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

A

ActionDelegate - Class in com.algosome.common.util

Delegates actions to the appropriate listeners.

ActionDelegate() - Constructor for class com.algosome.common.util.ActionDelegate

Creates a new ActionDelegate.

actionPerformed(ActionEvent) - Method in class com.algosome.common.actions.CloseAction

actionPerformed(ActionEvent) - Method in class com.algosome.common.util.ActionDelegate

Implementation of the ActionListener interface.

addAction(String, ActionListener) - Method in class com.algosome.common.util.ActionDelegate

Adds an action to this object.

addAction(ActionListener, String) - Method in interface com.algosome.common.util.Recorder

addChangeable(Changeable) - Method in class com.algosome.common.undoable.ChangeManager

Adds a Changeable to manage.

addChild(Node<T>) - Method in class com.algosome.common.util.Node

addListener(ChangeManagerListener) - Method in class com.algosome.common.undoable.ChangeManager

addListener(ThreadListener) - Method in class com.algosome.common.util.NotificationThread

Adds the parameter listener

addPreferenceChangeListener(PreferenceChangeListener) - Method in interface com.algosome.common.util.preferences.PreferenceManager

addPreferenceChangeListener(PreferenceChangeListener) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

addSelectionListener(IndexSelectionListener) - Method in interface com.algosome.common.event.IndexSelectionModel

Adds the parameter listener

addSelectionListener(IndexSelectionListener) - Method in class com.algosome.common.event.IndexSelectionModelImpl

addSelectionListener(ContiguousSelectionListener) - Method in interface com.algosome.common.event.Selectable

addSelectionListener(ContiguousSelectionListener) - Method in class com.algosome.common.event.SelectableImpl

animate - Variable in class com.algosome.common.swing.gui.ProgressDial

Flag to indicate whether this Panel is animating or not

animatorThread - Variable in class com.algosome.common.swing.gui.ProgressDial

A thread used for animation of this dial.

B

backtrackTo(Changeable) - Method in class com.algosome.common.undoable.ChangeManager

Backtracks to the parameter changeable, or the start if the parameter does not exists in this list (changeable and elements in the list are compared by the equals method)

ButtonPanel - Class in com.algosome.common.swing.gui

A JPanel with a horizontal/LINE_AXIS layout and maximum/minimum size constrained for JButtons (max 35 height)

ButtonPanel() - Constructor for class com.algosome.common.swing.gui.ButtonPanel

Creates a new JPanel with a horizontal/LINE_AXIS layout.

C

Callback - Interface in com.algosome.common.util

Simple interface to allow for callback events.

callback(Object) - Method in interface com.algosome.common.util.Callback

Callback function after a given process.

canPerform() - Method in class com.algosome.common.util.FalsePerformEvaluator

canPerform() - Method in interface com.algosome.common.util.PerformEvaluator

canPerform() - Method in class com.algosome.common.util.TruePerformEvaluator

canRedo() - Method in interface com.algosome.common.undoable.ChangeCando

Determines if a redo can be performed.

canRedo() - Method in class com.algosome.common.undoable.ChangeManager

Determines if a redo can be performed.

canUndo() - Method in interface com.algosome.common.undoable.ChangeCando

Determines if an Undo can be performed.

canUndo() - Method in class com.algosome.common.undoable.ChangeManager

Determines if an undo can be performed.

Changeable - Interface in com.algosome.common.undoable

Defines that an object can undo and redo a state.

ChangeableHistoryPanel - Class in com.algosome.common.undoable

History panel displaying a ChangeManager history.

ChangeableHistoryPanel(ChangeManager) - Constructor for class com.algosome.common.undoable.ChangeableHistoryPanel

ChangeCando - Interface in com.algosome.common.undoable

Interface defining methods which identify whether an undo or redo can be performed.

ChangeManager - Class in com.algosome.common.undoable

Manages a Queue of Changables to perform undo and/or redo operations.

ChangeManager() - Constructor for class com.algosome.common.undoable.ChangeManager

Creates a new ChangeManager object which is initially empty.

ChangeManager(ChangeManager) - Constructor for class com.algosome.common.undoable.ChangeManager

Creates a new ChangeManager which is a duplicate of the parameter in both contents and current index.

ChangeManagerEvent - Class in com.algosome.common.undoable

Descriptor class with information regarding a ChangeManager change event.

ChangeManagerEvent(ChangeManager) - Constructor for class com.algosome.common.undoable.ChangeManagerEvent

Constructs a new Event.

ChangeManagerListener - Interface in com.algosome.common.undoable

Listener interface to listen to a ChangeManager, and when changes occur.

ChangeManagerModel - Interface in com.algosome.common.undoable

changeOccurred(ChangeManagerEvent) - Method in interface com.algosome.common.undoable.ChangeManagerListener

Fired when a change occurs within a ChangeManager

clear() - Method in class com.algosome.common.undoable.ChangeManager

Clears all Changables contained in this manager.

CloseAction - Class in com.algosome.common.actions

Action that closes a JFrame.

