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

A

accept(File) - Method in class org.biolegato.gdesupport.canvas.colourmask.CharacterColourMaskReader

Determines whether a file is of type "character colour mask"

accept(File) - Method in class org.biolegato.gdesupport.canvas.colourmask.GDEColourMaskFile

actionPerformed(ActionEvent) - Method in class org.biolegato.gdesupport.canvas.colourmask.ImportFileAction

Performs all of the import file functionality.

actionPerformed(ActionEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDESequenceWindow

Adds an action handler to update the sequence data based on the window's values.

actionPerformed(ActionEvent) - Method in class org.biolegato.gdesupport.canvas.list.SelectByNameWindow

Handles the button commands for the given window.

addCursorListener(CursorListener) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Adds a cursor listener to the BLTextArea.

addListDataListener(ListDataListener) - Method in class org.biolegato.gdesupport.canvas.list.SequenceListModel

Adds a data listener to the list model

addMasks(ColourMap[], JComboBox) - Static method in class org.biolegato.gdesupport.canvas.colourmask.ImportFileAction

Loads colour masks into biolegato.

addModeListener(ModeListener) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Adds a cursor listener to the BLTextArea.

addPopupMenuItem(JMenuItem) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Adds an item to the GDEList's popup menu

addPopupMenuItem(JMenuItem) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Adds an item to the BLTextArea's right-click popup menu.

addUndo(Undoable) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Adds an undoable object to the undo stack.

addUndo(Undoable) - Method in class org.biolegato.gdesupport.canvas.undo.UndoMulti

Adds an undoable to the undo multi

B

background - Variable in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

The current default background colour of normal unselected text

backgroundSelect - Variable in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

The current default background colour of normal selected text

BLComponent - Class in org.biolegato.gdesupport.canvas.textarea

BLComponent() - Constructor for class org.biolegato.gdesupport.canvas.textarea.BLComponent

Creates a new instance of BLComponent

BLTextArea - Class in org.biolegato.gdesupport.canvas.textarea

A general canvas with more functionality support than JTextArea.

BLTextArea() - Constructor for class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Creates a new instance of BLTextArea

blTextAreaSelf - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Self-reference for inner classes.

C

changeCase() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Changes the case of the currently selected sequence (if the sequence is of inconsistent case, the case of the entire sequence is changed to the opposite case of the first character in the sequence.

changeCase() - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Changes the case of the currently selected sequence (if the sequence is of inconsistent case, the case of the entire sequence is changed to the opposite case of the first character in the sequence.

changeCase() - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Changes the case of the currently selected sequence (if the sequence is of inconsistent case, the case of the entire sequence is changed to the opposite case of the first character in the sequence.

changeCaseAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

The action "Change Case"

changePosition(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Updates/moves the cursor to the new position.

CharacterColourMap - Class in org.biolegato.gdesupport.canvas.colourmap

A colour map class that will give support for GDE style colour schemes

CharacterColourMap(String, Hashtable<Character, Color>) - Constructor for class org.biolegato.gdesupport.canvas.colourmap.CharacterColourMap

Creates a new instance of GDECharColourMap

CharacterColourMaskReader - Class in org.biolegato.gdesupport.canvas.colourmask

Used to select colour masks.

CharacterColourMaskReader() - Constructor for class org.biolegato.gdesupport.canvas.colourmask.CharacterColourMaskReader

Creates a new instance of GDEColourMaskFile

ColourMap - Class in org.biolegato.gdesupport.canvas.colourmap

The superclass of all colour maps.

ColourMap() - Constructor for class org.biolegato.gdesupport.canvas.colourmap.ColourMap

The abstract constructor for colour maps.

