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BioLegato sequence canvas support v1.1.0 API
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.sequence.data.FastAFile
Determines whether a specified file is of type FASTA file (based on extension).
accept(File) - Method in class org.biolegato.sequence.data.GDEFile
Determines whether a specified file is of type GDE file (based on extension).
accept(File) - Method in class org.biolegato.sequence.data.GDEFlatfile
Determines whether a specified file is of type GDE flat file (based on extension).
accept(File) - Method in class org.biolegato.sequence.data.GenBankFile2008
Determines whether a specified file is of type GenBank file (based on extension).
actionPerformed(ActionEvent) - Method in class org.biolegato.sequence.canvas.SequenceCanvasProperties
Handles close-button and bold check box clicks (updates the font and closes the window).
actionPerformed(ActionEvent) - Method in class org.biolegato.sequence.data.SequenceWindow
Updates sequence data based on the values selected in the window.
add(int, Seq) - Method in class org.biolegato.sequence.data.Dataset
Adds a sequence to the Dataset sequence object container.
addSequences(int, Collection<Seq>) - Method in class org.biolegato.sequence.data.Dataset
Adds sequences to the Dataset sequence object container.
autodetect(Scanner) - Static method in class org.biolegato.sequence.data.DataFormat
Used to auto-detect file formats.

B

blTextAreaSelf - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
Self-reference (used for inner-classes).

C

canvas - Variable in class org.biolegato.sequence.canvas.SequenceList
Canvas object which owns this SequenceList instance.
changeCase() - Method in interface org.biolegato.sequence.canvas.SequenceCanvasObject
Changes the case of the currently selected sequence.
changeCase() - Method in class org.biolegato.sequence.canvas.SequenceList
Changes the case of the currently selected sequence.
changeCase() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Changes the case of the currently selected sequence.
changeCaseAction - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The "Change case" menu item action.
changePosition(boolean, int, int) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Updates/moves the cursor to a new position.
CHAR_MASK_FILTER - Static variable in class org.biolegato.sequence.canvas.ColourMask
The colour mask file reader for GDE's position-based colour mask files.
clearSelection() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Clears the current text selection (does NOT delete any text).
clone() - Method in class org.biolegato.sequence.data.Seq
Clones the current sequence object.
col - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
The current column number/X-coordinate of the text caret cursor.
ColourMask - Class in org.biolegato.sequence.canvas
Colour mask support file
ColourMask(ColourMask.MaskType, String, Color[]) - Constructor for class org.biolegato.sequence.canvas.ColourMask
Creates a new instance of a colour mask
ColourMask.MaskType - Enum in org.biolegato.sequence.canvas
The type of mask defined by the colour mask class (i.e.
colourMasks - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The list of all colour masks loaded in the system.
colWidth - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
The width of each column in the text area.
contentsChanged(ListDataEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
This method is called when a field in a sequence is modified.
convertFrom(Dataset, Scanner, int, int) - Method in class org.biolegato.sequence.data.DataFormat
Converts a string from the given file format into the BioLegato internal format.
convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.DataFormat
Converts a single sequence from a scanner into BioLegato.
convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.FastAFile
Translates a single sequence from a scanner into BioLegato
convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.GDEFile
Translates a single sequence from a scanner into BioLegato
convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.GDEFlatfile
Translates a single sequence from a scanner into BioLegato
convertSequence(Dataset, Scanner, int, int, boolean) - Method in class org.biolegato.sequence.data.GenBankFile2008
Converts a single sequence from a scanner into BioLegato
convertTo(Appendable, Dataset, int) - Method in class org.biolegato.sequence.data.DataFormat
Converts data from the BioLegato's sequence canvas internal format to the given file format specified by the DataFormat object.
convertTo(Appendable, Dataset, int, int, int) - Method in class org.biolegato.sequence.data.DataFormat
Converts data from the BioLegato's sequence canvas internal format to the given file format.
convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.DataFormat
Converts data from the BioLegato's sequence canvas internal format to the given file format.
convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.FastAFile
Translates data from the BioLegato's sequence canvas internal format to the given file format.
convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.GDEFile
Translates data from the BioLegato's sequence canvas internal format to the given file format.
convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.GDEFlatfile
Translates data from the BioLegato's sequence canvas internal format to the given file format.
convertTo(Appendable, Seq, int, int) - Method in class org.biolegato.sequence.data.GenBankFile2008
Converts data from the BioLegato's sequence canvas internal format to the given file format.
copyAct - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The "Copy" menu item action.
copyClipboard() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Copies the currently selected sequences or text from the sequence canvas to the clipboard.
cursorChange(int, int) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
This method receives cursor updates for use in the status bar, and updates the row and column number displayed in the sequence canvas's status bar.
cutAct - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The "Cut" menu item action.