CloseAction(Window) - Constructor for class com.algosome.common.actions.CloseAction

CollapsableJSplitPane - Class in com.algosome.common.swing.gui

Convenience class which sets the one touch expandable

CollapsableJSplitPane(int, JComponent, JComponent) - Constructor for class com.algosome.common.swing.gui.CollapsableJSplitPane

COLOR_LIGHT_GRAY - Static variable in class com.algosome.common.util.UIUtils

colorForRow(int) - Method in class com.algosome.common.swing.gui.CustomJTable

Returns the appropriate background color for the given row.

com.algosome.common.actions - package com.algosome.common.actions

com.algosome.common.event - package com.algosome.common.event

com.algosome.common.io - package com.algosome.common.io

com.algosome.common.swing.gui - package com.algosome.common.swing.gui

com.algosome.common.undoable - package com.algosome.common.undoable

com.algosome.common.util - package com.algosome.common.util

com.algosome.common.util.io - package com.algosome.common.util.io

com.algosome.common.util.preferences - package com.algosome.common.util.preferences

Compare - Interface in com.algosome.common.util

Interface used to perform comparisons in sorting.

compare(Object, Object) - Method in class com.algosome.common.util.Sort

Compares to objects which implements the Compare interface.

compareThisTo(Compare) - Method in interface com.algosome.common.util.Compare

Compares the object implementing this interface against the parameter.

ContiguousSelectionEvent - Class in com.algosome.common.event

Defines an event that specifies a selection change in a linear, contiguous array.

ContiguousSelectionEvent(Object, int, int) - Constructor for class com.algosome.common.event.ContiguousSelectionEvent

ContiguousSelectionListener - Interface in com.algosome.common.event

Listener notified of changes to the underlying selection model.

convertToObjectType(String, int) - Static method in class com.algosome.common.util.preferences.Field

countOccurancesOf(String, String) - Static method in class com.algosome.common.util.StringAnalyzer

Counts and returns the number of times string b occures in String a

COURIER12 - Static variable in class com.algosome.common.util.UIUtils

COURIER13 - Static variable in class com.algosome.common.util.UIUtils

CustomJTable - Class in com.algosome.common.swing.gui

A better-looking table than JTable.

CustomJTable() - Constructor for class com.algosome.common.swing.gui.CustomJTable

CustomJTable(Vector, Vector) - Constructor for class com.algosome.common.swing.gui.CustomJTable

CustomJTable(String[][], String[]) - Constructor for class com.algosome.common.swing.gui.CustomJTable

CustomJTable(Object[][], Object[]) - Constructor for class com.algosome.common.swing.gui.CustomJTable

D

disableCopyPasteForComponent(JComponent) - Static method in class com.algosome.common.util.UIUtils

doQuery(InputStreamParser) - Method in class com.algosome.common.io.URLConnect

Performs an HTTP request to NCBI: sets the URL based upon the current query method, then calls retrieveURLOutput.

doRun() - Method in class com.algosome.common.util.NotificationThread

Abstract method called from run() after notification of all listeners that the thread has started.

Draw(Graphics) - Method in class com.algosome.common.swing.gui.TextBox

drawGradient(Graphics, int) - Static method in class com.algosome.common.swing.gui.Gradient

E

encoding - Variable in class com.algosome.common.io.URLConnect

The type of encoding to use for the URL submission.

ErrorHandler - Interface in com.algosome.common.event

Handles a particular error.

errorOccurred(Object) - Method in interface com.algosome.common.event.ErrorHandler

F

FalsePerformEvaluator - Class in com.algosome.common.util

Basic implementation of PerformEvaluator that always returns false

FalsePerformEvaluator() - Constructor for class com.algosome.common.util.FalsePerformEvaluator

Field - Class in com.algosome.common.util.preferences

Represents Fields for preferences.

Field() - Constructor for class com.algosome.common.util.preferences.Field

Field.FieldBoolean - Class in com.algosome.common.util.preferences

Field.FieldBoolean(String, boolean) - Constructor for class com.algosome.common.util.preferences.Field.FieldBoolean

Field.FieldBrowse - Class in com.algosome.common.util.preferences

Field.FieldBrowse(String, String, int) - Constructor for class com.algosome.common.util.preferences.Field.FieldBrowse

Field.FieldColor - Class in com.algosome.common.util.preferences

Field.FieldColor(String, Color) - Constructor for class com.algosome.common.util.preferences.Field.FieldColor

Field.FieldComboBox - Class in com.algosome.common.util.preferences

Field.FieldComboBox(String, List<Object>) - Constructor for class com.algosome.common.util.preferences.Field.FieldComboBox

Field.FieldComboBox(String, List<Object>, Object) - Constructor for class com.algosome.common.util.preferences.Field.FieldComboBox

Field.FieldDouble - Class in com.algosome.common.util.preferences

Field.FieldDouble(String, double) - Constructor for class com.algosome.common.util.preferences.Field.FieldDouble

Field.FieldInteger - Class in com.algosome.common.util.preferences

Field.FieldInteger(String, int) - Constructor for class com.algosome.common.util.preferences.Field.FieldInteger

Field.FieldLabel - Class in com.algosome.common.util.preferences

Field.FieldLabel(String, String) - Constructor for class com.algosome.common.util.preferences.Field.FieldLabel

Field.FieldLabel(String, String, float) - Constructor for class com.algosome.common.util.preferences.Field.FieldLabel

Field.FieldText - Class in com.algosome.common.util.preferences

Field.FieldText(String, String) - Constructor for class com.algosome.common.util.preferences.Field.FieldText

Field.FieldType - Class in com.algosome.common.util.preferences

Field.FieldType(String) - Constructor for class com.algosome.common.util.preferences.Field.FieldType

FieldFactory - Class in com.algosome.common.util.preferences

Factory class to retrieve the Field.FieldType of a given object based upon its class type.

