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

A

aa1 - Static variable in class org.bdgp.util.DNAUtils

Genetic Code in 1-character amino acid codes

aa3 - Static variable in class org.bdgp.util.DNAUtils

Genetic Code in 3-character amino acid codes

AbstractDataAdapter - class org.bdgp.io.AbstractDataAdapter.

An implementation of VisualDataAdapter that provides implementations of the listener code.

AbstractDataAdapter() - Constructor for class org.bdgp.io.AbstractDataAdapter

AbstractDataAdapterUI - class org.bdgp.swing.AbstractDataAdapterUI.

AbstractDataAdapterUI() - Constructor for class org.bdgp.swing.AbstractDataAdapterUI

actionPerformed(ActionEvent) - Method in class org.bdgp.util.MethodRunnerActionListener

Runs the method named in the constructor.

adapterAtIndexSupports(int, IOOperation) - Method in class org.bdgp.io.DataAdapterRegistry

Returns a boolean indicated whether the data adapter at the given index supports the given IOOperation.

adapterList - Variable in class org.bdgp.swing.widget.DataAdapterChooser

adapterSupports(String, IOOperation) - Method in class org.bdgp.io.DataAdapterRegistry

Returns a boolean indicating whether a data adapter supports a particular IOOperation.

add() - Method in class org.bdgp.swing.ListEditor

add() - Method in class org.bdgp.cv.gui.DAGComponent

add(TreePath) - Method in interface org.bdgp.cv.datamodel.MutableTreeModel

Creates a new node and adds it as a child of the node given by target.

add(TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

addChild(TreePath, Object) - Method in interface org.bdgp.cv.datamodel.MutableTreeModel

Adds a node to the tree at target.

addDataAdapterUIListener(DataAdapterUIListener) - Method in class org.bdgp.swing.AbstractDataAdapterUI

addDataAdapterUIListener(DataAdapterUIListener) - Method in interface org.bdgp.io.InteractiveDataAdapterUI

addDragTreeEventListener(DragTreeEventListener) - Method in class org.bdgp.swing.DragTree

addFilter(VectorFilter) - Method in class org.bdgp.util.BooleanFilter

addItem(XMLLayout.LayoutItem) - Method in class org.bdgp.swing.XMLLayout.BoxElement

addListSelectionListener(ListSelectionListener) - Method in class org.bdgp.swing.ListEditor

addProgressListener(ProgressListener) - Method in interface org.bdgp.io.VisualDataAdapter

Adds a progress listener to this adapter.

addProgressListener(ProgressListener) - Method in class org.bdgp.io.AbstractDataAdapter

addProgressListener(ProgressListener) - Method in class org.bdgp.io.GenericVisualDataAdapter

addProgressListener(ProgressListener) - Method in class org.bdgp.io.ProgressableFileInputStream

adjustHoverLoc(int, int) - Method in class org.bdgp.swing.DragTree

allowAdd(TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

allowCopy(TreePath[], TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

allowDelete(TreePath[]) - Method in class org.bdgp.cv.gui.DAGComponent

allowMerge(TreePath, TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

allowMove(TreePath[], TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

allowSplit(TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

allowStructureEdits - Variable in class org.bdgp.cv.gui.DAGComponent

ALWAYS - Static variable in class org.bdgp.swing.XMLLayout.ScrollerElement

AND - Static variable in class org.bdgp.util.BooleanFilter

AS_NEEDED - Static variable in class org.bdgp.swing.XMLLayout.ScrollerElement

attributes - Variable in class org.bdgp.swing.XMLLayout.LayoutNode

autocommit - Variable in class org.bdgp.swing.ListEditor

autosizeRows() - Method in class org.bdgp.swing.MultiheightTable

B

backgroundImage - Variable in class org.bdgp.swing.BackgroundImagePanel

BackgroundImagePanel - class org.bdgp.swing.BackgroundImagePanel.

Implementation of JPanel that allows the background to be set to an image.

BackgroundImagePanel() - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel with no image and with scaling turned off.

BackgroundImagePanel(boolean) - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel with no image specified.

BackgroundImagePanel(Image) - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel using the specified Image object as the background.

BackgroundImagePanel(Image, boolean) - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel using the specified Image object as the background.

BackgroundImagePanel(String) - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel using the image at the given path on the local filesystem.

BackgroundImagePanel(String, boolean) - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel using the image at the given path on the local filesystem.

BackgroundImagePanel(URL) - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel using the image at the given URL.

BackgroundImagePanel(URL, boolean) - Constructor for class org.bdgp.swing.BackgroundImagePanel

Constructs a BackgroundImagePanel using the image at the given URL.

binarySearch(Vector, Object) - Static method in class org.bdgp.util.VectorUtil

binarySearch(Vector, Object, boolean) - Static method in class org.bdgp.util.VectorUtil

Binary searches for object o, assuming that all the objects in the array are Comparable

binarySearch(Vector, Object, Comparator, boolean) - Static method in class org.bdgp.util.VectorUtil

Binary searches for object o using the given comparator.

blockUntilImagePrepared(Image) - Static method in class org.bdgp.swing.SwingUtil

Forces the current thread to yield until the given image has completely loaded.

BooleanFilter - class org.bdgp.util.BooleanFilter.

BooleanFilter(int) - Constructor for class org.bdgp.util.BooleanFilter

buildGUI() - Method in class org.bdgp.swing.ListEditor

buildGUI() - Method in class org.bdgp.swing.widget.DataAdapterChooser

buttonColor - Variable in class org.bdgp.swing.ListEditor

C

cancel() - Method in class org.bdgp.swing.widget.DataAdapterChooser

cancel() - Method in interface org.bdgp.util.Commitable

cancelButton - Variable in class org.bdgp.swing.widget.DataAdapterChooser

cancelled - Variable in class org.bdgp.swing.widget.DataAdapterChooser

center - Variable in class org.bdgp.swing.XMLLayout.PanelElement

center(Window) - Static method in class org.bdgp.swing.SwingUtil

Places a Window in the center of the screen.

checkForClickInExpandControl(TreePath, int, int) - Method in class org.bdgp.swing.dragtree.DragTreeUI

children() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

chunkReverse(String, int, int) - Static method in class org.bdgp.util.DNAUtils

determines the reverse of a part of a sequence of nucleotides.

clearRect(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

clipRect(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

clone() - Method in interface org.bdgp.cv.datamodel.DAGNode

clone() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

cloneObject(Object) - Static method in class org.bdgp.util.ObjectUtil

collapsedIcon - Variable in class org.bdgp.swing.dragtree.DragTreeUI

collapsePath(TreePath) - Method in class org.bdgp.cv.gui.DAGView

collapseRow(int) - Method in class org.bdgp.cv.gui.DAGView

commit() - Method in class org.bdgp.swing.ListEditor

commit() - Method in class org.bdgp.swing.widget.DataAdapterChooser

commit() - Method in interface org.bdgp.util.Commitable

commit(Object) - Method in class org.bdgp.swing.ListEditor

Commitable - interface org.bdgp.util.Commitable.

An interface for any object that allows commit/cancel behavior.

Comparable - interface org.bdgp.util.Comparable.

ComparableComparator - class org.bdgp.util.ComparableComparator.

ComparableComparator() - Constructor for class org.bdgp.util.ComparableComparator

Comparator - interface org.bdgp.util.Comparator.

compare(Object, Object) - Method in interface org.bdgp.util.Comparator

compare(Object, Object) - Method in class org.bdgp.util.ReverseComparator

compare(Object, Object) - Method in class org.bdgp.util.ComparableComparator

compare(Range, Range) - Static method in class org.bdgp.util.RangeHash

compareTo(Object) - Method in interface org.bdgp.util.Comparable

compareTo(Object) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

ComparisonConstants - interface org.bdgp.util.ComparisonConstants.

COMPLEMENT - Static variable in class org.bdgp.util.DNAUtils

complement(String) - Static method in class org.bdgp.util.DNAUtils

determines the complement of a sequence of nucleotides.

complementBuffer(StringBuffer) - Static method in class org.bdgp.util.DNAUtils

determines the complement of a sequence of nucleotides.

component - Variable in class org.bdgp.swing.dragtree.event.DragTreeEvent

ComponentNameResolver - interface org.bdgp.swing.ComponentNameResolver.

Interface for defining a name resolver for a XMLLayoutPanel.

configureComponent(Component, XMLLayout.LayoutItem) - Method in class org.bdgp.swing.XMLLayoutPanel

contains(DAGNode, DAGNode) - Static method in class org.bdgp.cv.datamodel.DAGUtil

contains(Range, int) - Static method in class org.bdgp.util.RangeHash

contains(TreeModel, Object, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

controllingObject - Variable in class org.bdgp.swing.AbstractDataAdapterUI

copy(TreePath[], TreePath) - Method in interface org.bdgp.cv.datamodel.MutableDAGModel

Adds the specified nodes as children of dest WITHOUT removing them from their current location.

copy(TreePath[], TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

copyArea(int, int, int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

create() - Method in class org.bdgp.swing.FastTranslatedGraphics

create(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

createDefaultModel() - Method in class org.bdgp.swing.NumericField

createMouseListener() - Method in class org.bdgp.swing.dragtree.DragTreeUI

createNewValue() - Method in interface org.bdgp.swing.GenericEditorComponent

createNewValue() - Method in class org.bdgp.swing.StringEditorComponent

createNewValue() - Method in class org.bdgp.swing.DefaultEditorComponent

currentAdapter - Variable in class org.bdgp.swing.widget.DataAdapterChooser

currentEditTransaction - Variable in class org.bdgp.swing.ListEditor

currentEditValue - Variable in class org.bdgp.swing.ListEditor

currentGUI - Variable in class org.bdgp.swing.widget.DataAdapterChooser

CursorResource - class org.bdgp.swing.dragtree.CursorResource.