D

DataFormat - Class in org.biolegato.sequence.data
Class to represent reading of data formats.
DataFormat() - Constructor for class org.biolegato.sequence.data.DataFormat
Creates a new instance of DataFormat
datamodel - Variable in class org.biolegato.sequence.canvas.SequenceList
Used for the relationship between the data model and the list.
datamodel - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
This reference is used to connect the data model/Dataset sequence object container to the text area.
Dataset - Class in org.biolegato.sequence.data
The internal document format for BioLegato.
Dataset(SequenceCanvas) - Constructor for class org.biolegato.sequence.data.Dataset
Creates a new instance of the Dataset object.
DBL_CLICK_TIME - Static variable in class org.biolegato.sequence.canvas.SequenceList
The amount of time (ms) between clicks to be considered a double click.
DEFAULT_FONT - Static variable in class org.biolegato.sequence.canvas.SequenceCanvas
The default font for the canvas (12pt monospaced).
DEFAULT_MASK - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The default colour mask for BioLegato.
delete(int, int, int, int, boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Deletes characters from the textarea's underlying Dataset NOTE: deletions are performed in a sequential manner
delete(int, int, int, boolean) - Method in class org.biolegato.sequence.data.Dataset
Deletes a portion of a sequence from the Dataset sequence object container.
deleteSelection() - Method in interface org.biolegato.sequence.canvas.SequenceCanvasObject
Cuts/deletes the content selected in the sequence canvas object.
deleteSelection() - Method in class org.biolegato.sequence.canvas.SequenceList
Deletes the currently selected sequences.
deleteSelection(boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Deletes any text currently selected.
deleteSelection() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Deletes any text currently selected.
detectType(StringBuffer) - Static method in class org.biolegato.sequence.data.Seq
This function detects the type of a sequence (RNA, DNA, or protein).
display() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Displays the canvas.
drawString(Graphics, char[], int, int, int, int) - Method in class org.biolegato.sequence.canvas.ColourMask
Draws a character string using the character colour coding specified by the ColourMask object.

F

FASTA - Static variable in class org.biolegato.sequence.data.DataFormat
A static final object used for handling FastA files.
FastAFile - Class in org.biolegato.sequence.data
FastA file format parser.
FastAFile() - Constructor for class org.biolegato.sequence.data.FastAFile
Creates a new instance of FastAFile
FOREG - Static variable in class org.biolegato.sequence.canvas.ColourMask
The current default FOREG colour of normal unselected text
FORMAT_LIST - Static variable in class org.biolegato.sequence.data.DataFormat
The list of available file formats

