Serialized Form

Package org.biolegato.gdesupport.canvas

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

serialVersionUID: 7526472295622777011L

Serialized Fields

canvas

GDECanvas canvas

fontSizeSP

javax.swing.SpinnerNumberModel fontSizeSP

boldCB

javax.swing.JCheckBox boldCB

closeB

javax.swing.JButton closeB

Class org.biolegato.gdesupport.canvas.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

list

GDEList list

Self reference.

popup

javax.swing.JPopupMenu popup

The right click menu for the GDE sequence list.

datamodel

Dataset datamodel

Used for the relationship between the data model and the list

listListeners

java.util.List<E> listListeners

The list of listeners to the data in 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"

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.GDETextArea extends javax.swing.JComponent implements Serializable

serialVersionUID: 7526472295622777004L

Serialized Fields

rowHeight

int rowHeight

The height of each row in the textarea

columnWidth

int columnWidth

The width of each column in the textarea

canvas

GDECanvas canvas

The canvas associtated with the textarea.

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)

minsx

int minsx

The minimum X co-ordinate for the current selection (cached for faster drawing) NOTE: this should only be modified by changePosition!!!

minsy

int minsy

The minimum Y co-ordinate for the current selection (cached for faster drawing) NOTE: this should only be modified by changePosition!!!

maxsx

int maxsx

The maximum X co-ordinate for the current selection (cached for faster drawing) NOTE: this should only be modified by changePosition!!!

maxsy

int maxsy

The maximum Y co-ordinate for the current selection (cached for faster drawing) NOTE: this should only be modified by changePosition!!!

popup

javax.swing.JPopupMenu popup

The right click menu for the text area.

datamodel

Dataset datamodel

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

blTextAreaSelf

GDETextArea blTextAreaSelf

Self-reference for inner classes.

longestline

int longestline

Stores the length of the longest line in the textarea

Class org.biolegato.gdesupport.canvas.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.data

Class org.biolegato.gdesupport.data.Dataset extends javax.swing.AbstractListModel implements Serializable

Serialized Fields

lines

java.util.List<E> lines

This linked list used to store all of the height in the document.

Each y is stored as a linked list of sequence wrappers. Each sequence wrapper is characterized by a sequence and a highindex offset. The highindex offset is used to determine the offset of the sequence within the document.

See Also:

org.biolegato.core.data.seqdoc.SeqWrap

maxGroup

int maxGroup

Keeps track of the maximum groupID number in usage.

group2seq

java.util.Set<E>[] group2seq

A hashtable used to map all groups to sequences

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

serialVersionUID: 7526472295622777013L

Serialized Fields

sequences

int[] sequences

The sequence associated with the window

maskbox

javax.swing.JComboBox maskbox

The combobox containing all colour masks

namebox

javax.swing.JTextField namebox

The text area used to obtain the sequence namebox 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

typebox

javax.swing.JComboBox typebox

The combobox used for modifying the sequence's typebox

directionbox

javax.swing.JComboBox directionbox

The combobox used for modifying the sequence's directionbox

topologybox

javax.swing.JComboBox topologybox

The combobox used for modifying the sequence's topologybox

strandednessbox

javax.swing.JComboBox strandednessbox

The combobox used for modifying the sequence's strandednessbox

datamodel

Dataset datamodel

The data model to associate with the sequences

Class org.biolegato.gdesupport.data.Seq extends java.lang.Object implements Serializable

serialVersionUID: 7526472295622777024L

Serialized Fields

type

Seq.Type type

name

java.lang.String name

sequence

java.lang.StringBuffer sequence

direction

Seq.Direction direction

strandedness

Seq.Strandedness strandedness

topology

Seq.Topology topology

original

java.lang.StringBuilder original