Serialized Form

Package jebl.evolution.graphs

Class jebl.evolution.graphs.Graph.NoEdgeException extends Exception implements Serializable

Package jebl.evolution.io

Class jebl.evolution.io.ImportException extends Exception implements Serializable

Class jebl.evolution.io.ImportException.BadFormatException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.DuplicateFieldException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.DuplicateTaxaException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.MissingFieldException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.ShortSequenceException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.TooFewTaxaException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.UnknownTaxonException extends ImportException implements Serializable

Class jebl.evolution.io.ImportException.UnparsableDataException extends ImportException implements Serializable

Class jebl.evolution.io.NexusImporter.MissingBlockException extends ImportException implements Serializable

Package jebl.evolution.sequences

Class jebl.evolution.sequences.SequenceStateException extends Exception implements Serializable

Package jebl.evolution.substmodel

Class jebl.evolution.substmodel.AbstractRateMatrix extends Object implements Serializable

Serialized Fields

dimension

int dimension

dimension

frequency

double[] frequency

stationary frequencies (sum = 1.0)

rate

double[][] rate

rate matrix (transition: from 1st index to 2nd index)

sequenceType

SequenceType sequenceType

data type

parameterStore_

double[] parameterStore_

Class jebl.evolution.substmodel.AminoAcidModel extends AbstractRateMatrix implements Serializable

Class jebl.evolution.substmodel.MatrixExponential extends Object implements Serializable

Serialized Fields

Eval

double[] Eval

Evec

double[][] Evec

Ievc

double[][] Ievc

iexp

double[][] iexp

ordr

int[] ordr

evali

double[] evali

amat

double[][] amat

dimension_

int dimension_

dimension of rate matrix

transProb

double[][] transProb

transition probability matrix

cr

double cr

ci

double ci

Class jebl.evolution.substmodel.WAG extends AminoAcidModel implements Serializable

Package jebl.evolution.taxa

Class jebl.evolution.taxa.MissingTaxonException extends Throwable implements Serializable

Package jebl.gui.trees.treecomponent

Class jebl.gui.trees.treecomponent.RootedTreeComponent extends JComponent implements Serializable

Serialized Fields

tree

RootedTree tree

the tree

treePainter

RootedTreePainter treePainter

the tree painter

listeners

Vector<E> listeners

Package jebl.gui.trees.treeviewer

Class jebl.gui.trees.treeviewer.MultipleTreeViewer extends TreeViewer implements Serializable

Serialized Fields

labelSize

int labelSize

multipleTreeControlsProvider

ControlsProvider multipleTreeControlsProvider

trees

List<E> trees

Class jebl.gui.trees.treeviewer.TreePane extends JComponent implements Serializable

Serialized Fields

controlPalette

ControlPalette controlPalette

transformCheck

JCheckBox transformCheck

controls

Controls controls

treeSelectionListeners

Set<E> treeSelectionListeners

originalTree

RootedTree originalTree

tree

RootedTree tree

treeLayout

TreeLayout treeLayout

orderBranches

boolean orderBranches

branchOrdering

SortedRootedTree.BranchOrdering branchOrdering

transformBranches

boolean transformBranches

branchTransform

TransformedRootedTree.Transform branchTransform

treeBounds

Rectangle2D treeBounds

treeScale

double treeScale

insets

Insets insets

selectedNodes

Set<E> selectedNodes

selectedTaxa

Set<E> selectedTaxa

rulerHeight

double rulerHeight

dragRectangle

Rectangle2D dragRectangle

branchDecorator

BranchDecorator branchDecorator

labelXOffset

float labelXOffset

taxonLabelPainter

Painter<T> taxonLabelPainter

taxonLabelWidth

double taxonLabelWidth

nodeLabelPainter

Painter<T> nodeLabelPainter

branchLabelPainter

Painter<T> branchLabelPainter

scaleBarPainter

Painter<T> scaleBarPainter

scaleBarBounds

Rectangle2D scaleBarBounds

branchLineStroke

Stroke branchLineStroke

taxonCalloutStroke

Stroke taxonCalloutStroke

selectionStroke

Stroke selectionStroke

selectionPaint

Paint selectionPaint

calibrated

boolean calibrated

transform

AffineTransform transform

showingRootBranch

boolean showingRootBranch

showingTaxonCallouts

boolean showingTaxonCallouts

taxonLabelTransforms

Map<K,V> taxonLabelTransforms

taxonLabelBounds

Map<K,V> taxonLabelBounds

taxonLabelJustifications

Map<K,V> taxonLabelJustifications

nodeLabelTransforms

Map<K,V> nodeLabelTransforms

nodeLabelBounds

Map<K,V> nodeLabelBounds

nodeLabelJustifications

Map<K,V> nodeLabelJustifications

branchLabelTransforms

Map<K,V> branchLabelTransforms

branchLabelBounds

Map<K,V> branchLabelBounds

branchLabelJustifications

Map<K,V> branchLabelJustifications

calloutPaths

Map<K,V> calloutPaths

transforNanchesPREFSkey

String transforNanchesPREFSkey

orderBranchesPREFSkey

String orderBranchesPREFSkey

showRootPREFSkey

String showRootPREFSkey

branchWeightPREFSkey

String branchWeightPREFSkey

Class jebl.gui.trees.treeviewer.TreeViewer extends JPanel implements Serializable