FieldFactory() - Constructor for class com.algosome.common.util.preferences.FieldFactory

FileFormatException - Exception in com.algosome.common.io

FileFormatException() - Constructor for exception com.algosome.common.io.FileFormatException

FileFormatException(String) - Constructor for exception com.algosome.common.io.FileFormatException

FileHistoryJFrame - Class in com.algosome.common.undoable

JFrame which display history based upon the items in a ChangeManager.

FileHistoryJFrame() - Constructor for class com.algosome.common.undoable.FileHistoryJFrame

FileIO - Class in com.algosome.common.util.io

FileIO() - Constructor for class com.algosome.common.util.io.FileIO

FileSelector - Interface in com.algosome.common.io

finalize() - Method in class com.algosome.common.swing.gui.ProgressDial

FixedSizeTextField - Class in com.algosome.common.swing.gui

FixedSizeTextField(int) - Constructor for class com.algosome.common.swing.gui.FixedSizeTextField

FixedSizeTextField(String, int) - Constructor for class com.algosome.common.swing.gui.FixedSizeTextField

FixedSizeTextField(String) - Constructor for class com.algosome.common.swing.gui.FixedSizeTextField

FontManager - Class in com.algosome.common.util

Singleton class to manage Fonts.

forwardTo(Changeable) - Method in class com.algosome.common.undoable.ChangeManager

Fastforwards to the parameter changeable, or the end if the parameter does not exists in this list (changeable and elements in the list are compared by the equals method)

G

GENEVA12 - Static variable in class com.algosome.common.util.UIUtils

get(String, String) - Method in interface com.algosome.common.util.preferences.PreferenceManager

get(String, String) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getActionCommand() - Method in class com.algosome.common.util.RecordedAction

getActionCommands() - Method in class com.algosome.common.util.ActionDelegate

Retrieves

getActionCommands() - Method in interface com.algosome.common.util.Recorder

getBoolean(String, boolean) - Method in interface com.algosome.common.util.preferences.PreferenceManager

getBoolean(String, boolean) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getChangeable() - Method in class com.algosome.common.util.RecordedAction

getChangeables() - Method in interface com.algosome.common.undoable.ChangeManagerModel

getChildren() - Method in class com.algosome.common.util.Node

getClassComponent(String, Object) - Static method in class com.algosome.common.util.preferences.FieldFactory

getCompareValue() - Method in interface com.algosome.common.util.Compare

Retrieves the value object to compare.

getCurrentIndex() - Method in interface com.algosome.common.undoable.ChangeManagerModel

getDate(String, Date) - Method in interface com.algosome.common.util.preferences.PreferenceManager

getDate(String, Date) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getDate() - Static method in class com.algosome.common.util.Util

Retrieves the current date for Genbank Formatting.

getDefaultFontHeight() - Method in class com.algosome.common.util.FontManager

getDouble(String, double) - Method in interface com.algosome.common.util.preferences.PreferenceManager

getDouble(String, double) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldBoolean

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldBrowse

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldColor

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldComboBox

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldDouble

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldInteger

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldLabel

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldText

getEditingComponent() - Method in class com.algosome.common.util.preferences.Field.FieldType

getEncoding() - Method in class com.algosome.common.io.URLConnect

Retrieves the encoding of this object.

getEnd() - Method in class com.algosome.common.event.ContiguousSelectionEvent

getEnd() - Method in class com.algosome.common.swing.gui.Line

getFontHeights() - Method in class com.algosome.common.util.FontManager

Retrieves a Map keyed with a Font and valued with its true drawing font height that may differ between OS's.

getFontManager() - Static method in class com.algosome.common.util.FontManager

getFonts() - Method in class com.algosome.common.util.FontManager

getHeight() - Method in class com.algosome.common.swing.gui.TextBox

getInt(String, int) - Method in interface com.algosome.common.util.preferences.PreferenceManager

getInt(String, int) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getIntegerValue() - Method in class com.algosome.common.swing.gui.IntegerTextField

Retrieves the integer value of the user input.

getKey() - Method in class com.algosome.common.util.preferences.PreferenceChangeEvent

getKeys() - Method in interface com.algosome.common.util.preferences.PreferenceManager

getKeys() - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getList(String, List) - Method in interface com.algosome.common.util.preferences.PreferenceManager

getList(String, List) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getListeners() - Method in interface com.algosome.common.event.IndexSelectionModel

Retrieves all Listeners.

getListeners() - Method in class com.algosome.common.event.IndexSelectionModelImpl

getListeners() - Method in class com.algosome.common.undoable.ChangeManager

getListeners() - Method in class com.algosome.common.util.NotificationThread

Retrieves all listeners.