CursorResource() - Constructor for class org.bdgp.swing.dragtree.CursorResource

D

DAGComponent - class org.bdgp.cv.gui.DAGComponent.

DAGComponent.SelectionWrapper - class org.bdgp.cv.gui.DAGComponent.SelectionWrapper.

DAGComponent.SelectionWrapper(DAGComponent, DAGComponent) - Constructor for class org.bdgp.cv.gui.DAGComponent.SelectionWrapper

DAGComponent(DAGModel) - Constructor for class org.bdgp.cv.gui.DAGComponent

DAGComponent(DAGModel, boolean) - Constructor for class org.bdgp.cv.gui.DAGComponent

DAGModel - interface org.bdgp.cv.datamodel.DAGModel.

DAGNode - interface org.bdgp.cv.datamodel.DAGNode.

Defines the requirements for a node in a DAG.

DAGUtil - class org.bdgp.cv.datamodel.DAGUtil.

DAGUtil() - Constructor for class org.bdgp.cv.datamodel.DAGUtil

DAGView - class org.bdgp.cv.gui.DAGView.

DAGView.DAGViewRenderer - class org.bdgp.cv.gui.DAGView.DAGViewRenderer.

DAGView.DAGViewRenderer(DAGView) - Constructor for class org.bdgp.cv.gui.DAGView.DAGViewRenderer

DAGView() - Constructor for class org.bdgp.cv.gui.DAGView

DAGView(DAGModel, Object) - Constructor for class org.bdgp.cv.gui.DAGView

DAGView(DAGNode) - Constructor for class org.bdgp.cv.gui.DAGView

data - Variable in class org.bdgp.swing.ListEditor

data - Variable in class org.bdgp.util.Queue

data - Variable in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

DataAdapter - interface org.bdgp.io.DataAdapter.

A Generic starter interface for DataAdapter components.

DataAdapterChooser - class org.bdgp.swing.widget.DataAdapterChooser.

DataAdapterChooser.CommitRunnable - class org.bdgp.swing.widget.DataAdapterChooser.CommitRunnable.

DataAdapterChooser.CommitRunnable(DataAdapterChooser) - Constructor for class org.bdgp.swing.widget.DataAdapterChooser.CommitRunnable

DataAdapterChooser(DataAdapterRegistry, IOOperation, String, Object, boolean) - Constructor for class org.bdgp.swing.widget.DataAdapterChooser

DataAdapterChooser(Dialog, DataAdapterRegistry, IOOperation, String, Object, boolean) - Constructor for class org.bdgp.swing.widget.DataAdapterChooser

DataAdapterChooser(Frame, DataAdapterRegistry, IOOperation, String, Object, boolean) - Constructor for class org.bdgp.swing.widget.DataAdapterChooser

DataAdapterException - exception org.bdgp.io.DataAdapterException.

DataAdapterException(String) - Constructor for class org.bdgp.io.DataAdapterException

DataAdapterException(Throwable, String) - Constructor for class org.bdgp.io.DataAdapterException

DataAdapterRegistry - class org.bdgp.io.DataAdapterRegistry.

A registry of data adapters.

DataAdapterRegistry() - Constructor for class org.bdgp.io.DataAdapterRegistry

Creates a new DataAdapterRegistry

DataAdapterUI - interface org.bdgp.io.DataAdapterUI.

An abstract representation of a DataAdapter user interface.

DataAdapterUIEvent - class org.bdgp.io.DataAdapterUIEvent.

DataAdapterUIEvent(Object, DataAdapterUI) - Constructor for class org.bdgp.io.DataAdapterUIEvent

DataAdapterUIListener - interface org.bdgp.io.DataAdapterUIListener.

A listener for changes to a DataAdapterUI.

defaultDividerSize - Variable in class org.bdgp.swing.ListEditor

DefaultDragTreeCellRenderer - class org.bdgp.swing.DefaultDragTreeCellRenderer.

DefaultDragTreeCellRenderer - class org.bdgp.swing.dragtree.DefaultDragTreeCellRenderer.

DefaultDragTreeCellRenderer() - Constructor for class org.bdgp.swing.DefaultDragTreeCellRenderer

DefaultDragTreeCellRenderer() - Constructor for class org.bdgp.swing.dragtree.DefaultDragTreeCellRenderer

DefaultEditorComponent - class org.bdgp.swing.DefaultEditorComponent.

DefaultEditorComponent() - Constructor for class org.bdgp.swing.DefaultEditorComponent

DefaultMutableDAGNode - class org.bdgp.cv.datamodel.DefaultMutableDAGNode.

DefaultMutableDAGNode(Object) - Constructor for class org.bdgp.cv.datamodel.DefaultMutableDAGNode

defaultNoSelectionComponent() - Static method in class org.bdgp.swing.ListEditor

del() - Method in class org.bdgp.swing.ListEditor

delete() - Method in class org.bdgp.cv.gui.DAGComponent

delete(TreePath[]) - Method in interface org.bdgp.cv.datamodel.MutableTreeModel

Deletes the specified nodes from the tree.

delete(TreePath[]) - Method in class org.bdgp.cv.gui.DAGComponent

dequeue() - Method in class org.bdgp.util.Queue

Takes a value off the front of the queue

displayCurrentGUI() - Method in class org.bdgp.swing.widget.DataAdapterChooser

displayNode(DAGNode) - Static method in class org.bdgp.cv.datamodel.DAGUtil

displayNode(TreeModel, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

dispose() - Method in class org.bdgp.swing.FastTranslatedGraphics

dividerLoc - Variable in class org.bdgp.swing.ListEditor

DNAUtils - class org.bdgp.util.DNAUtils.

a collection of constants and static methods useful in manipulating ascii representations of DNA sequences.

DNAUtils() - Constructor for class org.bdgp.util.DNAUtils

doCommit() - Method in class org.bdgp.swing.widget.DataAdapterChooser

doCommitWithExceptions() - Method in class org.bdgp.swing.widget.DataAdapterChooser

doObjectRender(Component, TreePath, Object) - Method in class org.bdgp.swing.dragtree.DefaultDragTreeCellRenderer

doOperation(Object) - Method in class org.bdgp.swing.AbstractDataAdapterUI

doOperation(Object) - Method in interface org.bdgp.io.DataAdapterUI

The method that actually performs the data adapter operation (presumably by delegating to a data adapter).

doStore(Object) - Method in class org.bdgp.swing.ListEditor

drag(DragTreeEvent) - Method in interface org.bdgp.swing.dragtree.event.DragTreeEventListener

drag(DragTreeEvent) - Method in class org.bdgp.swing.dragtree.event.DragTreeEventAdapter

dragAllowed - Variable in class org.bdgp.swing.DragTree

DragTree - class org.bdgp.swing.DragTree.

DragTree() - Constructor for class org.bdgp.swing.DragTree

DragTree(TreeModel) - Constructor for class org.bdgp.swing.DragTree

DragTree(TreeNode) - Constructor for class org.bdgp.swing.DragTree

DragTreeEvent - class org.bdgp.swing.dragtree.event.DragTreeEvent.

DragTreeEvent(Component, TreePath, MouseEvent) - Constructor for class org.bdgp.swing.dragtree.event.DragTreeEvent

DragTreeEventAdapter - class org.bdgp.swing.dragtree.event.DragTreeEventAdapter.

DragTreeEventAdapter() - Constructor for class org.bdgp.swing.dragtree.event.DragTreeEventAdapter

DragTreeEventListener - interface org.bdgp.swing.dragtree.event.DragTreeEventListener.

dragTreeEventListeners - Variable in class org.bdgp.swing.DragTree

DragTreeUI - class org.bdgp.swing.dragtree.DragTreeUI.

DragTreeUI.AutoscrollThread - class org.bdgp.swing.dragtree.DragTreeUI.AutoscrollThread.

DragTreeUI.AutoscrollThread(DragTreeUI, int, int, JViewport, int) - Constructor for class org.bdgp.swing.dragtree.DragTreeUI.AutoscrollThread

DragTreeUI.DragTreeKeyHandler - class org.bdgp.swing.dragtree.DragTreeUI.DragTreeKeyHandler.

DragTreeUI.DragTreeKeyHandler(DragTreeUI, DragTree) - Constructor for class org.bdgp.swing.dragtree.DragTreeUI.DragTreeKeyHandler

DragTreeUI.DragTreeMouseHandler - class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler.

DragTreeUI.DragTreeMouseHandler(DragTreeUI, DragTree) - Constructor for class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

Invoked when a mouse button has been pressed on a component.

DragTreeUI() - Constructor for class org.bdgp.swing.dragtree.DragTreeUI

draw3DRect(int, int, int, int, boolean) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawArc(int, int, int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawBytes(byte[], int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawChars(char[], int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawImage(Image, int, int, Color, ImageObserver) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawImage(Image, int, int, ImageObserver) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawImage(Image, int, int, int, int, Color, ImageObserver) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawImage(Image, int, int, int, int, ImageObserver) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawImage(Image, int, int, int, int, int, int, int, int, Color, ImageObserver) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawImage(Image, int, int, int, int, int, int, int, int, ImageObserver) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawLine(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawOval(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawPolygon(int[], int[], int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawPolygon(Polygon) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawPolyline(int[], int[], int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawRect(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawRoundRect(int, int, int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawString(AttributedCharacterIterator, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

drawString(String, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

driver - Variable in class org.bdgp.swing.AbstractDataAdapterUI

drop(DragTreeEvent) - Method in interface org.bdgp.swing.dragtree.event.DragTreeEventListener

drop(DragTreeEvent) - Method in class org.bdgp.swing.dragtree.event.DragTreeEventAdapter

E

east - Variable in class org.bdgp.swing.XMLLayout.PanelElement

EAST - Static variable in class org.bdgp.swing.dragtree.DragTreeUI

editable - Variable in class org.bdgp.swing.ListEditor

EditableString - class org.bdgp.util.EditableString.