Serialized Fields

controlsProvider

ControlsProvider controlsProvider

zoomPending

boolean zoomPending

zoom

double zoom

verticalExpansion

double verticalExpansion

tree

RootedTree tree

treePane

TreePane treePane

treePaneSelector

TreePaneSelector treePaneSelector

viewport

JViewport viewport

splitPane

JSplitPane splitPane

controlPalette

ControlPalette controlPalette

Package jebl.gui.trees.treeviewer_dev

Class jebl.gui.trees.treeviewer_dev.MultipleTreeViewer extends TreeViewer implements Serializable

Serialized Fields

trees

List<E> trees

currentTreeIndex

int currentTreeIndex

Class jebl.gui.trees.treeviewer_dev.TreePane extends JComponent implements Serializable

Serialized Fields

COLLAPSE_ATTRIBUTE_NAME

String COLLAPSE_ATTRIBUTE_NAME

treeSelectionListeners

Set<E> treeSelectionListeners

listeners

List<E> listeners

originalTree

RootedTree originalTree

tree

RootedTree tree

treeLayout

TreeLayout treeLayout

orderBranchesOn

boolean orderBranchesOn

branchOrdering

SortedRootedTree.BranchOrdering branchOrdering

transformBranchesOn

boolean transformBranchesOn

branchTransform

TransformedRootedTree.Transform branchTransform

treeBounds

Rectangle2D treeBounds

treeScale

double treeScale

insets

Insets insets

selectedNodes

Set<E> selectedNodes

selectedTips

Set<E> selectedTips

rulerHeight

double rulerHeight

dragRectangle

Rectangle2D dragRectangle

branchDecorator

Decorator branchDecorator

branchColouringDecorator

Decorator branchColouringDecorator

branchColouringAttribute

String branchColouringAttribute

labelXOffset

float labelXOffset

tipLabelPainter

LabelPainter<T> tipLabelPainter

tipLabelWidth

double tipLabelWidth

nodeLabelPainter

LabelPainter<T> nodeLabelPainter

branchLabelPainter

LabelPainter<T> branchLabelPainter

nodeBarPainter

NodeBarPainter nodeBarPainter

scaleBarPainter

Painter<T> scaleBarPainter

scaleBarBounds

Rectangle2D scaleBarBounds

branchLineStroke

BasicStroke branchLineStroke

calloutStroke

BasicStroke calloutStroke

selectionStroke

Stroke selectionStroke

selectionPaint

Paint selectionPaint

calibrated

boolean calibrated

transform

AffineTransform transform

showingTipCallouts

boolean showingTipCallouts

tipLabelTransforms

Map<K,V> tipLabelTransforms

tipLabelBounds

Map<K,V> tipLabelBounds

tipLabelJustifications

Map<K,V> tipLabelJustifications

nodeLabelTransforms

Map<K,V> nodeLabelTransforms

nodeLabelBounds

Map<K,V> nodeLabelBounds

nodeLabelJustifications

Map<K,V> nodeLabelJustifications

branchLabelTransforms

Map<K,V> branchLabelTransforms

branchLabelBounds

Map<K,V> branchLabelBounds

branchLabelJustifications

Map<K,V> branchLabelJustifications

nodeBars

Map<K,V> nodeBars

calloutPaths

Map<K,V> calloutPaths

Class jebl.gui.trees.treeviewer_dev.TreeViewer extends JPanel implements Serializable

Serialized Fields

zoomPending

boolean zoomPending

zoom

double zoom

verticalExpansion

double verticalExpansion

listeners

List<E> listeners

treePane

TreePane treePane

treePaneSelector

TreePaneSelector treePaneSelector

viewport

JViewport viewport

Class jebl.gui.trees.treeviewer_dev.TreeViewerPanel extends JPanel implements Serializable

Serialized Fields

treeViewer

TreeViewer treeViewer

controlPalette

ControlPalette controlPalette

Package jebl.math

Class jebl.math.MatrixCalcException extends Exception implements Serializable

Class jebl.math.MatrixCalcException.NotSquareMatrixException extends MatrixCalcException implements Serializable

Class jebl.math.MatrixCalcException.PositiveDefiniteException extends MatrixCalcException implements Serializable