getManager() - Method in class com.algosome.common.util.preferences.PreferenceChangeEvent

getModel() - Method in class com.algosome.common.event.IndexSelectionEvent

getModel() - Method in class com.algosome.common.undoable.ChangeManager

getName() - Method in class com.algosome.common.util.preferences.Field.FieldType

getName() - Method in interface com.algosome.common.util.preferences.PreferenceManager

getName() - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getName() - Method in interface com.algosome.common.util.Recorder

getNext() - Method in class com.algosome.common.io.SourceEvent

getObject(String, Object) - Method in interface com.algosome.common.util.preferences.PreferenceManager

getObject(String, Object) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

getObjectType(Object) - Static method in class com.algosome.common.util.preferences.Field

Retrieves an int which represents the Field type

getOperatingSystem() - Static method in enum com.algosome.common.util.OSType

Retrieves the Operating System type.

getOptions() - Method in class com.algosome.common.util.ListSelection

getParameter(String) - Method in class com.algosome.common.io.URLConnect

Retrieves the value to a parameter, or null if none has been set.

getPrevious() - Method in class com.algosome.common.io.SourceEvent

getQueryMethod() - Method in class com.algosome.common.io.URLConnect

Retrieves the HTTP method for query strings.

getQueryString() - Method in class com.algosome.common.io.URLConnect

Retrieves a query string based upon the current parameters.

getRect() - Method in class com.algosome.common.swing.gui.TextBox

getScrollableTracksViewportHeight() - Method in class com.algosome.common.swing.gui.CustomJTable

Changes the behavior of a table in a JScrollPane to be more like the behavior of JList, which expands to fill the available space.

getSelectedFiles() - Method in interface com.algosome.common.io.FileSelector

getSelectedIndeces() - Method in interface com.algosome.common.event.IndexSelectionModel

Retrieves the selected indeces, or {-1}.

getSelectedIndeces() - Method in class com.algosome.common.event.IndexSelectionModelImpl

getSelectedIndex() - Method in interface com.algosome.common.event.IndexSelectionModel

Retrieves the selected index.

getSelectedIndex() - Method in class com.algosome.common.event.IndexSelectionModelImpl

getSelection() - Method in class com.algosome.common.util.ListSelection

getSelectionEnd() - Method in class com.algosome.common.event.SelectableImpl

getSelectionEnd() - Method in interface com.algosome.common.event.Selection

getSelectionEnd() - Method in class com.algosome.common.event.SelectionImpl

getSelectionListeners() - Method in interface com.algosome.common.event.Selectable

getSelectionListeners() - Method in class com.algosome.common.event.SelectableImpl

getSelectionMode() - Method in interface com.algosome.common.event.IndexSelectionModel

Retrieves the mode.

getSelectionMode() - Method in class com.algosome.common.event.IndexSelectionModelImpl

getSelectionStart() - Method in class com.algosome.common.event.SelectableImpl

getSelectionStart() - Method in interface com.algosome.common.event.Selection

getSelectionStart() - Method in class com.algosome.common.event.SelectionImpl

getSource() - Method in class com.algosome.common.event.ContiguousSelectionEvent

getSource() - Method in interface com.algosome.common.io.Source

Retrieves the source as a URI

getSource() - Method in class com.algosome.common.io.SourceEvent

getSource() - Method in class com.algosome.common.undoable.ChangeManagerEvent

Retrieves the source ChangeManager.

getStart() - Method in class com.algosome.common.event.ContiguousSelectionEvent

getStart() - Method in class com.algosome.common.swing.gui.Line

getText() - Method in class com.algosome.common.swing.gui.TextBox

getType() - Method in interface com.algosome.common.io.Source

Retrieves the type of source this is

getURL() - Method in class com.algosome.common.io.URLConnect

Retrieves the URL associated with this object.

getUserObject() - Method in class com.algosome.common.util.Node

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldBoolean

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldBrowse

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldColor

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldComboBox

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldDouble

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldInteger

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldLabel

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldText

getValue() - Method in class com.algosome.common.util.preferences.Field.FieldType

getValue() - Method in class com.algosome.common.util.preferences.PreferenceChangeEvent

getWidth() - Method in class com.algosome.common.swing.gui.TextBox

getX() - Method in class com.algosome.common.swing.gui.TextBox

getY() - Method in class com.algosome.common.swing.gui.TextBox

Gradient - Class in com.algosome.common.swing.gui

Utility class to draw a gradient using a provided graphics object.

Gradient() - Constructor for class com.algosome.common.swing.gui.Gradient

H

hasAction(String) - Method in class com.algosome.common.util.ActionDelegate

Determines if the parameter action command has an action

HorizontalDivider - Class in com.algosome.common.swing.gui

Class which just draws a horizontal line based upon its width.

HorizontalDivider() - Constructor for class com.algosome.common.swing.gui.HorizontalDivider

HPanel - Class in com.algosome.common.swing.gui

A convenience JPanel with its layout set to a horizontal BoxLayout.

HPanel() - Constructor for class com.algosome.common.swing.gui.HPanel

I

IChangeManager - Interface in com.algosome.common.undoable

Marker interface for convenience

IconButton - Class in com.algosome.common.swing.gui

Utility class for a JButton with an icon.

IconButton(Icon, String) - Constructor for class com.algosome.common.swing.gui.IconButton

Constructs a new IconButton with a specified icon and tool tip text.

