Serialized Form

Package org.biolegato.gdesupport.canvas

Class org.biolegato.gdesupport.canvas.GDECanvas extends javax.swing.Box implements Serializable

serialVersionUID: 7526472295622776154L

Serialized Fields

datamodel

GDEModel datamodel

The current dataset for the GDE canvas

nameList

GDEList nameList

Used for selecting genes

dataCollector

GDETextArea dataCollector

The text area for data manipulation

altDataCollector

GDETextArea altDataCollector

The alternate text area for data manipulation (for splits)

currentPane

GDECanvasObject currentPane

Stores which canvas contains the cursor and any current data selections.

dataPane

javax.swing.JScrollPane dataPane

The scroll pane containing the main canvas

altDataPane

javax.swing.JScrollPane altDataPane

The scroll pane containing the split canvas

canvasPane

javax.swing.Box canvasPane

The box to store all split canvases

splitPane

javax.swing.JSplitPane splitPane

The split pane for split canvases

canvasSelf

GDECanvas canvasSelf

Reference pointer to self

status

javax.swing.JLabel status

Stores the row and column position status

insertStatus

javax.swing.JLabel insertStatus

Stores the insertion mode status

undoStack

java.util.Stack<E> undoStack

The stack of undoable events.

Every time an event occurs within the BLTextArea that is undoable, an undo object is created and added to this stack. This allows one to undo performed SeqDoc actions. To undo an action, pop the top object off of the stack and call its undo method. This will perform the undo and the undo method will return a redo object. The resulting redo object can then be added to the redoStack stack.

redoStack

java.util.Stack<E> redoStack

The stack of redoable events

Every time an event is undone, a redo object is created and added to this stack. A redo object is essentially an undo object created to "undo an undo". To perform a redo, pop the top object off the stact and call its undo method. This will perform the redo and the undo method will return an undo object. The resulting undo object can then be added to the undoStack stack.

splitAction

javax.swing.AbstractAction splitAction

Action for splitting the canvas

joinAction

javax.swing.AbstractAction joinAction

Action for joining split canvases

cutAction

javax.swing.AbstractAction cutAction

The action "Cut"

copyAction

javax.swing.AbstractAction copyAction

The action "Copy"

pasteAction

javax.swing.AbstractAction pasteAction

The action "Paste"

undoAction

javax.swing.AbstractAction undoAction

The action "Undo"

redoAction

javax.swing.AbstractAction redoAction

The action "Redo"

changeCaseAction

javax.swing.AbstractAction changeCaseAction

The action "Change Case"

selectByNameMenuItem

javax.swing.JMenuItem selectByNameMenuItem

The menu item "Select sequence by name"

splitMenuItem

javax.swing.JMenuItem splitMenuItem

Action for splitting the canvas

joinMenuItem

javax.swing.JMenuItem joinMenuItem

The menu item for joining split canvases

cutMenuItem

javax.swing.JMenuItem cutMenuItem

The menu itemaction "Cut"

copyMenuItem

javax.swing.JMenuItem copyMenuItem

The menu item "Copy"

pasteMenuItem

javax.swing.JMenuItem pasteMenuItem

The menu item "Paste"

undoMenuItem

javax.swing.JMenuItem undoMenuItem

The menu item "Undo"

redoMenuItem

javax.swing.JMenuItem redoMenuItem

The menu item "Redo"

changeCaseMenuItem

javax.swing.JMenuItem changeCaseMenuItem

The menu item "Change Case"

selectGroupMenuItem

javax.swing.JMenuItem selectGroupMenuItem

The menu item "Select group"

selectAllMenuItem

javax.swing.JMenuItem selectAllMenuItem

The menu item "Select All"

groupMenuItem

javax.swing.JMenuItem groupMenuItem

The menu item for grouping sequences in the canvas

ungroupMenuItem

javax.swing.JMenuItem ungroupMenuItem

The menu item for ungrouping sequences in the canvas

getInfoMenuItem

javax.swing.JMenuItem getInfoMenuItem

The menu item for "Get Info..."

gdeCanvasSelf

GDECanvas gdeCanvasSelf

Self-reference for inner classes.

