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

A

AbstractMapPoint - class jadex.swing.map.AbstractMapPoint.
Default implementation of MapPoint.
AbstractMapPoint() - Constructor for class jadex.swing.map.AbstractMapPoint
Default constructor.
AbstractMapPoint(String, float) - Constructor for class jadex.swing.map.AbstractMapPoint
An overloaded construcor.
accessorPropertyDescriptor() - Method in class jadex.swing.AceModelBeanInfo
Gets the accessor property descriptor.
aceAccessorPropertyDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the aceAccessor property descriptor.
AceDBCloneFetcher - class jadex.swing.sequence.AceDBCloneFetcher.
This class is used to fetch SequenceMap information from AceDB directly for SequenceMap display.
AceDBCloneFetcher() - Constructor for class jadex.swing.sequence.AceDBCloneFetcher
Default constructor
AceDBCloneFetcher(JSAceAccessor, String) - Constructor for class jadex.swing.sequence.AceDBCloneFetcher
Third constructor: AceAccessor and Sequence_map name.
AceDBCloneFetcher(String, int, String) - Constructor for class jadex.swing.sequence.AceDBCloneFetcher
Second constructor: AceDB host, port and Sequene_map object name.
AceDBFrame - class jadex.swing.AceDBFrame.
This is the entry point for Java AceDB browser.
aceDBFrame_WindowClosed(WindowEvent) - Method in class jadex.swing.AceDBFrame
 
AceDBFrame() - Constructor for class jadex.swing.AceDBFrame
Constructor
AceDBFrame(String, int) - Constructor for class jadex.swing.AceDBFrame
Another constructor with host and port arguments
AceDBFrameBeanInfo - class jadex.swing.AceDBFrameBeanInfo.
The bean information class for jadex.swing.AceDBFrame.
AceDBFrameBeanInfo() - Constructor for class jadex.swing.AceDBFrameBeanInfo
 
AceModel - class jadex.swing.AceModel.
This class handles all data related to class displaying.
AceModel() - Constructor for class jadex.swing.AceModel
AceModel constructor comment.
AceModel(Accessor) - Constructor for class jadex.swing.AceModel
An Overloaded constructur with Accessor as the sole argument.
AceModel(String, int) - Constructor for class jadex.swing.AceModel
Another constructor with host and port as the arguaments
AceModelBeanInfo - class jadex.swing.AceModelBeanInfo.
The bean information class for jadex.swing.AceModel.
AceModelBeanInfo() - Constructor for class jadex.swing.AceModelBeanInfo
 
actionPerformed_javaawteventActionEventMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the actionPerformed(java.awt.event.ActionEvent) method descriptor.
actionPerformed(ActionEvent) - Method in class jadex.swing.map.OpenFileAction
Actual method to open the file.
actionPerformed(ActionEvent) - Method in class jadex.swing.map.ZoomButtonControl
Processing all button actions.
actionPerformed(ActionEvent) - Method in class jadex.swing.sequence.CloneOpenFileAction
 
actionPerformed(ActionEvent) - Method in class jadex.swing.ClassListMediator
The actionListener method.
actionPerformed(ActionEvent) - Method in class jadex.swing.ClassViewController.CancellAction
 
actionPerformed(ActionEvent) - Method in class jadex.swing.ProgressPanel
Method to handle events for the ActionListener interface.
actionPerformed(ActionEvent) - Method in class jadex.swing.SearchPanel
Method to handle events for the ActionListener interface.
add(ProgressPanelListener, ProgressPanelListener) - Static method in class jadex.swing.ProgressPanelListenerEventMulticaster
Add new listener to support multicast events.
addAction() - Method in class jadex.swing.map.RangeControlPanel
Add actionlistenes to the buttons.
addActionListener_javaawteventActionListenerMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the addActionListener(java.awt.event.ActionListener) method descriptor.
addActionListener(ActionListener) - Method in class jadex.swing.ProgressPanel
This method was created in VisualAge.
addCancelActionListener(ActionListener) - Method in class jadex.swing.ClassViewController
Add a actionListener for Cancel button.
addFrame(String, JFrame) - Method in class jadex.swing.OpenFrames
Register a displaying AceObject.
addInterval(IntervalUI) - Method in class jadex.swing.map.IntervalContainer
Individual IntervalUI can be added into this container.
addInterval(IntervalUI) - Method in class jadex.swing.map.IntervalPanel
Individual IntervalUI can be added by this method.
addIntervalPanel(IntervalPanel) - Method in class jadex.swing.map.IntervalContainer
Individual IntervalPanel can be added into this container.
addLocus(LocusUI) - Method in class jadex.swing.map.LocusPanel
Add an individual LocusUI.
addMouseListener_int_javaawteventMouseListenerMethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the addMouseListener(int, java.awt.event.MouseListener) method descriptor.
addMouseListener_javaawteventMouseListenerMethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the addMouseListener(java.awt.event.MouseListener) method descriptor.
addMouseListener(int, MouseListener) - Method in class jadex.swing.IndexSelector
Add a mouselistener to a specified JLabel at position.
addMouseListener(MouseListener) - Method in interface jadex.swing.util.Zoomable
Add a mouseListener.
addMouseListener(MouseListener) - Method in class jadex.swing.IndexSelector
Add a mouselistener to all JLabels.
addMouseMotionListener(MouseMotionListener) - Method in interface jadex.swing.util.Zoomable
Add a mouseMotionLister.
addPanel(String, JPanel) - Method in class jadex.swing.classView.MapViewContainer
Add a JPanel for displaying.
addPoint(MapPoint) - Method in class jadex.swing.map.DisplayModel
Add a MapPoint.
addPoint(MapPoint) - Method in class jadex.swing.map.LocusShow
Add an individual MapPoint to the display.
addProgressPanelListener_jadexswingProgressPanelListenerMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the addProgressPanelListener(jadex.swing.ProgressPanelListener) method descriptor.
addProgressPanelListener(ProgressPanelListener) - Method in class jadex.swing.ProgressPanel
 
addPropertyChangeListener_javabeansPropertyChangeListenerMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the addPropertyChangeListener(java.beans.PropertyChangeListener) method descriptor.
addPropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.map.MapControl
Add a PropertyChangeListener to the listener list.
addPropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.sequence.RangeSpecifyDialog
Add propertychange listener
addPropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.ClassListModel
The addPropertyChangeListener method was generated to support the propertyChange field.
addPropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.ClassViewController
The addPropertyChangeListener method was generated to support the propertyChange field.
addSelectionListener(SequenceSelectionListener) - Method in class jadex.swing.sequence.SequenceSelectionModel
Register a selection listener
addViewMenuItem(String, JPanel) - Method in class jadex.swing.classView.MapViewContainerMenuBar
Add controllable View Items to the View Menu Item.
aqlSequenceDump(Element, String) - Method in class jadex.xml.SequenceMapXMLDump
Dump sequence by aql from acedb
assignClones(List) - Method in class jadex.swing.sequence.CloneControl
The algorithim to distribute the clones.
assignPoints(float) - Method in class jadex.swing.map.DisplayModel
Distribute all MapPoints.
assignPoints(MapPoint[], float) - Method in class jadex.swing.map.DisplayModel
Distribute a MapPoint array.

B

boxes - Variable in class jadex.swing.sequence.SequenceLayoutModel
 

C

CancellactionPerformed_javaawteventActionEventMethodEventDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the CancellactionPerformed(java.awt.event.ActionEvent) method descriptor.
CancellactionPerformed(EventObject) - Method in interface jadex.swing.ProgressPanelListener
 
CancellactionPerformed(EventObject) - Method in class jadex.swing.ProgressPanelListenerEventMulticaster
 
CancellEnabledPropertyDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the CancellEnabled property descriptor.
categoryPropertyDescriptor() - Method in class jadex.swing.AceModelBeanInfo
Gets the category property descriptor.
CategoryTreeSelectionListener - class jadex.swing.CategoryTreeSelectionListener.
This class is used to control the selection activity in CategoryTree.
CategoryTreeSelectionListener() - Constructor for class jadex.swing.CategoryTreeSelectionListener
Default constructor.
CategoryTreeSelectionListener(JTabbedPane) - Constructor for class jadex.swing.CategoryTreeSelectionListener
An overloaded constructor with a JTabbedPane as the only argument.
checkAdding(IntervalUI) - Method in class jadex.swing.map.IntervalPanel
Check if IntervalUI can be added onto this panel.
checkAdding(LocusUI) - Method in class jadex.swing.map.LocusPanel
Check if a LocusUI can be added.
checkGUI(int) - Method in class jadex.swing.ClassListDisplayer
 
checkKnobs() - Method in class jadex.swing.map.DisplayControl
Check the arrow of two knobs.
checkMapRange(MapRange) - Method in class jadex.swing.map.DisplayControl
See if the maprange is out of the full scale.
checkShowMenu() - Method in class jadex.swing.map.DisplayPopup
Checking the enability of show menuitems.
children() - Method in class jadex.swing.sequence.SequenceTreeNode
Get all children in an Enumeration.
ClassDisplayer - class jadex.swing.ClassDisplayer.
This class displays object numbers by counting their names' leading letter.
ClassDisplayer() - Constructor for class jadex.swing.ClassDisplayer
Default constructor.
ClassDisplayer(ClassDisplayerModel) - Constructor for class jadex.swing.ClassDisplayer
A overloaded constructor with ClassDisplayModel as the sole argument.
ClassDisplayer(String, int) - Constructor for class jadex.swing.ClassDisplayer
Another overloaded constructor with class name and number as the arguments.
ClassDisplayerBeanInfo - class jadex.swing.ClassDisplayerBeanInfo.
The bean information class for jadex.swing.ClassDisplayer.
ClassDisplayerBeanInfo() - Constructor for class jadex.swing.ClassDisplayerBeanInfo
 
ClassDisplayerModel - class jadex.swing.ClassDisplayerModel.
This is the model class to store all class counting information for ClassDisplayer.
ClassDisplayerModel() - Constructor for class jadex.swing.ClassDisplayerModel
Default constructor.
ClassDisplayerModel(String, int, JLabel[], JLabel) - Constructor for class jadex.swing.ClassDisplayerModel
A overloaded construcotr.
ClassListDisplayer - class jadex.swing.ClassListDisplayer.
This class lists objects in a specific class.
ClassListDisplayer() - Constructor for class jadex.swing.ClassListDisplayer
Constructor
ClassListDisplayer(ClassListModel) - Constructor for class jadex.swing.ClassListDisplayer
Constructor
ClassListMediator - class jadex.swing.ClassListMediator.
This is an adapter class to mediate the activities between ClassListdisplayer and ClassListModel.
ClassListMediator() - Constructor for class jadex.swing.ClassListMediator
Default constructor.
ClassListMediator(ClassListDisplayer, ClassListModel) - Constructor for class jadex.swing.ClassListMediator
An overloaded constructor.
ClassListModel - class jadex.swing.ClassListModel.
This model class stores all object information in a specified class to be displayed in the ClasslistDisplayer.
ClassListModel() - Constructor for class jadex.swing.ClassListModel
Default constructor.
ClassListModel(AceAccessor, JLabel, ClassDisplayerModel) - Constructor for class jadex.swing.ClassListModel
An overloaded construtor.
ClassListModelBeanInfo - class jadex.swing.ClassListModelBeanInfo.
The bean information class for jadex.swing.ClassListModel.
ClassListModelBeanInfo() - Constructor for class jadex.swing.ClassListModelBeanInfo
 
classNamePropertyDescriptor() - Method in class jadex.swing.ClassViewControllerBeanInfo
Gets the className property descriptor.
ClassView - class jadex.swing.classView.ClassView.
This is the super class for all ClassView.
ClassView() - Constructor for class jadex.swing.classView.ClassView
 
ClassViewController - class jadex.swing.ClassViewController.
This class is used to control the activities in ClassDisplayer and ClassListDisplayer.
ClassViewController.CancellAction - class jadex.swing.ClassViewController.CancellAction.
 
