(). Constructor for class duploss.cmd.CommandArgException
Construct a command exception with no detailed message.
CommandArgException(String). Constructor for class duploss.cmd.CommandArgException
Construct a command exception with a detailed message.
CommandException(). Constructor for class duploss.cmd.CommandException
Construct a command exception with no detailed message.
CommandException(String). Constructor for class duploss.cmd.CommandException
Construct a command exception with a detailed message.
CommandFormatException(). Constructor for class duploss.cmd.CommandFormatException
Construct a command exception with no detailed message.
CommandFormatException(String). Constructor for class duploss.cmd.CommandFormatException
Construct a command exception with a detailed message.
CommandInterpreter(DupLossEnv). Constructor for class duploss.cmd.CommandInterpreter
Construct a command interpreter.
CommandInterpreter(DupLossEnv, boolean). Constructor for class duploss.cmd.CommandInterpreter
Construct a command interpreter.
CommandInterpreter(Reader, PrintWriter, DupLossEnv). Constructor for class duploss.cmd.CommandInterpreter
Construct a command interpreter.
CommandInterpreter(Reader, PrintWriter, DupLossEnv, boolean). Constructor for class duploss.cmd.CommandInterpreter
Construct a command interpreter.
CommandReader(Reader). Constructor for class duploss.cmd.CommandReader
Construct a command reader.
CommandTokenizer(Reader). Constructor for class duploss.cmd.CommandTokenizer
Constructs a tokenizer.
componentHidden(ComponentEvent). Method in class duploss.gui.DupLossFrame
Does nothing (ComponentListener implementation).
componentMoved(ComponentEvent). Method in class duploss.gui.DupLossFrame
Does nothing (ComponentListener implementation).
componentResized(ComponentEvent). Method in class duploss.gui.DupLossFrame
Recomputes canvas sizes and rescale trees every time the window is resized.
componentShown(ComponentEvent). Method in class duploss.gui.DupLossFrame
Does nothing (ComponentListener implementation).
computeCoordinates(). Method in class duploss.tree.Tree
Computes the coordinates for each node in the tree.
computeCoordinates(double, double). Method in class duploss.tree.Tree
Computes the coordinates of each node.
computeLabelLeafMapping(). Method in class duploss.tree.Tree
Precomputes all mappings label to leaf.
computeLCA(). Method in class duploss.tree.Tree
Computes the LCA for all pair of nodes.
computeMapping(SpeciesTree). Method in class duploss.tree.GeneTree
Computes the mappings.
computeSpace(). Method in class duploss.tree.Tree
Computes the space required by the tree rooted at each node.
CONTROL_WIN_HEIGHT. Static variable in class duploss.gui.DupLossFrame
Height in pixel of control panel.
ControlListener(DupLossFrame, TextField, TextField, TextField, TextArea, ResultCanvas). Constructor for class duploss.gui.ControlListener
Constructs a control listener.

D

desc. Variable in class duploss.Option
Optional short description (recommended).
destroy(). Method in class duploss.plus.DupLossApplet
Releases resources used.
discard(). Method in class duploss.cmd.CommandReader
Reads until it reaches either EOL or EOF, discarding any characters encountered.
distance(DPoint). Method in class duploss.geo.DPoint
Computes the distance between two points.
DPoint(double, double). Constructor for class duploss.geo.DPoint
Constructs a point (x,y).
DPoint(DPoint). Constructor for class duploss.geo.DPoint
Constructs a point that is a copy of p.
draw(Graphics). Method in class duploss.tree.Tree
Draws the tree.
drawCircle(Graphics, DPoint, int). Static method in class duploss.Tools
Draws a filled circle.
drawCircle(Graphics, int, int, int). Static method in class duploss.Tools
Draws a filled circle.
drawDashedLine(Graphics, double, double, double, double). Static method in class duploss.Tools
Draws a dashed line representing a gene loss.
drawDashedLine(Graphics, DPoint, DPoint). Static method in class duploss.Tools
Draws a dashed line representing a gene loss.
drawGeneTree(Graphics). Method in class duploss.tree.GeneTree
Draws the gene tree inside the species tree.
drawLine(Graphics, DPoint, double, double). Static method in class duploss.Tools
Draws a line between two points.
drawLine(Graphics, DPoint, DPoint). Static method in class duploss.Tools
Draws a line between two points.
drawRectCenter(Graphics, double, double, double, double). Static method in class duploss.Tools
Draws a filled rectangle.
drawRectCenter(Graphics, DPoint, double, double). Static method in class duploss.Tools
Draws a filled rectangle.
drawSpeciesTree(Graphics). Method in class duploss.tree.SpeciesTree
Draws the species tree (as a large tree).
drawSquare(Graphics, double, double, double). Static method in class duploss.Tools
Draws a filled square.
drawSquare(Graphics, DPoint, double). Static method in class duploss.Tools
Draws a filled square.
DUPLOSS_TITLE. Static variable in class duploss.DupLoss
Constant string containing the title of the application.
DUPLOSS_VERSION. Static variable in class duploss.DupLoss
Constant string containing the current version information.
DupLossApplet(). Constructor for class duploss.plus.DupLossApplet
DupLossFrame(). Constructor for class duploss.gui.DupLossFrame
Constructs the main window.
DupLossServer(int). Constructor for class duploss.plus.DupLossServer
Constructs a server that will listen on the specified port.