EditableString(String) - Constructor for class org.bdgp.util.EditableString

editor - Variable in class org.bdgp.swing.ListEditor

endDocument() - Method in class org.bdgp.swing.XMLLayout.LayoutBuilder

endElement(String, String, String) - Method in class org.bdgp.swing.XMLLayout.LayoutBuilder

enqueue(Object) - Method in class org.bdgp.util.Queue

Adds a value to the end of the queue

ensureExists(File, ClassLoader, String) - Static method in class org.bdgp.io.FileUtil

Checks to see if a file exists.

ensureExists(File, String) - Static method in class org.bdgp.io.FileUtil

Checks to see if a file exists.

ensureVisible(Object) - Method in class org.bdgp.cv.gui.DAGComponent

EQUAL_TO - Static variable in interface org.bdgp.util.ComparisonConstants

equals(Object) - Method in class org.bdgp.util.EditableString

equals(Object) - Method in class org.bdgp.io.IOOperation

Indicates whether this IOOperation equals another.

equals(Object, Object) - Static method in class org.bdgp.util.ObjectUtil

equals(Range, Range) - Static method in class org.bdgp.util.RangeHash

exception - Variable in class org.bdgp.swing.widget.DataAdapterChooser

expandedIcon - Variable in class org.bdgp.swing.dragtree.DragTreeUI

expandPath(TreePath) - Method in class org.bdgp.cv.gui.DAGView

expandRow(int) - Method in class org.bdgp.cv.gui.DAGView

F

failed - Variable in class org.bdgp.swing.widget.DataAdapterChooser

failfast - Variable in class org.bdgp.swing.widget.DataAdapterChooser

FastTranslatedGraphics - class org.bdgp.swing.FastTranslatedGraphics.

FastTranslatedGraphics(Graphics) - Constructor for class org.bdgp.swing.FastTranslatedGraphics

FileUtil - class org.bdgp.io.FileUtil.

FileUtil() - Constructor for class org.bdgp.io.FileUtil

fill3DRect(int, int, int, int, boolean) - Method in class org.bdgp.swing.FastTranslatedGraphics

fillArc(int, int, int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

fillOval(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

fillPolygon(int[], int[], int) - Method in class org.bdgp.swing.FastTranslatedGraphics

fillPolygon(Polygon) - Method in class org.bdgp.swing.FastTranslatedGraphics

fillRect(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

fillRoundRect(int, int, int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

filter(VectorFilter, Enumeration) - Static method in class org.bdgp.util.VectorUtil

filter(VectorFilter, Vector) - Static method in class org.bdgp.util.VectorUtil

filter(VectorFilter, VectorTransformer, Enumeration) - Static method in class org.bdgp.util.VectorUtil

filter(VectorFilter, VectorTransformer, Vector) - Static method in class org.bdgp.util.VectorUtil

filters - Variable in class org.bdgp.util.BooleanFilter

finalize() - Method in class org.bdgp.swing.FastTranslatedGraphics

fireDataAdapterUIEvent(DataAdapterUIEvent) - Method in class org.bdgp.swing.AbstractDataAdapterUI

fireDragEvent(DragTreeEvent) - Method in class org.bdgp.swing.DragTree

fireDropEvent(DragTreeEvent) - Method in class org.bdgp.swing.DragTree

fireListSelectionEvent(ListSelectionEvent) - Method in class org.bdgp.swing.ListEditor

fireProgressEvent(ProgressEvent) - Method in interface org.bdgp.io.VisualDataAdapter

Fires a progress event.

fireProgressEvent(ProgressEvent) - Method in class org.bdgp.io.AbstractDataAdapter

fireProgressEvent(ProgressEvent) - Method in class org.bdgp.io.ProgressableFileInputStream

fireProgressEventIfNecessary() - Method in class org.bdgp.io.ProgressableFileInputStream

fireRightClickEvent(DragTreeEvent) - Method in class org.bdgp.swing.DragTree

first - Variable in class org.bdgp.swing.XMLLayout.DividerElement

fontify() - Method in class org.bdgp.swing.ListEditor

FORWARD_SPLICED_TRANSLATION - Static variable in class org.bdgp.util.DNAUtils

FRAME_MAPPING - Static variable in class org.bdgp.util.DNAUtils

FRAME_NEG_ONE - Static variable in class org.bdgp.util.DNAUtils

FRAME_NEG_THREE - Static variable in class org.bdgp.util.DNAUtils

FRAME_NEG_TWO - Static variable in class org.bdgp.util.DNAUtils

FRAME_ONE - Static variable in class org.bdgp.util.DNAUtils

FRAME_THREE - Static variable in class org.bdgp.util.DNAUtils

FRAME_TWO - Static variable in class org.bdgp.util.DNAUtils

G

g - Variable in class org.bdgp.swing.FastTranslatedGraphics

GCcontent(String) - Static method in class org.bdgp.util.DNAUtils

GCcontent(StringBuffer) - Static method in class org.bdgp.util.DNAUtils

GenericEditorComponent - interface org.bdgp.swing.GenericEditorComponent.

GenericVisualDataAdapter - class org.bdgp.io.GenericVisualDataAdapter.

An implementation of AbstractDataAdapter that delegates all the real data adapter work to another adapter.

GenericVisualDataAdapter() - Constructor for class org.bdgp.io.GenericVisualDataAdapter

Creates a GenericVisualDataAdapter without setting a DataAdapter for delegation.

GenericVisualDataAdapter(DataAdapter) - Constructor for class org.bdgp.io.GenericVisualDataAdapter

Creates a GenericVisualDataAdapter with a DataAdapter for delegation

get(int) - Method in class org.bdgp.util.RangeHash

Returns the value whose key range contains the given key, or null if no range contains that key.

get(int, int) - Method in class org.bdgp.util.RangeHash

getAdapter(String) - Method in class org.bdgp.io.DataAdapterRegistry

Returns a new instance of a driver with the given class name.

getAdapterNames() - Method in class org.bdgp.io.DataAdapterRegistry

Returns the class names of all installed adapters.

getAdapterNames(IOOperation) - Method in class org.bdgp.io.DataAdapterRegistry

Returns the class names of all installed adapters that support the given IOOperation.

getAdapterNames(IOOperation, boolean) - Method in class org.bdgp.io.DataAdapterRegistry

Returns the class names of all installed adapters that support the given IOOperation.

getAllowedDNACharacters() - Static method in class org.bdgp.util.DNAUtils

return an array of all allowed characters used to represent nucleotides This _should_ follow IUPAC spec, but doesn't yet

getAllowsChildren() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getCellRect(int, int, boolean) - Method in class org.bdgp.swing.MultiheightTable

getChildAt(int) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getChildCount() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getClickTarget() - Method in class org.bdgp.swing.DragTree

getClip() - Method in class org.bdgp.swing.FastTranslatedGraphics

getClipBounds() - Method in class org.bdgp.swing.FastTranslatedGraphics

getClipBounds(Rectangle) - Method in class org.bdgp.swing.FastTranslatedGraphics

getClipRect() - Method in class org.bdgp.swing.FastTranslatedGraphics

Deprecated. As of JDK 1.2

getCollapsedIcon() - Method in class org.bdgp.swing.dragtree.DragTreeUI

getColor() - Method in class org.bdgp.swing.FastTranslatedGraphics

getComponent() - Method in class org.bdgp.swing.HotkeyedMenuItem

getComponent(XMLLayout.BoxElement) - Method in class org.bdgp.swing.XMLLayoutPanel

getComponent(XMLLayout.ComponentElement) - Method in class org.bdgp.swing.XMLLayoutPanel

getComponent(XMLLayout.DividerElement) - Method in class org.bdgp.swing.XMLLayoutPanel

getComponent(XMLLayout.LayoutItem) - Method in class org.bdgp.swing.XMLLayoutPanel

getComponent(XMLLayout.PanelElement) - Method in class org.bdgp.swing.XMLLayoutPanel

getComponent(XMLLayout.ScrollerElement) - Method in class org.bdgp.swing.XMLLayoutPanel

getCopyCursor() - Static method in class org.bdgp.swing.dragtree.CursorResource

getCursorForDrag(int) - Method in class org.bdgp.swing.dragtree.DragTreeUI

getDAGChildAt(int) - Method in interface org.bdgp.cv.datamodel.DAGNode

Returns the child TreeNode at index childIndex as a DAGNode.

getDAGChildAt(int) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getData() - Method in class org.bdgp.swing.ListEditor

getDataAdapter() - Method in class org.bdgp.swing.widget.DataAdapterChooser

getDataAdapter() - Method in class org.bdgp.io.GenericVisualDataAdapter

Returns the data adapter that is being used for delegation

getDefinedInterval() - Method in class org.bdgp.util.RangeHash

getDefinedInterval(int) - Method in class org.bdgp.util.RangeHash

getDescription() - Method in class org.bdgp.util.ProgressEvent

getDragAllowed() - Method in class org.bdgp.swing.DragTree

getDragImage(int[]) - Method in class org.bdgp.swing.dragtree.DragTreeUI

getException() - Method in class org.bdgp.swing.widget.DataAdapterChooser

getExpandedIcon() - Method in class org.bdgp.swing.dragtree.DragTreeUI

getExpandedPaths() - Method in class org.bdgp.cv.gui.DAGComponent

getFilters() - Method in class org.bdgp.util.BooleanFilter

getFirst() - Method in class org.bdgp.swing.XMLLayout.DividerElement

getFont() - Method in class org.bdgp.swing.FastTranslatedGraphics

getFontMetrics() - Method in class org.bdgp.swing.FastTranslatedGraphics

getFontMetrics(Font) - Method in class org.bdgp.swing.FastTranslatedGraphics

getGeneticCodeOne() - Static method in class org.bdgp.util.DNAUtils

gets a representation of the genetic code.