Package org.virion.jam.app

Class org.virion.jam.app.Arguments.ArgumentException extends Exception implements Serializable

Package org.virion.jam.components

Class org.virion.jam.components.JVerticalLabel extends JLabel implements Serializable

Serialized Fields

clockwise

boolean clockwise

Class org.virion.jam.components.RealNumberField extends JTextField implements Serializable

Serialized Fields

changeListeners

EventListenerList changeListeners

min

double min

max

double max

range_check

boolean range_check

range_checked

boolean range_checked

Class org.virion.jam.components.WholeNumberField extends JTextField implements Serializable

Serialized Fields

changeListeners

EventListenerList changeListeners

min

int min

max

int max

range_check

boolean range_check

range_checked

boolean range_checked

Package org.virion.jam.console

Class org.virion.jam.console.ConsoleFrame extends DocumentFrame implements Serializable

Serialized Fields

piOut

PipedInputStream piOut

piErr

PipedInputStream piErr

poOut

PipedOutputStream poOut

poErr

PipedOutputStream poErr

textArea

JTextArea textArea

Package org.virion.jam.controlpalettes

Class org.virion.jam.controlpalettes.BasicControlPalette extends JPanel implements Serializable

Serialized Fields

controllerListener

ControllerListener controllerListener

listeners

List<E> listeners

preferredWidth

int preferredWidth

displayMode

BasicControlPalette.DisplayMode displayMode

openingSpeed

int openingSpeed

currentlyOpen

int currentlyOpen

controllers

List<E> controllers

disclosurePanels

List<E> disclosurePanels

controlsStates

List<E> controlsStates

Class org.virion.jam.controlpalettes.PinnedButton extends JToggleButton implements Serializable

Package org.virion.jam.controlpanels

Class org.virion.jam.controlpanels.BasicControlPalette extends JPanel implements Serializable

Serialized Fields

listeners

List<E> listeners

preferredWidth

int preferredWidth

displayMode

BasicControlPalette.DisplayMode displayMode

openingSpeed

int openingSpeed

titleColor

Color titleColor

currentlyOpen

int currentlyOpen

providers

List<E> providers

disclosurePanels

List<E> disclosurePanels

controlsList

List<E> controlsList

Package org.virion.jam.demo

Class org.virion.jam.demo.DemoFrame extends DocumentFrame implements Serializable

Serialized Fields

statusBar

StatusBar statusBar

filterPanel

SearchPanel filterPanel

filterPopup

JPopupMenu filterPopup

firstAction

AbstractAction firstAction

secondAction

AbstractAction secondAction

Package org.virion.jam.disclosure

Class org.virion.jam.disclosure.DisclosureButton extends JToggleButton implements Serializable

Serialized Fields

timer

Timer timer

opening

boolean opening

listeners

List<E> listeners

animationSpeed

int animationSpeed

current

int current

listener

ActionListener listener

Class org.virion.jam.disclosure.DisclosurePanel extends JPanel implements Serializable

Serialized Fields

button

DisclosureButton button

titleComponent

Component titleComponent

panel

JPanel panel

listeners

List<E> listeners

Package org.virion.jam.framework

Class org.virion.jam.framework.AboutBox extends AbstractFrame implements Serializable

Class org.virion.jam.framework.AbstractFrame extends JFrame implements Serializable

Serialized Fields

menuBar

JMenuBar menuBar

isDirty

boolean isDirty

saveAction

AbstractAction saveAction

saveAsAction

AbstractAction saveAsAction

importAction

Action importAction

exportAction

Action exportAction

printAction

AbstractAction printAction

closeWindowAction

AbstractAction closeWindowAction

zoomWindowAction

AbstractAction zoomWindowAction

minimizeWindowAction

AbstractAction minimizeWindowAction

cutAction

AbstractAction cutAction

copyAction

AbstractAction copyAction

pasteAction

AbstractAction pasteAction

deleteAction

AbstractAction deleteAction

selectAllAction

AbstractAction selectAllAction

findAction

AbstractAction findAction

Class org.virion.jam.framework.AuxilaryFrame extends AbstractFrame implements Serializable

Serialized Fields

documentFrame

DocumentFrame documentFrame

contentsPanel

JPanel contentsPanel

Class org.virion.jam.framework.DocumentFrame extends AbstractFrame implements Serializable

Serialized Fields

documentFile

File documentFile

saveAction

AbstractAction saveAction

saveAsAction

AbstractAction saveAsAction

Package org.virion.jam.html

Class org.virion.jam.html.HTMLViewer extends JFrame implements Serializable

Serialized Fields

editorPane

JEditorPane editorPane

Package org.virion.jam.panels

Class org.virion.jam.panels.ActionPanel extends JPanel implements Serializable

Serialized Fields

addButton

JButton addButton

removeButton

JButton removeButton

actionButton

JButton actionButton

addIcon

Icon addIcon

removeIcon

Icon removeIcon

actionIcon

Icon actionIcon

Class org.virion.jam.panels.AddRemovePanel extends JPanel implements Serializable