E

EnterLabelDialog(Frame, Vector). Constructor for class duploss.gui.EnterLabelDialog
Constructs the dialog window.
EOF_CMD. Static variable in class duploss.cmd.CommandReader
Special command type : No more commands, end-of-file has been read.
eps. Variable in class duploss.geo.DPoint
Maximum difference allowed between corresponding coordinates of two points for them to be considered as equal.
eps. Static variable in class duploss.geo.Line
Acceptable difference for equality to zero in some computations.
equals(Object). Method in class duploss.geo.DPoint
Checks if this point is equal to p.
equals(Object). Method in class duploss.tree.NodePair
Checks for equality.
EXIT_CMD_STR. Static variable in class duploss.cmd.CommandReader
The exit command string.

F

flush(). Method in class duploss.gui.TextAreaWriter
Flushes the buffer to the stream.

G

GENE1_TYPE_STR. Static variable in class duploss.cmd.CommandReader
Gene tree type string.
GENE2_TYPE_STR. Static variable in class duploss.cmd.CommandReader
Gene tree type string.
GENE_TREE_TYPE. Static variable in class duploss.tree.TreeReader
Tree of type GeneTree.
GeneLeafNode(). Constructor for class duploss.tree.GeneLeafNode
Constructs a leaf node with no labels.
GeneLeafNode(String). Constructor for class duploss.tree.GeneLeafNode
Constructs a leaf node and sets its label.
GeneNode(). Constructor for class duploss.tree.GeneNode
Constructs a node with no children.
GeneNode(GeneNode, GeneNode). Constructor for class duploss.tree.GeneNode
Constructs a node and sets its children.
GENERAL_TREE_TYPE. Static variable in class duploss.tree.TreeReader
Tree of type Tree.
GeneTree(). Constructor for class duploss.tree.GeneTree
Construct an empty gene tree.
GeneTree(GeneNode). Constructor for class duploss.tree.GeneTree
Construct a gene tree.
get(Node, Node). Method in class duploss.tree.LCA
Returns the LCA of u and v.
get(NodePair). Method in class duploss.tree.LCA
Returns the LCA of the pair of nodes.
getAppletInfo(). Method in class duploss.plus.DupLossApplet
Returns a string containing info about the applet.
getB(). Method in class duploss.geo.Line
Returns the y-intercept.
getCommand(). Method in class duploss.gui.MessageDialog
Returns the user's choice.
getCopyNb(). Method in class duploss.tree.GeneNode
Gets the copy number.
getFactor(). Method in class duploss.gui.ZoomFrame
Returns the zoom factor.
getGeneTree(). Method in interface duploss.gui.DupLossEnv
Returns the gene tree.
getGeneTree(). Method in class duploss.gui.DupLossFrame
Returns the gene tree currently set.
getGeneTree(). Method in class duploss.gui.ResultCanvas
Returns the gene tree.
getHeight(). Method in class duploss.tree.Node
Returns the height of the tree.
getHeight(). Method in class duploss.tree.SpeciesTree
Returns this tree height.
getHeight(). Method in class duploss.tree.Tree
Returns the height of the tree.
getLabel(). Method in class duploss.tree.GeneLeafNode
Returns the label.
getLabel(). Method in interface duploss.tree.Leaf
Returns the label associated with a Leaf
getLabel(). Method in class duploss.tree.LeafNode
Returns the label.
getLabel(). Method in class duploss.tree.SpeciesLeafNode
Returns the label.
getLeft(). Method in class duploss.tree.Node
Returns the left child.
getLeftPoint(). Method in class duploss.tree.SpeciesNode
Returns the left point.
getMapping(). Method in class duploss.tree.GeneNode
Returns the mapping.
getMiddlePoint(). Method in class duploss.tree.SpeciesNode
Returns the middle point.
getNode(String). Method in class duploss.tree.Tree
Returns the node labelled label.
getNormalAt(DPoint). Method in class duploss.geo.Line
Computes the normal.
getOption(String). Method in class duploss.OptionsTable
Gets an option.
getParameterInfo(). Method in class duploss.plus.DupLossApplet