G

GDE_MASK_FILTER - Static variable in class org.biolegato.sequence.canvas.ColourMask
The colour mask file reader for BioLegato's character-based colour mask files.
GDEFILE - Static variable in class org.biolegato.sequence.data.DataFormat
A static final object used for handling normal GDE files.
GDEFile - Class in org.biolegato.sequence.data
This class acts as a parser/translator for standard GDE files.
GDEFile() - Constructor for class org.biolegato.sequence.data.GDEFile
Creates a new instance of GDEFile
GDEFLAT - Static variable in class org.biolegato.sequence.data.DataFormat
A static final object used for handling GDE flat-files.
GDEFlatfile - Class in org.biolegato.sequence.data
This class acts as a parser/translator for GDE flat files.
GDEFlatfile() - Constructor for class org.biolegato.sequence.data.GDEFlatfile
Creates a new instance of GDEFlatfile
GENBANK - Static variable in class org.biolegato.sequence.data.DataFormat
A static final object used for handling GenBank files.
GenBankFile2008 - Class in org.biolegato.sequence.data
This class acts as a parser/translator for GenBank files (using the file specification current to 2008).
GenBankFile2008() - Constructor for class org.biolegato.sequence.data.GenBankFile2008
Creates a new instance of GenBankFile2008
getDefaultMask() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Load the default colour masks into BioLegato (this was the only way I was able to get the default colour mask to load properly and efficiently).
getDescription() - Method in class org.biolegato.sequence.data.FastAFile
Returns a description of the file format that can be displayed to the user.
getDescription() - Method in class org.biolegato.sequence.data.GDEFile
Returns a description of the file format that can be displayed to the user.
getDescription() - Method in class org.biolegato.sequence.data.GDEFlatfile
Returns a description of the file format that can be displayed to the user.
getDescription() - Method in class org.biolegato.sequence.data.GenBankFile2008
Returns a description of the file format that can be displayed to the user.
getElementAt(int) - Method in class org.biolegato.sequence.data.Dataset
Returns the names of sequences based on their Y-coordinate/"line number".
getFormat(String) - Static method in class org.biolegato.sequence.data.DataFormat
Finds the file type that corresponds to a given GDE/PCD file format hashname (returns the GDE flat file, by default, if not successful).
getgroup(int) - Method in class org.biolegato.sequence.data.Dataset
Obtains all of the line numbers of the sequences in a particular group.
getInfoAction - Variable in class org.biolegato.sequence.canvas.SequenceList
The menu item "Get info..."
getMask(int) - Method in class org.biolegato.sequence.data.Dataset
Retrieves the colour mask object for a given sequence 'line' in the Dataset sequence object container.
getPluginName() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Deprecated.
vestigial code from a previous BioLegato framework structure.
getSequence(char[], int, int, int) - Method in class org.biolegato.sequence.data.Dataset
Retrieves the text contained within a sequence object in the Dataset.
getSequenceLength(int) - Method in class org.biolegato.sequence.data.Dataset
Retrieves the length (in characters) of a given sequence 'line' in the Dataset sequence object container.
getSize() - Method in class org.biolegato.sequence.data.Dataset
Returns a count of the total number of sequences (lines) in the Dataset sequence object container.
group(int[]) - Method in class org.biolegato.sequence.data.Dataset
Creates a new sequence-group comprised of the sequences specified by Y-coordinate/"line numbers" in the array parameter 'sequences'.
groupAction - Variable in class org.biolegato.sequence.canvas.SequenceList
Action for grouping sequences in the canvas

H

HASH_SIZE - Static variable in class org.biolegato.sequence.canvas.ColourMask
The functional maximum size of the hashtable.