ColourMaskReader - Class in org.biolegato.gdesupport.canvas.colourmask

ColourMaskReader() - Constructor for class org.biolegato.gdesupport.canvas.colourmask.ColourMaskReader

colourMasks - Static variable in class org.biolegato.gdesupport.canvas.colourmask.ImportFileAction

The list of all colour masks loaded in the system.

column - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The current column of the caret.

column2X(int) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Converts a column number into a X co-ordinate

column2X(int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Converts a column number into a X co-ordinate

columnSize() - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Returns the size of one column of the textarea.

columnWidth - Variable in class org.biolegato.gdesupport.canvas.textarea.BLComponent

The width of each column in the textarea

copy() - Method in interface org.biolegato.gdesupport.canvas.Editable

Copies content from the current Editable object to the clipboads.

copy() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Copies content from the current Editable object to the clipboads.

copy() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Copies content from the current Editable object.

copy() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Copies content from the current Editable object.

copyAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

The action "Copy"

currentMap - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles printing text

cursorChange(BLTextArea, int, int) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Receives cursor updates for use in the status bar.

cursorChange(BLTextArea, int, int) - Method in interface org.biolegato.gdesupport.canvas.listeners.CursorListener

Communicates a change in cursor position.

CursorListener - Interface in org.biolegato.gdesupport.canvas.listeners

Used to communicate changes in the canvas cursor position.

cursorListeners - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Linked list to store all cursor listeners

cut() - Method in interface org.biolegato.gdesupport.canvas.Editable

Cuts content from the current Editable object to the clipboads.

cut() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Cuts content from the current Editable object to the clipboads.

cut() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Cuts content from the current Editable object.

cut() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Cuts content from the current Editable object.

cut() - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Cuts content from the current Editable object.

cut() - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Cuts content from the current Editable object.

cutAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

The action "Cut"

D

defaultColourMap - Static variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The default colour map for regular text in BLTextAreas

defaultGreyColourMap - Static variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The default colour map for greyed out text in BLTextAreas

delete() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Displays a window to edit the currently selected sequence's properties

delete(int, int, int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Deletes characters from the textarea's underlying SeqDoc NOTE: deletions are performed in a sequential manner

delete(int, int, int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Removes text from a document.

deleteSelection() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Used to delete the current selection before an insertion or as part of a deletion.

drawChars(BLTextArea, Graphics, int, int, char[], int, int, Color, Color) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

This is a function to help ensure proper spacing.

E

Editable - Interface in org.biolegato.gdesupport.canvas

An interface to group together all objects which support cut/copy/paste.

F

focusGained(FocusEvent) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

This function is used to determine whether to return the data in the JTextArea or JList when getData is called.

focusGained(FocusEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Used to control list display (when focused the list is colourful)

focusGained(FocusEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles activating the text area (changing colours from greyed out to normal).

focusLost(FocusEvent) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

This function is currently unused.

focusLost(FocusEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Used to control list display (when not focused the list is greyed out)

focusLost(FocusEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles deactivating the text area (changing colours from normal to greyed out).

foreground - Variable in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

The current default foreground colour of normal unselected text

foregroundSelect - Variable in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

The current default foreground colour of normal selected text

G

GDECanvas - Class in org.biolegato.gdesupport.canvas

The GDE-style sequence-based canvas class

GDECanvas() - Constructor for class org.biolegato.gdesupport.canvas.GDECanvas

Creates a new instance of BLGDECanvas

GDECanvasProperties - Class in org.biolegato.gdesupport.canvas

A class for adding GDE canvas specific properties to.

GDECanvasProperties(BLProperties) - Constructor for class org.biolegato.gdesupport.canvas.GDECanvasProperties

Creates a new GDECanvasProperties object.

gdeCanvasSelf - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

Self-reference for inner classes.

GDECharColourMap - Class in org.biolegato.gdesupport.canvas.colourmap

A colour map class that will give support for GDE style colour schemes

GDECharColourMap() - Constructor for class org.biolegato.gdesupport.canvas.colourmap.GDECharColourMap

Creates a new instance of GDECharColourMap

GDECharColourMap(Color, Color, Color, Color) - Constructor for class org.biolegato.gdesupport.canvas.colourmap.GDECharColourMap

Creates a new instance of GDECharColourMap

GDEColourMaskFile - Class in org.biolegato.gdesupport.canvas.colourmask

Used to select colour masks.