IndexSelectionEvent - Class in com.algosome.common.event

IndexSelectionEvent(IndexSelectionModel) - Constructor for class com.algosome.common.event.IndexSelectionEvent

IndexSelectionListener - Interface in com.algosome.common.event

Listener notified when an underlying selection has changed.

IndexSelectionModel - Interface in com.algosome.common.event

Model for selections of a single or multiple (discontiguous) indexes.

IndexSelectionModelImpl - Class in com.algosome.common.event

Implementation of the IndexSelectionModel interface.

IndexSelectionModelImpl() - Constructor for class com.algosome.common.event.IndexSelectionModelImpl

InputStreamParser - Interface in com.algosome.common.io

Inteface to parse an InputStream.

IntegerTextField - Class in com.algosome.common.swing.gui

Customized JTextField class that only allows integers to be input.

IntegerTextField() - Constructor for class com.algosome.common.swing.gui.IntegerTextField

A new empty IntegerTextField

IntegerTextField(int) - Constructor for class com.algosome.common.swing.gui.IntegerTextField

A new IntegerTextField with the specified integer value.

isCellEditable(int, int) - Method in class com.algosome.common.swing.gui.CustomJTable

isRecording() - Method in interface com.algosome.common.util.Recorder

isRightClick(MouseEvent) - Static method in class com.algosome.common.util.UIUtils

isRunning - Variable in class com.algosome.common.swing.gui.ProgressDial.Animator

isRunning() - Method in class com.algosome.common.swing.gui.ProgressDial

J

JRegionColorChooser - Class in com.algosome.common.swing.gui

Creates a simple JColorChooser that is modified so the Preview Panel is gone

JRegionColorChooser() - Constructor for class com.algosome.common.swing.gui.JRegionColorChooser

Creates a simple JColorChooser that is modified so the Preview Panel is gone

L

length() - Method in class com.algosome.common.swing.gui.Line

Line - Class in com.algosome.common.swing.gui

Class used to store values for drawing a line.

Line(Point, Point) - Constructor for class com.algosome.common.swing.gui.Line

ListSelection<T> - Class in com.algosome.common.util

Wraps a List with a selected value.

ListSelection(List<T>) - Constructor for class com.algosome.common.util.ListSelection

ListSelection(List<T>, T) - Constructor for class com.algosome.common.util.ListSelection

M

MULTI_SELECTION_MODE - Static variable in interface com.algosome.common.event.IndexSelectionModel

N

NAME_PATTERN - Static variable in class com.algosome.common.util.preferences.Field

Node<T> - Class in com.algosome.common.util

Defines a Node in a Tree data structure

Node(T) - Constructor for class com.algosome.common.util.Node

NotificationThread - Class in com.algosome.common.util

Runnable implementation which allows Listeners to be added to the class and listen for events within the run method (started, finished, etc...)

NotificationThread() - Constructor for class com.algosome.common.util.NotificationThread

notifyOfEvent(Object) - Method in interface com.algosome.common.util.ThreadListener

Called by the thread to notify clients of an event.

notifyOfEvent(Object) - Method in class com.algosome.common.util.ThreadListenerAdapter

O

opacity - Static variable in class com.algosome.common.util.UIUtils

Static variables used for window events - used to see if this window is already open

OSType - Enum in com.algosome.common.util

Defines different operating system types.

P

PaddedHPanel - Class in com.algosome.common.swing.gui

PaddedHPanel(int) - Constructor for class com.algosome.common.swing.gui.PaddedHPanel

PaddedLabel - Class in com.algosome.common.swing.gui

PaddedLabel(String, int) - Constructor for class com.algosome.common.swing.gui.PaddedLabel

paint(Graphics) - Method in class com.algosome.common.swing.gui.CustomJTable

Paints empty rows too, after letting the UI delegate do its painting.

paintComponent(Graphics) - Method in class com.algosome.common.swing.gui.HorizontalDivider

paintComponent(Graphics) - Method in class com.algosome.common.swing.gui.ProgressDial

The drawing routine for this dial.

paintEmptyRows(Graphics) - Method in class com.algosome.common.swing.gui.CustomJTable

Paints the backgrounds of the implied empty rows when the table model is insufficient to fill all the visible area available to us.

parameters - Variable in class com.algosome.common.io.URLConnect

HashMap defining parameters and values for a GET or PUT query string.

parseFrom(int) - Method in interface com.algosome.common.io.InputStreamParser

Specifies a start location to parse from.

parseInput(InputStream) - Method in interface com.algosome.common.io.InputStreamParser

Specifies an implementation to parse the given InputStream.

parseTo(int) - Method in interface com.algosome.common.io.InputStreamParser

Specifies an end location to parse to.

percentFinishedChanged(double) - Method in interface com.algosome.common.util.ProgressListener

PerformEvaluator - Interface in com.algosome.common.util

Basic interface that defines if something can be performed.

preferenceChanged(PreferenceChangeEvent) - Method in interface com.algosome.common.util.preferences.PreferenceChangeListener

PreferenceChangeEvent - Class in com.algosome.common.util.preferences

PreferenceChangeEvent(PreferenceManager, String, Object) - Constructor for class com.algosome.common.util.preferences.PreferenceChangeEvent

PreferenceChangeListener - Interface in com.algosome.common.util.preferences

This interface is opted over the java.util.pref.PreferenceChangeListener interface due to the reliance of that listener and event on the Preferences class and String new value constraint.