I

insert(int, int, char[], boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Inserts a string into the textarea's underlying Dataset object.
insert(int, int, char[], int, int, boolean) - Method in class org.biolegato.sequence.data.Dataset
Inserts text into the Dataset sequence object container.
insertionMode(boolean) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Thie method receives insertion mode change updates for use in the status bar.
insertionMode(boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
This method receives insertion mode change updates.
insertMode - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
If set to true, when the user types text, it will overwrite whatever existing text is already under the cursor.
intervalAdded(ListDataEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Called when a sequence is added to a Dataset.
intervalRemoved(ListDataEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Called when a sequence is removed from a Dataset.
isFormat(Scanner) - Method in class org.biolegato.sequence.data.DataFormat
Used as part of the DataFormat auto-detection algorithm.
isFormat(Scanner) - Method in class org.biolegato.sequence.data.FastAFile
Used as part of the DataFormat auto-detection algorithm.
isFormat(Scanner) - Method in class org.biolegato.sequence.data.GDEFile
Used as part of the DataFormat auto-detection algorithm.
isFormat(Scanner) - Method in class org.biolegato.sequence.data.GDEFlatfile
Used as part of the DataFormat auto-detection algorithm.
isFormat(Scanner) - Method in class org.biolegato.sequence.data.GenBankFile2008
Used as part of the DataFormat auto-detection algorithm.
isProtectionsOn(Seq.Type, boolean, boolean, boolean, char[], int, int) - Static method in class org.biolegato.sequence.data.Dataset
Checks a string against all of a sequence's protection settings.
isSelectionEmpty() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Tests if the text selection shape is empty (i.e.
itemStateChanged(ItemEvent) - Method in class org.biolegato.sequence.data.SequenceWindow
Handles sequence-type changes made (this includes greying out parameters which are not applicable to the current sequence type).

J

joinAction - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
Action for joining a split text area back into one text area.

K

keyPressed(KeyEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Processes key presses within the text area.
keyReleased(KeyEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Processes key releases within the text area.
keyTyped(KeyEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Processes keys typed within the text area.

M

main(String[]) - Static method in class org.biolegato.sequence.canvas.SequenceCanvas
Starts a new instance of BioLegato, using the sequence canvas.
mouseClicked(MouseEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Handles mouse clicks, by moving the text caret cursor.
mouseDragged(MouseEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Handles mouse drags.
mouseEntered(MouseEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Handles the mouse entering the text area.
mouseExited(MouseEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Handles the mouse exiting the text area.
mouseMoved(MouseEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Handles general mouse movements.
mousePressed(MouseEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Handles mouse button presses.
mouseReleased(MouseEvent) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Handles mouse button releases.
MULTIPLE_SELECTED - Static variable in class org.biolegato.sequence.data.SequenceWindow
The text to display in comboboxes when more than one option is selected.

O

openAction - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The "Open..." menu item action.
org.biolegato.sequence.canvas - package org.biolegato.sequence.canvas
 
org.biolegato.sequence.data - package org.biolegato.sequence.data
 

P

paintComponent(Graphics) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Paints the current sequence text area component to a graphics object.
pasteAct - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The "Paste" menu item action.
pasteClipboard() - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Pastes the current contents of the clipboard (null if empty) into the canvas at the current cursor position (within either the text area or the sequence list).
popup - Variable in class org.biolegato.sequence.canvas.SequenceList
The right click menu for the Sequence sequence list.
popup - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
The right click menu for the text area.
propertiesAction - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The "Properties..." menu item action.

Q

quote(String) - Static method in class org.biolegato.sequence.data.GDEFile
Quotes a GDE string (replaces " with ' and {} with [])

R

readCharMaskFile(File) - Static method in class org.biolegato.sequence.canvas.ColourMask
Reads and parses a character colour mask file.
readFile(String, Reader, boolean, boolean) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Reads a data into the canvas.
readIn(DataFormat, Scanner, boolean) - Method in interface org.biolegato.sequence.canvas.SequenceCanvasObject
Reads contents into the current sequence canvas object.
readIn(DataFormat, Scanner, boolean) - Method in class org.biolegato.sequence.canvas.SequenceList
Reads data into the sequence list.
readIn(DataFormat, Scanner, boolean) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Reads contents into the text area.
readPosMaskFile(File) - Static method in class org.biolegato.sequence.canvas.ColourMask
Reads and parses a position colour mask file.
refreshSize() - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Refreshes the size of the text area (for scroll size purposes).
removeSequences(int[]) - Method in class org.biolegato.sequence.data.Dataset
Removes multiple sequences from the Dataset sequence object container.
row - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
The current row number/Y-coordinate of the text caret cursor.
row2Y(int) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Converts a Dataset sequence container row number into a Y coordinate "on the screen" (in the Graphics object).
rowHeight - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
The height of each row (in pixels) in the text area.