Class org.biolegato.gdesupport.canvas.GDECanvasProperties extends javax.swing.JDialog implements Serializable

serialVersionUID: 7526472295622777011L

Serialized Fields

properties

org.biolegato.core.properties.BLProperties properties

The BLProperties object to associate the properties extension with.

Class org.biolegato.gdesupport.canvas.PropertiesCheckbox extends javax.swing.JCheckBox implements Serializable

serialVersionUID: 7526472295622777010L

Serialized Fields

propertyKey

java.lang.String propertyKey

The key in ther properties hashtable that corresponds to the widget.

properties

org.biolegato.core.properties.BLProperties properties

The BLProperties object to associate the widget to.

Class org.biolegato.gdesupport.canvas.PropertiesNumber extends javax.swing.Box implements Serializable

serialVersionUID: 7526472295622777036L

Serialized Fields

spinner

javax.swing.JSpinner spinner

The JSpinner object to set the value with.

propertyKey

java.lang.String propertyKey

The key in ther properties hashtable that corresponds to the widget.

properties

org.biolegato.core.properties.BLProperties properties

The BLProperties object to associate the widget to.

Package org.biolegato.gdesupport.canvas.colourmask

Class org.biolegato.gdesupport.canvas.colourmask.ImportFileAction extends javax.swing.Box implements Serializable

serialVersionUID: 7526472295622777037L

Serialized Fields

window

javax.swing.JDialog window

The window to associate the import with.

combobox

javax.swing.JComboBox combobox

The combobox to use for selecting imported colour masks from.

Package org.biolegato.gdesupport.canvas.data

Class org.biolegato.gdesupport.canvas.data.Cell extends java.util.Hashtable<java.lang.String,java.lang.Object> implements Serializable

serialVersionUID: 7526472295622777024L

Serialized Fields

listeners

java.util.List<E> listeners

This linked list stores all sequence listeners

Package org.biolegato.gdesupport.canvas.list

Class org.biolegato.gdesupport.canvas.list.GDEList extends javax.swing.JList implements Serializable

serialVersionUID: 7526472295622777009L

Serialized Fields

lastClickTime

long lastClickTime

The last time the mouse was clicked (used for double click detection)

lastClickEntry

int lastClickEntry

The entry selected on the last click

listSelf

GDEList listSelf

Self reference.

canvas

GDECanvas canvas

Stores a symbolic link to the parent canvas.

popup

javax.swing.JPopupMenu popup

The right click menu for the GDE sequence list.

datamodel

GDEModel datamodel

Used for the relationship between the data model and the list

selectGroupAction

javax.swing.AbstractAction selectGroupAction

The menu item "Select group"

getInfoAction

javax.swing.AbstractAction getInfoAction

The menu item "Get info..."

deleteMenuItem

javax.swing.JMenuItem deleteMenuItem

The menu item "Delete"

cutMenuItem

javax.swing.JMenuItem cutMenuItem

The menu item "Cut"

copyMenuItem

javax.swing.JMenuItem copyMenuItem

The menu item "Copy"

pasteMenuItem

javax.swing.JMenuItem pasteMenuItem

The menu item "Paste"

selectAllAction

javax.swing.AbstractAction selectAllAction

The menu item "Select All"

selectByNameAction

javax.swing.AbstractAction selectByNameAction

The abstract action "Select sequence by name"

groupAction

javax.swing.AbstractAction groupAction

Action for grouping sequences in the canvas

ungroupAction

javax.swing.AbstractAction ungroupAction

Action for ungrouping sequences in the canvas

Class org.biolegato.gdesupport.canvas.list.GDESequenceWindow extends javax.swing.JDialog implements Serializable

