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

accept(File) - Method in class org.biolegato.gdesupport.formats.FastAFile

Determines whether or not a specified file is of type GenBank file (based on extension).

accept(File) - Method in class org.biolegato.gdesupport.formats.GDEFile

Determines whether or not a specified file is of type GDE file (based on extension) Currently the only extension supported is ".gde".

accept(File) - Method in class org.biolegato.gdesupport.formats.GDEFlatfile

Determines whether or not a specified file is of type GDE flat file (based on extension).

accept(File) - Method in class org.biolegato.gdesupport.formats.GenBankFile2008

Determines whether or not a specified file is of type GenBank file (based on extension).

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.

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

Handles changes in the status of the checkbox.

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

Adds a cursor listener to the BLTextArea.

addFormats(JFileChooser, String) - Static method in class org.biolegato.gdesupport.formats.DataFormat

This function loads all of the available file formats into a JFileChooser.

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

Adds a data listener to the list model

addListener(CellListener) - Method in class org.biolegato.gdesupport.canvas.data.Cell

Adds a sequence listener to keep track of sequence modifications.

addListener(DatasetListener) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Adds a listener object to the data container.

addListener(GDEModelListener) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Adds a listener object to the data container.

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.

addRow(int, Cell) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Adds a sequence to the data container.

addSequence(int, Cell) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Adds a sequence to the data container.

addSequences(Cell[]) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

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

auto(File) - Static method in class org.biolegato.gdesupport.formats.DataFormat

Used to auto-detect and parse files into BioLegato sequence objects.

auto(InputStream) - Static method in class org.biolegato.gdesupport.formats.DataFormat

Used to auto-detect and parse an input stream's data into BioLegato sequence objects.

auto(BufferedReader) - Static method in class org.biolegato.gdesupport.formats.DataFormat

Used to auto-detect and parse data into BioLegato sequence objects.

B

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

The current default background colour of normal unselected 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(GDEModel) - 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

Cell - Class in org.biolegato.gdesupport.canvas.data

This class is used to contain all sequence related functions and data.

Cell() - Constructor for class org.biolegato.gdesupport.canvas.data.Cell

Constructs new instances of Cell objects.

Cell(String) - Constructor for class org.biolegato.gdesupport.canvas.data.Cell

Constructs new instances of Cell objects.

Cell(Map<String, Object>) - Constructor for class org.biolegato.gdesupport.canvas.data.Cell

Constructs new instances of sequence.

Cell.CharacterClass - Enum in org.biolegato.gdesupport.canvas.data

Used for typing characters within a sequence.

Cell.Direction - Enum in org.biolegato.gdesupport.canvas.data

Used for typing/storing sequence direction.

Cell.Strandedness - Enum in org.biolegato.gdesupport.canvas.data

Used for typing/storing sequence strandedness.

Cell.Topology - Enum in org.biolegato.gdesupport.canvas.data

Used for typing/storing sequence topology.

Cell.Type - Enum in org.biolegato.gdesupport.canvas.data

This enum is used for typing/storing sequence types.

CellListener - Interface in org.biolegato.gdesupport.canvas.data

This listener received change events from sequences.

changeCase() - Method in interface org.biolegato.gdesupport.canvas.GDECanvasObject

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

Updates/moves the cursor to the new position.

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

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

charType(char) - Method in class org.biolegato.gdesupport.canvas.data.Cell

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

Clears the current text selection

ClipboardWrapper - Class in org.biolegato.gdesupport.canvas

ClipboardWrapper(Cell[]) - Constructor for class org.biolegato.gdesupport.canvas.ClipboardWrapper

Creates a new instance of ClipboardWrapper

clone() - Method in class org.biolegato.gdesupport.canvas.data.Cell

Clones the current sequence object.

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 class org.biolegato.gdesupport.canvas.GDECanvas

Copies content from the current Editable object to the clipboads.

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

Copies content from the current Editable object.