ClassViewController.CancellAction(ClassViewController) - Constructor for class jadex.swing.ClassViewController.CancellAction
 
ClassViewController() - Constructor for class jadex.swing.ClassViewController
Default constructor.
ClassViewController(String, AceModel) - Constructor for class jadex.swing.ClassViewController
TA overloaded constructor.
ClassViewControllerBeanInfo - class jadex.swing.ClassViewControllerBeanInfo.
The bean information class for jadex.swing.ClassViewController.
ClassViewControllerBeanInfo() - Constructor for class jadex.swing.ClassViewControllerBeanInfo
 
clear() - Method in class jadex.swing.classView.SequenceView
Clear up.
clear() - Method in class jadex.swing.sequence.SequenceDisplay
Clear up and force to release all resources.
clear() - Method in class jadex.swing.sequence.SequenceDisplayAndTreeAdapter
Clear up
clear() - Method in class jadex.swing.sequence.SequenceTreeDisplay
Clear up.
clear() - Method in class jadex.swing.sequence.SequenceViewFactory
Clear up method.
clearSelection() - Method in class jadex.swing.sequence.SequenceDisplay
Clear all selected sequences.
clearSelection() - Method in class jadex.swing.sequence.SequenceSelectionModel
Remove all selected sequence from selection
Clone - class jadex.swing.sequence.Clone.
This wrapper class contains information about a clone.
Clone() - Constructor for class jadex.swing.sequence.Clone
Creates new Clone
Clone(String) - Constructor for class jadex.swing.sequence.Clone
Another constructor with name as a argument
Clone(String, MapRange) - Constructor for class jadex.swing.sequence.Clone
Third constructor with name and maprange as arguements
Clone(String, MapRange, Contig) - Constructor for class jadex.swing.sequence.Clone
Fourth constructor with name, mapRange, and contig
CloneControl - class jadex.swing.sequence.CloneControl.
A subclass of DisplayControl to control CloneDisplay.
CloneControl() - Constructor for class jadex.swing.sequence.CloneControl
Default constructor
CloneControl(CloneDisplay) - Constructor for class jadex.swing.sequence.CloneControl
Second constructor with CloneDisplay as the argument
CloneControl(CloneDisplay, CloneFetcher) - Constructor for class jadex.swing.sequence.CloneControl
Third constrcutor with clonedisplay and clonefetcher as the arguement
CloneControl(CloneDisplay, DisplayModel) - Constructor for class jadex.swing.sequence.CloneControl
Fourth constructor with clonedisplay and displaymodel as the argumetns
CloneDisplay - class jadex.swing.sequence.CloneDisplay.
This is the class used to show clones in the chromosome.
CloneDisplay() - Constructor for class jadex.swing.sequence.CloneDisplay
Default constructor
CloneDisplay(CloneControl) - Constructor for class jadex.swing.sequence.CloneDisplay
Second constructor: CloneControl as the argument
CloneDisplay(DisplayModel) - Constructor for class jadex.swing.sequence.CloneDisplay
Third constructor: DisplayModel as the argument
CloneFetcher - class jadex.swing.sequence.CloneFetcher.
This class is used to get clone data from a datasource, such as AceDB or local files.
CloneFetcher() - Constructor for class jadex.swing.sequence.CloneFetcher
 
CloneOpenFileAction - class jadex.swing.sequence.CloneOpenFileAction.
This class is used to open a sequnece_map file.
CloneOpenFileAction() - Constructor for class jadex.swing.sequence.CloneOpenFileAction
Default constructor
CloneOpenFileAction(MapViewContainer) - Constructor for class jadex.swing.sequence.CloneOpenFileAction
Second constructor with container as the argument
CloneOpenFileAction(MapViewContainer, SequenceMapView) - Constructor for class jadex.swing.sequence.CloneOpenFileAction
Third constructor with container and SequenceMapView as the arguments
CloneUI - class jadex.swing.sequence.CloneUI.
The vertical bar for representing the clone on the left to the chromosome line on the CloneDisplay.
CloneUI() - Constructor for class jadex.swing.sequence.CloneUI
Creates new CloneUI
CloneUI(Clone) - Constructor for class jadex.swing.sequence.CloneUI
One more constructor with clone as the argument
CloneUI(String) - Constructor for class jadex.swing.sequence.CloneUI
Another constructor with name as the argument
COLUMN_LAYOUT - Static variable in class jadex.swing.map.DisplayPopup
 
combine(MapRange) - Method in class jadex.swing.map.MapRange
Add two maprange together and return a changed this maprange
contain(long) - Method in class jadex.swing.map.MapRange
Check if this maprange contains a specific value.
Contig - class jadex.swing.sequence.Contig.
A wrapper class for Contig.
Contig() - Constructor for class jadex.swing.sequence.Contig
Creates new Contig
Contig(String) - Constructor for class jadex.swing.sequence.Contig
Second constructor with name as the arguemnt
Contig(String, String) - Constructor for class jadex.swing.sequence.Contig
Third constructor with name, map as the arguement
Contig(String, String, MapRange, MapRange) - Constructor for class jadex.swing.sequence.Contig
Fourth constructor with all properties as the arguments
control - Variable in class jadex.swing.map.Knob
 
ControlPanel - class jadex.swing.map.ControlPanel.
This is a JPanel to control the displaying items in the MapView.
ControlPanel() - Constructor for class jadex.swing.map.ControlPanel
Creates new form ControlPanel
ControlPanel(Container) - Constructor for class jadex.swing.map.ControlPanel
 
countPropertyDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the count property descriptor.
createXMLFile(String) - Method in class jadex.xml.SequenceMapXMLDump
A template to create xml files
currentPanelPropertyDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the currentPanel property descriptor.
currentPanelPropertyDescriptor() - Method in class jadex.swing.ClassViewControllerBeanInfo
Gets the currentPanel property descriptor.

D

defaultCloseOperationPropertyDescriptor() - Method in class jadex.swing.AceDBFrameBeanInfo
Gets the defaultCloseOperation property descriptor.
deSearch() - Method in class jadex.swing.map.DisplayControl
Remove all label and close all extra locusUI.
deSelectedElements(List) - Method in class jadex.swing.sequence.SequenceSelectionModel
DeSelect a list of elements.
deSelectSequence(Element) - Method in class jadex.swing.sequence.SequenceDisplay
Remove selected sequence.
deSelectSequence(Element) - Method in class jadex.swing.sequence.SequenceSelectionModel
Remove a selected sequence.
disableGUI() - Method in class jadex.swing.ClassListDisplayer
This method was created in VisualAge.
DisplayControl - class jadex.swing.map.DisplayControl.
This is a control class for LocusDisplay.
DisplayControl() - Constructor for class jadex.swing.map.DisplayControl
Default constructor.
DisplayControl(DisplayModel) - Constructor for class jadex.swing.map.DisplayControl
An overloaded constructor.
DisplayModel - class jadex.swing.map.DisplayModel.
This is a datamodel used for both GeneticMap and SequenceMap displays.
DisplayModel() - Constructor for class jadex.swing.map.DisplayModel
Creates new DisplayModel
DisplayPopup - class jadex.swing.map.DisplayPopup.
This is a JPopupMenu used in LocusDisplay.
DisplayPopup(MapPointDisplay, DisplayControl) - Constructor for class jadex.swing.map.DisplayPopup
Constructor by using MapPointDisplay and DisplayControl.
DisplayPopup(MapPointDisplay, DisplayControl, String) - Constructor for class jadex.swing.map.DisplayPopup
Another constructor.
distance - Variable in class jadex.swing.sequence.SequenceLayoutModel
 
doSearch(String) - Method in class jadex.swing.map.DisplayControl
Consider to change this method in the future.
doSearch(String) - Method in class jadex.swing.map.IntervalContainer
Search Intervals which names containing s.
doSearch(String) - Method in class jadex.swing.map.LocusShow
Locus can be searched based on name.
doSearch(String) - Method in class jadex.swing.map.LocusDisplay
Search loci with names containg pattern.
DownKnob - class jadex.swing.map.DownKnob.
This Knob is used in the south end in the chromosome line in the LocusDisplay or SequenceMapDisplay.
DownKnob() - Constructor for class jadex.swing.map.DownKnob
Default constructor.
DownKnob(DisplayControl) - Constructor for class jadex.swing.map.DownKnob
An overloaded constructor.
doZooming() - Method in class jadex.swing.map.LocusDisplay
Actual zooming method.
doZooming() - Method in class jadex.swing.sequence.CloneDisplay
Do zooming.
doZooming() - Method in class jadex.swing.util.TestPanel
 
doZooming() - Method in interface jadex.swing.util.Zoomable
How zooming should be implemented.
drawNames(float, float, float, float, Graphics2D) - Method in class jadex.swing.map.LocusLayout
The actual layout method.
drawNames(float, float, float, float, Graphics2D) - Method in class jadex.swing.map.SmartLocusLayout
Actual layout methods.
DTD_NAME - Static variable in class jadex.xml.SequenceMapXMLDump
 
dump(String) - Method in class jadex.xml.SequenceMapXMLDump
A template method to dump the sequnece from acedb
dumpAll() - Method in class jadex.xml.SequenceMapXMLDump
This method to dump all chromosomes from acedb into six xml and six jar files
DumpClassView - class jadex.swing.classView.DumpClassView.
This is a simple AceObject view.
DumpClassView() - Constructor for class jadex.swing.classView.DumpClassView
Default constructor.

E

equals(Clone) - Method in class jadex.swing.sequence.Clone
Comparae if two clones are equal.
equals(MapRange) - Method in class jadex.swing.map.MapRange
Compare two mapranges.
equals(Object) - Method in class jadex.swing.sequence.SequenceTreeNode
Comparing if two elements are equal.
equalsF(MapRange) - Method in class jadex.swing.map.MapRange
Deprecated. use equals(MapRange rg).

F

fetchClone() - Method in class jadex.swing.sequence.CloneFetcher
The main method to be called by Model or other class to get the data.
fetchObjects(String, int, int) - Method in class jadex.swing.ClassListModel
Fetch the objects with leading letter as letter from start to start + legnth -1.
fieldProgressPanelListenerEventMulticaster - Variable in class jadex.swing.ProgressPanel
 
FileCloneFetcher - class jadex.swing.sequence.FileCloneFetcher.
This subclass of CloneFetcher is used to get clone information from local file systems.
FileCloneFetcher() - Constructor for class jadex.swing.sequence.FileCloneFetcher
Creates new FileCloneFetcher
FileCloneFetcher(String) - Constructor for class jadex.swing.sequence.FileCloneFetcher
Second constructor.
fileToURL(File) - Method in class jadex.xml.XMLParserDemo
 
findMethod(Class, String, int) - Static method in class jadex.swing.AceDBFrameBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
findMethod(Class, String, int) - Static method in class jadex.swing.AceModelBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
findMethod(Class, String, int) - Static method in class jadex.swing.ClassDisplayerBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
findMethod(Class, String, int) - Static method in class jadex.swing.ClassListModelBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
findMethod(Class, String, int) - Static method in class jadex.swing.ClassViewControllerBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
findMethod(Class, String, int) - Static method in class jadex.swing.IndexSelectorBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
findMethod(Class, String, int) - Static method in class jadex.swing.ProgressPanelBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
findMethod(Class, String, int) - Static method in class jadex.swing.WelcomePaneBeanInfo
Find the method by comparing (name & parameter size) against the methods in the class.
fireCancellactionPerformed(EventObject) - Method in class jadex.swing.ProgressPanel
Method to support listener events.
firePropertyChange_javalangString_javalangObject_javalangObjectMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object) method descriptor.
firePropertyChange(String, Object, Object) - Method in class jadex.swing.sequence.SequenceDisplay
Release proteced access to public, so its package class can call it.
firePropertyChange(String, Object, Object) - Method in class jadex.swing.ClassListModel
The firePropertyChange method was generated to support the propertyChange field.
firePropertyChange(String, Object, Object) - Method in class jadex.swing.ClassViewController
The firePropertyChange method was generated to support the propertyChange field.
fireSelectionValueChanged(Element, boolean) - Method in class jadex.swing.sequence.SequenceSelectionModel
Notify all selection listeners a selection has changed
fireSelectionValueChanged(List, boolean) - Method in class jadex.swing.sequence.SequenceSelectionModel
Notify all selection listeners a selection has changed
fromBpToX(long) - Method in class jadex.swing.sequence.SequenceLayoutModel
Transform from the bp on chromsome to the graphics coordinate system
fromXtoBp(float) - Method in class jadex.swing.sequence.SequenceLayoutModel
The opposite method of the above method

G

geneDump(Element, String) - Method in class jadex.xml.SequenceMapXMLDump
Dump a possible gene
GeneRenderer - class jadex.swing.sequence.GeneRenderer.
A customized JComponent for rendering gene structures in SequenceView.
GeneRenderer() - Constructor for class jadex.swing.sequence.GeneRenderer
Default constructor
GeneticMapApplet - class jadex.swing.GeneticMapApplet.
This applet is used to launch GeneticMapView applet.
GeneticMapApplet() - Constructor for class jadex.swing.GeneticMapApplet
 
GeneTransform - class jadex.xml.GeneTransform.
 
GeneTransform() - Constructor for class jadex.xml.GeneTransform
 
getAccessor() - Method in class jadex.swing.sequence.AceDBCloneFetcher
Get the AceAccessor used in this Sequence_map dislay.
getAccessor() - Method in class jadex.swing.AceModel
Gets the accessor property (jade.db.AceAccessor) value.
getAccessor() - Method in class jadex.xml.SequenceMapXMLDump
 
getAceAccessor() - Method in class jadex.swing.map.LocusUI
Get the AceAccessor.
getAceAccessor() - Method in class jadex.swing.ClassListModel
Get the AceAccessor.
getAceAccessorMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the getAceAccessor() method descriptor.
getAceModel() - Method in class jadex.swing.AceDBFrame
Return the AceModel property value.
getAceModel() - Method in class jadex.swing.ClassViewController
 
getAceObject() - Method in class jadex.swing.map.Locus
Get the AceObject.
getAceObject() - Method in class jadex.swing.map.LocusUI
Get the AceObject attached to this LocusUI.
getAceObject() - Method in class jadex.swing.sequence.Clone
Get the wrapped AceObject for this clone.
getAceObject() - Method in class jadex.swing.sequence.Contig
Get the wrapped AceObject for this Contig.
getAceObject() - Method in class jadex.swing.ObjectViewController
Get the AceObject.
getActions() - Method in class jadex.swing.sequence.SequenceActions
Expose the actions set
getAdditionalBeanInfo() - Method in class jadex.swing.AceDBFrameBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAdditionalBeanInfo() - Method in class jadex.swing.AceModelBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAdditionalBeanInfo() - Method in class jadex.swing.ClassDisplayerBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAdditionalBeanInfo() - Method in class jadex.swing.ClassListModelBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAdditionalBeanInfo() - Method in class jadex.swing.ClassViewControllerBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAdditionalBeanInfo() - Method in class jadex.swing.IndexSelectorBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAdditionalBeanInfo() - Method in class jadex.swing.ProgressPanelBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAdditionalBeanInfo() - Method in class jadex.swing.WelcomePaneBeanInfo
Returns the BeanInfo of the superclass of this bean to inherit its features.
getAllButton() - Method in class jadex.swing.ClassListDisplayer
Return the JToolBarButton3 property value.
getAllowsChildren() - Method in class jadex.swing.sequence.SequenceTreeNode
Get if this node allows children.
getApplet() - Method in class jadex.swing.OpenFrames
Get the applet.
getAssignedClones() - Method in class jadex.swing.sequence.CloneControl
Get the distributed clones.
getBeanClass() - Static method in class jadex.swing.AceDBFrameBeanInfo
Gets the bean class.
getBeanClass() - Static method in class jadex.swing.AceModelBeanInfo
Gets the bean class.
getBeanClass() - Static method in class jadex.swing.ClassDisplayerBeanInfo
Gets the bean class.
getBeanClass() - Static method in class jadex.swing.ClassListModelBeanInfo
Gets the bean class.
getBeanClass() - Static method in class jadex.swing.ClassViewControllerBeanInfo
Gets the bean class.
getBeanClass() - Static method in class jadex.swing.IndexSelectorBeanInfo
Gets the bean class.
getBeanClass() - Static method in class jadex.swing.ProgressPanelBeanInfo
Gets the bean class.
getBeanClass() - Static method in class jadex.swing.WelcomePaneBeanInfo
Gets the bean class.
getBeanClassName() - Static method in class jadex.swing.AceDBFrameBeanInfo
Gets the bean class name.
getBeanClassName() - Static method in class jadex.swing.AceModelBeanInfo
Gets the bean class name.
getBeanClassName() - Static method in class jadex.swing.ClassDisplayerBeanInfo
Gets the bean class name.
getBeanClassName() - Static method in class jadex.swing.ClassListModelBeanInfo
Gets the bean class name.
getBeanClassName() - Static method in class jadex.swing.ClassViewControllerBeanInfo
Gets the bean class name.
getBeanClassName() - Static method in class jadex.swing.IndexSelectorBeanInfo
Gets the bean class name.
getBeanClassName() - Static method in class jadex.swing.ProgressPanelBeanInfo
Gets the bean class name.
getBeanClassName() - Static method in class jadex.swing.WelcomePaneBeanInfo
Gets the bean class name.
getBeanDescriptor() - Method in class jadex.swing.AceDBFrameBeanInfo
 
