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

A

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

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

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

Determines whether a specified file is of type GenBank file (based on extension).

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

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

Determines whether 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.files.GDEFlatfile

Determines whether a specified file is of type GDE flat file (based on extension).

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

Determines whether a specified file is of type GenBank file (based on extension).

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

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

Handles the button commands for the given window.

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

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

addSequence(int, Seq) - Method in class org.biolegato.gdesupport.data.Dataset

Adds a sequence to the data container.

addSequences(int, Collection<Seq>) - Method in class org.biolegato.gdesupport.data.Dataset

Adds sequences to the data container.

autodetect(BufferedReader) - Static method in class org.biolegato.gdesupport.files.DataFormat

Used to auto-detect file formats.

AVG_SEQ_LENGTH - Static variable in class org.biolegato.gdesupport.files.GenBankFile2008

B

blTextAreaSelf - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

Self-reference for inner classes.

C

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.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.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.

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

The action "Change Case"

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

Updates/moves the cursor to the new position.

CharacterColourMaskReader - Class in org.biolegato.gdesupport.files

Used to select colour masks.

CharacterColourMaskReader() - Constructor for class org.biolegato.gdesupport.files.CharacterColourMaskReader

Creates a new instance of GDEColourMaskFile

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

Clears the current text selection

ClipboardWrapper - Class in org.biolegato.gdesupport.data

ClipboardWrapper(Seq[]) - Constructor for class org.biolegato.gdesupport.data.ClipboardWrapper

Creates a new instance of ClipboardWrapper

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

Clones the current sequence object.

ColourMask - Class in org.biolegato.gdesupport.data

ColourMask(ColourMask.MaskType, String, Color[]) - Constructor for class org.biolegato.gdesupport.data.ColourMask

ColourMask.MaskType - Enum in org.biolegato.gdesupport.data

column - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

The current column of the caret.

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

Returns the size of one column of the textarea.

columnWidth - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

The width of each column in the textarea

contentsChanged(ListDataEvent) - Method in class org.biolegato.gdesupport.canvas.GDETextArea

Called when a field in a sequence is modified.

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

The action "Copy"

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

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

Returns the currently selected data in the list.

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

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

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

Receives cursor updates for use in the status bar.

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

The action "Cut"

D

DataFormat - Class in org.biolegato.gdesupport.files

Class to represent reading of data formats.

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

Creates a new instance of DataFormat

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

Used for the relationship between the data model and the list

datamodel - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

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

Dataset - Class in org.biolegato.gdesupport.data

The internal document format for BioLegato.

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

Creates a new instance of Dataset

DEFAULT_FONT - Static variable in class org.biolegato.gdesupport.canvas.GDECanvas

The default font for the canvas

DEFAULT_MASK - Static variable in class org.biolegato.gdesupport.data.Seq

The default colour mask for BioLegato

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

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

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

Cuts content from the current Editable object.

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

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

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

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

detectType(StringBuffer) - Static method in class org.biolegato.gdesupport.data.Seq

This function detects the type of a sequence

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

Displays the canvas

drawString(Graphics, char[], int, int, int, int) - Method in class org.biolegato.gdesupport.data.ColourMask

F

FASTA - Static variable in class org.biolegato.gdesupport.files.DataFormat

FastAFile - Class in org.biolegato.gdesupport.files

FastA file format parser.

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

Creates a new instance of FastAFile

FOREG - Static variable in class org.biolegato.gdesupport.data.ColourMask

The current default FOREG colour of normal unselected text

FORMAT_LIST - Static variable in class org.biolegato.gdesupport.files.DataFormat

The list of available file formats

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, GDECanvas) - Constructor for class org.biolegato.gdesupport.canvas.GDECanvasProperties

Creates a new GDECanvasProperties object.

GDEColourMaskFile - Class in org.biolegato.gdesupport.files

Used to select colour masks.

GDEColourMaskFile() - Constructor for class org.biolegato.gdesupport.files.GDEColourMaskFile

Creates a new instance of GDEColourMaskFile

GDEFILE - Static variable in class org.biolegato.gdesupport.files.DataFormat

GDEFile - Class in org.biolegato.gdesupport.files

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

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

Creates a new instance of GDEFile

GDEFLAT - Static variable in class org.biolegato.gdesupport.files.DataFormat

GDEFlatfile - Class in org.biolegato.gdesupport.files

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

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

Creates a new instance of GDEFlatfile

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

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

GDEList - Class in org.biolegato.gdesupport.canvas

The JList of sequences in the GDE canvas.

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

Constructs a new GDEList

GDESequenceWindow - Class in org.biolegato.gdesupport.data

A window for editing sequence properties.

GDESequenceWindow(Dataset, JFrame, int[]) - Constructor for class org.biolegato.gdesupport.data.GDESequenceWindow

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

GDETextArea - Class in org.biolegato.gdesupport.canvas

A general canvas with more functionality support than JTextArea.