GDEColourMaskFile() - Constructor for class org.biolegato.gdesupport.canvas.colourmask.GDEColourMaskFile

Creates a new instance of GDEColourMaskFile

GDEList - Class in org.biolegato.gdesupport.canvas.list

The JList of sequences in the GDE canvas.

GDEList(GDECanvas) - Constructor for class org.biolegato.gdesupport.canvas.list.GDEList

Constructs a new GDEList

GDESequenceWindow - Class in org.biolegato.gdesupport.canvas.list

A window for editing sequence properties.

GDESequenceWindow(JFrame, Sequence[]) - Constructor for class org.biolegato.gdesupport.canvas.list.GDESequenceWindow

Creates a window for editing the properties of a given array of sequences.

GDETextArea - Class in org.biolegato.gdesupport.canvas.textarea

Custom text area for allowing box selection

GDETextArea() - Constructor for class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Constructs a new instance of GDETextArea.

getBackground() - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Returns the current default background colour for painting portions of the canvas without text.

getData() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Returns the current/selected data in the canvas.

getData() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Returns the currently selected data in the list.

getData() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Used to obtain all of the text selected within the document.

getDefaultColour(int) - Static method in class org.biolegato.gdesupport.canvas.colourmask.GDEColourMaskFile

Returns a standard colour from the properties

getDescription() - Method in class org.biolegato.gdesupport.canvas.colourmask.CharacterColourMaskReader

Returns the description of "character colour mask"

getDescription() - Method in class org.biolegato.gdesupport.canvas.colourmask.GDEColourMaskFile

getElementAt(int) - Method in class org.biolegato.gdesupport.canvas.list.SequenceListModel

Returns the names of sequences based on their line number.

getForeground() - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Returns the current default foreground colour for painting portions of the canvas without text.

getInfo() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Displays a window to edit the currently selected sequence's properties

getInfoAction - Variable in class org.biolegato.gdesupport.canvas.list.GDEList

The menu item "Get info..."

getInsertMode() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Returns the insertion mode status of the textarea.

getListModel() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Returns the current list model.

getMaxSX() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the maximum X co-ordinate of the selection area.

getMaxSY() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the maximum Y co-ordinate of the selection area.

getMinSX() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the minimum X co-ordinate of the selection area.

getMinSY() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the minimum Y co-ordinate of the selection area.

getName() - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Returns the name of the colour map.

getProtectAlignment(Sequence, String) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Checks a string against a sequence's alignment gap protection settings.

getProtectAmbiguous(Sequence, String) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Checks a string against a sequence's ambiguous character protection settings.

getProtectUnambiguous(Sequence, String) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Checks a string against a sequence's unambiguous character protection settings.

getSelectedItem() - Method in class org.biolegato.gdesupport.canvas.colourmask.ImportFileAction

Returns the current selected colour mask for the sequence.

getSeqDoc() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Returns the SeqDoc associated with the BLTextArea

getSize() - Method in class org.biolegato.gdesupport.canvas.list.SequenceListModel

Returns the number of sequences in the sequence document.

getSX1() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the starting X co-ordinate of the selection area.

getSX2() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the ending X co-ordinate of the selection area.

getSY1() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the starting Y co-ordinate of the selection area.

getSY2() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Gets the ending Y co-ordinate of the selection area.

getTabName() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Returns the name to display in the canvas tab for

greyedOutMap - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The colour map to use when the textarea is greyed out.

groupAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

Action for grouping sequences in the canvas

I

ImportFileAction - Class in org.biolegato.gdesupport.canvas.colourmask

The menu item to handle importing colour masks

ImportFileAction(JDialog, Object) - Constructor for class org.biolegato.gdesupport.canvas.colourmask.ImportFileAction

Creates a new ImportFileAction object.