Serialized Fields

addIcon

Icon addIcon

addRolloverIcon

Icon addRolloverIcon

addPressedIcon

Icon addPressedIcon

removeIcon

Icon removeIcon

removeRolloverIcon

Icon removeRolloverIcon

removePressedIcon

Icon removePressedIcon

removeAction

AbstractAction removeAction

panels

ArrayList<E> panels

Class org.virion.jam.panels.OptionsPanel extends JPanel implements Serializable

Serialized Fields

gridbag

GridBagLayout gridbag

hGap

int hGap

vGap

int vGap

Class org.virion.jam.panels.RulesPanel extends JPanel implements Serializable

Serialized Fields

addIcon

Icon addIcon

addRolloverIcon

Icon addRolloverIcon

addPressedIcon

Icon addPressedIcon

removeIcon

Icon removeIcon

removeRolloverIcon

Icon removeRolloverIcon

removePressedIcon

Icon removePressedIcon

removeAction

AbstractAction removeAction

ruleModel

RuleModel ruleModel

rules

ArrayList<E> rules

Class org.virion.jam.panels.SearchPanel extends JPanel implements Serializable

Serialized Fields

listeners

ArrayList<E> listeners

searchTextEmpty

boolean searchTextEmpty

emptyLabel

String emptyLabel

continuousSearch

boolean continuousSearch

findButton

JButton findButton

searchText

JTextField searchText

cancelButton

JButton cancelButton

comboBox

JComboBox comboBox

Class org.virion.jam.panels.StatusBar extends StatusPanel implements Serializable

Class org.virion.jam.panels.StatusPanel extends JPanel implements Serializable

Serialized Fields

statusLabel

JLabel statusLabel

statusText

String statusText

statusButton

JButton statusButton

status

int status

statusProvider

StatusProvider statusProvider

timer

Timer timer

lastUpdate

long lastUpdate

pendingUpdate

boolean pendingUpdate

pendingText

String pendingText

current

int current

listener

ActionListener listener

Package org.virion.jam.table

Class org.virion.jam.table.ColorEditor extends AbstractCellEditor implements Serializable

Serialized Fields

currentColor

Color currentColor

button

JButton button

colorChooser

JColorChooser colorChooser

dialog

JDialog dialog

Class org.virion.jam.table.ColorRenderer extends JLabel implements Serializable

Serialized Fields

unselectedBorder

Border unselectedBorder

selectedBorder

Border selectedBorder

isBordered

boolean isBordered

Class org.virion.jam.table.HeaderRenderer extends DefaultTableCellRenderer implements Serializable

Class org.virion.jam.table.RealNumberCellEditor extends DefaultCellEditor implements Serializable

Serialized Fields

editor

RealNumberField editor

Class org.virion.jam.table.TableRenderer extends DefaultTableCellRenderer implements Serializable

Serialized Fields

bg1

Color bg1

bg2

Color bg2

striped

boolean striped

Class org.virion.jam.table.WholeNumberCellEditor extends DefaultCellEditor implements Serializable

Serialized Fields

editor

WholeNumberField editor

Package org.virion.jam.toolbar

Class org.virion.jam.toolbar.GenericToolbarItem extends JPanel implements Serializable

Serialized Fields

label

JLabel label

Class org.virion.jam.toolbar.Toolbar extends JToolBar implements Serializable

Serialized Fields

options

ToolbarOptions options

iconTextMenuItem

JRadioButtonMenuItem iconTextMenuItem

iconOnlyMenuItem

JRadioButtonMenuItem iconOnlyMenuItem

textOnlyMenuItem

JRadioButtonMenuItem textOnlyMenuItem

smallSizeMenuItem

JCheckBoxMenuItem smallSizeMenuItem

toolbarItems

List<E> toolbarItems

Class org.virion.jam.toolbar.ToolbarAction extends AbstractAction implements Serializable

Serialized Fields

label

String label

toolTipText

String toolTipText

icon

Icon icon

disabledIcon

Icon disabledIcon

pressedIcon

Icon pressedIcon

Class org.virion.jam.toolbar.ToolbarButton extends JButton implements Serializable

Serialized Fields

action

ToolbarAction action

Package org.virion.jam.util

Class org.virion.jam.util.JExceptionDialog extends JDialog implements Serializable

Serialized Fields

buttonPanel

JPanel buttonPanel

okButton

JButton okButton

jScrollPane1

JScrollPane jScrollPane1

exceptionTextArea

JTextArea exceptionTextArea