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 class org.biolegato.gdesupport.canvas.GDECanvas

Cuts content from the current Editable object to the clipboads.

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

Cuts content from the current Editable object.

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

DataFormat - Class in org.biolegato.gdesupport.formats

Class to represent reading of data formats.

DataFormat() - Constructor for class org.biolegato.gdesupport.formats.DataFormat

Creates a new instance of DataFormat

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

Used for the relationship between the data model and the list

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

Used for the relationship between the data model and the text area

Dataset - Class in org.biolegato.gdesupport.canvas.data

The internal document format for BioLegato.

Dataset() - Constructor for class org.biolegato.gdesupport.canvas.data.Dataset

Creates a new instance of Dataset

Dataset(Cell[]) - Constructor for class org.biolegato.gdesupport.canvas.data.Dataset

Creates a new instance of Dataset using the existing sequence list

DatasetListener - Interface in org.biolegato.gdesupport.canvas.data

The listener class for sequence document objects.

delete(int, int, int) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Removes text from the document.

delete(int, int, int, int) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Removes text from the document.

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 Dataset 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.

F

FastAFile - Class in org.biolegato.gdesupport.formats

FastA file format parser.

FastAFile() - Constructor for class org.biolegato.gdesupport.formats.FastAFile

Creates a new instance of FastAFile

finalize() - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Finalizes the object - removes all references to itself

finalize() - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Finalizes the object - removes all references to itself

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

The current default foreground colour of normal unselected 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

GDECanvasObject - Interface in org.biolegato.gdesupport.canvas

GDECanvasProperties - Class in org.biolegato.gdesupport.canvas

A class for adding GDE canvas specific properties to.

GDECanvasProperties(JFrame, 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.

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

GDEFile - Class in org.biolegato.gdesupport.formats

This class acts as a parser/translator for standard GDE files.

GDEFile() - Constructor for class org.biolegato.gdesupport.formats.GDEFile

Creates a new instance of GDEFile

GDEFlatfile - Class in org.biolegato.gdesupport.formats

This class acts as a parser/translator for GDE flat files.

GDEFlatfile() - Constructor for class org.biolegato.gdesupport.formats.GDEFlatfile

Creates a new instance of GDEFlatfile

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

GDEModel - Class in org.biolegato.gdesupport.canvas.data

The internal document format for BioLegato.

GDEModel() - Constructor for class org.biolegato.gdesupport.canvas.data.GDEModel

Creates a new instance of Dataset

GDEModelListener - Interface in org.biolegato.gdesupport.canvas.data

The listener class for sequence document objects.

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

A window for editing sequence properties.

GDESequenceWindow(GDEModel, JFrame, Cell[]) - 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(GDECanvas) - Constructor for class org.biolegato.gdesupport.canvas.textarea.GDETextArea

Constructs a new instance of GDETextArea.

GenBankFile2008 - Class in org.biolegato.gdesupport.formats

This class acts as a parser/translator for GenBank files (using the file specification current to 2008).

GenBankFile2008() - Constructor for class org.biolegato.gdesupport.formats.GenBankFile2008

Creates a new instance of GenBankFile2008

get(Object) - Method in class org.biolegato.gdesupport.canvas.data.Cell

Obtains a value for a field of the sequence.

get(int) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Retrieves a sequence object from the Dataset specified by its line number.

get(int) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Retrieves a sequence object from the Dataset specified by its line line.

getClipboard() - Static method in class org.biolegato.gdesupport.canvas.GDECanvas

Obtains the current contents of the clipboard (null if empty).

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

Returns the current/selected data in the canvas.

getData() - Method in interface org.biolegato.gdesupport.canvas.GDECanvasObject

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

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.

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

Passes the current datamodel to any GDE canvas related components

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

Returns the Dataset associated with the BLTextArea

getDefault(String) - Static method in class org.biolegato.gdesupport.canvas.data.Cell

This function obtains the default value of a field for a Cell.