getGeneticCodeThree() - Static method in class org.bdgp.util.DNAUtils

gets a representation of the genetic code.

getHalt() - Method in class org.bdgp.swing.dragtree.DragTreeUI.AutoscrollThread

getHigh() - Method in interface org.bdgp.util.Range

getHighlightedRow() - Method in class org.bdgp.swing.DragTree

getHighlightRow() - Method in class org.bdgp.swing.DragTree

getHoverImage() - Method in class org.bdgp.swing.DragTree

getHoverRect() - Method in class org.bdgp.swing.DragTree

getHoverX() - Method in class org.bdgp.swing.DragTree

getHoverY() - Method in class org.bdgp.swing.DragTree

getIconHeight() - Method in class org.bdgp.swing.dragtree.TreeIcon

getIconHeight() - Method in class org.bdgp.cv.gui.TreeIcon

getIconWidth() - Method in class org.bdgp.swing.dragtree.TreeIcon

getIconWidth() - Method in class org.bdgp.cv.gui.TreeIcon

getID() - Method in class org.bdgp.swing.XMLLayout.ComponentElement

getIndex(TreeNode) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getIndexOfAdapter(String) - Method in class org.bdgp.io.DataAdapterRegistry

Returns the index of the given adapter

getIndexOfParent(Object, Object) - Method in interface org.bdgp.cv.datamodel.DAGModel

getInterval(int) - Method in class org.bdgp.util.RangeHash

getIntervalIndex(int, int) - Method in class org.bdgp.util.RangeHash

getIntervalIndex(int, int, boolean) - Method in class org.bdgp.util.RangeHash

getItemAtIndex(int) - Method in class org.bdgp.util.RangeHash

getItems() - Method in class org.bdgp.swing.XMLLayout.BoxElement

getKeyHead(String) - Method in class org.bdgp.util.MultiProperties

getKeyTail(String) - Method in class org.bdgp.util.MultiProperties

getLayout(File) - Static method in class org.bdgp.swing.XMLLayout

getLayout(InputSource) - Static method in class org.bdgp.swing.XMLLayout

getLayout(InputStream) - Static method in class org.bdgp.swing.XMLLayout

getLayout(String) - Static method in class org.bdgp.swing.XMLLayout

getLayout(URL) - Static method in class org.bdgp.swing.XMLLayout

getListPanel() - Method in class org.bdgp.swing.ListEditor

getLow() - Method in interface org.bdgp.util.Range

getMaximumSize(JComponent) - Method in class org.bdgp.swing.multiheighttable.MultiheightTableUI

Return the maximum size of the table.

getMergeCursor() - Static method in class org.bdgp.swing.dragtree.CursorResource

getMinimalDAG(DAGModel, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getMinimalDAG(DAGNode) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getMinimumSize(JComponent) - Method in class org.bdgp.swing.multiheighttable.MultiheightTableUI

Return the minimum size of the table.

getMouseEvent() - Method in class org.bdgp.swing.dragtree.event.DragTreeEvent

getMoveCursor() - Static method in class org.bdgp.swing.dragtree.CursorResource

getNACharToIdMap() - Static method in class org.bdgp.util.DNAUtils

gets a map from letters to numbers each representing nucleotides.

getNAIdToCharMap() - Static method in class org.bdgp.util.DNAUtils

gets a map from numbers to letters each representing nucleotides.

getName() - Method in class org.bdgp.io.GenericVisualDataAdapter

Returns the name of the delegation DataAdapter

getName() - Method in class org.bdgp.io.IOOperation

Returns the name of this IOOperation

getName() - Method in interface org.bdgp.io.DataAdapter

Returns the name of this data adapter

getNameForAdapter(String) - Method in class org.bdgp.io.DataAdapterRegistry

Returns the name of the data adapter with the given class name.

getOrientation() - Method in class org.bdgp.swing.XMLLayout.BoxElement

getOrientation() - Method in class org.bdgp.swing.XMLLayout.DividerElement

getOutput() - Method in class org.bdgp.swing.widget.DataAdapterChooser

getParent() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getParent(Object, int) - Method in interface org.bdgp.cv.datamodel.DAGModel

getParentAt(int) - Method in interface org.bdgp.cv.datamodel.DAGNode

Returns the parent DAGNode at index parentIndex.

getParentAt(int) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getParentCount() - Method in interface org.bdgp.cv.datamodel.DAGNode

Returns the number of parent DAGNodes the receiver contains.

getParentCount() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getParentCount(Object) - Method in interface org.bdgp.cv.datamodel.DAGModel

getPathExists(TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

getPathsToNode(DAGModel, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPathsToNode(DAGNode) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPathsToNodeAsVector(DAGModel, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPathsToNodeAsVector(DAGNode) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPathsToNodes(DAGModel, Vector) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPathsToNodes(Vector) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPathsToNodesAsVector(DAGModel, Vector) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPathsToNodesAsVector(Vector) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getPercentIncremement() - Method in class org.bdgp.io.ProgressableFileInputStream

getPreferredRowHeight(int) - Method in class org.bdgp.swing.MultiheightTable

getPreferredSize(JComponent) - Method in class org.bdgp.swing.multiheighttable.MultiheightTableUI

Return the preferred size of the table.

getPresentationName() - Method in class org.bdgp.swing.NamedCompoundEdit

getProperties() - Method in class org.bdgp.swing.AbstractDataAdapterUI

getProperties() - Method in class org.bdgp.swing.XMLLayout.ComponentElement

getProperties() - Method in class org.bdgp.swing.widget.DataAdapterChooser

getProperties() - Method in interface org.bdgp.io.DataAdapterUI

Returns the UI properties for this DataAdapterUI.

getProperties(String) - Method in class org.bdgp.util.MultiProperties

getRedoPresentationName() - Method in class org.bdgp.swing.NamedCompoundEdit

getResidueChar(int) - Static method in class org.bdgp.util.DNAUtils

gets a nucleotide code.

getResidueID(char) - Static method in class org.bdgp.util.DNAUtils

gets an index into an array of codes for nucleotides.

getRightClickMenu() - Method in class org.bdgp.cv.gui.DAGComponent

getRoot() - Method in class org.bdgp.swing.XMLLayout

getRoot() - Method in class org.bdgp.swing.XMLLayout.LayoutBuilder

getRoot(TreeNode) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getRowHeight() - Method in class org.bdgp.swing.MultiheightTable

getRowHeight(boolean) - Method in class org.bdgp.swing.MultiheightTable

getRowHeight(int) - Method in class org.bdgp.swing.MultiheightTable

getSecond() - Method in class org.bdgp.swing.XMLLayout.DividerElement

getSelectedItem() - Method in class org.bdgp.swing.ListEditor

getSelectedNodes() - Method in class org.bdgp.cv.gui.DAGComponent

getSubThrowable() - Method in class org.bdgp.util.NestedException

getSupportedOperations() - Method in class org.bdgp.io.GenericVisualDataAdapter

Returns the supported operations of the delegation data adapter

getSupportedOperations() - Method in interface org.bdgp.io.DataAdapter

Returns a list of all operations supported by this data adapter

getSupportedOperations(String) - Method in class org.bdgp.io.DataAdapterRegistry

Returns the supported operations of the data adapter with the given class name.

getSystemClassLoader() - Static method in class org.bdgp.io.FileUtil

getTarget() - Method in class org.bdgp.swing.dragtree.event.DragTreeEvent

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.bdgp.swing.DefaultDragTreeCellRenderer

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.bdgp.swing.dragtree.DefaultDragTreeCellRenderer

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.bdgp.cv.gui.DAGView.DAGViewRenderer

getType() - Method in class org.bdgp.io.GenericVisualDataAdapter

Returns the type of the delegation data adapter

getType() - Method in interface org.bdgp.io.DataAdapter

Returns the type of data handled by this data adapter

getTypeForAdapter(String) - Method in class org.bdgp.io.DataAdapterRegistry

Returns the type of the data adapter with the given class name.

getUI() - Method in class org.bdgp.io.DataAdapterUIEvent

getUI(IOOperation) - Method in interface org.bdgp.io.VisualDataAdapter

Returns a user interface for the requested IOOperation.

getUI(IOOperation) - Method in class org.bdgp.io.GenericVisualDataAdapter

Returns the user interface for an io operation, based on what was set for that operation in a previous call to GenericVisualDataAdapter.setUI(IOOperation, DataAdapterUI)

getUndoPresentationName() - Method in class org.bdgp.swing.NamedCompoundEdit

getUniqueNodes(DAGNode) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getUniqueNodes(TreeModel, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

getUsableAdapterList() - Method in class org.bdgp.swing.widget.DataAdapterChooser

getUserObject() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

getValue() - Method in class org.bdgp.util.ProgressEvent

getVector(Enumeration) - Static method in class org.bdgp.util.VectorUtil

getWidth() - Method in class org.bdgp.swing.XMLLayout.DividerElement

getWrappedException() - Method in class org.bdgp.util.NestedError

GREATER_THAN - Static variable in interface org.bdgp.util.ComparisonConstants

H

halt - Variable in class org.bdgp.swing.dragtree.DragTreeUI.AutoscrollThread

halt() - Method in class org.bdgp.swing.dragtree.DragTreeUI.AutoscrollThread

haltThread(DragTreeUI.AutoscrollThread) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

handleAutoscroll(int, int) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

handleEdit(Object) - Method in class org.bdgp.swing.ListEditor

hideList() - Method in class org.bdgp.swing.ListEditor

highlightDropTarget(int) - Method in class org.bdgp.swing.DragTree

highlightedRow - Variable in class org.bdgp.swing.DragTree

hitClip(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

horiz - Variable in class org.bdgp.swing.XMLLayout.ScrollerElement

HORIZONTAL - Static variable in class org.bdgp.swing.XMLLayout.BoxElement

HORIZONTAL - Static variable in class org.bdgp.swing.XMLLayout.DividerElement

hotkeyDesc - Variable in class org.bdgp.swing.HotkeyedMenuItem

HotkeyedMenuItem - class org.bdgp.swing.HotkeyedMenuItem.