S

saveAsAction - Variable in class org.biolegato.sequence.canvas.SequenceCanvas
The "Save ALL As..." menu item action.
selectAllAction - Variable in class org.biolegato.sequence.canvas.SequenceList
The menu item "Select All"
SELECTBG - Static variable in class org.biolegato.sequence.canvas.SequenceTextArea
The background colour of selected text.
selectByNameAction - Variable in class org.biolegato.sequence.canvas.SequenceList
The abstract action "Select sequence by name"
SELECTFG - Static variable in class org.biolegato.sequence.canvas.SequenceTextArea
The foreground colour of selected text.
selectGroupAction - Variable in class org.biolegato.sequence.canvas.SequenceList
The menu item "Select group"
selectionMade(SequenceTextArea) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Manages mutual exclusion between the textareas and the list This method listens to the sequence text area, and deselects any sequences in the sequence list, and the other text area (if the text area is split), whenever something is selected in one of the sequence text areas.
selectionMouse - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
Used to track mouse holds and releases.
selectionMove - Variable in class org.biolegato.sequence.canvas.SequenceTextArea
Used to track whether the shift key is pressed.
Seq - Class in org.biolegato.sequence.data
This class is used to contain all sequence related functions.
Seq() - Constructor for class org.biolegato.sequence.data.Seq
Constructs new instances of a sequence object.
Seq(Seq.Type, String, StringBuffer) - Constructor for class org.biolegato.sequence.data.Seq
Constructs new instances of a sequence object.
Seq(Seq.Type, String, StringBuffer, String) - Constructor for class org.biolegato.sequence.data.Seq
Constructs new instances of a sequence object.
Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness) - Constructor for class org.biolegato.sequence.data.Seq
Constructs new instances of a sequence object.
Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness, CharSequence) - Constructor for class org.biolegato.sequence.data.Seq
Constructs new instances of a sequence object.
Seq(Seq.Type, String, StringBuffer, Seq.Direction, Seq.Topology, Seq.Strandedness, int, String) - Constructor for class org.biolegato.sequence.data.Seq
Constructs new instances of a sequence object.
Seq(Seq) - Constructor for class org.biolegato.sequence.data.Seq
Constructs new instance of a sequence object by copying data from another, pre-existing sequence object.
Seq.Direction - Enum in org.biolegato.sequence.data
Used for typing/storing sequence direction.
Seq.Strandedness - Enum in org.biolegato.sequence.data
Used for typing/storing sequence strandedness.
Seq.Topology - Enum in org.biolegato.sequence.data
Used for typing/storing sequence topology.
Seq.Type - Enum in org.biolegato.sequence.data
This enum is used for typing/storing sequence types.
SequenceCanvas - Class in org.biolegato.sequence.canvas
The BioLegato sequence-based canvas class (based on GDE).
SequenceCanvas() - Constructor for class org.biolegato.sequence.canvas.SequenceCanvas
Creates a new instance of a SequenceCanvas.
SequenceCanvas(Map<? extends Object, ? extends Object>) - Constructor for class org.biolegato.sequence.canvas.SequenceCanvas
Creates a new instance of a SequenceCanvas.
SequenceCanvasObject - Interface in org.biolegato.sequence.canvas
An interface for abstracting the two canvas objects (SequenceTextArea and SequenceList) within BioLegato's Sequence canvas.
SequenceCanvasProperties - Class in org.biolegato.sequence.canvas
A class for setting properties for the Sequence canvas.
SequenceCanvasProperties(JFrame, SequenceCanvas) - Constructor for class org.biolegato.sequence.canvas.SequenceCanvasProperties
Creates a new SequenceCanvasProperties object.
SequenceList - Class in org.biolegato.sequence.canvas
The JList of sequences in the Sequence canvas (to the left of the text-area).
SequenceList(SequenceCanvas, Dataset) - Constructor for class org.biolegato.sequence.canvas.SequenceList
Constructs a new SequenceList
SequenceTextArea - Class in org.biolegato.sequence.canvas
A general canvas with more functionality support than JTextArea.
SequenceTextArea(SequenceCanvas, Dataset) - Constructor for class org.biolegato.sequence.canvas.SequenceTextArea
Creates a new instance of a SequenceTextArea.
SequenceWindow - Class in org.biolegato.sequence.data
A window for editing/viewing the properties of sequences in the canvas.
SequenceWindow(SequenceCanvas, Dataset, JFrame, int[]) - Constructor for class org.biolegato.sequence.data.SequenceWindow
Creates a window for editing the properties of selected sequences.
serialVersionUID - Static variable in class org.biolegato.sequence.canvas.SequenceTextArea
This constant is used for serialization purposes.
serialVersionUID - Static variable in class org.biolegato.sequence.data.SequenceWindow
Used for serialization purposes.
setFont(Font) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Updates the font for the text area.
stateChanged(ChangeEvent) - Method in class org.biolegato.sequence.canvas.SequenceCanvasProperties
Handles changes to the font size spinner (updates the font on spinner value change).
STDCOLOURS - Static variable in class org.biolegato.sequence.canvas.ColourMask
These are the default colours specified in GDE colour mask files.