serialVersionUID: 7526472295622777013L

Serialized Fields

sequences

Cell[] sequences

The sequence associated with the window

name

javax.swing.JTextField name

The text area used to obtain the sequence name from

protectAlignmentCB

javax.swing.JCheckBox protectAlignmentCB

The checkbox used to modify the protection of the sequence's alignment gaps

protectAmbiguousCB

javax.swing.JCheckBox protectAmbiguousCB

The checkbox used to modify the protection of the sequence's ambiguous characters

protectUnambiguousCB

javax.swing.JCheckBox protectUnambiguousCB

The checkbox used to modify the protection of the sequence's unambiguous characters

type

javax.swing.JComboBox type

The combobox used for modifying the sequence's type

direction

javax.swing.JComboBox direction

The combobox used for modifying the sequence's direction

topology

javax.swing.JComboBox topology

The combobox used for modifying the sequence's topology

strandedness

javax.swing.JComboBox strandedness

The combobox used for modifying the sequence's strandedness

mask

ImportFileAction mask

The colour mask selection component

datamodel

GDEModel datamodel

The data model to associate with the sequences

Class org.biolegato.gdesupport.canvas.list.SelectByNameWindow extends javax.swing.JDialog implements Serializable

serialVersionUID: 7526472295622776150L

Serialized Fields

list

javax.swing.JList list

The list to search for and select/deselect sequences from.

nameSelector

javax.swing.JTextField nameSelector

Used for obtaining the name to search for

selectButton

javax.swing.JButton selectButton

The button used to select the sequences based on their name

deselectButton

javax.swing.JButton deselectButton

The button used to deselect the sequences based on their name

closeButton

javax.swing.JButton closeButton

The button used to close the window

Package org.biolegato.gdesupport.canvas.textarea

Class org.biolegato.gdesupport.canvas.textarea.BLComponent extends javax.swing.JComponent implements Serializable

Serialized Fields

rowHeight

int rowHeight

The height of each row in the textarea

columnWidth

int columnWidth

The width of each column in the textarea

Class org.biolegato.gdesupport.canvas.textarea.BLTextArea extends BLComponent implements Serializable

serialVersionUID: 7526472295622777004L

Serialized Fields

insertMode

boolean insertMode

If true new text will overwrite existing text.

selectionMove

boolean selectionMove

Used to track the shift key. If this is false, cancel the current selection on moving using the direction arrows. If this is true, stretch the current selection on moving using the direction arrows.

selectionMouse

boolean selectionMouse

Used to track mouse holds and releases. If this is false, cancel the current selection on any mouse click. If this is true, stretch the current selection on mouse movement.

row

int row

The current row of the caret

column

int column

The current column of the caret.

sx

int sx

The start column of the selection (no selection if sx = column)

sy

int sy

The start row of the selection (no selection if sy = row)

currentMap

ColourMap currentMap

Handles printing text

popup

javax.swing.JPopupMenu popup

The right click menu for the text area.

cursorListeners

java.util.List<E> cursorListeners

Linked list to store all cursor listeners

modeListeners

java.util.List<E> modeListeners

Linked list to store all mode change listeners

active

boolean active

Stores the state of whether the canvas's selection is active

datamodel

GDEModel datamodel

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

invalidzone

java.awt.Color invalidzone

The colour of invalid areas in the textarea.

blTextAreaSelf

BLTextArea blTextAreaSelf

Self-reference for inner classes.

Class org.biolegato.gdesupport.canvas.textarea.GDETextArea extends BLTextArea implements Serializable

serialVersionUID: 7526472295622777017L

Serialized Fields

canvas

GDECanvas canvas

The canvas associtated with the textarea.

Class org.biolegato.gdesupport.canvas.textarea.UndoableGDETextArea extends GDETextArea implements Serializable

serialVersionUID: 7526472295622777017L

Serialized Fields

canvas

GDECanvas canvas

Stores a symbolic link to the parent canvas.

ugdeTextAreaSelf

UndoableGDETextArea ugdeTextAreaSelf

Self-reference for inner classes.