PreferenceManager - Interface in com.algosome.common.util.preferences

Manages Preferences.

PreferenceManagerImpl - Class in com.algosome.common.util.preferences

Implementation of the PreferenceManager interface backed by a Map to store the key/value pairs.

PreferenceManagerImpl() - Constructor for class com.algosome.common.util.preferences.PreferenceManagerImpl

PreferenceManagerImpl(String) - Constructor for class com.algosome.common.util.preferences.PreferenceManagerImpl

PreferenceManagerImpl(Map<String, Object>) - Constructor for class com.algosome.common.util.preferences.PreferenceManagerImpl

PreferenceManagerImpl(PreferenceManager) - Constructor for class com.algosome.common.util.preferences.PreferenceManagerImpl

PreferenceManagerImpl(String, Map<String, Object>) - Constructor for class com.algosome.common.util.preferences.PreferenceManagerImpl

prepareRenderer(TableCellRenderer, int, int) - Method in class com.algosome.common.swing.gui.CustomJTable

Shades alternate rows in different colors.

ProgressDial - Class in com.algosome.common.swing.gui

An animated progress dial similar to the Cocoa presentation of a progress dial.

ProgressDial() - Constructor for class com.algosome.common.swing.gui.ProgressDial

Creates a new Progress Dial with a preferred, max, and minimum size of 24 pixels.

ProgressDial(int) - Constructor for class com.algosome.common.swing.gui.ProgressDial

Creates a new Progress Dial with a preferred, max, and minimum size of the parameter size.

ProgressDial.Animator - Class in com.algosome.common.swing.gui

ProgressDial.Animator() - Constructor for class com.algosome.common.swing.gui.ProgressDial.Animator

ProgressDialog - Class in com.algosome.common.swing.gui

A JDialog containing a JProgressBar and no decorations.

ProgressDialog() - Constructor for class com.algosome.common.swing.gui.ProgressDialog

Constructs a new dialog containing a progress bar and indication label which, by default, contains the text loading.

ProgressDialog(ActionListener) - Constructor for class com.algosome.common.swing.gui.ProgressDialog

Constructs a new GenecoderProgressDialog containing a ProgressBar, Label, and an action listener that defines a cancel action.

ProgressListener - Interface in com.algosome.common.util

Q

query_method - Variable in class com.algosome.common.io.URLConnect

Indicates whether GET or PUT will be used to contact a server.

R

readfileWhole(String) - Static method in class com.algosome.common.util.io.FileIO

RecordedAction - Class in com.algosome.common.util

RecordedAction(String, Changeable) - Constructor for class com.algosome.common.util.RecordedAction

Recorder - Interface in com.algosome.common.util

Defines a recorder.

redo() - Method in interface com.algosome.common.undoable.Changeable

Redoes the state.

redo() - Method in class com.algosome.common.undoable.ChangeManager

Redoes the Changable at the current index.

reloadData() - Method in class com.algosome.common.swing.gui.CustomJTable

removeAction(String, ActionListener) - Method in class com.algosome.common.util.ActionDelegate

Removes the parameter action specified by the string key.

removeAllActionsFor(String) - Method in class com.algosome.common.util.ActionDelegate

Removes all actions for the parameter action command

removeListener(ChangeManagerListener) - Method in class com.algosome.common.undoable.ChangeManager

removeListener(ThreadListener) - Method in class com.algosome.common.util.NotificationThread

Removes the parameter listener.

removePreferenceChangeListener(PreferenceChangeListener) - Method in interface com.algosome.common.util.preferences.PreferenceManager

removePreferenceChangeListener(PreferenceChangeListener) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

removeSelectionListener(IndexSelectionListener) - Method in interface com.algosome.common.event.IndexSelectionModel

Removes the parameter listener.

removeSelectionListener(IndexSelectionListener) - Method in class com.algosome.common.event.IndexSelectionModelImpl

removeSelectionListener(ContiguousSelectionListener) - Method in interface com.algosome.common.event.Selectable

removeSelectionListener(ContiguousSelectionListener) - Method in class com.algosome.common.event.SelectableImpl

retrieveURLOutput(String, InputStreamParser) - Method in class com.algosome.common.io.URLConnect

Retrieves the output from the given url parameter.

RIGHT_MOUSE_CLICK - Static variable in class com.algosome.common.util.UIUtils

run() - Method in class com.algosome.common.swing.gui.ProgressDial.Animator

run() - Method in class com.algosome.common.util.NotificationThread

S

Selectable - Interface in com.algosome.common.event

Defines an Object or its contents are selectable.

SelectableImpl - Class in com.algosome.common.event

Basic implementation of the Selectable interface.

SelectableImpl() - Constructor for class com.algosome.common.event.SelectableImpl

Selection - Interface in com.algosome.common.event

Defines an object that has a selection start and end.

selectionChanged(ContiguousSelectionEvent) - Method in interface com.algosome.common.event.ContiguousSelectionListener

Called when the underlying selection has changed.

selectionChanged(IndexSelectionEvent) - Method in interface com.algosome.common.event.IndexSelectionListener

A change in the selection.