T

textLengthChanged(int, int, int) - Static method in class org.biolegato.sequence.canvas.SequenceCanvas
Coordinates text length changes between split text areas.
textLengthChanged(int, int, int) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Manages text length changes.
toString() - Method in class org.biolegato.sequence.canvas.ColourMask
Returns the name of the colour mask.
toString() - Method in class org.biolegato.sequence.data.Seq
Creates a string representation of the Seq and its fields This representation is limited to '[GROUP#|_] NAME' because the toString method will be called when the sequence is displayed in any JList.

U

ungroup(int[]) - Method in class org.biolegato.sequence.data.Dataset
Ungroups an array of sequences by iteratively calling the single-sequence ungroup function for each sequence number in the array.
ungroupAction - Variable in class org.biolegato.sequence.canvas.SequenceList
Action for ungrouping/degrouping sequences in the canvas
updateFont(int, boolean) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Updates the font for the Sequence canvas and its sub-objects
updateLength(int, int) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Updates the internal counter which stores the length of the longest line in the text area.

V

valueChanged(ListSelectionEvent) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
This method listens to the sequence list, and deselects any text in the sequence text area(s) whenever something is selected in the sequence list.
valueOf(String) - Static method in enum org.biolegato.sequence.canvas.ColourMask.MaskType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Direction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Strandedness
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Topology
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.biolegato.sequence.data.Seq.Type
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.biolegato.sequence.canvas.ColourMask.MaskType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biolegato.sequence.data.Seq.Direction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biolegato.sequence.data.Seq.Strandedness
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biolegato.sequence.data.Seq.Topology
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.biolegato.sequence.data.Seq.Type
Returns an array containing the constants of this enum type, in the order they are declared.

W

writeFile(String, Appendable, boolean) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Writes data out from the canvas to an Appendable object.
writeFile(DataFormat, Appendable, boolean) - Method in class org.biolegato.sequence.canvas.SequenceCanvas
Writes data out from the canvas.
writeOut(DataFormat, Appendable) - Method in interface org.biolegato.sequence.canvas.SequenceCanvasObject
Writes the current contents of the canvas object to an Appendable object.
writeOut(DataFormat, Appendable) - Method in class org.biolegato.sequence.canvas.SequenceList
Writes the selected sequences out to an appendable object
writeOut(DataFormat, Appendable) - Method in class org.biolegato.sequence.canvas.SequenceTextArea
Writes the current contents of the canvas object to an Appendable object.
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BioLegato sequence canvas support v1.1.0 API

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