HotkeyedMenuItem(String) - Constructor for class org.bdgp.swing.HotkeyedMenuItem

hoverHeight - Variable in class org.bdgp.swing.DragTree

hoverImage - Variable in class org.bdgp.swing.DragTree

hoverVisible - Variable in class org.bdgp.swing.DragTree

hoverWidth - Variable in class org.bdgp.swing.DragTree

hoverX - Variable in class org.bdgp.swing.DragTree

hoverY - Variable in class org.bdgp.swing.DragTree

I

id - Variable in class org.bdgp.swing.XMLLayout.ComponentElement

id_to_letter - Static variable in class org.bdgp.util.DNAUtils

ascii character codes for each nucleotide (or set of nucleotides).

IdentityTransformation - class org.bdgp.util.IdentityTransformation.

IdentityTransformation() - Constructor for class org.bdgp.util.IdentityTransformation

imageObserverInfoflagToString(int) - Static method in class org.bdgp.swing.SwingUtil

Decodes the bits of a java.awt.image.ImageObserver infoflag into a human readable string.

indicateClickTarget(int) - Method in class org.bdgp.swing.DragTree

init() - Method in class org.bdgp.io.GenericVisualDataAdapter

Calls init() on the delegation data adapter

init() - Method in interface org.bdgp.io.DataAdapter

For initialization, like opening files or database connections.

init(DataAdapterRegistry, IOOperation, Object, boolean) - Method in class org.bdgp.swing.widget.DataAdapterChooser

initButtons() - Method in class org.bdgp.swing.ListEditor

initGUI() - Method in class org.bdgp.cv.gui.DAGView

input - Variable in class org.bdgp.swing.widget.DataAdapterChooser

insert(MutableTreeNode, int) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

insertionSort(Enumeration, Comparator) - Static method in class org.bdgp.util.VectorUtil

insertParent(MutableDAGNode, int) - Method in interface org.bdgp.cv.datamodel.MutableDAGNode

Adds parent to the receiver at index.

insertParent(MutableDAGNode, int) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

installDataAdapter(String) - Method in class org.bdgp.io.DataAdapterRegistry

Installs a data adapter to this registry.

installListeners() - Method in class org.bdgp.swing.dragtree.DragTreeUI

installListeners() - Method in class org.bdgp.swing.widget.DataAdapterChooser

InteractiveDataAdapterUI - interface org.bdgp.io.InteractiveDataAdapterUI.

IOOperation - class org.bdgp.io.IOOperation.

An input/output operation.

IOOperation(String) - Constructor for class org.bdgp.io.IOOperation

Creates a named IOOperation

isCancelled() - Method in class org.bdgp.swing.widget.DataAdapterChooser

isComponentTag(String) - Method in class org.bdgp.swing.XMLLayout.LayoutBuilder

isEmpty() - Method in class org.bdgp.util.Queue

Indicates whether or not the queue is empty

isFailure() - Method in class org.bdgp.swing.widget.DataAdapterChooser

isInstalled(String) - Method in class org.bdgp.io.DataAdapterRegistry

isLeaf() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

isParentOf(DAGModel, Object, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

isStructureEditable() - Method in class org.bdgp.cv.gui.DAGComponent

item - Variable in class org.bdgp.swing.XMLLayout.ScrollerElement

item - Variable in class org.bdgp.swing.XMLLayout.LayoutNode

J

junkVector() - Static method in class org.bdgp.swing.ListEditor

K

keyPressed(KeyEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeKeyHandler

keyReleased(KeyEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeKeyHandler

L

layout - Variable in class org.bdgp.swing.XMLLayoutPanel

LESS_THAN - Static variable in interface org.bdgp.util.ComparisonConstants

letter_to_id - Static variable in class org.bdgp.util.DNAUtils

ordinal numbers of nucleotides associated with each possible ascii character code.

LETTERS - Static variable in class org.bdgp.util.DNAUtils

number of "letters" that are valid in a string of nucleotide codes.

ListEditor - class org.bdgp.swing.ListEditor.

A component for editing vectors of objects

ListEditor(GenericEditorComponent) - Constructor for class org.bdgp.swing.ListEditor

ListEditor(GenericEditorComponent, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.bdgp.swing.ListEditor

ListEditor(GenericEditorComponent, Component, Vector, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.bdgp.swing.ListEditor

ListEditor(GenericEditorComponent, Vector) - Constructor for class org.bdgp.swing.ListEditor

listeners - Variable in class org.bdgp.swing.AbstractDataAdapterUI

listeners - Variable in class org.bdgp.swing.ListEditor

listeners - Variable in class org.bdgp.io.AbstractDataAdapter

listListener - Variable in class org.bdgp.swing.ListEditor

listResizable - Variable in class org.bdgp.swing.ListEditor

load(Object) - Method in interface org.bdgp.swing.GenericEditorComponent

load(Object) - Method in class org.bdgp.swing.StringEditorComponent

load(Object) - Method in class org.bdgp.swing.DefaultEditorComponent

M

main(String[]) - Static method in class org.bdgp.swing.XMLLayoutPanel

main(String[]) - Static method in class org.bdgp.swing.MultiheightTable

main(String[]) - Static method in class org.bdgp.swing.ListEditor

main(String[]) - Static method in class org.bdgp.util.RangeHash

masterUndolist - Variable in class org.bdgp.swing.ListEditor

menuFont - Variable in class org.bdgp.cv.gui.DAGComponent

merge() - Method in class org.bdgp.cv.gui.DAGComponent

merge(TreePath, TreePath) - Method in interface org.bdgp.cv.datamodel.MutableTreeModel

Merges two nodes in the Tree.

merge(TreePath, TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

mergeVectors(Vector, Vector) - Static method in class org.bdgp.util.VectorUtil

MethodRunnerActionListener - class org.bdgp.util.MethodRunnerActionListener.

MethodRunnerActionListener(Object, String) - Constructor for class org.bdgp.util.MethodRunnerActionListener

methodName is the name of the method to run (no parens) (the method must not take any args) target is the object to run the method on if the method does not exist for that object, an exception is thrown

minDividerSize - Variable in class org.bdgp.swing.ListEditor

minimalDAGHelper(MinimalDAGModel, DAGModel, Object) - Static method in class org.bdgp.cv.datamodel.DAGUtil

MINUS - Static variable in class org.bdgp.swing.dragtree.TreeIcon

MINUS - Static variable in class org.bdgp.cv.gui.TreeIcon

mouseClicked(MouseEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

mouseDragged(MouseEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

mouseEvent - Variable in class org.bdgp.swing.dragtree.event.DragTreeEvent

mouseMoved(MouseEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

mousePressed(MouseEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

mouseReleased(MouseEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI.DragTreeMouseHandler

move(TreePath[], TreePath) - Method in interface org.bdgp.cv.datamodel.MutableTreeModel

Adds the specified nodes as children of dest, and removes them from their current location.

move(TreePath[], TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

MultiheightTable - class org.bdgp.swing.MultiheightTable.

MultiheightTable() - Constructor for class org.bdgp.swing.MultiheightTable

MultiheightTable(int, int) - Constructor for class org.bdgp.swing.MultiheightTable

MultiheightTable(Object[][], Object[]) - Constructor for class org.bdgp.swing.MultiheightTable

MultiheightTable(TableModel) - Constructor for class org.bdgp.swing.MultiheightTable

MultiheightTable(TableModel, TableColumnModel) - Constructor for class org.bdgp.swing.MultiheightTable

MultiheightTable(TableModel, TableColumnModel, ListSelectionModel) - Constructor for class org.bdgp.swing.MultiheightTable

MultiheightTable(Vector, Vector) - Constructor for class org.bdgp.swing.MultiheightTable

MultiheightTableUI - class org.bdgp.swing.multiheighttable.MultiheightTableUI.

MultiheightTableUI() - Constructor for class org.bdgp.swing.multiheighttable.MultiheightTableUI

MultiProperties - class org.bdgp.util.MultiProperties.

MultiProperties() - Constructor for class org.bdgp.util.MultiProperties

multiPropertyNames() - Method in class org.bdgp.util.MultiProperties

MutableDAGModel - interface org.bdgp.cv.datamodel.MutableDAGModel.

MutableDAGNode - interface org.bdgp.cv.datamodel.MutableDAGNode.

Defines the requirements for a DAG node object that can change -- by adding or removing parent or child nodes, or by changing the contents of a user object stored in the node.

MutableTreeModel - interface org.bdgp.cv.datamodel.MutableTreeModel.

N

name - Variable in class org.bdgp.io.IOOperation

NamedCompoundEdit - class org.bdgp.swing.NamedCompoundEdit.