Returns info about valid parameters.
getParent(). Method in class duploss.tree.Node
Returns the parent.
getPoint(). Method in class duploss.tree.Node
Returns the coordinates.
getResultGTree(). Method in class duploss.gui.DupLossFrame
Returns the gene tree displayed in the result window.
getResultSTree(). Method in class duploss.gui.DupLossFrame
Returns the species tree displayed in the result window.
getRight(). Method in class duploss.tree.Node
Returns the right child.
getRightPoint(). Method in class duploss.tree.SpeciesNode
Returns the right point.
getRoot(). Method in class duploss.tree.Tree
Returns the root.
getSlope(). Method in class duploss.geo.Line
Returns the slope.
getSpeciesTree(). Method in interface duploss.gui.DupLossEnv
Returns the species tree.
getSpeciesTree(). Method in class duploss.gui.DupLossFrame
Returns the species tree currently set.
getSpeciesTree(). Method in class duploss.gui.ResultCanvas
Returns the species tree.
getStringRep(). Method in class duploss.tree.GeneLeafNode
Returns a string represention of the leaf.
getStringRep(). Method in class duploss.tree.LeafNode
Returns a string represention of the leaf.
getStringRep(). Method in class duploss.tree.Node
Returns a string represention of the tree rooted at this node.
getStringRep(). Method in class duploss.tree.SpeciesLeafNode
Returns a string represention of the leaf.
getStringRep(). Method in class duploss.tree.Tree
Returns the string representation of the tree.
getValue(String). Method in class duploss.OptionsTable
Returns the value of an option.
getWidth(). Method in class duploss.tree.Node
Returns the width of the tree.
getWidth(). Method in class duploss.tree.SpeciesTree
Returns this tree width.
getWidth(). Method in class duploss.tree.Tree
Returns the width of the tree.
getX(). Method in class duploss.tree.Node
Returns the x-coordinate.
getXScale(). Method in class duploss.tree.Tree
Returns the horizontal scaling factor.
getY(). Method in class duploss.tree.Node
Returns the y-coordinate.
getYScale(). Method in class duploss.tree.Tree
Returns the vertical scaling factor.

H

hashCode(). Method in class duploss.tree.NodePair
Returns a hash code for this pair.
height. Variable in class duploss.tree.Node
Height of rectangle enclosing subtree rooted at this node.
heightSpacing. Variable in class duploss.tree.Tree
Minimum vertical space between a node and any of its children.
HELP_CMD. Static variable in class duploss.cmd.CommandReader
The help command type.
HELP_CMD_STR. Static variable in class duploss.cmd.CommandReader
The help command string.
HELP_STRING. Static variable in class duploss.cmd.CommandInterpreter
String describing all available commands.
hTreeMargin. Variable in class duploss.tree.Tree
Top and bottom margin.

I

in. Variable in class duploss.tree.TreeReader
The stream where this tree reader takes its input.
init(). Method in class duploss.plus.DupLossApplet
Initializes the applet.
InputTreeFrame(DupLossFrame, PrintWriter). Constructor for class duploss.gui.InputTreeFrame
Construct a window to input a tree.
intersect(Line). Method in class duploss.geo.Line
Computes the intersection point of this line and line l2.
intersectsUnique(Line). Method in class duploss.geo.Line
Checks if this line intersects with l2 at a unique point.
isDuplication(). Method in class duploss.tree.GeneNode
Checks if this node is a duplication node.
isLeaf(). Method in class duploss.tree.Node
Returns true if it is a Leaf.
isRoot(). Method in class duploss.tree.Node
Returns true if it is the root.
isSet(). Method in class duploss.Option
Checks if it is on.
isSet(String). Method in class duploss.OptionsTable
Checks if an option is set.
itemStateChanged(ItemEvent). Method in class duploss.gui.ControlListener
Invoked when an ItemEvent is received.