SelectionImpl - Class in com.algosome.common.event

Implementation of the Selection interface

SelectionImpl(int, int) - Constructor for class com.algosome.common.event.SelectionImpl

Defines a start and end of a selection

set(String, String) - Method in interface com.algosome.common.util.preferences.PreferenceManager

set(String, String) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

setBoolean(String, boolean) - Method in interface com.algosome.common.util.preferences.PreferenceManager

setBoolean(String, boolean) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

setChangeManager(ChangeManager) - Method in class com.algosome.common.undoable.ChangeableHistoryPanel

setChangeManager(ChangeManager) - Method in class com.algosome.common.undoable.FileHistoryJFrame

setDate(String, Date) - Method in interface com.algosome.common.util.preferences.PreferenceManager

setDate(String, Date) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

setDouble(String, double) - Method in interface com.algosome.common.util.preferences.PreferenceManager

setDouble(String, double) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

setEncoding(String) - Method in class com.algosome.common.io.URLConnect

Sets the encoding of this object.

setHeight(int) - Method in class com.algosome.common.swing.gui.TextBox

setIndeterminate(boolean) - Method in class com.algosome.common.swing.gui.ProgressDial

setIndeterminate(boolean) - Method in class com.algosome.common.swing.gui.ProgressDialog

Sets the progress bar to indeterminate.

setInt(String, int) - Method in interface com.algosome.common.util.preferences.PreferenceManager

setInt(String, int) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

setList(String, List) - Method in interface com.algosome.common.util.preferences.PreferenceManager

setList(String, List) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

setLocation(Point) - Method in class com.algosome.common.swing.gui.TextBox

setMaxSize(int) - Static method in class com.algosome.common.undoable.ChangeManager

Sets the max size for this.

setObject(String, Object) - Method in interface com.algosome.common.util.preferences.PreferenceManager

setObject(String, Object) - Method in class com.algosome.common.util.preferences.PreferenceManagerImpl

setOperation(String) - Method in class com.algosome.common.swing.gui.ProgressDialog

Sets the operation text being performed.

setParameter(String, String) - Method in class com.algosome.common.io.URLConnect

Sets the value to a parameter for dynamic websites.

setProgressValue(int) - Method in class com.algosome.common.swing.gui.ProgressDialog

Set the progress value of the Progress Bar.

setQueryMethod(boolean) - Method in class com.algosome.common.io.URLConnect

Sets the HTTP method for query strings.

setRecorder(Recorder) - Method in class com.algosome.common.util.ActionDelegate

Sets a recorder.

setRect(Rectangle) - Method in class com.algosome.common.swing.gui.TextBox

setSelection(int...) - Method in interface com.algosome.common.event.IndexSelectionModel

Sets the selection.

setSelection(int...) - Method in class com.algosome.common.event.IndexSelectionModelImpl

setSelection(T) - Method in class com.algosome.common.util.ListSelection

setSelectionEnd(int) - Method in interface com.algosome.common.event.Selectable

setSelectionEnd(int) - Method in class com.algosome.common.event.SelectableImpl

setSelectionMode(int) - Method in interface com.algosome.common.event.IndexSelectionModel

Sets the mode.

setSelectionMode(int) - Method in class com.algosome.common.event.IndexSelectionModelImpl

setSelectionStart(int) - Method in interface com.algosome.common.event.Selectable

setSelectionStart(int) - Method in class com.algosome.common.event.SelectableImpl

setSource(URI) - Method in interface com.algosome.common.io.Source

setText(String) - Method in class com.algosome.common.swing.gui.TextBox

setURL(String) - Method in class com.algosome.common.io.URLConnect

Sets the main URL to retrieve

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldBoolean

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldBrowse

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldColor

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldComboBox

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldDouble

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldInteger

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldLabel

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldText

setValue(Object) - Method in class com.algosome.common.util.preferences.Field.FieldType

setWidth(int) - Method in class com.algosome.common.swing.gui.TextBox

setX(int) - Method in class com.algosome.common.swing.gui.TextBox

setY(int) - Method in class com.algosome.common.swing.gui.TextBox

SINGLE_SELECTION_MODE - Static variable in interface com.algosome.common.event.IndexSelectionModel

Sort - Class in com.algosome.common.util

A class which sorts any object that implements the Compare interface.

Sort() - Constructor for class com.algosome.common.util.Sort

Source - Interface in com.algosome.common.io

Defines a source for a sequence or sequences.

Source.Type - Enum in com.algosome.common.io

sourceChanged(SourceEvent) - Method in interface com.algosome.common.io.SourceListener

SourceEvent - Class in com.algosome.common.io

SourceEvent(Object, Source, Source) - Constructor for class com.algosome.common.io.SourceEvent

SourceListener - Interface in com.algosome.common.io

startAnimation() - Method in class com.algosome.common.swing.gui.ProgressDial

stopAnimation() - Method in class com.algosome.common.swing.gui.ProgressDial

StringAnalyzer - Class in com.algosome.common.util

Class used to Strings.