NamedCompoundEdit() - Constructor for class org.bdgp.swing.NamedCompoundEdit

NamedCompoundEdit(String) - Constructor for class org.bdgp.swing.NamedCompoundEdit

NestedError - error org.bdgp.util.NestedError.

A general purpose Error that can wrap another Throwable object.

NestedError() - Constructor for class org.bdgp.util.NestedError

NestedError(String) - Constructor for class org.bdgp.util.NestedError

NestedError(Throwable) - Constructor for class org.bdgp.util.NestedError

NestedError(Throwable, String) - Constructor for class org.bdgp.util.NestedError

NestedException - exception org.bdgp.util.NestedException.

A general perpose Exception that can wrap another exception.

NestedException() - Constructor for class org.bdgp.util.NestedException

NestedException(String) - Constructor for class org.bdgp.util.NestedException

NestedException(Throwable) - Constructor for class org.bdgp.util.NestedException

NestedException(Throwable, String) - Constructor for class org.bdgp.util.NestedException

NEVER - Static variable in class org.bdgp.swing.XMLLayout.ScrollerElement

newStringValue - Variable in class org.bdgp.swing.StringEditorComponent

north - Variable in class org.bdgp.swing.XMLLayout.PanelElement

NORTH - Static variable in class org.bdgp.swing.dragtree.DragTreeUI

noSelectionComponent - Variable in class org.bdgp.swing.ListEditor

NOT - Static variable in class org.bdgp.util.BooleanFilter

NUCLEOTIDES - Static variable in class org.bdgp.util.DNAUtils

NumericField - class org.bdgp.swing.NumericField.

NumericField(int) - Constructor for class org.bdgp.swing.NumericField

O

ObjectUtil - class org.bdgp.util.ObjectUtil.

ObjectUtil() - Constructor for class org.bdgp.util.ObjectUtil

okButton - Variable in class org.bdgp.swing.widget.DataAdapterChooser

ONE_LETTER_CODE - Static variable in class org.bdgp.util.DNAUtils

op - Variable in class org.bdgp.swing.widget.DataAdapterChooser

operation - Variable in class org.bdgp.util.BooleanFilter

OR - Static variable in class org.bdgp.util.BooleanFilter

org.bdgp.cv.datamodel - package org.bdgp.cv.datamodel

org.bdgp.cv.gui - package org.bdgp.cv.gui

org.bdgp.io - package org.bdgp.io

org.bdgp.swing - package org.bdgp.swing

org.bdgp.swing.dragtree - package org.bdgp.swing.dragtree

org.bdgp.swing.dragtree.event - package org.bdgp.swing.dragtree.event

org.bdgp.swing.multiheighttable - package org.bdgp.swing.multiheighttable

org.bdgp.swing.widget - package org.bdgp.swing.widget

org.bdgp.util - package org.bdgp.util

orientation - Variable in class org.bdgp.swing.XMLLayout.BoxElement

orientation - Variable in class org.bdgp.swing.XMLLayout.DividerElement

original_data - Variable in class org.bdgp.swing.ListEditor

output - Variable in class org.bdgp.swing.widget.DataAdapterChooser

overlaps(Range, Range) - Static method in class org.bdgp.util.RangeHash

P

paint(Graphics) - Method in class org.bdgp.swing.BackgroundImagePanel

paint(Graphics, JComponent) - Method in class org.bdgp.swing.multiheighttable.MultiheightTableUI

paintComponent(Graphics) - Method in class org.bdgp.swing.DragTree

paintComponent(Graphics) - Method in class org.bdgp.swing.DefaultDragTreeCellRenderer

paintComponent(Graphics) - Method in class org.bdgp.swing.dragtree.DefaultDragTreeCellRenderer

paintIcon(Component, Graphics, int, int) - Method in class org.bdgp.swing.dragtree.TreeIcon

paintIcon(Component, Graphics, int, int) - Method in class org.bdgp.cv.gui.TreeIcon

parents() - Method in interface org.bdgp.cv.datamodel.DAGNode

Returns the parents of the reciever as an Enumeration.

parents() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

peek() - Method in class org.bdgp.util.Queue

Returns the value at the front of the queue

pluginBorder - Variable in class org.bdgp.swing.widget.DataAdapterChooser

PLUS - Static variable in class org.bdgp.swing.dragtree.TreeIcon

PLUS - Static variable in class org.bdgp.cv.gui.TreeIcon

printStackTrace() - Method in class org.bdgp.util.NestedError

printStackTrace() - Method in class org.bdgp.util.NestedException

printStackTrace(PrintStream) - Method in class org.bdgp.util.NestedError

printStackTrace(PrintStream) - Method in class org.bdgp.util.NestedException

printStackTrace(PrintWriter) - Method in class org.bdgp.util.NestedError

printStackTrace(PrintWriter) - Method in class org.bdgp.util.NestedException

ProgressableFileInputStream - class org.bdgp.io.ProgressableFileInputStream.

ProgressableFileInputStream(File) - Constructor for class org.bdgp.io.ProgressableFileInputStream

ProgressableFileInputStream(String) - Constructor for class org.bdgp.io.ProgressableFileInputStream

progressBar - Variable in class org.bdgp.swing.widget.DataAdapterChooser

ProgressEvent - class org.bdgp.util.ProgressEvent.

An event indicating that some progress has been made

ProgressEvent(Object, Double, String) - Constructor for class org.bdgp.util.ProgressEvent

progressListener - Variable in class org.bdgp.swing.widget.DataAdapterChooser

ProgressListener - interface org.bdgp.util.ProgressListener.

Listener for ProgressEvents.

progressMade(ProgressEvent) - Method in interface org.bdgp.util.ProgressListener

Fired when some sort of progress has been made on the object to which we are listening

props - Variable in class org.bdgp.swing.XMLLayout.ComponentElement

put(int, int, Object) - Method in class org.bdgp.util.RangeHash

put(Range, Object) - Method in class org.bdgp.util.RangeHash

Q

Queue - class org.bdgp.util.Queue.

A run of the mill FIFO queue.

Queue() - Constructor for class org.bdgp.util.Queue

Create a new, empty Queue

Queue(Vector) - Constructor for class org.bdgp.util.Queue

Creates a queue containing the data in the provided Vector

quickSort(Vector) - Static method in class org.bdgp.util.VectorUtil

quickSort(Vector, Comparator) - Static method in class org.bdgp.util.VectorUtil

R

Range - interface org.bdgp.util.Range.

RangeHash - class org.bdgp.util.RangeHash.

RangeHash() - Constructor for class org.bdgp.util.RangeHash

ranges() - Method in class org.bdgp.util.RangeHash

READ - Static variable in class org.bdgp.io.IOOperation

A predefined IOOperation for "read"

read() - Method in class org.bdgp.io.ProgressableFileInputStream

read(byte[]) - Method in class org.bdgp.io.ProgressableFileInputStream

read(byte[], int, int) - Method in class org.bdgp.io.ProgressableFileInputStream

redo() - Method in class org.bdgp.cv.gui.DAGComponent

refresh() - Method in class org.bdgp.swing.ListEditor

refresh() - Method in class org.bdgp.cv.gui.DAGView

registerHotkeys() - Method in class org.bdgp.cv.gui.DAGComponent

registerListeners() - Method in class org.bdgp.cv.gui.DAGComponent

registry - Variable in class org.bdgp.swing.widget.DataAdapterChooser

reload() - Method in class org.bdgp.swing.XMLLayoutPanel

reload() - Method in class org.bdgp.swing.ListEditor

remove(int) - Method in class org.bdgp.util.RangeHash

Removes and returns the value whose key range contains the given key.

remove(int) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

remove(int, int) - Method in class org.bdgp.util.RangeHash

Removes the EXACT range defined by (low,high).

remove(MutableTreeNode) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

removeAll() - Method in class org.bdgp.util.RangeHash

Removes every element

removeAllChildren() - Method in interface org.bdgp.cv.datamodel.MutableDAGNode

Removes all children from the receiver, and deletes receiver from the child nodes' parent lists

removeAllChildren() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

removeAllParents() - Method in interface org.bdgp.cv.datamodel.MutableDAGNode

Removes all parents from the receiver

removeAllParents() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

removeDataAdapter(String) - Method in class org.bdgp.io.DataAdapterRegistry

Uninstalls an adapter.

removeDataAdapterUIListener(DataAdapterUIListener) - Method in class org.bdgp.swing.AbstractDataAdapterUI

removeDataAdapterUIListener(DataAdapterUIListener) - Method in interface org.bdgp.io.InteractiveDataAdapterUI

removeDragTreeEventListener(DragTreeEventListener) - Method in class org.bdgp.swing.DragTree

removeFilter(VectorFilter) - Method in class org.bdgp.util.BooleanFilter

removeFromParent() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

removeListSelectionListener(ListSelectionListener) - Method in class org.bdgp.swing.ListEditor

removeParent(int) - Method in interface org.bdgp.cv.datamodel.MutableDAGNode

Removes the parent at index from the receiver.

removeParent(int) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

removeParent(MutableDAGNode) - Method in interface org.bdgp.cv.datamodel.MutableDAGNode

Removes parent node from the receiver.

removeParent(MutableDAGNode) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

removeProgressListener(ProgressListener) - Method in interface org.bdgp.io.VisualDataAdapter

Remove a progress listener to this adapter.

removeProgressListener(ProgressListener) - Method in class org.bdgp.io.AbstractDataAdapter

removeProgressListener(ProgressListener) - Method in class org.bdgp.io.GenericVisualDataAdapter

removeProgressListener(ProgressListener) - Method in class org.bdgp.io.ProgressableFileInputStream

removeProperties(String) - Method in class org.bdgp.util.MultiProperties

removeRange(int, int) - Method in class org.bdgp.util.RangeHash

Removes every element within the range (low,high)

repaintRow(int) - Method in class org.bdgp.swing.dragtree.DragTreeUI

repeat(char, int) - Static method in class org.bdgp.util.StringUtil

repeat(String, int) - Static method in class org.bdgp.util.StringUtil

resetRowHeight() - Method in class org.bdgp.swing.MultiheightTable

resetRowHeight(int) - Method in class org.bdgp.swing.MultiheightTable

resizeImage() - Method in class org.bdgp.swing.BackgroundImagePanel

Forces the background image cache to be recalculated.

resolveName(String, Properties) - Method in interface org.bdgp.swing.ComponentNameResolver

Returns a component based on the id provided.

resolver - Variable in class org.bdgp.swing.XMLLayoutPanel

restoreState(Hashtable) - Method in class org.bdgp.util.EditableString

restoreState(Hashtable) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

restoreState(Hashtable) - Method in class org.bdgp.cv.gui.DAGComponent.SelectionWrapper

REVERSE_SPLICED_TRANSLATION - Static variable in class org.bdgp.util.DNAUtils

reverse(String) - Static method in class org.bdgp.util.DNAUtils

determines the reverse of a sequence of nucleotides.