L

labelHeight. Variable in class duploss.tree.Tree
Height of label text.
LabelListener(Frame, TextField, Leaf). Constructor for class duploss.gui.LabelListener
Contructs a label listener.
labelSpace. Variable in class duploss.tree.Tree
Vertical space between leaf nodes and leaf labels.
LCA(). Constructor for class duploss.tree.LCA
Constructs an empty LCA collection.
LeafNode(). Constructor for class duploss.tree.LeafNode
Constructs a leaf node with no labels.
LeafNode(String). Constructor for class duploss.tree.LeafNode
Constructs a leaf node and sets its label.
leafWidth. Variable in class duploss.tree.Tree
Horizontal space allocated for a leaf.
left. Variable in class duploss.tree.Node
This node's left child.
LegendCanvas(). Constructor for class duploss.gui.LegendCanvas
Constructs a legend canvas.
Line(double, double). Constructor for class duploss.geo.Line
Constructs a line.
Line(double, DPoint). Constructor for class duploss.geo.Line
Constructs a line.
Line(DPoint, DPoint). Constructor for class duploss.geo.Line
Constructs a line.
lineWrap(String, int). Static method in class duploss.Tools
Splits a single line String to multiple lines of maximum width w.
LIST_CMD. Static variable in class duploss.cmd.CommandReader
The list command type.
LIST_CMD_STR. Static variable in class duploss.cmd.CommandReader
The list command string.
LIST_WIDTH. Static variable in class duploss.cmd.CommandInterpreter
Width in characters of directory listing.
LOAD_CMD. Static variable in class duploss.cmd.CommandReader
The load command type.
LOAD_CMD_STR. Static variable in class duploss.cmd.CommandReader
The load command string.
LOADTREE_CMD. Static variable in class duploss.cmd.CommandReader
The loadtree command type.
LOADTREE_CMD_STR. Static variable in class duploss.cmd.CommandReader
The loadtree command string.

M

main(String[]). Static method in class duploss.DupLoss
Entry point of program.
main(String[]). Static method in class duploss.plus.DupLossServer
Runs the server.
MappingException(). Constructor for class duploss.tree.MappingException
Constructs a mapping exception with no specific message.
MappingException(String). Constructor for class duploss.tree.MappingException
Constructs a mapping exception with message msg.
MessageDialog(Frame, String, String, int). Constructor for class duploss.gui.MessageDialog
Contructs a message dialog window.
MessageFrame(String, String). Constructor for class duploss.gui.MessageFrame
Constructs a new message window.
mouseClicked(MouseEvent). Method in class duploss.gui.InputTreeFrame
Receives and processes MouseEvent.
mouseClicked(MouseEvent). Method in class duploss.gui.ZoomFrame
Moves trees in zoom window to show the region identified by a mouse click in the result canvas.
mouseEntered(MouseEvent). Method in class duploss.gui.InputTreeFrame
Does nothing (MouseListener implementation).
mouseEntered(MouseEvent). Method in class duploss.gui.ZoomFrame
Does nothing (MouseListener implementation).
mouseExited(MouseEvent). Method in class duploss.gui.InputTreeFrame
Does nothing (MouseListener implementation).
mouseExited(MouseEvent). Method in class duploss.gui.ZoomFrame
Does nothing (MouseListener implementation).
mousePressed(MouseEvent). Method in class duploss.gui.InputTreeFrame
Does nothing (MouseListener implementation).
mousePressed(MouseEvent). Method in class duploss.gui.ZoomFrame
Does nothing (MouseListener implementation).
mouseReleased(MouseEvent). Method in class duploss.gui.InputTreeFrame
Does nothing (MouseListener implementation).
mouseReleased(MouseEvent). Method in class duploss.gui.ZoomFrame
Does nothing (MouseListener implementation).
move(double). Method in class duploss.geo.Line
Moves a line in its normal direction.