getBeanDescriptor() - Method in class jadex.swing.AceModelBeanInfo
 
getBeanDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
 
getBeanDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
 
getBeanDescriptor() - Method in class jadex.swing.ClassViewControllerBeanInfo
 
getBeanDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
 
getBeanDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
 
getBeanDescriptor() - Method in class jadex.swing.WelcomePaneBeanInfo
 
getBounds(Element, int, boolean) - Method in class jadex.swing.sequence.SequenceLayoutModel
Calculate the positon of sequence element based on its positions on the chromosome
getBoxAboveY(float) - Method in class jadex.swing.sequence.SequenceLayoutModel
Get the box just above or containing a given y
getBoxBelowY(float) - Method in class jadex.swing.sequence.SequenceLayoutModel
Get the box just below or containing a given y
getBoxFromY(float, float) - Method in class jadex.swing.sequence.SequenceLayoutModel
A helper to get the box number for a point
getButtonAllEnable() - Method in class jadex.swing.ClassDisplayer
Export if the JRadioButton, ButtonAll, is enabled.
getCategory() - Method in class jadex.swing.AceModel
Gets the category property (java.util.Vector) value.
getChildAt(int) - Method in class jadex.swing.sequence.SequenceTreeNode
Get a treeNode given the index of the child.
getChildCount() - Method in class jadex.swing.sequence.SequenceTreeNode
Get the total number of the children.
getClassName() - Method in class jadex.swing.ClassDisplayer
Get the class name displayed.
getClassName() - Method in class jadex.swing.ClassDisplayerModel
Get the displayed class name.
getClassName() - Method in class jadex.swing.ClassListModel
 
getClassName() - Method in class jadex.swing.ClassViewController
Gets the className property (java.lang.String) value.
getClone() - Method in class jadex.swing.sequence.CloneFetcher
Get the clones.
getClone() - Method in class jadex.swing.sequence.CloneUI
Get the displayed clone.
getClone(String) - Method in class jadex.swing.sequence.CloneFetcher
Parse clone information from String.
getCloneControl() - Method in class jadex.swing.classView.SequenceMapView
Get the CloneControl used in this SequenceMapView.
getCloneInfor() - Method in class jadex.swing.sequence.CloneFetcher
Get the clone information for the Sequence_map into a String.
getCloneInfor() - Method in class jadex.swing.sequence.AceDBCloneFetcher
Get all information about clones in the Sequence_map in a String.
getCloneInfor() - Method in class jadex.swing.sequence.FileCloneFetcher
Fetch all clone information into a String.
getClones() - Method in class jadex.swing.sequence.CloneControl
Get the clones displayed in the CloneDisplay.
getClosestElement(int, int) - Method in class jadex.swing.sequence.SequenceLayoutModel
Get the sequence element by a point coordinate on the graphics
getColor() - Method in class jadex.swing.sequence.CloneUI
Get the color of this cloneUI.
getComparator() - Method in class jadex.swing.map.DisplayModel
Get the comparator for sorting the MapPoints.
getContig() - Method in class jadex.swing.sequence.CloneFetcher
Get the contigs in this Sequence_maps.
getCount() - Method in class jadex.swing.ClassDisplayer
Get the total object entries of the class.
getCount() - Method in class jadex.swing.ClassDisplayerModel
Get the total count of the displayed class.
getCountMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the getCount() method descriptor.
getCurrentPanel() - Method in class jadex.swing.ClassListDisplayer
Comment
getCurrentPanel() - Method in class jadex.swing.ClassListModel
Gets the currentPanel property (javax.swing.JPanel) value.
getCurrentPanel() - Method in class jadex.swing.ClassViewController
Gets the currentPanel property (javax.swing.JPanel) value.
getData() - Method in class jadex.swing.map.DisplayModel
Get all MapPoint in an array.
getDbFrame() - Method in class jadex.swing.SearchPanel
This method was created in VisualAge.
getDbFrame() - Method in class jadex.swing.ViewSettingPanel
 
getDirection() - Method in class jadex.swing.map.Knob
The name of direction: up, down or no.
getDirection() - Method in class jadex.swing.map.DownKnob
Get the direction of the Knob.
getDirection() - Method in class jadex.swing.map.UpKnob
Get the direction as a string.
getDisplay() - Method in class jadex.swing.map.DisplayControl
Display should be provided by subclass.
getDisplay() - Method in class jadex.swing.map.LocusControl
Get the display.
getDisplay() - Method in class jadex.swing.sequence.CloneControl
Return CloneDisplay implementing MapPointDisplay
getDocument() - Method in interface jadex.swing.sequence.SequenceFetcher
The xml document: based on JDOM documentation, JDOM document is not loaded in the memory.
getDocument() - Method in class jadex.swing.sequence.SequenceModel
Get the xml document from fetcher.
getDocument() - Method in class jadex.swing.sequence.SequenceXMLFetcher
Get the XML document containing all Sequence element information.
getDocument() - Method in class jadex.xml.SequenceMapXMLDump
Get the document to display the contents
getElementsBetween(Rectangle) - Method in class jadex.swing.sequence.SequenceLayoutModel
Get a list of sequence elements in a rectangele
getEnd() - Method in class jadex.swing.map.IntervalUI
Get the end value.
getEnd() - Method in class jadex.swing.map.MapRange
Get the end value.
getEndF() - Method in class jadex.swing.map.MapRange
Get the end value in float.
getError() - Method in class jadex.swing.map.AbstractMapPoint
Get the error of this position.
getError() - Method in class jadex.swing.map.Locus
 
getError() - Method in interface jadex.swing.map.MapPoint
Get the error of the position of this MapPoint.
getError() - Method in class jadex.swing.sequence.Clone
No error data from AceDB
getEventSetDescriptors() - Method in class jadex.swing.AceDBFrameBeanInfo
Return the event set descriptors for this bean.
getEventSetDescriptors() - Method in class jadex.swing.AceModelBeanInfo
Return the event set descriptors for this bean.
getEventSetDescriptors() - Method in class jadex.swing.ClassDisplayerBeanInfo
Return the event set descriptors for this bean.
getEventSetDescriptors() - Method in class jadex.swing.ClassListModelBeanInfo
Return the event set descriptors for this bean.
getEventSetDescriptors() - Method in class jadex.swing.ClassViewControllerBeanInfo
Return the event set descriptors for this bean.
getEventSetDescriptors() - Method in class jadex.swing.IndexSelectorBeanInfo
Return the event set descriptors for this bean.
getEventSetDescriptors() - Method in class jadex.swing.ProgressPanelBeanInfo
Return the event set descriptors for this bean.
getEventSetDescriptors() - Method in class jadex.swing.WelcomePaneBeanInfo
Return the event set descriptors for this bean.
getExitAction() - Method in class jadex.swing.sequence.SequenceActions
Get the exit action.
getExtend() - Method in class jadex.swing.map.MapRange
Get the total length of this MapRange.
getExtend() - Method in class jadex.swing.sequence.Contig
 
getExtendF() - Method in class jadex.swing.map.MapRange
How to include the two ends? This is a question?
getExtendF() - Method in class jadex.swing.sequence.Contig
 
getFetcher() - Method in class jadex.swing.sequence.SequenceModel
Get the data source.
getForOutColor() - Method in class jadex.swing.map.LocusUI
Get the foreground color used when mouse is not in.
getFrame(String) - Method in class jadex.swing.OpenFrames
Get the JFrame with the title.
getFullMapRange() - Method in class jadex.swing.sequence.HorizontalMiniMapCartoon
Get the full maprange
getGeneBounds(Rectangle) - Method in class jadex.swing.sequence.SequenceLayoutModel
Get a gene bounds from it parent sequence's bounds
getGeneRenderer() - Method in class jadex.swing.sequence.SequenceDisplay
Get the gene renderer.
getGeneRenderer(Element, JComponent, long) - Method in class jadex.swing.sequence.GeneRenderer
Get the gene renderer for a gene element.
getHelpAction() - Method in class jadex.swing.sequence.SequenceActions
Get the help action.
getIndex_intMethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the getIndex(int) method descriptor.
getIndex() - Method in class jadex.swing.IndexSelector
Get all JLabels for index.
getIndex(int) - Method in class jadex.swing.IndexSelector
Get the JLabel at position.
getIndex(TreeNode) - Method in class jadex.swing.sequence.SequenceTreeNode
Get the index of a child node.
getIndexMethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the getIndex() method descriptor.
getIndexSelector1Index_intMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the getIndexSelector1Index(int) method descriptor.
getIndexSelector1Index() - Method in class jadex.swing.ClassDisplayer
Method generated to support the promotion of the indexSelector1Index attribute.
getIndexSelector1Index(int) - Method in class jadex.swing.ClassDisplayer
Method generated to support the promotion of the indexSelector1Index attribute.
getIndexSelector1IndexMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the getIndexSelector1Index() method descriptor.
getInstance() - Static method in class jadex.swing.sequence.SequenceActions
The method to get an instance of this class.
getInstance() - Static method in class jadex.swing.OpenFrames
This is the only method to get the instance of this class.
getInstance(boolean) - Static method in class jadex.swing.sequence.SequenceActions
Another method to get an instance of this class.
getIntervals() - Method in class jadex.swing.map.OpenFileAction
 
getJButton1() - Method in class jadex.swing.ProgressPanel
Return the JButton1 property value.
getJButton1Enabled() - Method in class jadex.swing.ProgressPanel
Method generated to support the promotion of the CancellEnabled attribute.
getJLabel1() - Method in class jadex.swing.ClassDisplayer
Return the total entry label.
getJLabel1MethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the getJLabel1() method descriptor.
getJTreeView() - Method in class jadex.swing.classView.TreeClassView
This method is too heavy, and should be refactored.
getLabelAll() - Method in class jadex.swing.ClassDisplayerModel
 
getLabels() - Method in class jadex.swing.ClassDisplayerModel
Get all 26 labels, each of which is for one letter.
getLabels(int) - Method in class jadex.swing.ClassDisplayerModel
Get a indexed JLabel from the JLabel array.
getLayer(Element) - Static method in class jadex.xml.XMLUtilities
Get the layer of a element in XML document from root element, i.e., Chromosome.
getLayoutModel() - Method in class jadex.swing.sequence.SequenceDisplay
Get the layoutModel used in this SequenceDisplay.
getLeftEnd() - Method in class jadex.swing.map.MapRange
Get the left end of this maprange
getLetter() - Method in class jadex.swing.ClassListMediator
Get the selected letter.
getLetterBox() - Method in class jadex.swing.ClassListDisplayer
Return the JComboBox2 property value.
getLetterLabel() - Method in class jadex.swing.ClassListDisplayer
Return the JLabel2 property value.
getLetterList() - Method in class jadex.swing.ClassListModel
 
getLetterListMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the getLetterList() method descriptor.
getList_intMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the getList(int) method descriptor.
getListMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the getList() method descriptor.
getLoci() - Method in class jadex.swing.map.OpenFileAction
 
getLocusControl() - Method in class jadex.swing.map.LocusShow
Get the LocusControl for this LocusShow.
getLocusControl() - Method in class jadex.swing.map.LocusDisplay
Get the LocusControl used by this display.
getMap() - Method in class jadex.swing.map.MapCartoon
Get the total MaRange for the chromosome.
getMap() - Method in class jadex.swing.map.MapControl
Get the total MapRange.
getMap() - Method in class jadex.swing.sequence.Contig
Get the name of the Sequence_map this contig is in.
getMapControl() - Method in class jadex.swing.classView.MapViewContainer
Get the MapControl used in this MapContainer.
getMapControl() - Method in class jadex.swing.map.DisplayControl
Get the central controller.
getMapName() - Method in class jadex.swing.sequence.CloneFetcher
Get the name of the Sequence_map to be displayed.
getMapPoints(int) - Method in class jadex.swing.map.DisplayModel
Get the MapPointn with the number of size.
getMapPoints(MapRange) - Method in class jadex.swing.map.DisplayModel
Giving a maprange, get all mappoints in this range.
getMapPoints(MapRange, int) - Method in class jadex.swing.map.DisplayModel
Giving a maprange and showing number, get the mappoints.
getMapRange() - Method in class jadex.swing.sequence.Clone
Get the MapRange of the clone.
getMapRange() - Method in class jadex.swing.sequence.HorizontalMiniMapCartoon
Get the current maprange
getMapRange() - Method in class jadex.swing.sequence.SequenceDisplay
Get the current maprange
getMapRange() - Method in class jadex.swing.sequence.SequenceLayoutModel
Get the currently displayed MapRange.
getMapRange(Element) - Static method in class jadex.xml.XMLUtilities
Extract the maprange information from sequence element
getMapRange(Element, Namespace) - Static method in class jadex.xml.XMLUtilities
Extract the maprange information from sequence element
getMapScale() - Method in class jadex.swing.sequence.CloneFetcher
Get the total MapRange for the Sequence_map.
getMapView() - Method in class jadex.swing.map.MapMenuBar
Get the MapView this Menubar controlled.
getMarker() - Method in class jadex.swing.map.MiniMapCartoon
Get the markers.
getMarkers() - Method in class jadex.swing.map.OpenFileAction
 