ReverseComparator - class org.bdgp.util.ReverseComparator.

A ReverseComparator wraps another Comparator and returns the reverse ordering of the wrapped comparator.

ReverseComparator(Comparator) - Constructor for class org.bdgp.util.ReverseComparator

reverseComplement(String) - Static method in class org.bdgp.util.DNAUtils

determines the reverse complement of a sequence of nucleotides.

rightClick(DragTreeEvent) - Method in interface org.bdgp.swing.dragtree.event.DragTreeEventListener

rightClick(DragTreeEvent) - Method in class org.bdgp.swing.dragtree.event.DragTreeEventAdapter

root - Variable in class org.bdgp.swing.XMLLayout

rowAtPoint(Point) - Method in class org.bdgp.swing.MultiheightTable

rowHeights - Variable in class org.bdgp.swing.MultiheightTable

run() - Method in class org.bdgp.swing.dragtree.DragTreeUI.AutoscrollThread

run() - Method in class org.bdgp.swing.widget.DataAdapterChooser.CommitRunnable

S

satisfies(Object) - Method in interface org.bdgp.util.VectorFilter

satisfies(Object) - Method in class org.bdgp.util.BooleanFilter

scaleImage - Variable in class org.bdgp.swing.BackgroundImagePanel

second - Variable in class org.bdgp.swing.XMLLayout.DividerElement

select(int) - Method in class org.bdgp.swing.ListEditor

select(Object) - Method in class org.bdgp.cv.gui.DAGComponent

select(Object, boolean) - Method in class org.bdgp.cv.gui.DAGComponent

select(TreePath[], boolean) - Method in class org.bdgp.cv.gui.DAGComponent

select(Vector, boolean) - Method in class org.bdgp.cv.gui.DAGComponent

selectPathForEvent(TreePath, MouseEvent) - Method in class org.bdgp.swing.dragtree.DragTreeUI

setAccelerator(String, String) - Method in class org.bdgp.swing.HotkeyedMenuItem

setBackground(Image) - Method in class org.bdgp.swing.BackgroundImagePanel

Sets the background image to the given Image.

setBackground(String) - Method in class org.bdgp.swing.BackgroundImagePanel

Sets the background image to the image at the given path on the local filesystem.

setBackground(URL) - Method in class org.bdgp.swing.BackgroundImagePanel

Sets the background image to the image at the given URL.

setBounds(int, int, int, int) - Method in class org.bdgp.swing.BackgroundImagePanel

setBounds(Rectangle) - Method in class org.bdgp.swing.BackgroundImagePanel

setButtonColor(Color) - Method in class org.bdgp.swing.ListEditor

setClickBorderColor(Color) - Method in class org.bdgp.swing.dragtree.DefaultDragTreeCellRenderer

setClip(int, int, int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

setClip(Shape) - Method in class org.bdgp.swing.FastTranslatedGraphics

setColor(Color) - Method in class org.bdgp.swing.FastTranslatedGraphics

setControllingObject(Commitable) - Method in class org.bdgp.swing.AbstractDataAdapterUI

setControllingObject(Commitable) - Method in interface org.bdgp.io.InteractiveDataAdapterUI

setData(Vector) - Method in class org.bdgp.swing.ListEditor

setData(Vector, boolean) - Method in class org.bdgp.swing.ListEditor

setDataAdapter(DataAdapter) - Method in class org.bdgp.swing.AbstractDataAdapterUI

setDataAdapter(DataAdapter) - Method in interface org.bdgp.io.DataAdapterUI

Sets the data adapter for this UI.

setDataAdapter(DataAdapter) - Method in class org.bdgp.io.GenericVisualDataAdapter

Sets the data adapter for delegation

setDefaultDividerLoc(int) - Method in class org.bdgp.swing.ListEditor

setDragAllowed(boolean) - Method in class org.bdgp.swing.DragTree

setEditable(boolean) - Method in class org.bdgp.swing.StringEditorComponent

setEditable(boolean) - Method in class org.bdgp.swing.ListEditor

setEditable(boolean) - Method in class org.bdgp.swing.DefaultEditorComponent

setEnabled(boolean) - Method in class org.bdgp.swing.widget.DataAdapterChooser

setFirst(XMLLayout.LayoutItem) - Method in class org.bdgp.swing.XMLLayout.DividerElement

setFont(Font) - Method in class org.bdgp.swing.FastTranslatedGraphics

setFont(Font) - Method in class org.bdgp.swing.ListEditor

setHighlightColor(Color) - Method in class org.bdgp.swing.dragtree.DefaultDragTreeCellRenderer

setHoverCoords(int, int) - Method in class org.bdgp.swing.DragTree

setHoverImage(Image) - Method in class org.bdgp.swing.DragTree

setHoverVisible(boolean) - Method in class org.bdgp.swing.DragTree

setItem(XMLLayout.LayoutItem) - Method in class org.bdgp.swing.XMLLayout.ScrollerElement

setMenuFont(Font) - Method in class org.bdgp.cv.gui.DAGComponent

setName(String) - Method in class org.bdgp.swing.NamedCompoundEdit

setNewUI(DataAdapterUIEvent) - Method in interface org.bdgp.io.DataAdapterUIListener

setNode(DAGModel, Object) - Method in class org.bdgp.cv.gui.DAGView

setNode(DAGNode) - Method in class org.bdgp.cv.gui.DAGView

setPaintMode() - Method in class org.bdgp.swing.FastTranslatedGraphics

setParent(MutableTreeNode) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

setPercentIncrement(double) - Method in class org.bdgp.io.ProgressableFileInputStream

setProperties(MultiProperties) - Method in class org.bdgp.swing.widget.DataAdapterChooser

setProperties(Properties) - Method in class org.bdgp.swing.AbstractDataAdapterUI

setProperties(Properties) - Method in interface org.bdgp.io.DataAdapterUI

Sets UI properties for this DataAdapterUI.

setProperties(String, Properties) - Method in class org.bdgp.util.MultiProperties

setPropertiesFile(File) - Method in class org.bdgp.swing.widget.DataAdapterChooser

setPropertiesFile(String) - Method in class org.bdgp.swing.widget.DataAdapterChooser

setProperty(String, String) - Method in class org.bdgp.util.MultiProperties

setResolver(ComponentNameResolver) - Method in class org.bdgp.swing.XMLLayoutPanel

setRoot(TreeNode) - Method in class org.bdgp.swing.DragTree

setRowHeight(int, int) - Method in class org.bdgp.swing.MultiheightTable

setScaleImage(boolean) - Method in class org.bdgp.swing.BackgroundImagePanel

Enable/disable scaling of the background image.

setSecond(XMLLayout.LayoutItem) - Method in class org.bdgp.swing.XMLLayout.DividerElement

setSelection() - Method in class org.bdgp.cv.gui.DAGComponent.SelectionWrapper

setShowListPanel(boolean) - Method in class org.bdgp.swing.ListEditor

setSize(Dimension) - Method in class org.bdgp.swing.BackgroundImagePanel

setSize(int, int) - Method in class org.bdgp.swing.BackgroundImagePanel

setStructureEditable(boolean) - Method in class org.bdgp.cv.gui.DAGComponent

setUI(Component) - Method in class org.bdgp.swing.widget.DataAdapterChooser

setUI(IOOperation, DataAdapterUI) - Method in class org.bdgp.io.GenericVisualDataAdapter

Sets a user interface to be used for a particular io operation.

setUndoManager(UndoManager) - Method in class org.bdgp.cv.gui.DAGComponent

setUserObject(Object) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

setValue(String) - Method in class org.bdgp.util.EditableString

setVectorEditable(boolean) - Method in class org.bdgp.swing.ListEditor

setXMLLayout(XMLLayout) - Method in class org.bdgp.swing.XMLLayoutPanel

setXORMode(Color) - Method in class org.bdgp.swing.FastTranslatedGraphics

show() - Method in class org.bdgp.swing.widget.DataAdapterChooser

showList() - Method in class org.bdgp.swing.ListEditor

size() - Method in class org.bdgp.util.RangeHash

size() - Method in class org.bdgp.util.Queue

The number of elements in the Queue

sizeToPreferred(Component) - Static method in class org.bdgp.swing.SwingUtil

Resizes a Component to its preferred size

sizeToPreferred(JDialog) - Static method in class org.bdgp.swing.SwingUtil

Resizes a JDialog to its preferred size.