N

name. Variable in class duploss.Option
Option name.
NEW_CMD. Static variable in class duploss.cmd.CommandReader
The new command type.
NEW_CMD_STR. Static variable in class duploss.cmd.CommandReader
The new command string.
nextToken(). Method in class duploss.cmd.CommandTokenizer
Reads the next token.
NO. Static variable in class duploss.gui.MessageDialog
Constant for NO.
NO_CMD. Static variable in class duploss.cmd.CommandReader
Special command type: The "empty" command, a blank line.
Node(). Constructor for class duploss.tree.Node
Constructs a node with no children.
Node(Node, Node). Constructor for class duploss.tree.Node
Constructs a node and sets its children.
NodePair(Node, Node). Constructor for class duploss.tree.NodePair
Constructs a pair of nodes.
nodeRadius. Variable in class duploss.tree.Tree
Radius of a node.
NoMappingException(). Constructor for class duploss.tree.NoMappingException
Constructs a no mapping exception.

O

OK. Static variable in class duploss.gui.MessageDialog
Constant for OK.
Option(String). Constructor for class duploss.Option
Constructs an option with the specified name.
Option(String, boolean). Constructor for class duploss.Option
Constructs an option.
Option(String, String, boolean). Constructor for class duploss.Option
Constructs an option.
options. Static variable in class duploss.DupLoss
Options of the application.
options(). Method in class duploss.OptionsTable
Returns an enumeration of all Option objects contained in the table.
OPTIONS_CMD. Static variable in class duploss.cmd.CommandReader
The options command type.
OPTIONS_CMD_STR. Static variable in class duploss.cmd.CommandReader
The options command string.
OptionsTable(). Constructor for class duploss.OptionsTable
Constructs an empty option table.
OptionsTable(Option[]). Constructor for class duploss.OptionsTable
Constructs an option table.
OTHER_TYPE_STR. Static variable in class duploss.cmd.CommandReader
Other tree type string.

P

paint(Graphics). Method in class duploss.gui.LegendCanvas
Draws the legend.
paint(Graphics). Method in class duploss.gui.ResultCanvas
Draws the trees.
paint(Graphics). Method in class duploss.gui.TreeCanvas
Draws the tree and the title.
parent. Variable in class duploss.tree.Node
This node's parent.
point. Variable in class duploss.tree.Node
Coordinates of the node.
prepare(). Method in class duploss.tree.Tree
Prepares the tree to be drawn.
prepareOther(). Method in class duploss.tree.SpeciesTree
Computes other necessary values.
prepareOther(). Method in class duploss.tree.Tree
Does any other compution needed to prepare the tree.
put(Node, Node, Node). Method in class duploss.tree.LCA
Stores a new LCA information.
put(NodePair, Node). Method in class duploss.tree.LCA
Stores a new LCA information.

Q

QUIT_CMD. Static variable in class duploss.cmd.CommandReader
The quit command type.
QUIT_CMD_STR. Static variable in class duploss.cmd.CommandReader
The quit command string.

R

read(char[], int, int). Method in class duploss.tree.TreeReader
Reads characters into cbuf.
readArg(). Method in class duploss.cmd.CommandReader
Reads a command argument.
readEOL(). Method in class duploss.cmd.CommandReader
Reads end-of-line.
readGeneTree(). Method in class duploss.tree.TreeReader
Reads a gene tree.
readSpeciesTree(). Method in class duploss.tree.TreeReader
Reads a species tree.
readTree(). Method in class duploss.tree.TreeReader
Reads a tree.
readTree(int). Method in class duploss.tree.TreeReader
Reads a tree.
readTreeType(). Method in class duploss.cmd.CommandReader
Reads a tree type argument.
readType(). Method in class duploss.cmd.CommandReader
Reads the command key word.
recomputeCoordInS(). Method in class duploss.tree.GeneTree
Recomputes the coordinates of the gene tree inside the species tree.
recomputeTrees(). Method in interface duploss.gui.DupLossEnv
Performs all coordinates computations and rescaling on both trees.
recomputeTrees(). Method in class duploss.gui.DupLossFrame
Recomputes coordinates and rescaling of both trees.
removeGeneTree(). Method in class duploss.gui.DupLossFrame
Removes the gene tree.
removeSpeciesTree(). Method in class duploss.gui.DupLossFrame
Removes the species tree.
removeTrees(). Method in interface duploss.gui.DupLossEnv
Removes all trees.
removeTrees(). Method in class duploss.gui.DupLossFrame
Removes all trees.
rescaleOther(). Method in class duploss.tree.SpeciesTree
Rescales length variables.
rescaleOther(). Method in class duploss.tree.Tree
Rescales other lengths variables and tree components.
rescaleOtherLengths(). Method in class duploss.tree.GeneTree
Rescales gene tree specific length variables.
rescaleOtherLengths(). Method in class duploss.tree.Tree
Rescales other lengths variables.
reset(). Method in class duploss.Option
Turns off the option.
RESET_CMD. Static variable in class duploss.cmd.CommandReader
The reset command type.
RESET_CMD_STR. Static variable in class duploss.cmd.CommandReader
The reset command string.
resetOption(String). Method in class duploss.OptionsTable
Turns off an option
ResultCanvas(). Constructor for class duploss.gui.ResultCanvas
Constructs an empty result canvas.
ResultCanvas(SpeciesTree, GeneTree). Constructor for class duploss.gui.ResultCanvas
Constructs a result canvas containing the specified tree.
rezoom(). Method in class duploss.gui.ControlListener
Updates the zoom window if it is opened.
rezoom(). Method in class duploss.gui.ZoomFrame
Rezooms using current factor.
right. Variable in class duploss.tree.Node
This node's right child
root. Variable in class duploss.tree.Tree
Root of the tree.
run(). Method in class duploss.cmd.CommandInterpreter
Runs the command interpreter.