getMaximum() - Method in class jadex.swing.ProgressPanel
Method generated to support the promotion of the TotalNumber attribute.
getMaximumMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the getMaximum() method descriptor.
getMessage() - Method in class jadex.swing.ProgressPanel
Method generated to support the promotion of the message attribute.
getMessage() - Method in class jadex.swing.WelcomePane
Gets the message property (java.lang.String) value.
getMessageMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the getMessage() method descriptor.
getMethodDescriptors() - Method in class jadex.swing.AceDBFrameBeanInfo
Return the method descriptors for this bean.
getMethodDescriptors() - Method in class jadex.swing.AceModelBeanInfo
Return the method descriptors for this bean.
getMethodDescriptors() - Method in class jadex.swing.ClassDisplayerBeanInfo
Return the method descriptors for this bean.
getMethodDescriptors() - Method in class jadex.swing.ClassListModelBeanInfo
Return the method descriptors for this bean.
getMethodDescriptors() - Method in class jadex.swing.ClassViewControllerBeanInfo
Return the method descriptors for this bean.
getMethodDescriptors() - Method in class jadex.swing.IndexSelectorBeanInfo
Return the method descriptors for this bean.
getMethodDescriptors() - Method in class jadex.swing.ProgressPanelBeanInfo
Return the method descriptors for this bean.
getMethodDescriptors() - Method in class jadex.swing.WelcomePaneBeanInfo
Return the method descriptors for this bean.
getModel() - Method in class jadex.swing.map.DisplayControl
Get the DisplayModel this control controlled.
getModel() - Method in class jadex.swing.map.LocusDisplay
Get the displaymodel.
getModel() - Method in class jadex.swing.sequence.SequenceDisplay
Get the sequence model.
getModel() - Method in class jadex.swing.ClassDisplayer
Get the ClassDisplayerModel.
getModel() - Method in class jadex.swing.ClassListDisplayer
Return the model property value.
getMouseAt() - Method in class jadex.swing.sequence.SequenceDisplay
Get the mouse position in bp unit
getMouseAt() - Method in class jadex.swing.sequence.SequenceLayoutModel
Get the current mouse position in bp unit
getMoveLeftAction() - Method in class jadex.swing.sequence.SequenceActions
Get the moveLeft Action.
getMoveRightAction() - Method in class jadex.swing.sequence.SequenceActions
Get the moveRight action.
getName() - Method in class jadex.swing.classView.SequenceMapView
Get the name of the Sequence_map displayed in the SequenceMapView.
getName() - Method in class jadex.swing.map.AbstractMapPoint
Get the name of this MapPoint.
getName() - Method in class jadex.swing.map.IntervalUI
Get the name of this intervalUI.
getName() - Method in class jadex.swing.map.Locus
Get the name of this Locus.
getName() - Method in class jadex.swing.map.LocusLayout
Get the name of this layout.
getName() - Method in class jadex.swing.map.LocusUI
Get the name for this display.
getName() - Method in interface jadex.swing.map.MapPoint
The name of the MapPoint.
getName() - Method in class jadex.swing.map.SmartLocusLayout
Get the specified name for this LocusLayout.
getName() - Method in class jadex.swing.sequence.AceDBCloneFetcher
Get the name of the displayed Sequence_map.
getName() - Method in class jadex.swing.sequence.Clone
Get the name of the clone.
getName() - Method in class jadex.swing.sequence.CloneUI
Get the name of the clone.
getName() - Method in class jadex.swing.sequence.Contig
Get the name of the contig.
getName() - Method in class jadex.swing.ClassDisplayer
Get the displayed class name.
getName() - Method in class jadex.swing.ClassListDisplayer
 
getName(Element) - Static method in class jadex.xml.XMLUtilities
Get the name of the sequence from its attribute.
getNameLayout() - Method in class jadex.swing.map.LocusDisplay
Get the Layout for Names.
getNameLayout() - Method in interface jadex.swing.map.MapPointDisplay
Get the layout name.
getNameLayout() - Method in class jadex.swing.sequence.CloneDisplay
Get the name layout used in this CloneDisplay.
getNameMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the getName() method descriptor.
getNames() - Method in class jadex.swing.AceDBFrame
Gets the names property (java.util.Vector) value.
getNamespace() - Method in interface jadex.swing.sequence.SequenceFetcher
The namespace of the root if any.
getNamespace() - Method in class jadex.swing.sequence.SequenceModel
Get the namespace of this document
getNamespace() - Method in class jadex.swing.sequence.SequenceXMLFetcher
The namespace of the root if any.
getNamespace() - Static method in class jadex.xml.XMLUtilities
Deprecated. please don't use this method anymore.
getNextButton() - Method in class jadex.swing.ClassListDisplayer
Return the JToolBarButton2 property value.
getObject() - Method in class jadex.swing.classView.ClassView
Get the displayed AceObject.
getObject() - Method in class jadex.swing.classView.DumpClassView
Get the AceObject displayed.
getObject() - Method in class jadex.swing.classView.MapView
Get the Aceobject displayed.
getObject() - Method in class jadex.swing.classView.SequenceMapView
Deprecated. the AceObject will be null.
getObject() - Method in class jadex.swing.classView.SequenceView
No aceobject anymore.
getObject() - Method in class jadex.swing.classView.TreeClassView
Get the displayed AceObject.
getObjectView() - Method in class jadex.swing.ObjectViewController
Based on the types of AceObject, privide different views of AceObjects.
getPageBox() - Method in class jadex.swing.ClassListDisplayer
Return the JComboBox1 property value.
getParent() - Method in class jadex.swing.sequence.SequenceTreeNode
Get the parent of this TreeNode.
getPMap() - Method in class jadex.swing.sequence.Contig
 
getPopup() - Method in class jadex.swing.map.LocusDisplay
Get the JPopupMenu used by this Display.
getPopup() - Method in class jadex.swing.sequence.CloneDisplay
Get the PopupMenu used in this CloneDisplay.
getPopup() - Method in class jadex.swing.sequence.SequenceDisplay
Expose the popup to the classes at the same package
getPosition() - Method in class jadex.swing.map.AbstractMapPoint
Get the position of this MapPoint.
getPosition() - Method in class jadex.swing.map.Locus
Get the position of this Locus.
getPosition() - Method in class jadex.swing.map.LocusUI
Get the position of the Locus.
getPosition() - Method in interface jadex.swing.map.MapPoint
Get the position of this MapPoint.
getPosition() - Method in class jadex.swing.sequence.Clone
Get the position of the clone.
getPositions(Element) - Static method in class jadex.xml.XMLUtilities
Get the position of the sequence element.
getPositions(Element, Namespace) - Static method in class jadex.xml.XMLUtilities
Get the position of the sequence element.
getPreferredScrollableViewportSize() - Method in class jadex.swing.sequence.SequenceDisplay
 
getPreferredSize() - Method in class jadex.swing.map.Knob
Get the size of this Knob.
getPreviouseButton() - Method in class jadex.swing.ClassListDisplayer
Return the JToolBarButton1 property value.
getPropertyChange() - Method in class jadex.swing.ClassListModel
Accessor for the propertyChange field.
getPropertyChange() - Method in class jadex.swing.ClassViewController
Accessor for the propertyChange field.
getPropertyDescriptors() - Method in class jadex.swing.AceDBFrameBeanInfo
Return the property descriptors for this bean.
getPropertyDescriptors() - Method in class jadex.swing.AceModelBeanInfo
Return the property descriptors for this bean.
getPropertyDescriptors() - Method in class jadex.swing.ClassDisplayerBeanInfo
Return the property descriptors for this bean.
getPropertyDescriptors() - Method in class jadex.swing.ClassListModelBeanInfo
Return the property descriptors for this bean.
getPropertyDescriptors() - Method in class jadex.swing.ClassViewControllerBeanInfo
Return the property descriptors for this bean.
getPropertyDescriptors() - Method in class jadex.swing.IndexSelectorBeanInfo
Return the property descriptors for this bean.
getPropertyDescriptors() - Method in class jadex.swing.ProgressPanelBeanInfo
Return the property descriptors for this bean.
getPropertyDescriptors() - Method in class jadex.swing.WelcomePaneBeanInfo
Return the property descriptors for this bean.
getRange() - Method in class jadex.swing.map.MapCartoon
Getter for property range.
getRange() - Method in class jadex.swing.map.MapControl
Getter for property range.
getRange() - Method in class jadex.swing.map.MapScale
Getter for property range.
getRange() - Method in class jadex.swing.map.MapScale1
Get the displayed MapRange.
getRange() - Method in class jadex.swing.map.MiniMapCartoon
Get the displayed MapRange.
getRange() - Method in class jadex.swing.sequence.HorizontalMapScale
Get the currently displayed MapRange.
getRangeFromPMap(MapRange) - Method in class jadex.swing.sequence.Contig
Transfer the PMap range to SequenceMap range.
getRenderer() - Method in class jadex.swing.sequence.SequenceDisplay
Get the sequence renderer.
getResetAction() - Method in class jadex.swing.sequence.SequenceActions
Get the Reset Action.
getRightEnd() - Method in class jadex.swing.map.MapRange
Get the right end of this maprange
getRoot() - Method in interface jadex.swing.sequence.SequenceFetcher
An xml root element: for a whole chromosome, this should be the chromsome element.
getRoot() - Method in class jadex.swing.sequence.SequenceModel
Get the root element.
getRoot() - Method in class jadex.swing.sequence.SequenceXMLFetcher
Get the root of the chromosome XML document.
getScrollableBlockIncrement(Rectangle, int, int) - Method in class jadex.swing.sequence.SequenceDisplay
 
getScrollableTracksViewportHeight() - Method in class jadex.swing.sequence.SequenceDisplay
Horizontal is always in a whole view
getScrollableTracksViewportWidth() - Method in class jadex.swing.sequence.SequenceDisplay
 
getScrollableUnitIncrement(Rectangle, int, int) - Method in class jadex.swing.sequence.SequenceDisplay
 
getSearchAction() - Method in class jadex.swing.sequence.SequenceActions
Get the search Action.
getSelected() - Method in class jadex.swing.sequence.SequenceSelectionModel
Return the selected or deselected element.
getSelectedElement() - Method in class jadex.swing.sequence.SequenceSelectionModel
Get the selected element.
getSelectedPage() - Method in class jadex.swing.ClassListMediator
Get the selected page.
getSelectedSequence() - Method in class jadex.swing.sequence.SequenceDisplay
Get the selected sequence element.
getSelectedSequences() - Method in class jadex.swing.sequence.SequenceDisplay
Get the selected sequence elemnet list.
getSelection() - Method in class jadex.swing.sequence.SequenceSelectionModel
Get the selected list
getSelectionModel() - Method in class jadex.swing.sequence.SequenceDisplay
Get the selectionModel used in this SequenceDisplay.
getSequence() - Method in class jadex.swing.sequence.SequenceSelectionEvent
Get the selected sequence.
getSequence() - Method in class jadex.swing.sequence.SequenceTreeNode
Get the wrapped sequence element.
getSequenceAndGeneBounds(Element, int, boolean) - Method in class jadex.swing.sequence.SequenceLayoutModel
Calculte a bounds for a sequence elemement containing a gene
getSequenceDisplay() - Method in class jadex.swing.sequence.SequenceViewFactory
Get the SequenceDisplay in this object.
getSequenceRenderer(Element, boolean, boolean) - Method in class jadex.swing.sequence.SequenceRenderer
An overloaded for get SequenceRenderer.
getSequenceRenderer(String, long, long, boolean, boolean) - Method in class jadex.swing.sequence.SequenceRenderer
Get the SequenceRenderer.
getSequences() - Method in class jadex.swing.sequence.SequenceSelectionEvent
For multiselection, get the selected sequences.
getSequenceView() - Method in class jadex.swing.sequence.SequenceElementTableView
Get this SequenceView.
getSequenceView() - Method in interface jadex.swing.sequence.SequenceElementView
Get the JComponent used to display the Sequence elemnet.
getShowNumber() - Method in class jadex.swing.map.DisplayControl
Get the number of shown LocusUI.
getShowNumber() - Method in class jadex.swing.map.LocusControl
The number of shown LocusUI.
getStart() - Method in class jadex.swing.map.IntervalUI
Get the start value.
getStart() - Method in class jadex.swing.map.MapRange
Get the start value.
getStartF() - Method in class jadex.swing.map.MapRange
Get the start value in float.
getStartingLabel() - Method in class jadex.swing.ClassListModel
 
getStartingLabelMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the getStartingLabel() method descriptor.
getSubSequences(Element) - Static method in class jadex.xml.XMLUtilities
Get the subsequences from a sequence element or a chromosome (root).
getSubSequences(Element, Namespace) - Static method in class jadex.xml.XMLUtilities
Get the subsequences from a sequenc element.
getTabbedPane() - Method in class jadex.swing.CategoryTreeSelectionListener
Export the JTabbedPane
getTable() - Method in class jadex.swing.sequence.SequenceElementTableView
Expose the table.
getTotalEntriesMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the getTotalEntries() method descriptor.
getTotalMapRange() - Method in class jadex.swing.map.DisplayControl
Get the total MapRange.
getTotalPage() - Method in class jadex.swing.ClassListDisplayer
 