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

Returns a standard colour from the properties

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

Returns the default colour mask

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

getDescription() - Method in class org.biolegato.gdesupport.formats.FastAFile

Returns a description of the file format that can be displayed to the user.

getDescription() - Method in class org.biolegato.gdesupport.formats.GDEFile

Returns a description of the file format that can be displayed to the user.

getDescription() - Method in class org.biolegato.gdesupport.formats.GDEFlatfile

Returns a description of the file format that can be displayed to the user.

getDescription() - Method in class org.biolegato.gdesupport.formats.GenBankFile2008

Returns a description of the file format that can be displayed to the user.

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

Returns the names of sequences based on their line number.

getFormat(String) - Static method in class org.biolegato.gdesupport.formats.DataFormat

Finds the filetype that corresponds to the given hashname (null if not successful).

getgroup(Integer) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

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.

getLineCount() - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Returns the number of lines in the document.

getLineLength(int) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Retrieves the length of a line in the document.

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

Returns the current list model.

getLongestLine() - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Returns the length of the longest line in the data container

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.

getName() - Method in class org.biolegato.gdesupport.formats.DataFormat

Obtains the name of the file format for File Chooser purposes

getName() - Method in class org.biolegato.gdesupport.formats.FastAFile

Obtains the internal name of the file format (this is great for hashtables storage and searching).

getName() - Method in class org.biolegato.gdesupport.formats.GDEFile

Obtains the internal name of the file format (this is great for hashtables storage and searching).

getName() - Method in class org.biolegato.gdesupport.formats.GDEFlatfile

Obtains the internal name of the file format (this is great for hashtables storage and searching).

getName() - Method in class org.biolegato.gdesupport.formats.GenBankFile2008

Obtains the internal name of the file format (this is great for hashtables storage and searching).

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

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

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

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

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

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

getRowCount() - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Returns the number of lines in the document.

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

Returns the current selected colour mask for the sequence.

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

Returns the number of sequences in the sequence document.

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

Returns the name to display in the canvas tab for

getTransferData(DataFlavor) - Method in class org.biolegato.gdesupport.canvas.ClipboardWrapper

Translates the Dataset to the given format

getTransferData(DataFlavor) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Translates the Dataset to the given format

getTransferData(DataFlavor) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Translates the Dataset to the given format

getTransferDataFlavors() - Method in class org.biolegato.gdesupport.canvas.ClipboardWrapper

Dictates what formats the Dataset can be converted to.

getTransferDataFlavors() - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Dictates what formats the Dataset can be converted to.

getTransferDataFlavors() - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Dictates what formats the Dataset can be converted to.

group(int[]) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

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

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.data.GDEModel

Inserts a string into the document on a given line.

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

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

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

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

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)

insertField(String, int, String) - Method in class org.biolegato.gdesupport.canvas.data.Cell

Inserts a string into field within the sequence.

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.

isDataFlavorSupported(DataFlavor) - Method in class org.biolegato.gdesupport.canvas.ClipboardWrapper

Dictates whether a given format is supported for conversion

isDataFlavorSupported(DataFlavor) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Dictates whether a given format is supported for conversion

isDataFlavorSupported(DataFlavor) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Dictates whether a given format is supported for conversion

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

Checks if the undo multi contains any undoable objects

isFormat(Reader) - Method in class org.biolegato.gdesupport.formats.DataFormat

Used to auto-detect Bio Legato formats

isFormat(Reader) - Method in class org.biolegato.gdesupport.formats.FastAFile

Used to auto-detect Bio Legato formats

isFormat(Reader) - Method in class org.biolegato.gdesupport.formats.GDEFile

Used to auto-detect Bio Legato formats

isFormat(Reader) - Method in class org.biolegato.gdesupport.formats.GDEFlatfile

Used to auto-detect Bio Legato formats

isFormat(Reader) - Method in class org.biolegato.gdesupport.formats.GenBankFile2008

Used to auto-detect Bio Legato formats

isProtectionsOn(Cell, 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.

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

Tests if the selection shape is empty

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

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

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) - 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.