skip(long) - Method in class org.bdgp.io.ProgressableFileInputStream

sort(Enumeration) - Static method in class org.bdgp.util.VectorUtil

This will empty the enumeration

sort(Enumeration, Comparator) - Static method in class org.bdgp.util.VectorUtil

This will empty the enumeration

sort(Enumeration, Comparator, boolean) - Static method in class org.bdgp.util.VectorUtil

This will empty the enumeration

sort(Vector) - Static method in class org.bdgp.util.VectorUtil

sort(Vector, boolean) - Static method in class org.bdgp.util.VectorUtil

sort(Vector, Comparator) - Static method in class org.bdgp.util.VectorUtil

sort(Vector, Comparator, boolean) - Static method in class org.bdgp.util.VectorUtil

south - Variable in class org.bdgp.swing.XMLLayout.PanelElement

SOUTH - Static variable in class org.bdgp.swing.dragtree.DragTreeUI

split() - Method in class org.bdgp.cv.gui.DAGComponent

split(TreePath) - Method in interface org.bdgp.cv.datamodel.MutableTreeModel

Splits a node in the tree.

split(TreePath) - Method in class org.bdgp.cv.gui.DAGComponent

startClickRow - Variable in class org.bdgp.swing.DragTree

startDocument() - Method in class org.bdgp.swing.XMLLayout.LayoutBuilder

startElement(String, String, String, Attributes) - Method in class org.bdgp.swing.XMLLayout.LayoutBuilder

store(Object) - Method in interface org.bdgp.swing.GenericEditorComponent

store(Object) - Method in class org.bdgp.swing.StringEditorComponent

store(Object) - Method in class org.bdgp.swing.DefaultEditorComponent

storeState(Hashtable) - Method in class org.bdgp.util.EditableString

storeState(Hashtable) - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

storeState(Hashtable) - Method in class org.bdgp.cv.gui.DAGComponent.SelectionWrapper

StringEditorComponent - class org.bdgp.swing.StringEditorComponent.

StringEditorComponent(String) - Constructor for class org.bdgp.swing.StringEditorComponent

StringUtil - class org.bdgp.util.StringUtil.

StringUtil() - Constructor for class org.bdgp.util.StringUtil

SwingUtil - class org.bdgp.swing.SwingUtil.

A pile of useful methods for Swing applications.

T

tableChanged(TableModelEvent) - Method in class org.bdgp.swing.MultiheightTable

tagName - Variable in class org.bdgp.swing.XMLLayout.LayoutNode

target - Variable in class org.bdgp.swing.dragtree.event.DragTreeEvent

tempImage - Variable in class org.bdgp.swing.BackgroundImagePanel

termFont - Variable in class org.bdgp.cv.gui.DAGView

termForeground - Variable in class org.bdgp.cv.gui.DAGView

THREE_LETTER_CODE - Static variable in class org.bdgp.util.DNAUtils

toString() - Method in class org.bdgp.swing.FastTranslatedGraphics

toString() - Method in class org.bdgp.util.RangeHash

toString() - Method in class org.bdgp.util.EditableString

toString() - Method in class org.bdgp.io.AbstractDataAdapter

toString() - Method in class org.bdgp.io.GenericVisualDataAdapter

Returns the name of the delegation data adapter

toString() - Method in class org.bdgp.cv.datamodel.DefaultMutableDAGNode

transform(Object) - Method in class org.bdgp.util.IdentityTransformation

transform(Object) - Method in interface org.bdgp.util.VectorTransformer

transform(Object) - Method in class org.bdgp.util.TransformStringToEditable

transform(VectorTransformer, Enumeration) - Static method in class org.bdgp.util.VectorUtil

transform(VectorTransformer, Vector) - Static method in class org.bdgp.util.VectorUtil

TransformStringToEditable - class org.bdgp.util.TransformStringToEditable.

Transformation that turns a java.lang.String object into a org.bdgp.util.EditableString

TransformStringToEditable() - Constructor for class org.bdgp.util.TransformStringToEditable

translate(int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

translate(String, int, int) - Static method in class org.bdgp.util.DNAUtils

gets a translation into amino acids of a string of nucleotides.

translate(String, int, int, String, String, String) - Static method in class org.bdgp.util.DNAUtils

gets a translation into amino acids of a string of nucleotides.

translate(String, int, String[][][], String, String, String) - Static method in class org.bdgp.util.DNAUtils

gets a translation into amino acids of a string of nucleotides.

translateAbsolute(int, int) - Method in class org.bdgp.swing.FastTranslatedGraphics

TreeIcon - class org.bdgp.swing.dragtree.TreeIcon.

TreeIcon - class org.bdgp.cv.gui.TreeIcon.

TreeIcon(int, Color) - Constructor for class org.bdgp.swing.dragtree.TreeIcon

TreeIcon(int, Color) - Constructor for class org.bdgp.cv.gui.TreeIcon

trueClone(Vector) - Static method in class org.bdgp.util.VectorUtil

U

ui - Variable in class org.bdgp.io.DataAdapterUIEvent

undo() - Method in class org.bdgp.swing.ListEditor

undo() - Method in class org.bdgp.cv.gui.DAGComponent

undoable - Variable in class org.bdgp.swing.ListEditor

undodad - Variable in class org.bdgp.cv.gui.DAGComponent

unregisterHotkeys() - Method in class org.bdgp.cv.gui.DAGComponent

unregisterListeners() - Method in class org.bdgp.cv.gui.DAGComponent

updateGUI() - Method in class org.bdgp.swing.ListEditor

V

valueList - Variable in class org.bdgp.swing.ListEditor

values() - Method in class org.bdgp.util.RangeHash

vectorEditable - Variable in class org.bdgp.swing.ListEditor

VectorFilter - interface org.bdgp.util.VectorFilter.

VectorTransformer - interface org.bdgp.util.VectorTransformer.

VectorUtil - class org.bdgp.util.VectorUtil.

VectorUtil() - Constructor for class org.bdgp.util.VectorUtil

vert - Variable in class org.bdgp.swing.XMLLayout.ScrollerElement

VERTICAL - Static variable in class org.bdgp.swing.XMLLayout.BoxElement

VERTICAL - Static variable in class org.bdgp.swing.XMLLayout.DividerElement

VisualDataAdapter - interface org.bdgp.io.VisualDataAdapter.

A data adapter that provides some sort of user interface.

W

west - Variable in class org.bdgp.swing.XMLLayout.PanelElement

WEST - Static variable in class org.bdgp.swing.dragtree.DragTreeUI

width - Variable in class org.bdgp.swing.XMLLayout.DividerElement

workingImage - Variable in class org.bdgp.swing.BackgroundImagePanel

WRITE - Static variable in class org.bdgp.io.IOOperation

A predifined IOOperation for "write"

X

XMLLayout - class org.bdgp.swing.XMLLayout.

Defines the layout used by XMLLayoutPanel.

XMLLayout.BoxElement - class org.bdgp.swing.XMLLayout.BoxElement.

XMLLayout.BoxElement(int) - Constructor for class org.bdgp.swing.XMLLayout.BoxElement

XMLLayout.ComponentElement - class org.bdgp.swing.XMLLayout.ComponentElement.

XMLLayout.ComponentElement(String, Properties) - Constructor for class org.bdgp.swing.XMLLayout.ComponentElement

XMLLayout.DividerElement - class org.bdgp.swing.XMLLayout.DividerElement.

XMLLayout.DividerElement(int, int) - Constructor for class org.bdgp.swing.XMLLayout.DividerElement

XMLLayout.DividerElement(XMLLayout.LayoutItem, XMLLayout.LayoutItem, int, int) - Constructor for class org.bdgp.swing.XMLLayout.DividerElement

XMLLayout.LayoutBuilder - class org.bdgp.swing.XMLLayout.LayoutBuilder.

XMLLayout.LayoutBuilder() - Constructor for class org.bdgp.swing.XMLLayout.LayoutBuilder

XMLLayout.LayoutItem - class org.bdgp.swing.XMLLayout.LayoutItem.

XMLLayout.LayoutItem() - Constructor for class org.bdgp.swing.XMLLayout.LayoutItem

XMLLayout.LayoutNode - class org.bdgp.swing.XMLLayout.LayoutNode.

XMLLayout.LayoutNode(XMLLayout) - Constructor for class org.bdgp.swing.XMLLayout.LayoutNode

XMLLayout.PanelElement - class org.bdgp.swing.XMLLayout.PanelElement.

XMLLayout.PanelElement() - Constructor for class org.bdgp.swing.XMLLayout.PanelElement

XMLLayout.PanelElement(XMLLayout.LayoutItem, XMLLayout.LayoutItem, XMLLayout.LayoutItem, XMLLayout.LayoutItem, XMLLayout.LayoutItem) - Constructor for class org.bdgp.swing.XMLLayout.PanelElement

XMLLayout.ScrollerElement - class org.bdgp.swing.XMLLayout.ScrollerElement.

XMLLayout.ScrollerElement(int, int) - Constructor for class org.bdgp.swing.XMLLayout.ScrollerElement

XMLLayout.ScrollerElement(XMLLayout.LayoutItem, int, int) - Constructor for class org.bdgp.swing.XMLLayout.ScrollerElement

XMLLayout(XMLLayout.LayoutItem) - Constructor for class org.bdgp.swing.XMLLayout

XMLLayoutPanel - class org.bdgp.swing.XMLLayoutPanel.

A JPanel whose contents and layout are determined by an XMLLayout.

XMLLayoutPanel() - Constructor for class org.bdgp.swing.XMLLayoutPanel

XMLLayoutPanel(ComponentNameResolver, XMLLayout) - Constructor for class org.bdgp.swing.XMLLayoutPanel

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