getTotalShowNumber() - Method in class jadex.swing.map.DisplayControl
Get the TotalShowNumber in this displayed maprange.
getTree() - Method in class jadex.swing.sequence.SequenceTreeDisplay
Get the JTree displaying these sequence elements.
getTreeDisplay() - Method in class jadex.swing.sequence.SequenceViewFactory
Get the SequenceTreeDisplay in this object.
getUI() - Method in class jadex.swing.sequence.SequenceDisplay
Get the SequenceUI used in this SequenceDisplay.
getURL() - Method in class jadex.swing.map.LocusUI
Get the name of the url linking to the detailed information.
getValue() - Method in class jadex.swing.ProgressPanel
Method generated to support the promotion of the currentValue attribute.
getValueMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the getValue() method descriptor.
getVerticalPosition() - Method in class jadex.swing.map.LocusDisplay
Get the position of the Chromosome line.
getVerticalPosition() - Method in class jadex.swing.sequence.CloneDisplay
Get the position of the chromosome line.
getVerticalPosition() - Method in class jadex.swing.util.TestPanel
 
getVerticalPosition() - Method in interface jadex.swing.util.Zoomable
The vertical line position.
getView() - Method in class jadex.swing.classView.ClassView
Get the JComponent used to display the AceObject.
getView() - Method in class jadex.swing.classView.DumpClassView
Get the JComponent displaying the AceObject.
getView() - Method in class jadex.swing.classView.MapView
Get the JComponent for displaying the AceObject.
getView() - Method in class jadex.swing.classView.SequenceMapView
Get the JComponent displaying the AceObject.
getView() - Method in class jadex.swing.classView.SequenceView
Get the JComponent holding this SequenceView.
getView() - Method in class jadex.swing.classView.TreeClassView
Get the JComponent displaying this AceObject.
getViewFrame() - Method in class jadex.swing.classView.ClassView
Get a self-showable JFrame displaying the AceObject.
getViewFrame() - Method in class jadex.swing.classView.MapView
Get the JFrame holding all these displays.
getViewFrame() - Method in class jadex.swing.classView.SequenceMapView
Get the JFrame holding this SequenceMapView.
getViewFrame() - Method in class jadex.swing.classView.SequenceView
Override the super method.
getZoomAction() - Method in class jadex.swing.sequence.SequenceActions
Get the zoomAction.
getZoomInAction() - Method in class jadex.swing.sequence.SequenceActions
Get the zoomInAction.
getZoomOutAction() - Method in class jadex.swing.sequence.SequenceActions
Get the zoomOutAction.

H

height - Variable in class jadex.swing.sequence.SequenceLayoutModel
 
HelpPane - class jadex.swing.map.HelpPane.
This is a JEditorPane to display a help HTML file for the MapView.
HelpPane() - Constructor for class jadex.swing.map.HelpPane
Creates new HelpTextPane
HelpPane(boolean) - Constructor for class jadex.swing.map.HelpPane
Another constructor to be used in applet.
HIGHLIGHT_COLOR - Variable in class jadex.swing.map.DisplayControl
 
highLightColor - Variable in class jadex.swing.map.LocusDisplay
 
HorizontalMapScale - class jadex.swing.sequence.HorizontalMapScale.
A horizonal mapscale to show bp position on the sequence map.
HorizontalMapScale() - Constructor for class jadex.swing.sequence.HorizontalMapScale
Default constructor: create a horizontal mapscale
HorizontalMapScale(MapRange) - Constructor for class jadex.swing.sequence.HorizontalMapScale
Second constructor
HorizontalMiniMapCartoon - class jadex.swing.sequence.HorizontalMiniMapCartoon.
A minimapcartoon to show the position of the displaying region on the whole chromosome.
HorizontalMiniMapCartoon() - Constructor for class jadex.swing.sequence.HorizontalMiniMapCartoon
Creates new HorizontalMiniMapCartoon
horizontalZoom(int) - Method in class jadex.swing.map.IntervalContainer
Expand or shrink on the horizontal direction.
horizontalZoom(int) - Method in interface jadex.swing.map.MapZoom
 

I

IN_FOREGROUND_COLOR - Static variable in class jadex.swing.MouseSenser
 
indexPropertyDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the index property descriptor.
IndexSelector - class jadex.swing.IndexSelector.
The class is used to display the index all the displayed class.
IndexSelector() - Constructor for class jadex.swing.IndexSelector
Default constructor.
indexSelector1AddMouseListener_int_javaawteventMouseListenerMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the indexSelector1AddMouseListener(int, java.awt.event.MouseListener) method descriptor.
indexSelector1AddMouseListener_javaawteventMouseListenerMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the indexSelector1AddMouseListener(java.awt.event.MouseListener) method descriptor.
indexSelector1AddMouseListener(int, MouseListener) - Method in class jadex.swing.ClassDisplayer
 
indexSelector1AddMouseListener(MouseListener) - Method in class jadex.swing.ClassDisplayer
 
indexSelector1IndexPropertyDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the indexSelector1Index property descriptor.
IndexSelectorBeanInfo - class jadex.swing.IndexSelectorBeanInfo.
The bean information class for jadex.swing.IndexSelector.
IndexSelectorBeanInfo() - Constructor for class jadex.swing.IndexSelectorBeanInfo
 
IndividualSequenceView - class jadex.swing.sequence.IndividualSequenceView.
This class is used to link sequence to the Wormbase, http://www.wormbase.org, in an applet or application.
IndividualSequenceView() - Constructor for class jadex.swing.sequence.IndividualSequenceView
 
init() - Method in class jadex.swing.sequence.SequenceViewApplet
Initialization method to set up all layout
init() - Method in class jadex.swing.GeneticMapApplet
Creates new form GeneticMapApplet
installDefaults() - Method in class jadex.swing.sequence.SequenceUI
initialize default settings
installListeners() - Method in class jadex.swing.sequence.SequenceUI
initialize listeners
installUI(JComponent) - Method in class jadex.swing.sequence.SequenceUI
Actually, an initializion method, following the model of ListUI
intersect(IntervalUI) - Method in class jadex.swing.map.IntervalUI
Check if two intervals intersect.
intersect(MapRange) - Method in class jadex.swing.map.MapRange
Check if two mapranges intersect.
IntervalContainer - class jadex.swing.map.IntervalContainer.
A customized JPanel is used to hold all IntervalPanel, and can be displayed in the MapView.
IntervalContainer() - Constructor for class jadex.swing.map.IntervalContainer
Default constructor
IntervalContainer(MapRange) - Constructor for class jadex.swing.map.IntervalContainer
Another constructor with maprange as the argument.
IntervalPanel - class jadex.swing.map.IntervalPanel.
This customized JPanel is used to hold IntervalUIs in a vertical way.
IntervalPanel() - Constructor for class jadex.swing.map.IntervalPanel
Default constructor.
IntervalPanel(MapRange) - Constructor for class jadex.swing.map.IntervalPanel
Another constructor with maprange as its argument.
IntervalUI - class jadex.swing.map.IntervalUI.
A customized JComponent to display a Interval.
IntervalUI() - Constructor for class jadex.swing.map.IntervalUI
Default constructor.
IntervalUI(AceObject) - Constructor for class jadex.swing.map.IntervalUI
Constructor with interval (aceobject) as only argument.
IntervalUI(float, float, String) - Constructor for class jadex.swing.map.IntervalUI
Constructor with start, end values and name of interval.
IS_LOW - Variable in class jadex.swing.sequence.SequenceLayoutModel
 
IS_UP - Variable in class jadex.swing.sequence.SequenceLayoutModel
 
isApplet() - Method in class jadex.swing.classView.MapView
See if this MapView is in an applet or not.
isClone() - Method in class jadex.swing.map.LocusUI
Check if this UI for CloneUI.
isConnectShown() - Method in class jadex.swing.map.LocusDisplay
Get the flag of connecting lines.
isConnectShown() - Method in interface jadex.swing.map.MapPointDisplay
Get the status of the connecting lines.
isConnectShown() - Method in class jadex.swing.sequence.CloneDisplay
Get the status of the connecting lines.
isInApplet() - Method in class jadex.swing.sequence.SequenceActions
Query if in applet.
isLeaf() - Method in class jadex.swing.sequence.SequenceTreeNode
See if this TreeNode is a leaf.
isLeaf(Element) - Method in class jadex.swing.sequence.SequenceModel
Check if the element is a lead
isMultiSelected() - Method in class jadex.swing.sequence.SequenceSelectionEvent
Query if this event is used in multi-selection.
isOdd(Element) - Static method in class jadex.xml.XMLUtilities
See the position of the sequence element in the subsequenc list is Odd or even.
isSelected() - Method in class jadex.swing.sequence.SequenceSelectionEvent
Query if this event is used in selection.
itemStateChanged(ItemEvent) - Method in class jadex.swing.ClassListMediator
ItemSelectionListener method.

J

jadex.swing - package jadex.swing
 
jadex.swing.classView - package jadex.swing.classView
 
jadex.swing.map - package jadex.swing.map
 
jadex.swing.sequence - package jadex.swing.sequence
 
jadex.swing.util - package jadex.swing.util
 
jadex.xml - package jadex.xml
 
jButton1_ActionPerformed(ActionEvent) - Method in class jadex.swing.SearchPanel
All main behavoirs are located in this method.
JLabel1PropertyDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the JLabel1 property descriptor.
JLabel1SetText_javalangStringMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the JLabel1SetText(java.lang.String) method descriptor.
jTree2_MouseClickEvents1(MouseEvent) - Method in class jadex.swing.AceDBFrame
Comment

K

Knob - class jadex.swing.map.Knob.
A little ornamenet used in the vertical line for chromosome in LocusDisplay or CloneDisplay.
Knob() - Constructor for class jadex.swing.map.Knob
Default constructor.
Knob(DisplayControl) - Constructor for class jadex.swing.map.Knob
Overloaded constructor.

L

letterListPropertyDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the letterList property descriptor.
LineMouse - class jadex.swing.map.LineMouse.
Lighten up label and line when mouse is in.
LineMouse(LocusUI, MapPointDisplay) - Constructor for class jadex.swing.map.LineMouse
The sole construcotr.
link - Static variable in class jadex.swing.sequence.CloneFetcher
 
listPropertyDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the list property descriptor.
Locus - class jadex.swing.map.Locus.
An implementataion of MapPoint.
Locus() - Constructor for class jadex.swing.map.Locus
Default constructor.
Locus(AceObject) - Constructor for class jadex.swing.map.Locus
An overloaded constructor.
Locus(String, float) - Constructor for class jadex.swing.map.Locus
An overloaded construtor.
Locus(String, float, AceObject) - Constructor for class jadex.swing.map.Locus
An overloaded constructor.
Locus(String, float, float, AceObject) - Constructor for class jadex.swing.map.Locus
An overloaded constructor.
LocusControl - class jadex.swing.map.LocusControl.
This is a control class for LocusDisplay.
LocusControl() - Constructor for class jadex.swing.map.LocusControl
Default constructor.
LocusControl(DisplayModel) - Constructor for class jadex.swing.map.LocusControl
Overloaded constructor.
LocusControl(DisplayModel, LocusDisplay) - Constructor for class jadex.swing.map.LocusControl
overloaded constructor.
LocusControl(LocusDisplay) - Constructor for class jadex.swing.map.LocusControl
Overloaded constructor.
LocusDisplay - class jadex.swing.map.LocusDisplay.
An implementation of MapPointDisplay for displaying Loci.
LocusDisplay() - Constructor for class jadex.swing.map.LocusDisplay
This constructor can only be used by classes in the same package
LocusDisplay(MapRange) - Constructor for class jadex.swing.map.LocusDisplay
Initialize the total range by the constructor.
LocusLayout - class jadex.swing.map.LocusLayout.
Layout for distribute the loci on the locusdisplay.
LocusLayout(float, int, boolean, Color) - Constructor for class jadex.swing.map.LocusLayout
The only constructor.
LocusPanel - class jadex.swing.map.LocusPanel.
This is another way to display loci.
LocusPanel() - Constructor for class jadex.swing.map.LocusPanel
Default constructor.
LocusPanel(MapRange) - Constructor for class jadex.swing.map.LocusPanel
Overloaded constructor.
LocusShow - class jadex.swing.map.LocusShow.
The super class of locus display, and designed as a general locus disply model.
LocusShow() - Constructor for class jadex.swing.map.LocusShow
 
LocusUI - class jadex.swing.map.LocusUI.
This customized JLabel is for displaying Locus or Clone information.
LocusUI() - Constructor for class jadex.swing.map.LocusUI
Default constructor.
LocusUI(MapPoint) - Constructor for class jadex.swing.map.LocusUI
A overloaded constructor.
LocusUI(String, float) - Constructor for class jadex.swing.map.LocusUI
A overloaded constructor.