N

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

Standard neutral colour

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

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

org.biolegato.gdesupport.formats - package org.biolegato.gdesupport.formats

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 class org.biolegato.gdesupport.canvas.GDECanvas

Pastes the current clipboard into the current Editable object.

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

Pastes content 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.

PropertiesCheckbox - Class in org.biolegato.gdesupport.canvas

Class used to create widgets to obtain boolean values for properties.

PropertiesCheckbox(BLProperties, String, String) - Constructor for class org.biolegato.gdesupport.canvas.PropertiesCheckbox

Creates a new instance of PropertiesCheckbox

PropertiesNumber - Class in org.biolegato.gdesupport.canvas

Class used to create widgets to obtain numerical values for properties.

PropertiesNumber(BLProperties, String, String, int, int) - Constructor for class org.biolegato.gdesupport.canvas.PropertiesNumber

Creates a new instance of PropertiesNumber

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)

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

Handles changes in the status of the associated properties key.

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

Handles changes in the status of the associated properties key.

put(String, Object) - Method in class org.biolegato.gdesupport.canvas.data.Cell

Changes a value of a field in the sequence.

Q

quote(String) - Static method in class org.biolegato.gdesupport.formats.GDEFile

Quotes a GDE string (replaces " with ' and {} with [])

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.

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

Reads a file into the canvas

readFile(File) - Method in class org.biolegato.gdesupport.formats.DataFormat

Reads a file's contained sequences using the file filter's translation.

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, Cell, char[], 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, Cell, char[], 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, Cell, char[], 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, Cell, char[], 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

removeListener(CellListener) - Method in class org.biolegato.gdesupport.canvas.data.Cell

Removes a sequence listener from keeping track of sequence modifications.

removeListener(DatasetListener) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Adds a listener object to the data container.

removeListener(GDEModelListener) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Adds a listener object to the data container.

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

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

removeRows(int[]) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Removes an array of sequences from the data container.

removeSequences(int[]) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Removes an array of sequences from the data container.

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(Cell, 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.list.GDEList

Selects all the sequences within the list.

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

The menu item "Select All"

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

The background colour of selected text

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, Cell, char[], int, int) - Method in class org.biolegato.gdesupport.canvas.colourmap.ColourMap

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

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

The foreground colour of selected text

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"

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

Manages mutual exclusion between the textarea and the list

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

Used to track mouse holds and releases.

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

Used to track the shift key.

seqDocFlavour - Static variable in class org.biolegato.gdesupport.canvas.data.Dataset

A data flavour representing the Dataset data type.

seqDocFlavour - Static variable in class org.biolegato.gdesupport.canvas.data.GDEModel

A data flavour representing the Dataset data type.

sequenceAdded(Dataset, int, Cell) - Method in interface org.biolegato.gdesupport.canvas.data.DatasetListener

This method is called when a sequence is added to a Dataset.

sequenceAdded(GDEModel, int, Cell) - Method in interface org.biolegato.gdesupport.canvas.data.GDEModelListener

This method is called when a sequence is added to a Dataset.

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

Passes any sequence additions to the data listeners.

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

Called when a sequence is added to a Dataset.

sequenceArrayFlavour - Static variable in class org.biolegato.gdesupport.canvas.ClipboardWrapper

A data flavour representing the raw Cell data type.

sequenceChanged(Cell, String) - Method in interface org.biolegato.gdesupport.canvas.data.CellListener

This method is called when a field in a sequence is modified.

sequenceChanged(Cell, String) - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Called when a field in a sequence is modified.

sequenceChanged(Dataset, int, Cell, String) - Method in interface org.biolegato.gdesupport.canvas.data.DatasetListener

This method is called when a field in a sequence is modified.

sequenceChanged(Cell, String) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

Called when a field in a sequence is modified.

sequenceChanged(GDEModel, int, Cell, String) - Method in interface org.biolegato.gdesupport.canvas.data.GDEModelListener

This method is called when a field in a sequence is modified.