insert(int, int, String) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Inserts a string into the textarea's underlying SeqDoc NOTE: this is a wrapper method for insert(x, y, data)

insert(int, int, Sequence[]) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Inserts an array of sequences into the textarea's underlying SeqDoc

insert(int, int, String) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Inserts a string into the textarea's underlying SeqDoc (NOTE: this should ONLY be called by sub-methods)

insertionMode(boolean) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Receives insertion mode change updates for use in the status bar.

insertionMode(boolean) - Method in interface org.biolegato.gdesupport.canvas.listeners.ModeListener

Communicates that the insertion mode has changed.

insertMode - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

If true new text will overwrite existing text.

invalidzone - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The colour of invalid areas in the textarea.

isEmpty() - Method in class org.biolegato.gdesupport.canvas.undo.UndoMulti

Checks if the undo multi contains any undoable objects

isEmptySelection() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Tests if the selection shape is empty

isProtectionsOn(Sequence, String) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Checks a string against all of a sequence's protection settings.

isSelectedLine(int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

This function is used to test if a line is selected.

isSelectedLine(int) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

This function is used to test if a line is selected.

itemStateChanged(ItemEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDESequenceWindow

Handles type changes made (this includes greying out those parameters which are not applicable to the current sequence type.

J

joinAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

Action for joining split canvases

K

keyPressed(KeyEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Processes key presses within the text area

keyPressed(KeyEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Processes key presses within the text area

keyReleased(KeyEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Processes key releases within the text area

keyTyped(KeyEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Processes the typing of keys within the text area

keyTyped(KeyEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Processes the typing of keys within the text area

L

load(File) - Static method in class org.biolegato.gdesupport.canvas.colourmask.ImportFileAction

Loads all of the colour masks contained in a file or directory.

M

maxColumns() - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Returns the current maximum number of visible columns

maxRows() - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Returns the current maximum number of visible rows

ModeListener - Interface in org.biolegato.gdesupport.canvas.listeners

Used to communicate changes in the canvas insertion mode.

modeListeners - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Linked list to store all mode change listeners

MonochromeColourMap - Class in org.biolegato.gdesupport.canvas.colourmap

A standard monochrome colour map.

MonochromeColourMap() - Constructor for class org.biolegato.gdesupport.canvas.colourmap.MonochromeColourMap

Creates a new instance of MonochromeColourMap

MonochromeColourMap(Color, Color, Color, Color) - Constructor for class org.biolegato.gdesupport.canvas.colourmap.MonochromeColourMap

Creates a new instance of MonochromeColourMap

mouseClicked(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Checks for double clicks.

mouseClicked(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles mouse clicks.

mouseDragged(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles mouse drags.

mouseEntered(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Currently does nothing

mouseEntered(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles the mouse entering the component.

mouseExited(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Currently does nothing

mouseExited(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles the mouse exiting the component.

mouseMoved(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles mouse movements.

mousePressed(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Checks for right clicks.

mousePressed(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles mouse button presses.

mouseReleased(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Checks for right clicks.

mouseReleased(MouseEvent) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Handles mouse button releases.

moveSelection(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Moves the start of a selection to a new co-ordinate

moveSelection(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Moves the start of a selection to a new co-ordinate

N

neutralColour - Static variable in class org.biolegato.gdesupport.canvas.colourmap.CharacterColourMap

Standard neutral colour

neutralColour - Static variable in class org.biolegato.gdesupport.canvas.colourmap.GDECharColourMap

Standard neutral colour

normalMap - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The colour map to use when the textarea is not greyed out.