M

Magnifier - class jadex.swing.util.Magnifier.
A mouse listener and mousemotion listener to zoom a range in a JPanel.
Magnifier(Zoomable) - Constructor for class jadex.swing.util.Magnifier
constructor to initialize panel
main_javalangString__MethodDescriptor() - Method in class jadex.swing.AceDBFrameBeanInfo
Gets the main(java.lang.String[]) method descriptor.
main_javalangString__MethodDescriptor() - Method in class jadex.swing.AceModelBeanInfo
Gets the main(java.lang.String[]) method descriptor.
main_javalangString__MethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the main(java.lang.String[]) method descriptor.
main_javalangString__MethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the main(java.lang.String[]) method descriptor.
main_javalangString__MethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the main(java.lang.String[]) method descriptor.
main_javalangString__MethodDescriptor() - Method in class jadex.swing.WelcomePaneBeanInfo
Gets the main(java.lang.String[]) method descriptor.
main(String[]) - Static method in class jadex.swing.classView.MapView
A test method for this MapView.
main(String[]) - Static method in class jadex.swing.classView.MapViewContainer
A test method.
main(String[]) - Static method in class jadex.swing.classView.SequenceMapView
A test method.
main(String[]) - Static method in class jadex.swing.classView.SequenceView
A test method.
main(String[]) - Static method in class jadex.swing.map.ControlPanel
 
main(String[]) - Static method in class jadex.swing.map.IntervalContainer
 
main(String[]) - Static method in class jadex.swing.map.LocusDisplay
 
main(String[]) - Static method in class jadex.swing.map.MapCartoon
 
main(String[]) - Static method in class jadex.swing.map.MapMenuBar
 
main(String[]) - Static method in class jadex.swing.map.RangeControlPanel
 
main(String[]) - Static method in class jadex.swing.map.ZoomButtonControl
A test method.
main(String[]) - Static method in class jadex.swing.sequence.AceDBCloneFetcher
 
main(String[]) - Static method in class jadex.swing.sequence.CloneDisplay
 
main(String[]) - Static method in class jadex.swing.sequence.CloneUI
 
main(String[]) - Static method in class jadex.swing.sequence.FileCloneFetcher
 
main(String[]) - Static method in class jadex.swing.sequence.HorizontalMapScale
 
main(String[]) - Static method in class jadex.swing.sequence.RangeSpecifyDialog
 
main(String[]) - Static method in class jadex.swing.sequence.SequenceDisplay
 
main(String[]) - Static method in class jadex.swing.sequence.SequenceTreeDisplay
 
main(String[]) - Static method in class jadex.swing.sequence.SequenceViewApplet
 
main(String[]) - Static method in class jadex.swing.util.TestPanel
 
main(String[]) - Static method in class jadex.swing.AceDBFrame
main entrypoint - starts the part when it is run as an application
main(String[]) - Static method in class jadex.swing.AceModel
Starts the application.
main(String[]) - Static method in class jadex.swing.ClassDisplayer
main entrypoint - starts the part when it is run as an application
main(String[]) - Static method in class jadex.swing.ClassListDisplayer
main entrypoint - starts the part when it is run as an application
main(String[]) - Static method in class jadex.swing.GeneticMapApplet
 
main(String[]) - Static method in class jadex.swing.IndexSelector
This method was created in VisualAge.
main(String[]) - Static method in class jadex.swing.ProgressPanel
main entrypoint - starts the part when it is run as an application
main(String[]) - Static method in class jadex.swing.SearchPanel
main entrypoint - starts the part when it is run as an application
main(String[]) - Static method in class jadex.swing.ViewSettingPanel
 
main(String[]) - Static method in class jadex.swing.WelcomePane
main entrypoint - starts the part when it is run as an application
main(String[]) - Static method in class jadex.xml.GeneTransform
 
main(String[]) - Static method in class jadex.xml.SequenceMapXMLDump
A tester
main(String[]) - Static method in class jadex.xml.XMLParserAndValidation
 
main(String[]) - Static method in class jadex.xml.XMLParserDemo
 
MapCartoon - class jadex.swing.map.MapCartoon.
This customized JPanel is used to show the displayed region on the chromosome.
MapCartoon() - Constructor for class jadex.swing.map.MapCartoon
Creates new MapCartoon
MapCartoon(float) - Constructor for class jadex.swing.map.MapCartoon
An overloaded constructor.
MapCartoon(long) - Constructor for class jadex.swing.map.MapCartoon
An overloaded constructor.
MapCartoon(MapRange) - Constructor for class jadex.swing.map.MapCartoon
An overloaded constructor.
MapControl - class jadex.swing.map.MapControl.
This is a invisible mediator to coordinate all zooming tools in a MapView or SequenceMapView.
MapControl() - Constructor for class jadex.swing.map.MapControl
Creates new MapControl
MapControl(MapRange) - Constructor for class jadex.swing.map.MapControl
An overloaded constructor.
MapMenuBar - class jadex.swing.map.MapMenuBar.
A customized JMenuBar used in a MapView.
MapMenuBar(JFrame) - Constructor for class jadex.swing.map.MapMenuBar
An overloaded constructor.
MapMenuBar(JInternalFrame) - Constructor for class jadex.swing.map.MapMenuBar
Creates new MapMenuBar.
MapMenuBar(MapView) - Constructor for class jadex.swing.map.MapMenuBar
An overloaded constructor.
MapPoint - interface jadex.swing.map.MapPoint.
This is the specification for objects which can be displayed in the LocusDisplay.
MapPointDisplay - interface jadex.swing.map.MapPointDisplay.
This is the specification of a MapPointDisplay.
MapRange - class jadex.swing.map.MapRange.
This is a utility class for storing the positions of the MapPoint, and processing the range calculations.
MapRange() - Constructor for class jadex.swing.map.MapRange
Default constructor
MapRange(float, float) - Constructor for class jadex.swing.map.MapRange
MapRange with float point numbers will be used in GeneticMap.
MapRange(long, long) - Constructor for class jadex.swing.map.MapRange
MapRange with integer numbers will be used in SequenceMap and PhysicalMap.
MapRange(String, String) - Constructor for class jadex.swing.map.MapRange
Construct a maprange with String arguments.
MapScale - class jadex.swing.map.MapScale.
This customized JSlider is used for the ruling of the MapRange in the MapView.
MapScale() - Constructor for class jadex.swing.map.MapScale
Creates new MapScale
MapScale1 - class jadex.swing.map.MapScale1.
A customized JPanel for the ruler of MapRange in a MapView.
MapScale1() - Constructor for class jadex.swing.map.MapScale1
Default constructor.
MapScale1(MapRange) - Constructor for class jadex.swing.map.MapScale1
An overloaded constructor.
MapView - class jadex.swing.classView.MapView.
This MapView is used to display Genetic_map.
MapView() - Constructor for class jadex.swing.classView.MapView
Default constructor.
MapView(AceObject) - Constructor for class jadex.swing.classView.MapView
An overloaded constructor.
MapView(AceObject, Applet) - Constructor for class jadex.swing.classView.MapView
Another constructor for applet
MapViewContainer - class jadex.swing.classView.MapViewContainer.
A JFrame as a container for both genetic and sequence map views.
MapViewContainer() - Constructor for class jadex.swing.classView.MapViewContainer
Default constructor
MapViewContainer(String) - Constructor for class jadex.swing.classView.MapViewContainer
Second construcotr with title as the argument
MapViewContainerMenuBar - class jadex.swing.classView.MapViewContainerMenuBar.
This is a JMenubar for MapViewContainer.
MapViewContainerMenuBar() - Constructor for class jadex.swing.classView.MapViewContainerMenuBar
Default constructor
MapViewContainerMenuBar(MapViewContainer) - Constructor for class jadex.swing.classView.MapViewContainerMenuBar
An overloaded constructor.
MapZoom - interface jadex.swing.map.MapZoom.
This is the specificaton for horizontal and vertical zooming.
maximumPropertyDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the maximum property descriptor.
messagePropertyDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the message property descriptor.
messagePropertyDescriptor() - Method in class jadex.swing.WelcomePaneBeanInfo
Gets the message property descriptor.
MiniMapCartoon - class jadex.swing.map.MiniMapCartoon.
A customized JPanel to display the zoomed region in the full chromosome.
MiniMapCartoon(MapRange) - Constructor for class jadex.swing.map.MiniMapCartoon
Creates new MiniMapCartoon.
mouseClicked(MouseEvent) - Method in class jadex.swing.map.Knob
 
mouseClicked(MouseEvent) - Method in class jadex.swing.map.IntervalContainer
Do nothing.
mouseClicked(MouseEvent) - Method in class jadex.swing.map.IntervalUI
For detailed information display.
mouseClicked(MouseEvent) - Method in class jadex.swing.map.LocusDisplay
Do nothing.
mouseClicked(MouseEvent) - Method in class jadex.swing.map.LocusUI
Do nothing.
mouseClicked(MouseEvent) - Method in class jadex.swing.map.MapCartoon
Do nothing here.
mouseClicked(MouseEvent) - Method in class jadex.swing.sequence.CloneDisplay
Do nothing.
mouseClicked(MouseEvent) - Method in class jadex.swing.sequence.CloneUI
 
mouseClicked(MouseEvent) - Method in class jadex.swing.util.Magnifier
Zooming in the drawn rectangle by clicking mouse.
mouseClicked(MouseEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the MouseListener interface.
mouseClicked(MouseEvent) - Method in class jadex.swing.ClassViewController
 
mouseClicked(MouseEvent) - Method in class jadex.swing.ObjectLabel
 
mouseDragged(MouseEvent) - Method in class jadex.swing.map.LocusDisplay
Do nothing.
mouseDragged(MouseEvent) - Method in class jadex.swing.map.MapCartoon
Zooming by creating rectangels.
mouseDragged(MouseEvent) - Method in class jadex.swing.util.Magnifier
Create a rectangle by mouse dragging.
mouseEntered(MouseEvent) - Method in class jadex.swing.map.Knob
 
mouseEntered(MouseEvent) - Method in class jadex.swing.map.IntervalContainer
Do nothing.
mouseEntered(MouseEvent) - Method in class jadex.swing.map.IntervalUI
For color change.
mouseEntered(MouseEvent) - Method in class jadex.swing.map.LineMouse
When Mouse eneters, set up the name of the LocusUI.
mouseEntered(MouseEvent) - Method in class jadex.swing.map.LocusDisplay
Do nothing.
mouseEntered(MouseEvent) - Method in class jadex.swing.map.LocusUI
Change color when mouse enters.
mouseEntered(MouseEvent) - Method in class jadex.swing.map.MapCartoon
Do nothing here.
mouseEntered(MouseEvent) - Method in class jadex.swing.sequence.CloneDisplay
Do nothing.
mouseEntered(MouseEvent) - Method in class jadex.swing.sequence.CloneUI
 
mouseEntered(MouseEvent) - Method in class jadex.swing.util.Magnifier
Do nothing.
mouseEntered(MouseEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the MouseListener interface.
mouseEntered(MouseEvent) - Method in class jadex.swing.ClassViewController
 
mouseEntered(MouseEvent) - Method in class jadex.swing.MouseSenser
MouseSenser constructor comment.
mouseEntered(MouseEvent) - Method in class jadex.swing.ObjectLabel
 
mouseExited(MouseEvent) - Method in class jadex.swing.map.Knob
 
mouseExited(MouseEvent) - Method in class jadex.swing.map.IntervalContainer
Do nothing.
mouseExited(MouseEvent) - Method in class jadex.swing.map.IntervalUI
 
mouseExited(MouseEvent) - Method in class jadex.swing.map.LineMouse
When Mouse exits, remove the selected name of the LocusUI.
mouseExited(MouseEvent) - Method in class jadex.swing.map.LocusDisplay
Do nothing.
mouseExited(MouseEvent) - Method in class jadex.swing.map.LocusUI
Change color when mouse exits.
mouseExited(MouseEvent) - Method in class jadex.swing.map.MapCartoon
Do nothing.
mouseExited(MouseEvent) - Method in class jadex.swing.sequence.CloneDisplay
 
mouseExited(MouseEvent) - Method in class jadex.swing.sequence.CloneUI
 
mouseExited(MouseEvent) - Method in class jadex.swing.util.Magnifier
Do nothing.
mouseExited(MouseEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the MouseListener interface.
mouseExited(MouseEvent) - Method in class jadex.swing.ClassViewController
 
mouseExited(MouseEvent) - Method in class jadex.swing.MouseSenser
MouseSenser constructor comment.
mouseExited(MouseEvent) - Method in class jadex.swing.ObjectLabel
 
mouseIn - Variable in class jadex.swing.map.Knob
 
mouseMoved(MouseEvent) - Method in class jadex.swing.map.LocusDisplay
Do nothing.
mouseMoved(MouseEvent) - Method in class jadex.swing.map.MapCartoon
Do nothing.
mouseMoved(MouseEvent) - Method in class jadex.swing.util.Magnifier
Detecting is mouse is in the drawn rectangle by mouse moving.
mousePressed(MouseEvent) - Method in class jadex.swing.map.Knob
 
mousePressed(MouseEvent) - Method in class jadex.swing.map.IntervalContainer
Showing popup.
mousePressed(MouseEvent) - Method in class jadex.swing.map.IntervalUI
For popupmenu showing up.
mousePressed(MouseEvent) - Method in class jadex.swing.map.LocusDisplay
Showing popup menu.
mousePressed(MouseEvent) - Method in class jadex.swing.map.LocusUI
Linking to the detailed information by using this method.
mousePressed(MouseEvent) - Method in class jadex.swing.map.MapCartoon
Start up the zooming.
mousePressed(MouseEvent) - Method in class jadex.swing.sequence.CloneDisplay
Show popup menu.
mousePressed(MouseEvent) - Method in class jadex.swing.sequence.CloneUI
 
mousePressed(MouseEvent) - Method in class jadex.swing.util.Magnifier
Do nothing.
mousePressed(MouseEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the MouseListener interface.
mousePressed(MouseEvent) - Method in class jadex.swing.ClassViewController
 
mousePressed(MouseEvent) - Method in class jadex.swing.ObjectLabel
 
mouseReleased(MouseEvent) - Method in class jadex.swing.map.Knob
 
mouseReleased(MouseEvent) - Method in class jadex.swing.map.IntervalContainer
For popup pop.
mouseReleased(MouseEvent) - Method in class jadex.swing.map.IntervalUI
For popupmenu showing up.
mouseReleased(MouseEvent) - Method in class jadex.swing.map.LocusDisplay
Showing popup menu.
mouseReleased(MouseEvent) - Method in class jadex.swing.map.LocusUI
Do nothing.
mouseReleased(MouseEvent) - Method in class jadex.swing.map.MapCartoon
End the zooming.
mouseReleased(MouseEvent) - Method in class jadex.swing.sequence.CloneDisplay
Show popup menu.
mouseReleased(MouseEvent) - Method in class jadex.swing.sequence.CloneUI
 
mouseReleased(MouseEvent) - Method in class jadex.swing.util.Magnifier
Do nothing.
mouseReleased(MouseEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the MouseListener interface.
mouseReleased(MouseEvent) - Method in class jadex.swing.ClassViewController
 
mouseReleased(MouseEvent) - Method in class jadex.swing.ObjectLabel
 
MouseSenser - class jadex.swing.MouseSenser.
This class is used to lighten up the label when mouse is in.
MouseSenser() - Constructor for class jadex.swing.MouseSenser
Default constructor.
MouseSenser(JComponent) - Constructor for class jadex.swing.MouseSenser
An overloaded constructor.
moveDown(int) - Method in class jadex.swing.map.MapRange
Move the current range to the lower direction.
moveLeft() - Method in class jadex.swing.sequence.SequenceLayoutModel
Moving the current range to the left
moveRight() - Method in class jadex.swing.sequence.SequenceLayoutModel
Moving the current range to the right
moveUp(int) - Method in class jadex.swing.map.MapRange
Move the current range to the up direction.
moving() - Method in class jadex.swing.map.Knob
 
moving() - Method in class jadex.swing.map.DownKnob
Move down the range.
moving() - Method in class jadex.swing.map.UpKnob
Move up the range.
movingDown() - Method in class jadex.swing.map.DisplayControl
Moving down the displayed range by knob.
movingDown() - Method in class jadex.swing.map.MapControl
Moving up the maprange.
movingUp() - Method in class jadex.swing.map.DisplayControl
Moving up the displayed range by knob.
movingUp() - Method in class jadex.swing.map.MapControl
Moving down the maprange.