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

Creates a new instance of GDETextArea

GENBANK - Static variable in class org.biolegato.gdesupport.files.DataFormat

GenBankFile2008 - Class in org.biolegato.gdesupport.files

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

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

Creates a new instance of GenBankFile2008

getClipboard() - Static method in class org.biolegato.gdesupport.data.ClipboardWrapper

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

getDefaultMask() - Static method in class org.biolegato.gdesupport.data.Seq

Load the default colour masks (this was the only way I was able to get this code to work properly).

getDescription() - Method in class org.biolegato.gdesupport.data.Seq

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

Returns the description of "character colour mask"

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

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

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

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

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

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

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

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

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

getDirection() - Method in class org.biolegato.gdesupport.data.Seq

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

Returns the names of sequences based on their y number.

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

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

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

getGroupID() - Method in class org.biolegato.gdesupport.data.Seq

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

The menu item "Get info..."

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

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

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

Retrieves the length of a line in the document.

getMask() - Method in class org.biolegato.gdesupport.data.Seq

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

Returns the name to display in the canvas tab for

getName() - Method in class org.biolegato.gdesupport.data.Seq

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

Obtains the name of the file format for File Chooser purposes

getOriginal() - Method in class org.biolegato.gdesupport.data.Seq

getProtectAlignment() - Method in class org.biolegato.gdesupport.data.Seq

getProtectAmbiguous() - Method in class org.biolegato.gdesupport.data.Seq

getProtectUnambiguous() - Method in class org.biolegato.gdesupport.data.Seq

getSequence() - Method in class org.biolegato.gdesupport.data.Seq

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

Returns the number of lines in the document.

getStrandedness() - Method in class org.biolegato.gdesupport.data.Seq

getTopology() - Method in class org.biolegato.gdesupport.data.Seq

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

Translates the Dataset to the given format

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

Dictates what formats the Dataset can be converted to.

getType() - Method in class org.biolegato.gdesupport.data.Seq

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

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

Action for grouping sequences in the canvas

H

hash(char) - Static method in class org.biolegato.gdesupport.data.ColourMask

HASH_SIZE - Static variable in class org.biolegato.gdesupport.data.ColourMask

The functional maximum size of the hashtable.

I

insert(int, int, char[], boolean) - Method in class org.biolegato.gdesupport.canvas.GDETextArea

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

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

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

insertMode - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

If true new text will overwrite existing text.

intervalAdded(ListDataEvent) - Method in class org.biolegato.gdesupport.canvas.GDETextArea

Called when a sequence is added to a Dataset.

intervalRemoved(ListDataEvent) - Method in class org.biolegato.gdesupport.canvas.GDETextArea

Called when a sequence is removed from a Dataset.

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

Dictates whether a given format is supported for conversion

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

Used to auto-detect Bio Legato formats

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

Used to auto-detect Bio Legato formats

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

Used to auto-detect Bio Legato formats

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

Used to auto-detect Bio Legato formats

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

Used to auto-detect Bio Legato formats

isProtectionsOn(Seq.Type, boolean, boolean, boolean, char[], int, int) - Method in class org.biolegato.gdesupport.canvas.GDETextArea

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

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

Tests if the selection shape is empty

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

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

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.GDETextArea

Processes key presses within the text area

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

Processes key releases within the text area

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

Processes the typing of keys within the text area

M

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

The main canvas display

modified() - Method in class org.biolegato.gdesupport.data.Seq

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

Checks for double clicks.

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

Handles mouse clicks.

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

Handles mouse drags.

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

Currently does nothing

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

Handles the mouse entering the component.

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

Currently does nothing

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

Handles the mouse exiting the component.

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

Handles mouse movements.

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

Checks for right clicks.

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

Handles mouse button presses.

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

Checks for right clicks.

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

Handles mouse button releases.

MULTIPLE_SELECTED - Static variable in class org.biolegato.gdesupport.data.GDESequenceWindow

The text to display in a combobox when more than one item is selected among the list of sequences

O

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

The action "Open..."

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

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

org.biolegato.gdesupport.files - package org.biolegato.gdesupport.files

P

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

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

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

Pastes content into the current Editable object.

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

Pastes content into the current Editable object.

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

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.GDETextArea

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

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

The right click menu for the GDE sequence list.

popup - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

The right click menu for the text area.

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

The action "Properties..."

Q

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

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

R

readColourMaskFile(File) - Static method in class org.biolegato.gdesupport.files.CharacterColourMaskReader

Reads and parses a colour mask file.

readColourMaskFile(File) - Static method in class org.biolegato.gdesupport.files.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(Dataset, File) - Static method in class org.biolegato.gdesupport.files.DataFormat

Reads a file into the canvas

readFile(Dataset, DataFormat, File) - Static method in class org.biolegato.gdesupport.files.DataFormat

Reads a file into the canvas

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

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

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

Removes an array of sequences from the data container.

row - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

The current row of the caret

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

Converts a row number into a Y co-ordinate

rowHeight - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

The height of each row in the textarea

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

Returns the size of one row of the textarea.

S

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

The action "Save As..."