S

SAVE_CMD. Static variable in class duploss.cmd.CommandReader
The save command type.
SAVE_CMD_STR. Static variable in class duploss.cmd.CommandReader
The save command string.
SAVEF_CMD. Static variable in class duploss.cmd.CommandReader
The save force command type.
SAVEF_CMD_STR. Static variable in class duploss.cmd.CommandReader
The save force command string.
scale(double). Method in class duploss.tree.Tree
Scales the tree by a factor.
scale(double, double). Method in class duploss.tree.Tree
Scales the tree by the specified factors.
scaleLengthsTo(double, double). Method in class duploss.tree.Tree
Scales only the length variables to the specified factors.
scaleTo(Dimension). Method in class duploss.tree.Tree
Scales the tree to the specified size.
scaleTo(double, double). Method in class duploss.tree.Tree
Scales the tree to the specified size.
SCREEN_MARGIN. Static variable in class duploss.gui.DupLossFrame
Extra fix amount of space between the main window and the border of the screen.
selectionSort(String[]). Static method in class duploss.Tools
Sorts an array of Strings in increasing order.
set(). Method in class duploss.Option
Turns on the option.
SET_CMD. Static variable in class duploss.cmd.CommandReader
The set command type.
SET_CMD_STR. Static variable in class duploss.cmd.CommandReader
The set command string.
setCopyNb(int). Method in class duploss.tree.GeneNode
Sets the copy number.
setDimensions(double, double). Method in class duploss.tree.Node
Sets the width and height a rectangle containing the tree rooted at this node.
setDuplication(boolean). Method in class duploss.tree.GeneNode
Marks this node as being a duplication node.
setGeneTree(GeneTree). Method in interface duploss.gui.DupLossEnv
Sets the gene tree.
setGeneTree(GeneTree). Method in class duploss.gui.DupLossFrame
Sets the gene tree.
setGeneTree(GeneTree). Method in class duploss.gui.ResultCanvas
Sets the gene tree.
setLabel(String). Method in class duploss.tree.GeneLeafNode
Sets the label.
setLabel(String). Method in interface duploss.tree.Leaf
Labels a Leaf
setLabel(String). Method in class duploss.tree.LeafNode
Sets the label.
setLabel(String). Method in class duploss.tree.SpeciesLeafNode
Sets the label.
setLeft(Node). Method in class duploss.tree.Node
Sets the left child.
setLeftPoint(DPoint). Method in class duploss.tree.SpeciesNode
Sets the left point.
setMapping(SpeciesNode). Method in class duploss.tree.GeneNode
Sets the mapping.
setMiddlePoint(DPoint). Method in class duploss.tree.SpeciesNode
Sets the middle point.
setOption(String). Method in class duploss.OptionsTable
Turns on an option
setParent(Node). Method in class duploss.tree.Node
Sets the parent.
setPoint(double, double). Method in class duploss.tree.Node
Sets the coordinates.
setPoint(DPoint). Method in class duploss.tree.Node
Sets the coordinates.
setPrompt(boolean). Method in class duploss.cmd.CommandInterpreter
Enables or disables the prompt.
setRight(Node). Method in class duploss.tree.Node
Sets the right child.
setRightPoint(DPoint). Method in class duploss.tree.SpeciesNode
Sets the right point.
setRoot(Node). Method in class duploss.tree.Tree
Sets the root.
setSpeciesTree(SpeciesTree). Method in interface duploss.gui.DupLossEnv
Sets the species tree.
setSpeciesTree(SpeciesTree). Method in class duploss.gui.DupLossFrame
Sets the species tree.
setSpeciesTree(SpeciesTree). Method in class duploss.gui.ResultCanvas
Sets the species tree.
setTree(Tree). Method in class duploss.gui.TreeCanvas
Sets the tree.
setTrees(SpeciesTree, GeneTree). Method in class duploss.gui.ResultCanvas
Sets the trees.
setValue(boolean). Method in class duploss.Option
Sets its value.
setValue(String, boolean). Method in class duploss.OptionsTable
Sets the value of an option.
size(). Method in class duploss.OptionsTable
Returns the number of options in the table.
slope(DPoint). Method in class duploss.geo.DPoint
Returns the slope between this point and p2.
spaces(int). Static method in class duploss.Tools
Returns a string of spaces.
SPECIES_TREE_TYPE. Static variable in class duploss.tree.TreeReader
Tree of type SpeciesTree.
SPECIES_TYPE_STR. Static variable in class duploss.cmd.CommandReader
Species tree type string.
SpeciesLeafNode(). Constructor for class duploss.tree.SpeciesLeafNode
Constructs a leaf node with no labels.
SpeciesLeafNode(String). Constructor for class duploss.tree.SpeciesLeafNode
Constructs a leaf node and sets its label.
SpeciesNode(). Constructor for class duploss.tree.SpeciesNode
Constructs a node with no children.
SpeciesNode(SpeciesNode, SpeciesNode). Constructor for class duploss.tree.SpeciesNode
Constructs a node and sets its children.
SpeciesTree(). Constructor for class duploss.tree.SpeciesTree
Contructs an empty tree.
SpeciesTree(SpeciesNode). Constructor for class duploss.tree.SpeciesTree
Contructs a tree with specified root.
start(). Method in class duploss.plus.DupLossApplet
Shows the window.
start(). Method in class duploss.plus.DupLossServer
Starts the server.
stop(). Method in class duploss.plus.DupLossApplet
Hides the window.
sval. Variable in class duploss.cmd.CommandTokenizer
This variable contains the word token that has been read.