N

NAME_SPACE - Static variable in class jadex.xml.SequenceMapXMLDump
 
namePropertyDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the name property descriptor.
namePropertyDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the name property descriptor.
namesPropertyDescriptor() - Method in class jadex.swing.AceDBFrameBeanInfo
Gets the names property descriptor.
nColor - Variable in class jadex.swing.map.LocusDisplay
 
NORMAL_COLOR - Variable in class jadex.swing.map.DisplayControl
 
NUMBER_PER_COLUMN - Static variable in class jadex.swing.map.DisplayControl
 

O

ObjectLabel - class jadex.swing.ObjectLabel.
A JLabel used to display the name of the AceObjects.
ObjectLabel(AceObject) - Constructor for class jadex.swing.ObjectLabel
ObjectLabel constructor comment.
ObjectLabel(String) - Constructor for class jadex.swing.ObjectLabel
An overloaded construtor.
ObjectViewController - class jadex.swing.ObjectViewController.
This class is used to control the display for individual AceObject.
ObjectViewController() - Constructor for class jadex.swing.ObjectViewController
Default constructor.
ObjectViewController(AceObject) - Constructor for class jadex.swing.ObjectViewController
A overloaded construcotr.
OpenFileAction - class jadex.swing.map.OpenFileAction.
This ActionListener is used to open a genetic_map file in the MapView menubar.
OpenFileAction() - Constructor for class jadex.swing.map.OpenFileAction
Creates new OpenFileAction
OpenFileAction(JFrame, MapView) - Constructor for class jadex.swing.map.OpenFileAction
An overloaded constructor.
OpenFrames - class jadex.swing.OpenFrames.
A singleton to control the individual AceObject displaying.
OpenFrames() - Constructor for class jadex.swing.OpenFrames
OpenFrames constructor comment.
OUT_FOREGROUND_COLOR - Static variable in class jadex.swing.MouseSenser
 
output(OutputStream) - Method in class jadex.xml.SequenceMapXMLDump
 
output(String) - Method in class jadex.xml.SequenceMapXMLDump
A utility to print out document at any time
outputSequenceList(List) - Method in class jadex.swing.sequence.SequenceLayoutModel
An convient method to output a sequence element list

P

paint(Graphics, JComponent) - Method in class jadex.swing.sequence.SequenceUI
Most of render activities are here
paintComponent(Graphics) - Method in class jadex.swing.map.DownKnob
Override the superclass' method.
paintComponent(Graphics) - Method in class jadex.swing.map.IntervalPanel
GUI painting.
paintComponent(Graphics) - Method in class jadex.swing.map.IntervalUI
 
paintComponent(Graphics) - Method in class jadex.swing.map.LocusDisplay
All painting activities are here.
paintComponent(Graphics) - Method in class jadex.swing.map.LocusPanel
 
paintComponent(Graphics) - Method in class jadex.swing.map.MapCartoon
The most important method.
paintComponent(Graphics) - Method in class jadex.swing.map.MapScale1
 
paintComponent(Graphics) - Method in class jadex.swing.map.MiniMapCartoon
 
paintComponent(Graphics) - Method in class jadex.swing.map.UpKnob
All paint activities.
paintComponent(Graphics) - Method in class jadex.swing.sequence.CloneDisplay
The most important method in this class.
paintComponent(Graphics) - Method in class jadex.swing.sequence.CloneUI
 
paintComponent(Graphics) - Method in class jadex.swing.sequence.GeneRenderer
All draw activites are here
paintComponent(Graphics) - Method in class jadex.swing.sequence.HorizontalMapScale
The most important method in this class.
paintComponent(Graphics) - Method in class jadex.swing.sequence.HorizontalMiniMapCartoon
 
paintComponent(Graphics) - Method in class jadex.swing.sequence.SequenceRenderer
 
paintComponent(Graphics) - Method in class jadex.swing.util.TestPanel
 
paintSelectedSequence(Element) - Method in class jadex.swing.sequence.SequenceUI
Paint a specfic sequence from outside of paint method, and is usually is called by some event listeners.
paintSequence(Graphics, SequenceRenderer, Element, int, boolean, List) - Method in class jadex.swing.sequence.SequenceUI
 
paintSequence(Graphics, SequenceRenderer, Element, List) - Method in class jadex.swing.sequence.SequenceUI
 
paintSingleSequence(Graphics, SequenceRenderer, Element, int, boolean, List) - Method in class jadex.swing.sequence.SequenceUI
 
parse(String, boolean) - Method in class jadex.xml.XMLParserDemo
parse with/out validataion
pattern - Variable in class jadex.swing.map.DisplayControl
 
patterns - Variable in class jadex.swing.map.DisplayControl
 
processFile(File) - Method in class jadex.swing.map.OpenFileAction
Processing the file
processMouseEvent(MouseEvent) - Method in class jadex.swing.ObjectLabel
This method was created in VisualAge.
ProgressPanel - class jadex.swing.ProgressPanel.
A JPanel to show the downloading progress.
ProgressPanel() - Constructor for class jadex.swing.ProgressPanel
Constructor
ProgressPanelBeanInfo - class jadex.swing.ProgressPanelBeanInfo.
The bean information class for jadex.swing.ProgressPanel.
ProgressPanelBeanInfo() - Constructor for class jadex.swing.ProgressPanelBeanInfo
 
progressPanelCancellactionPerformed_javautilEventObjectMethodEventDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the progressPanel.CancellactionPerformed(java.util.EventObject) method descriptor.
progressPanelEventSetDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the progressPanel event set descriptor.
ProgressPanelListener - interface jadex.swing.ProgressPanelListener.
An interface for controlling the ProgressPanel.
ProgressPanelListenerEventMulticaster - class jadex.swing.ProgressPanelListenerEventMulticaster.
This is the event multicaster class to support the jadex.swing.ProgressPanelListenerEventMulticaster interface.
ProgressPanelListenerEventMulticaster(ProgressPanelListener, ProgressPanelListener) - Constructor for class jadex.swing.ProgressPanelListenerEventMulticaster
Constructor to support multicast events.
propertyChange - Variable in class jadex.swing.ClassViewController
 
propertyChange - Variable in class jadex.swing.WelcomePane
 
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.map.DisplayControl
PropertyChangeListener method: for zoom property fired by mapcontrol
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.map.IntervalContainer
Property change listener for range property.
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.map.LocusShow
Used as a maprange change listener.
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.map.MapCartoon
Listening to the Range property change.
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.map.MapScale
 
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.map.MapScale1
Listening to the Range propety change.
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.map.MiniMapCartoon
Listen to the Range property change.
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.sequence.HorizontalMapScale
ProertyChangeListener method
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.sequence.HorizontalMiniMapCartoon
 
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.AceDBFrame
 
propertyChange(PropertyChangeEvent) - Method in class jadex.swing.ClassListDisplayer
Method to handle events for the PropertyChangeListener interface.
propertyChangeEventSetDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the propertyChange event set descriptor.
propertyChangepropertyChange_javabeansPropertyChangeEventMethodEventDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the propertyChange.propertyChange(java.beans.PropertyChangeEvent) method descriptor.

R

RangeControlPanel - class jadex.swing.map.RangeControlPanel.
This customized JPanel is used to set the displayed MapRange, i.e., zooming function.
RangeControlPanel() - Constructor for class jadex.swing.map.RangeControlPanel
Creates new form RangeControlPanel
RangeSpecifyDialog - class jadex.swing.sequence.RangeSpecifyDialog.
A customized JDialog to specify a MapRange for the SequenceView.
RangeSpecifyDialog(Frame, boolean) - Constructor for class jadex.swing.sequence.RangeSpecifyDialog
Creates new form RangeSpecifyDialog
relayout() - Method in class jadex.swing.sequence.SequenceLayoutModel
Do some initialization layout calculation
remove(ProgressPanelListener, ProgressPanelListener) - Static method in class jadex.swing.ProgressPanelListenerEventMulticaster
Remove listener to support multicast events.
removeFrame(String) - Method in class jadex.swing.OpenFrames
Remove the JFrame with title title.
removeMouseListener_int_javaawteventMouseListenerMethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the removeMouseListener(int, java.awt.event.MouseListener) method descriptor.
removeMouseListener_javaawteventMouseListenerMethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the removeMouseListener(java.awt.event.MouseListener) method descriptor.
removeMouseListener(int, MouseListener) - Method in class jadex.swing.IndexSelector
 
removeMouseListener(MouseListener) - Method in class jadex.swing.IndexSelector
 
removePanels() - Method in class jadex.swing.classView.MapViewContainer
Remove all displayed panels.
removeProgressPanelListener_jadexswingProgressPanelListenerMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the removeProgressPanelListener(jadex.swing.ProgressPanelListener) method descriptor.
removeProgressPanelListener(ProgressPanelListener) - Method in class jadex.swing.ProgressPanel
 
removePropertyChangeListener_javabeansPropertyChangeListenerMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the removePropertyChangeListener(java.beans.PropertyChangeListener) method descriptor.
removePropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.map.MapControl
Removes a PropertyChangeListener from the listener list.
removePropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.sequence.RangeSpecifyDialog
Remove propertychangelistener
removePropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.ClassListModel
The removePropertyChangeListener method was generated to support the propertyChange field.
removePropertyChangeListener(PropertyChangeListener) - Method in class jadex.swing.ClassViewController
The removePropertyChangeListener method was generated to support the propertyChange field.
removeSelectionListener(SequenceSelectionListener) - Method in class jadex.swing.sequence.SequenceSelectionModel
Unregister a selection listener
removeViewItem(String) - Method in class jadex.swing.classView.MapViewContainerMenuBar
Remove the view Item from the View MenuItem.
removeViewItems() - Method in class jadex.swing.classView.MapViewContainerMenuBar
Remove all menuitems except left and right mapscales
repaint() - Method in interface jadex.swing.util.Zoomable
Repaint to show the zoom rectangels.
reset() - Method in class jadex.swing.map.DisplayControl
Reset to the whole chromosome range.
reset() - Method in class jadex.swing.map.MapControl
Reset to the full MapRange.
reset() - Method in class jadex.swing.sequence.SequenceLayoutModel
Reset the maprange to the whole chromosome
resetBackground() - Method in class jadex.swing.map.IntervalPanel
Reset the background of each intervalUI to black.
resetBackground() - Method in class jadex.swing.map.IntervalUI
Reset the background to black.
resetUI() - Method in class jadex.swing.map.DisplayControl
UI should be reset after total points or showing points in range have been changed.
resetUI() - Method in class jadex.swing.map.LocusControl
Reset UI whenever the MapRange changed.
resetUI() - Method in class jadex.swing.sequence.CloneControl
UI should be reset after total points or showing points in range have been changed.
ROOT_NAME - Static variable in class jadex.xml.SequenceMapXMLDump
 

S

search(String) - Method in class jadex.swing.classView.SequenceView
Search a sequence object in the displayed chromosome.
search(String) - Method in class jadex.swing.sequence.SequenceDisplay
Search a sequence element with the name of name.
search(String) - Method in class jadex.swing.sequence.SequenceModel
Search a specific sequence element by its name.
search(String) - Method in class jadex.swing.sequence.SequenceViewFactory
Search a sequence element in the display
search(String, String) - Method in class jadex.swing.classView.MapView
Search Intercal or Locus by their names.
search(String, String) - Method in class jadex.swing.classView.SequenceMapView
Search a clone displayed in this SequenceMapView.
searchElement(int[], long) - Method in class jadex.swing.sequence.SequenceLayoutModel
Find an element based on box number and base pain positin on the chromosome.
SearchPanel - class jadex.swing.SearchPanel.
This class is used to search AceObject from AceDB.
SearchPanel() - Constructor for class jadex.swing.SearchPanel
Constructor
SequenceActions - class jadex.swing.sequence.SequenceActions.
This is the central repository to handle all actions in the whole Sequence Display.
SequenceDisplay - class jadex.swing.sequence.SequenceDisplay.
SequenceDisplay.java: Graphics Sequence display designed based on Swing MVC model and renderer method.
SequenceDisplay() - Constructor for class jadex.swing.sequence.SequenceDisplay
Default constructor
SequenceDisplay(SequenceModel) - Constructor for class jadex.swing.sequence.SequenceDisplay
Second constructor.
SequenceDisplayAndTreeAdapter - class jadex.swing.sequence.SequenceDisplayAndTreeAdapter.
An adapter to connect the selections of SequenceDisplay and SequenceTreeDisplay.
SequenceDisplayAndTreeAdapter(SequenceDisplay, SequenceTreeDisplay) - Constructor for class jadex.swing.sequence.SequenceDisplayAndTreeAdapter
Constructor
SequenceElementTableView - class jadex.swing.sequence.SequenceElementTableView.
This customized JPanel is used to display some more information for individual sequence element.
SequenceElementTableView() - Constructor for class jadex.swing.sequence.SequenceElementTableView
Creates new SequenceElementTableView
SequenceElementTableView(Element) - Constructor for class jadex.swing.sequence.SequenceElementTableView
Second constructor
SequenceElementView - interface jadex.swing.sequence.SequenceElementView.
This is the specificatio for individual Sequence element view.
SequenceFetcher - interface jadex.swing.sequence.SequenceFetcher.
This is the interface defining a specification for fetching data for SequenceView.
SequenceLayoutModel - class jadex.swing.sequence.SequenceLayoutModel.
This class is used to transform bp coordinate on the chromosome to the graphics coordinate, and the zoom and some layout processing.
SequenceLayoutModel() - Constructor for class jadex.swing.sequence.SequenceLayoutModel
Creates new SequenceLayoutCalculator
SequenceLayoutModel(int, SequenceDisplay) - Constructor for class jadex.swing.sequence.SequenceLayoutModel
Third constructor with a layer as a argument
SequenceLayoutModel(SequenceDisplay) - Constructor for class jadex.swing.sequence.SequenceLayoutModel
Second constructor with display as the argument
SequenceMapApplet - class jadex.swing.sequence.SequenceMapApplet.
This applet is used to launch the Sequnce_map View in an applet.
SequenceMapApplet() - Constructor for class jadex.swing.sequence.SequenceMapApplet
Creates new form SequenceMapApplet
SequenceMapView - class jadex.swing.classView.SequenceMapView.
All object views should be a subclss of classView
SequenceMapView() - Constructor for class jadex.swing.classView.SequenceMapView
Default constructor
SequenceMapView(String) - Constructor for class jadex.swing.classView.SequenceMapView
An overloaded constructor with name as the Argument.
SequenceMapView(String, Applet) - Constructor for class jadex.swing.classView.SequenceMapView
An overloaded constructor.
SequenceMapXMLDump - class jadex.xml.SequenceMapXMLDump.
 