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

The menu item "Select All"

SELECTBG - Static variable in class org.biolegato.gdesupport.canvas.GDETextArea

The BACKG colour of selected text

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

The abstract action "Select sequence by name"

SelectByNameWindow - Class in org.biolegato.gdesupport.canvas

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

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

Creates a new instance of SelectByNameWindow

SELECTFG - Static variable in class org.biolegato.gdesupport.canvas.GDETextArea

The FOREG colour of selected text

selectGroupAction - Variable in class org.biolegato.gdesupport.canvas.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.GDETextArea

Used to track mouse holds and releases.

selectionMove - Variable in class org.biolegato.gdesupport.canvas.GDETextArea

Used to track the shift key.

Seq - Class in org.biolegato.gdesupport.data

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

Seq() - Constructor for class org.biolegato.gdesupport.data.Seq

Constructs new instances of Cell objects.

Seq(Seq.Type, String, StringBuffer) - Constructor for class org.biolegato.gdesupport.data.Seq

Constructs new instances of sequence.

Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness) - Constructor for class org.biolegato.gdesupport.data.Seq

Constructs new instances of sequence.

Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness, StringBuilder) - Constructor for class org.biolegato.gdesupport.data.Seq

Constructs new instances of sequence.

Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness, int, String) - Constructor for class org.biolegato.gdesupport.data.Seq

Constructs new instances of sequence.

Seq(Seq) - Constructor for class org.biolegato.gdesupport.data.Seq

Constructs new instances of sequence.

Seq.CharacterClass - Enum in org.biolegato.gdesupport.data

Used for typing characters within a sequence.

Seq.Direction - Enum in org.biolegato.gdesupport.data

Used for typing/storing sequence direction.

Seq.Strandedness - Enum in org.biolegato.gdesupport.data

Used for typing/storing sequence strandedness.

Seq.Topology - Enum in org.biolegato.gdesupport.data

Used for typing/storing sequence topology.

Seq.Type - Enum in org.biolegato.gdesupport.data

This enum is used for typing/storing sequence types.

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

A data flavour representing the raw Cell data type.

serialVersionUID - Static variable in class org.biolegato.gdesupport.canvas.GDETextArea

This constant is used for serialization purposes.

serialVersionUID - Static variable in class org.biolegato.gdesupport.data.GDESequenceWindow

Used for serialization purposes

setClipboard(Seq[]) - Static method in class org.biolegato.gdesupport.data.ClipboardWrapper

Changes the current contents of the clipboard.

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

Updates the font for the canvas (ensures repaint)

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

Updates the font for the canvas (ensures repaint)

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

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

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

T

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

Dumps the data contained within the clipboard wrapper

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

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

Creates a string representation of the Cell and its fields

translateFrom(Dataset, BufferedReader) - Method in class org.biolegato.gdesupport.files.DataFormat

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

translateFrom(Dataset, BufferedReader) - Method in class org.biolegato.gdesupport.files.FastAFile

Translates data in the FastA file format to sequence objects

translateFrom(Dataset, BufferedReader) - Method in class org.biolegato.gdesupport.files.GDEFile

Translates data in the GDE file format to sequence objecte

translateFrom(Dataset, BufferedReader) - Method in class org.biolegato.gdesupport.files.GDEFlatfile

Translates data in the GDE flat file format to sequence objecte

translateFrom(Dataset, BufferedReader) - Method in class org.biolegato.gdesupport.files.GenBankFile2008

Translates data in the GenBank file format to sequence objecte

translateTo(Appendable, Seq, int, int) - Method in class org.biolegato.gdesupport.files.DataFormat

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

translateTo(Appendable, Seq, int, int) - Method in class org.biolegato.gdesupport.files.FastAFile

Translates a sequence into the FastA file format.

translateTo(Appendable, Seq, int, int) - Method in class org.biolegato.gdesupport.files.GDEFile

Translates a sequence into the GDE file format.

translateTo(Appendable, Seq, int, int) - Method in class org.biolegato.gdesupport.files.GDEFlatfile

Translates a sequence into the GDE flat file format.

translateTo(Appendable, Seq, int, int) - Method in class org.biolegato.gdesupport.files.GenBankFile2008

Translates a sequence into the GenBank file format.

U

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

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

Action for ungrouping sequences in the canvas

updateFont(int, boolean) - Method in class org.biolegato.gdesupport.canvas.GDECanvas

Updates the font for the GDE canvas and its sub-objects

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

Updates the internal counter storing the length of the longest line

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.data.ColourMask.MaskType

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

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

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

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

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

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

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

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

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

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

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

values() - Static method in enum org.biolegato.gdesupport.data.ColourMask.MaskType

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

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

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

W

writeAll(Dataset, DataFormat, File) - Static method in class org.biolegato.gdesupport.files.DataFormat

Writes a list of sequences to a file.

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

Writes a file out from the canvas

writeOut(DataFormat, Appendable) - Method in interface org.biolegato.gdesupport.canvas.GDECanvasObject

writeOut(DataFormat, Appendable) - Method in class org.biolegato.gdesupport.canvas.GDEList

writeOut(DataFormat, Appendable) - Method in class org.biolegato.gdesupport.canvas.GDETextArea

Writes the selected sequences out to an appendable object

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