T

TextAreaWriter(TextArea). Constructor for class duploss.gui.TextAreaWriter
Contructs a writer.
textValueChanged(TextEvent). Method in class duploss.gui.LabelListener
Invoked when the text field is modified.
Tools(). Constructor for class duploss.Tools
toString(). Method in class duploss.geo.DPoint
Returns a string describing this point.
toString(). Method in class duploss.geo.Line
Returns a string representation describing this line.
toString(). Method in class duploss.tree.Node
Returns a string describing the node.
toString(). Method in class duploss.tree.Tree
Returns a string describing the tree.
translate(Point). Method in class duploss.gui.ResultCanvas
Translates the origin.
Tree(). Constructor for class duploss.tree.Tree
Constructs the empty tree.
Tree(Node). Constructor for class duploss.tree.Tree
Constructs a tree with the given root.
TREE_CMD. Static variable in class duploss.cmd.CommandReader
The tree command type.
TREE_CMD_STR. Static variable in class duploss.cmd.CommandReader
The tree command string.
TreeCanvas(). Constructor for class duploss.gui.TreeCanvas
Constructs an empty tree canvas with no title.
TreeCanvas(String). Constructor for class duploss.gui.TreeCanvas
Constructs an empty tree canvas with the specified title.
TreeCanvas(Tree). Constructor for class duploss.gui.TreeCanvas
Constructs a tree canvas with the specified tree.
TreeCanvas(Tree, String). Constructor for class duploss.gui.TreeCanvas
Constructs a tree canvas with the specified tree and title.
TreeFormatException(String). Constructor for class duploss.tree.TreeFormatException
Constructs a tree format exception with a detailed message.
TreeFormatException(String, int). Constructor for class duploss.tree.TreeFormatException
Constructs a tree format exception with a detailed message.
TreeReader(Reader). Constructor for class duploss.tree.TreeReader
Constructs a tree reader that will read from in.
TT_EOF. Static variable in class duploss.cmd.CommandTokenizer
This constant indicates that the end of the file has been read.
TT_EOL. Static variable in class duploss.cmd.CommandTokenizer
This constant indicates that the end of line has been read.
TT_WORD. Static variable in class duploss.cmd.CommandTokenizer
This constant indicates that a word token has been read.
ttype. Variable in class duploss.cmd.CommandTokenizer
This variable contains the type of token read.