O

org.biolegato.gdesupport.canvas - package org.biolegato.gdesupport.canvas

org.biolegato.gdesupport.canvas.colourmap - package org.biolegato.gdesupport.canvas.colourmap

org.biolegato.gdesupport.canvas.colourmask - package org.biolegato.gdesupport.canvas.colourmask

org.biolegato.gdesupport.canvas.list - package org.biolegato.gdesupport.canvas.list

org.biolegato.gdesupport.canvas.listeners - package org.biolegato.gdesupport.canvas.listeners

org.biolegato.gdesupport.canvas.textarea - package org.biolegato.gdesupport.canvas.textarea

org.biolegato.gdesupport.canvas.undo - package org.biolegato.gdesupport.canvas.undo

P

paintComponent(Graphics) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Paints the current textarea (this uses the current clip bounds to determine the area to paint.

paste() - Method in interface org.biolegato.gdesupport.canvas.Editable

Pastes the current clipboard into the current Editable object.

paste() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Pastes the current clipboard into the current Editable object.

paste() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Pastes content into the current Editable object.

paste() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Pastes content into the current Editable object.

paste() - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Pastes content into the current Editable object.

paste() - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Pastes content into the current Editable object.

pasteAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

The action "Paste"

pdelete(int, int, int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Removes text from one line of a document (doesn't do any group processing - permission processing only).

pdeleteSelection() - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Used to delete the current selection before an insertion or as part of a deletion.

popup - Variable in class org.biolegato.gdesupport.canvas.list.GDEList

The right click menu for the GDE sequence list.

popup - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The right click menu for the text area.

PositionColourMap - Class in org.biolegato.gdesupport.canvas.colourmap

A colour map class that will give support for GDE colour masks

PositionColourMap(String, Color[], boolean) - Constructor for class org.biolegato.gdesupport.canvas.colourmap.PositionColourMap

Creates a new instance of GDEColourMaskMap.

propertiesComponent(Container) - Method in class org.biolegato.gdesupport.canvas.GDECanvasProperties

Displays all of the widgets available for modifying the associated properties.

propertiesUpdate(String, String) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Used to intercept font size changes (since the font size is stored in the properties)

R

readColourMapFile(File) - Method in class org.biolegato.gdesupport.canvas.colourmask.CharacterColourMaskReader

Reads and parses a colour mask file.

readColourMapFile(File) - Method in class org.biolegato.gdesupport.canvas.colourmask.ColourMaskReader

readColourMapFile(File) - Method in class org.biolegato.gdesupport.canvas.colourmask.GDEColourMaskFile

Reads and parses a colour mask file.

redo() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Redoes data modification.

redoAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

The action "Redo"

refreshSize() - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

refreshSize() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Refreshes the size of the textarea (for scroll size purposes)

regularDrawString(BLTextArea, Graphics, int, int, Sequence, int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.CharacterColourMap

Draws a sequence mapping the appropriate colours to each character rendered

regularDrawString(BLTextArea, Graphics, int, int, Sequence, int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Draws an unselected sequence while mapping the appropriate colours to each character rendered.

regularDrawString(BLTextArea, Graphics, int, int, Sequence, int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.GDECharColourMap

Draws a sequence mapping the appropriate colours to each character rendered

regularDrawString(BLTextArea, Graphics, int, int, Sequence, int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.MonochromeColourMap

Draws a sequence mapping the appropriate colours to each character rendered.

regularDrawString(BLTextArea, Graphics, int, int, Sequence, int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.PositionColourMap

Draws a sequence mapping the appropriate colours to each character rendered

removeListDataListener(ListDataListener) - Method in class org.biolegato.gdesupport.canvas.list.SequenceListModel

Removes a data listener from the list model

removePopupMenuItem(JMenuItem) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Removes an item from the BLTextArea's right-click popup menu.

resetSelection() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Resets the current selection to (0,0 - 0,0)

row - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

The current row of the caret

row2Y(int) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Converts a row number into a Y co-ordinate

row2Y(int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Converts a row number into a Y co-ordinate

rowHeight - Variable in class org.biolegato.gdesupport.canvas.textarea.BLComponent

The height of each row in the textarea

rowSize() - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Returns the size of one row of the textarea.