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

Passes any sequence modifications to the data listeners.

sequenceChanged(GDEModel, int, Cell, 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(GDEModel) - Constructor for class org.biolegato.gdesupport.canvas.list.SequenceListModel

Creates a new instance of SequenceListModel.

sequenceRemoved(Dataset, int, Cell) - Method in interface org.biolegato.gdesupport.canvas.data.DatasetListener

This method is called when a sequence is removed from the Dataset class.

sequenceRemoved(GDEModel, int, Cell) - Method in interface org.biolegato.gdesupport.canvas.data.GDEModelListener

This method is called when a sequence is removed from the Dataset class.

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

Passes any sequence deletions to the data listeners.

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

Called when a sequence is removed from a Dataset.

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

This constant is used for serialization purposes.

setClipboard(Cell[]) - Static method in class org.biolegato.gdesupport.canvas.GDECanvas

Changes the current contents of the clipboard.

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)

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.PropertiesNumber

Handles changes in the status of the spinner.

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

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

T

toArray() - Method in class org.biolegato.gdesupport.canvas.ClipboardWrapper

Dumps the data contained within the clipboard wrapper

toArray() - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Converts the Dataset into a sequence array representation

toArray() - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

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

Returns the name of the colour map.

toString() - Method in class org.biolegato.gdesupport.canvas.data.Cell

Creates a string representation of the Cell and its fields

toString() - Method in class org.biolegato.gdesupport.canvas.data.Dataset

Converts the Dataset into a string representation

translateFrom(BufferedReader) - Method in class org.biolegato.gdesupport.formats.DataFormat

Translates a string from the given file format into the BioLegato internal format.

translateFrom(BufferedReader) - Method in class org.biolegato.gdesupport.formats.FastAFile

Translates data in the FastA file format to sequence objecte

translateFrom(BufferedReader) - Method in class org.biolegato.gdesupport.formats.GDEFile

Translates data in the GDE file format to sequence objecte

translateFrom(BufferedReader) - Method in class org.biolegato.gdesupport.formats.GDEFlatfile

Translates data in the GDE flat file format to sequence objecte

translateFrom(BufferedReader) - Method in class org.biolegato.gdesupport.formats.GenBankFile2008

Translates data in the GenBank file format to sequence objecte

translateTo(Cell) - Method in class org.biolegato.gdesupport.formats.DataFormat

Translates a string from the BioLegato internal format to the given file format.

translateTo(Cell) - Method in class org.biolegato.gdesupport.formats.FastAFile

Translates a sequence into the FastA file format.

translateTo(Cell) - Method in class org.biolegato.gdesupport.formats.GDEFile

Translates a sequence into the GDE file format.

translateTo(Cell) - Method in class org.biolegato.gdesupport.formats.GDEFlatfile

Translates a sequence into the GDE flat file format.

translateTo(Cell) - Method in class org.biolegato.gdesupport.formats.GenBankFile2008

Translates a sequence into the GenBank file format.

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, Cell[]) - Method in class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea

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

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.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

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

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(List<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(GDEModel, int, Cell) - 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(GDEModel, int) - Constructor for class org.biolegato.gdesupport.canvas.undo.UndoRowInsertion

Creates a new instance of UndoRowInsertion

ungroup(int[]) - Method in class org.biolegato.gdesupport.canvas.data.GDEModel

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

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

V

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

Clears the data collector when an item is selected from the sequence list

valueOf(String) - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.CharacterClass

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Direction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Strandedness

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Topology

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Type

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.CharacterClass

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Direction

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Strandedness

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Topology

Returns an array containing the constants of this enum type, in the order they're declared.

values() - Static method in enum org.biolegato.gdesupport.canvas.data.Cell.Type

Returns an array containing the constants of this enum type, in the order they're declared.

W

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

Writes a file out from the canvas

writeFile(File, Cell[]) - Method in class org.biolegato.gdesupport.formats.DataFormat

Writes a list of sequences to a file.

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

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