U

u. Variable in class duploss.tree.NodePair
A node.
UnknownCommandException(String). Constructor for class duploss.cmd.UnknownCommandException
Constructs a command exception.
UnknownOptionException(String). Constructor for class duploss.UnknownOptionException
Constructs an unknown option exception.
updateGUIOptions(). Method in interface duploss.gui.DupLossEnv
Updates the GUI component displaying the current options (ex: check boxes).
updateGUIOptions(). Method in class duploss.gui.DupLossFrame
Updates the checkboxes state to reflect the options currently set.

V

v. Variable in class duploss.tree.NodePair
A node.
value. Variable in class duploss.Option
Flag stating whether the option is set or not.

W

width. Variable in class duploss.tree.Node
Width of rectangle enclosing subtree rooted at this node.
widthSpacing. Variable in class duploss.tree.Tree
Horizontal space between two leaves.
windowActivated(WindowEvent). Method in class duploss.gui.ControlListener
Does nothing (WindowListener implementation).
windowActivated(WindowEvent). Method in class duploss.gui.DupLossFrame
Does nothing (WindowListener implementation).
windowActivated(WindowEvent). Method in class duploss.gui.MessageFrame
Does nothing (WindowListener implementation).
windowClosed(WindowEvent). Method in class duploss.gui.ControlListener
Does nothing (WindowListener implementation).
windowClosed(WindowEvent). Method in class duploss.gui.DupLossFrame
Does nothing (WindowListener implementation).
windowClosed(WindowEvent). Method in class duploss.gui.MessageFrame
Does nothing (WindowListener implementation).
windowClosing(WindowEvent). Method in class duploss.gui.ControlListener
Closes the zoom window.
windowClosing(WindowEvent). Method in class duploss.gui.DupLossFrame
Exits the application.
windowClosing(WindowEvent). Method in class duploss.gui.MessageFrame
Closes the message window.
windowDeactivated(WindowEvent). Method in class duploss.gui.ControlListener
Does nothing (WindowListener implementation).
windowDeactivated(WindowEvent). Method in class duploss.gui.DupLossFrame
Does nothing (WindowListener implementation).
windowDeactivated(WindowEvent). Method in class duploss.gui.MessageFrame
Does nothing (WindowListener implementation).
windowDeiconified(WindowEvent). Method in class duploss.gui.ControlListener
Does nothing (WindowListener implementation).
windowDeiconified(WindowEvent). Method in class duploss.gui.DupLossFrame
Does nothing (WindowListener implementation).
windowDeiconified(WindowEvent). Method in class duploss.gui.MessageFrame
Does nothing (WindowListener implementation).
windowIconified(WindowEvent). Method in class duploss.gui.ControlListener
Does nothing (WindowListener implementation).
windowIconified(WindowEvent). Method in class duploss.gui.DupLossFrame
Does nothing (WindowListener implementation).
windowIconified(WindowEvent). Method in class duploss.gui.MessageFrame
Does nothing (WindowListener implementation).
windowOpened(WindowEvent). Method in class duploss.gui.ControlListener
Does nothing (WindowListener implementation).
windowOpened(WindowEvent). Method in class duploss.gui.DupLossFrame
Does nothing (WindowListener implementation).
windowOpened(WindowEvent). Method in class duploss.gui.MessageFrame
Does nothing (WindowListener implementation).
write(char[], int, int). Method in class duploss.gui.TextAreaWriter
Writes len bytes from cbuf[] starting at offset off.
wTreeMargin. Variable in class duploss.tree.Tree
Left and right margin.

X

x. Variable in class duploss.geo.DPoint
The x coordinate.
xDistance(DPoint). Method in class duploss.geo.DPoint
Computes the difference between the x-coordinates.
xScale. Variable in class duploss.tree.Tree
Horizontal scaling factor.

Y

y. Variable in class duploss.geo.DPoint
The y coordinate.
yDistance(DPoint). Method in class duploss.geo.DPoint
Computes the difference between the y-coordinates.
YES. Static variable in class duploss.gui.MessageDialog
Constant for YES.
yScale. Variable in class duploss.tree.Tree
Vertical scaling factor.