StringAnalyzer() - Constructor for class com.algosome.common.util.StringAnalyzer

StringFootnotePreference - Class in com.algosome.common.util.preferences

StringFootnotePreference(String) - Constructor for class com.algosome.common.util.preferences.StringFootnotePreference

StringPathPreference - Class in com.algosome.common.util.preferences

StringPathPreference(String) - Constructor for class com.algosome.common.util.preferences.StringPathPreference

StringTitlePreference - Class in com.algosome.common.util.preferences

StringTitlePreference(String) - Constructor for class com.algosome.common.util.preferences.StringTitlePreference

strip_count - Variable in class com.algosome.common.swing.gui.ProgressDial

The strip count for this dial.

T

TextBox - Class in com.algosome.common.swing.gui

Class to be used for drawing to a graphics object.

TextBox() - Constructor for class com.algosome.common.swing.gui.TextBox

TextBox(String) - Constructor for class com.algosome.common.swing.gui.TextBox

TextBox(String, Rectangle) - Constructor for class com.algosome.common.swing.gui.TextBox

TextBox(String, Point) - Constructor for class com.algosome.common.swing.gui.TextBox

TextBox(String, int, int) - Constructor for class com.algosome.common.swing.gui.TextBox

TextBox(String, int, int, int, int) - Constructor for class com.algosome.common.swing.gui.TextBox

threadFinished(Runnable) - Method in interface com.algosome.common.util.ThreadListener

Called after the Thread finishes.

threadFinished(Runnable) - Method in class com.algosome.common.util.ThreadListenerAdapter

ThreadListener - Interface in com.algosome.common.util

Can be used to monitor Thread progress

ThreadListenerAdapter - Class in com.algosome.common.util

Empty implementation of the ThreadListener interface to make implementation easier.

ThreadListenerAdapter() - Constructor for class com.algosome.common.util.ThreadListenerAdapter

threadStarted(Runnable) - Method in interface com.algosome.common.util.ThreadListener

Fired when the thread first starts.

threadStarted(Runnable) - Method in class com.algosome.common.util.ThreadListenerAdapter

toString() - Method in class com.algosome.common.swing.gui.CustomJTable

toString() - Method in class com.algosome.common.undoable.ChangeManager

toString() - Method in class com.algosome.common.util.preferences.StringFootnotePreference

toString() - Method in class com.algosome.common.util.preferences.StringPathPreference

toString() - Method in class com.algosome.common.util.preferences.StringTitlePreference

TruePerformEvaluator - Class in com.algosome.common.util

Implementation of PerformEvaluator that always returns true.

TruePerformEvaluator() - Constructor for class com.algosome.common.util.TruePerformEvaluator

TYPE_BOOLEAN - Static variable in class com.algosome.common.util.preferences.Field

TYPE_COLOR - Static variable in class com.algosome.common.util.preferences.Field

TYPE_DOUBLE - Static variable in class com.algosome.common.util.preferences.Field

TYPE_INTEGER - Static variable in class com.algosome.common.util.preferences.Field

TYPE_PATTERN - Static variable in class com.algosome.common.util.preferences.Field

TYPE_TEXT - Static variable in class com.algosome.common.util.preferences.Field

U

UIUtils - Class in com.algosome.common.util

This is the Globals class for GeneCoder.

UIUtils() - Constructor for class com.algosome.common.util.UIUtils

Constructor.

undo() - Method in interface com.algosome.common.undoable.Changeable

Undoes the state

undo() - Method in class com.algosome.common.undoable.ChangeManager

Undoes the Changeable at the current index.

UNICODE_BULLET - Static variable in class com.algosome.common.util.UIUtils

UNICODE_DOWN_ARROW - Static variable in class com.algosome.common.util.UIUtils

UNICODE_UP_ARROW - Static variable in class com.algosome.common.util.UIUtils

url - Variable in class com.algosome.common.io.URLConnect

Specifies a URL to look up.

URLConnect - Class in com.algosome.common.io

URLConnect is a class that can be used to connect to and read a website.

URLConnect() - Constructor for class com.algosome.common.io.URLConnect

Creates an empty URLConnect object containing no parameters.

URLConnect(String) - Constructor for class com.algosome.common.io.URLConnect

Creates a URLConnect object with a given URL

URLConnect(URLConnect) - Constructor for class com.algosome.common.io.URLConnect

Creates an URLConnect object from a previous URLConnect object.

UserWarner - Class in com.algosome.common.util

Warns the user of a particular notice.

UserWarner() - Constructor for class com.algosome.common.util.UserWarner

Util - Class in com.algosome.common.util

Utility class

Util() - Constructor for class com.algosome.common.util.Util

V

VALUE_PATTERN - Static variable in class com.algosome.common.util.preferences.Field

valueOf(String) - Static method in enum com.algosome.common.io.Source.Type

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

valueOf(String) - Static method in enum com.algosome.common.util.OSType

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

values() - Static method in enum com.algosome.common.io.Source.Type

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

values() - Static method in enum com.algosome.common.util.OSType

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

VPanel - Class in com.algosome.common.swing.gui

A convenience JPanel class with a vertical BoxLayout.

VPanel() - Constructor for class com.algosome.common.swing.gui.VPanel

W

warnUser() - Static method in class com.algosome.common.util.UserWarner

Warns the user.

warnUser(String) - Static method in class com.algosome.common.util.UserWarner

Warns the user with a particular message.

windowLocation - Static variable in class com.algosome.common.util.UIUtils

writeFile(String, String) - Static method in class com.algosome.common.util.io.FileIO

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