S

safesubstring(Sequence, int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Ensures all substrings do not excees the start or end of the sequence

selectAll() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Selects all the sequences within the canvas.

selectAll() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Selects all the sequences within the list.

selectAll() - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Selects all the sequences within the textarea.

selectAllAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

The action "Select All"

selectByNameAction - Variable in class org.biolegato.gdesupport.canvas.list.GDEList

The abstract action "Select sequence by name"

SelectByNameWindow - Class in org.biolegato.gdesupport.canvas.list

A class to provide the functionality of selecting/deselecting sequences based on name.

SelectByNameWindow(JFrame, JList) - Constructor for class org.biolegato.gdesupport.canvas.list.SelectByNameWindow

Creates a new instance of SelectByNameWindow

selectDrawString(BLTextArea, Graphics, int, int, Sequence, int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Draws a selected sequence while mapping the appropriate colours to each character rendered.

selectGroup() - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Selects the group members of the currently selected sequence(s)

selectGroupAction - Variable in class org.biolegato.gdesupport.canvas.list.GDEList

The menu item "Select group"

selectionMouse - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Used for mouse dragging.

selectionMove - Variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Used to track the shift key.

sequenceAdded(SeqDoc, int, Sequence) - Method in class org.biolegato.gdesupport.canvas.list.SequenceListModel

Passes any sequence additions to the data listeners.

sequenceAdded(SeqDoc, int, Sequence) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Called when a sequence is added to a SeqDoc.

sequenceChanged(SeqDoc, int, Sequence, String) - Method in class org.biolegato.gdesupport.canvas.list.SequenceListModel

Passes any sequence modifications to the data listeners.

sequenceChanged(SeqDoc, int, Sequence, String) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Called when a field in a sequence is modified.

SequenceListModel - Class in org.biolegato.gdesupport.canvas.list

A list model that is based on the sequence names in a sequence document.

SequenceListModel(SeqDoc) - Constructor for class org.biolegato.gdesupport.canvas.list.SequenceListModel

Creates a new instance of SequenceListModel.

sequenceRemoved(SeqDoc, int, Sequence) - Method in class org.biolegato.gdesupport.canvas.list.SequenceListModel

Passes any sequence deletions to the data listeners.

sequenceRemoved(SeqDoc, int, Sequence) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Called when a sequence is removed from a SeqDoc.

serialVersionUID - Static variable in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

This constant is used for serialization purposes.

setBackground(Color) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Changes the current default background colour for painting portions of the canvas without text.

setBackground(Color) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Changes the background of the canvas.

setColourMap(ColourMap) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Changes the current colour map for unselected text.

setFont(Font) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Updates the font for the canvas (ensures repaint)

setFont(Font) - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Updates the font for the canvas (ensures repaint)

setFont(Font) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Updates the font for the canvas (ensures repaint)

setForeground(Color) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Changes the current default foreground colour for painting portions of the canvas without text.

setGreyColourMap(ColourMap) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Changes the current colour map for unselected text.

setName(String) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Changes the name of the colour map.

stateChanged(ChangeEvent) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Refreshes the canvas on tab changes.

stretchSelection(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLTextArea

Stretches the selection by changing the co-ordinate of the selection's end

stretchSelection(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Stretches the selection by changing the co-ordinate of the selection's end

stringToInt(String) - Static method in class org.biolegato.gdesupport.canvas.colourmask.GDEColourMaskFile

Converts a string to an integer (note: returns 0 on failure).

T

toString() - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

Returns the name of the colour map.

U

uchangePosition(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

The undoable version of the "changePosition" function

udelete(int, int, int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Removes text from a document.

udeleteSelection() - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

The undoable version of the "deleteSelection" function

ugdeTextAreaSelf - Variable in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Self-reference for inner classes.

uinsert(int, int, String) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Inserts a string into the textarea's underlying SeqDoc (NOTE: this should ONLY be called by sub-methods)

uinsert(int, int, Sequence[]) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Inserts an array of sequences into the textarea's underlying SeqDoc

umoveSelection(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

The undoable version of the "moveSelection" function

undo() - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Undoes data modification.

undo() - Method in interface org.biolegato.gdesupport.canvas.undo.Undoable

Undoes an action represented by the undoable object.

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoChangePosition

Undoes the changing of caret position

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoDelete

Undoes a deletion

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoInsert

Undoes a text insertion

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoMoveSelection

Undoes the movement of a selection area

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoMulti

Undoes a multitude of undoable objects

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoRowDeletion

Undoes a row deletion

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoRowInsertion

Undoes a row insertion

undo() - Method in class org.biolegato.gdesupport.canvas.undo.UndoStretchSelection

Undoes the stretching of a selection

Undoable - Interface in org.biolegato.gdesupport.canvas.undo

This interface is used for generalizing all objects which perform undo-related actions.

UndoableGDETextArea - Class in org.biolegato.gdesupport.canvas.textarea

Custom text area for allowing box selection

UndoableGDETextArea(GDECanvas) - Constructor for class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Constructs a new instance of GDETextArea.

undoAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

The action "Undo"

UndoChangePosition - Class in org.biolegato.gdesupport.canvas.undo

This object handles undoing caret position changes within a GDETextArea.

UndoChangePosition(UndoableGDETextArea, int, int) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoChangePosition

Creates a new instance of UndoChangePosition

UndoDelete - Class in org.biolegato.gdesupport.canvas.undo

This object handles undoing text deletion within a GDETextArea

UndoDelete(UndoableGDETextArea, int, int, String) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoDelete

Creates a new instance of UndoInsert

UndoInsert - Class in org.biolegato.gdesupport.canvas.undo

This object handles undoing text insertion within a UndoableGDETextArea

UndoInsert(UndoableGDETextArea, int, int, int) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoInsert

Creates a new instance of UndoInsert

UndoInsert(UndoableGDETextArea, int, int, int, int) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoInsert

Creates a new instance of UndoInsert

UndoMoveSelection - Class in org.biolegato.gdesupport.canvas.undo

This object handles undoing selection movement within a UndoableGDETextArea.

UndoMoveSelection(UndoableGDETextArea, int, int) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoMoveSelection

Creates a new instance of UndoMoveSelection

UndoMulti - Class in org.biolegato.gdesupport.canvas.undo

This object contains a linked list of related undoable objects.

UndoMulti() - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoMulti

Creates a new instance of UndoMulti

UndoMulti(LinkedList<Undoable>) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoMulti

Creates a new instance of UndoMulti from a linked list

UndoRowDeletion - Class in org.biolegato.gdesupport.canvas.undo

This object handles undoing sequence row deletions

UndoRowDeletion(SeqDoc, int, Sequence) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoRowDeletion

Creates a new instance of UndoRowDeletion

UndoRowInsertion - Class in org.biolegato.gdesupport.canvas.undo

This object handles undoing sequence row inesrtions

UndoRowInsertion(SeqDoc, int) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoRowInsertion

Creates a new instance of UndoRowInsertion

UndoStretchSelection - Class in org.biolegato.gdesupport.canvas.undo

This object handles undoing selection stretches within a GDETextArea.

UndoStretchSelection(UndoableGDETextArea, int, int) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoStretchSelection

Creates a new instance of UndoChangePosition

ungroupAction - Variable in class org.biolegato.gdesupport.canvas.GDECanvas

Action for ungrouping sequences in the canvas

updelete(int, int, int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

Removes text from one line of a document (doesn't do any group processing - permission processing only).

updeleteSelection() - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

The undoable version of the "deleteSelection" function

ustretchSelection(int, int) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

The undoable version of the "stretchSelection" function

X

X2Column(int) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Converts a X co-ordinate into a column number

X2Column(int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Converts a X co-ordinate into a column number

Y

Y2Row(int) - Method in class org.biolegato.gdesupport.canvas.list.GDEList

Converts a Y co-ordinate into a row number

Y2Row(int) - Method in class org.biolegato.gdesupport.canvas.textarea.BLComponent

Converts a Y co-ordinate into a row number

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