SequenceMapXMLDump() - Constructor for class jadex.xml.SequenceMapXMLDump
Default constructor: Creates new SequenceMapXMLDump
SequenceMapXMLDump(String) - Constructor for class jadex.xml.SequenceMapXMLDump
Second constructor: Based on the name of the chromosome
SequenceMapXMLDump(String, int, boolean) - Constructor for class jadex.xml.SequenceMapXMLDump
Third constructor: provide the acedb server name and port number
SequenceMapXMLDump(String, String, int, boolean) - Constructor for class jadex.xml.SequenceMapXMLDump
Fourth constructor: Name and Acedb information as the argument
SequenceModel - class jadex.swing.sequence.SequenceModel.
This is the data model for SequenceDisplay.
SequenceModel() - Constructor for class jadex.swing.sequence.SequenceModel
Default constructor
SequenceModel(SequenceFetcher) - Constructor for class jadex.swing.sequence.SequenceModel
Second constructor
SequenceRenderer - class jadex.swing.sequence.SequenceRenderer.
This customized JPanel is used for rendering the Sequence elemnet in the SequenceDisplay.
SequenceRenderer() - Constructor for class jadex.swing.sequence.SequenceRenderer
Creates new SequenceRenderer
SequenceSelectionEvent - class jadex.swing.sequence.SequenceSelectionEvent.
A sequence selection event object.
SequenceSelectionEvent(Object, Element, boolean) - Constructor for class jadex.swing.sequence.SequenceSelectionEvent
Creates new SequenceSelectionEvent
SequenceSelectionEvent(Object, List, boolean) - Constructor for class jadex.swing.sequence.SequenceSelectionEvent
Second constructor
SequenceSelectionListener - interface jadex.swing.sequence.SequenceSelectionListener.
This is the EventListener all classes are interested in Sequence Selection should implement.
SequenceSelectionModel - class jadex.swing.sequence.SequenceSelectionModel.
This class processes and stores selections of sequnce on the sequence display.
SequenceSelectionModel() - Constructor for class jadex.swing.sequence.SequenceSelectionModel
Creates new SequenceSelectionModel
SequenceTreeDisplay - class jadex.swing.sequence.SequenceTreeDisplay.
Display a sequence in a JTree based on an xml document or element.
SequenceTreeDisplay() - Constructor for class jadex.swing.sequence.SequenceTreeDisplay
Creates new SequenceTreeDisplay
SequenceTreeNode - class jadex.swing.sequence.SequenceTreeNode.
A customized TreeNode used in SequenceTreeDisplay by using JDOM element.
SequenceTreeNode() - Constructor for class jadex.swing.sequence.SequenceTreeNode
Creates new SequenceTreeNode
SequenceTreeNode(Element) - Constructor for class jadex.swing.sequence.SequenceTreeNode
Second construcor
SequenceUI - class jadex.swing.sequence.SequenceUI.
A customized ComponentUI for processing SequenceDispay activities.
SequenceUI() - Constructor for class jadex.swing.sequence.SequenceUI
Default constructor
SequenceView - class jadex.swing.classView.SequenceView.
A Sequence graphics view for chromosome and other sequence objects
SequenceView() - Constructor for class jadex.swing.classView.SequenceView
Creates new SequenceView
SequenceView(String) - Constructor for class jadex.swing.classView.SequenceView
Second constructor
SequenceViewApplet - class jadex.swing.sequence.SequenceViewApplet.
The applet for displaying a SequenceView in the browser.
SequenceViewApplet() - Constructor for class jadex.swing.sequence.SequenceViewApplet
 
SequenceViewFactory - class jadex.swing.sequence.SequenceViewFactory.
This class is used to set up all GUIs for Sequence View in a JFrame or JApplet.
SequenceViewFactory(JApplet) - Constructor for class jadex.swing.sequence.SequenceViewFactory
Second constructor
SequenceViewFactory(JFrame) - Constructor for class jadex.swing.sequence.SequenceViewFactory
Frist constructor
SequenceXMLFetcher - class jadex.swing.sequence.SequenceXMLFetcher.
A subclass SequenceFetcher to get data from a XML document.
SequenceXMLFetcher() - Constructor for class jadex.swing.sequence.SequenceXMLFetcher
Default constructor
SequenceXMLFetcher(InputStream) - Constructor for class jadex.swing.sequence.SequenceXMLFetcher
Third constructor: more general than the second one
SequenceXMLFetcher(InputStream, String) - Constructor for class jadex.swing.sequence.SequenceXMLFetcher
Fourth constructor
SequenceXMLFetcher(String) - Constructor for class jadex.swing.sequence.SequenceXMLFetcher
Second constructor
setAccessor(AceAccessor) - Method in class jadex.swing.AceModel
Sets the accessor property (jade.db.AceAccessor) value.
setAccessor(JSAceAccessor) - Method in class jadex.swing.sequence.AceDBCloneFetcher
Set the AceAccessor for this object.
setAccessor(JSAceAccessor) - Method in class jadex.xml.SequenceMapXMLDump
Set and get AceAccessor: Query engine
setAceAccessor_jadedbAceAccessorMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setAceAccessor(jade.db.AceAccessor) method descriptor.
setAceAccessor(AceAccessor) - Method in class jadex.swing.map.LocusUI
Set the AceAccessor for fetching AceObject directly from the LocusUI.
setAceAccessor(AceAccessor) - Method in class jadex.swing.ClassListModel
Set AceAccessor for accessing the AceDB.
setAceModel(AceModel) - Method in class jadex.swing.ClassViewController
Set AceModel for displaying.
setAceObject(AceObject) - Method in class jadex.swing.map.IntervalUI
Set aceobject as the interval for this intervalUI.
setAceObject(AceObject) - Method in class jadex.swing.map.Locus
Set up the AceObject for this Locus.
setAceObject(AceObject) - Method in class jadex.swing.map.LocusUI
Set the AceObject for this LocusUI.
setAceObject(AceObject) - Method in class jadex.swing.sequence.Clone
The the wrapped AceObject for this clone.
setAceObject(AceObject) - Method in class jadex.swing.sequence.Contig
Set the wrapped AceObject for this Contig.
setAceObject(AceObject) - Method in class jadex.swing.ObjectViewController
Set the Aceobject to be displayed.
setApplet(Applet) - Method in class jadex.swing.OpenFrames
Set the applet.
setApplet(JApplet) - Static method in class jadex.swing.sequence.IndividualSequenceView
Set the applet used for SequenceView.
setBackground(Color) - Method in class jadex.swing.map.IntervalUI
Set the background color.
setBigIcon() - Method in class jadex.swing.sequence.SequenceActions
Use big icons
setCategory(Vector) - Method in class jadex.swing.AceModel
Sets the category property (java.util.Vector) value.
setClassName(String) - Method in class jadex.swing.map.DisplayPopup
Set the class name this popup used for.
setClassName(String) - Method in class jadex.swing.ClassDisplayer
 
setClassName(String) - Method in class jadex.swing.ClassDisplayerModel
Set the class name.
setClassName(String) - Method in class jadex.swing.ClassListModel
 
setClassName(String) - Method in class jadex.swing.ClassViewController
Sets the className property (java.lang.String) value.
setClone(Clone) - Method in class jadex.swing.sequence.CloneUI
set the clone to be displayed.
setCloneControl(CloneControl) - Method in class jadex.swing.classView.SequenceMapView
Set the CloneControl for this SequenceMapView.
setCloneControl(CloneControl) - Method in class jadex.swing.sequence.CloneDisplay
Set the control of the display.
setCloneDisplay(CloneDisplay) - Method in class jadex.swing.sequence.CloneControl
Set the clonedisplay.
setCloneFetcher(CloneFetcher) - Method in class jadex.swing.sequence.CloneControl
Set the clone fetcher, and get data from data source and initialize the clone model.
setClones(List) - Method in class jadex.swing.sequence.CloneDisplay
Set the clones.
setColor(Color) - Method in class jadex.swing.sequence.CloneUI
Set the color of this cloneUI.
setComparator(Comparator) - Method in class jadex.swing.map.DisplayModel
Set the comparator for sorting the MapPoints.
setConnect(boolean) - Method in class jadex.swing.map.LocusLayout
Set if the connecting lines should be displayed.
setConnectShown(boolean) - Method in class jadex.swing.map.LocusDisplay
The connecting line can be turn on or off by this method.
setConnectShown(boolean) - Method in interface jadex.swing.map.MapPointDisplay
Control if the connecting lines should be displayed or not.
setConnectShown(boolean) - Method in class jadex.swing.sequence.CloneDisplay
Set if the connecting lines should be displayed.
setContainer(MapViewContainer) - Method in class jadex.swing.sequence.CloneOpenFileAction
Set MapViewContainer
setContig(Contig) - Method in class jadex.swing.sequence.Clone
Set the contig this clone belongs to.
setCount_intMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the setCount(int) method descriptor.
setCount(int) - Method in class jadex.swing.ClassDisplayer
 
setCount(int) - Method in class jadex.swing.ClassDisplayerModel
Set the total count.
setCurrentPanel(JPanel) - Method in class jadex.swing.ClassListModel
Sets the currentPanel property (javax.swing.JPanel) value.
setCurrentPanel(JPanel) - Method in class jadex.swing.ClassViewController
Sets the currentPanel property (javax.swing.JPanel) value.
setCursor(Cursor) - Method in interface jadex.swing.util.Zoomable
Change the cursor for displaying zoomability when the mouse is in the rectangle.
setData(List) - Method in class jadex.swing.map.DisplayModel
Set the total displayable MapPoint data.
setData(MapPoint[]) - Method in class jadex.swing.map.DisplayModel
Set the total displayable MapPoint data from a MapPoint array.
setData(Vector) - Method in class jadex.swing.map.DisplayModel
Vector is a collection of MapPoint to be displayed.
setDbFrame(AceDBFrame) - Method in class jadex.swing.SearchPanel
Set the AceDBFrame.
setDbFrame(AceDBFrame) - Method in class jadex.swing.ViewSettingPanel
 
setDirection(boolean) - Method in class jadex.swing.map.Knob
Set the dircetion of this knob.
setDirection(boolean) - Method in class jadex.swing.map.DownKnob
Set the direction of this knob.
setDirection(boolean) - Method in class jadex.swing.map.UpKnob
Set the dircetion of this knob.
setDisplay(LocusDisplay) - Method in class jadex.swing.map.LocusControl
Set the LocusDisplay.
setDisplayControl(DisplayControl) - Method in class jadex.swing.map.Knob
Set up a DisplayControl for this Knob.
setDisplayer(ClassListDisplayer) - Method in class jadex.swing.ClassListMediator
 
setDocument(Document) - Method in class jadex.swing.sequence.SequenceXMLFetcher
Set the XML document containing all sequence element information.
setEnd(float) - Method in class jadex.swing.map.IntervalUI
Set the end value.
setEnd(long) - Method in class jadex.swing.map.MapRange
Set the end value.
setEndF(float) - Method in class jadex.swing.map.MapRange
Set the end value in float.
setError(float) - Method in class jadex.swing.map.AbstractMapPoint
Set the error of the position.
setError(float) - Method in class jadex.swing.map.Locus
 
setError(float) - Method in interface jadex.swing.map.MapPoint
Set the error of the position of this MapPoint.
setError(float) - Method in class jadex.swing.sequence.Clone
Do nothing
setExitAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set the exit action.
setExtend(MapRange) - Method in class jadex.swing.sequence.Contig
Set the MapRange if contig in Sequence_map.
setExtendF(MapRange) - Method in class jadex.swing.sequence.Contig
Set the MapRange of contig in GeneticMap
setFetcher(SequenceFetcher) - Method in class jadex.swing.sequence.SequenceModel
Set the datasouce for this SequenceModel.
setFile(String) - Method in class jadex.swing.sequence.FileCloneFetcher
Set the name of the file to be opened.
setFileMenu() - Method in class jadex.swing.classView.MapViewContainerMenuBar
Setup the file Menu.
setFileMenuForApplet() - Method in class jadex.swing.classView.MapViewContainerMenuBar
Applet File menu: quit only
setFileOpenAction(ActionListener) - Method in class jadex.swing.classView.MapViewContainerMenuBar
Set the actionListener for the file open MenuItem.
setForeOutColor(Color) - Method in class jadex.swing.map.LocusUI
Set the foreground color when mouse is out.
setFrame() - Method in class jadex.swing.classView.MapView
Setup the JFrame.
setFullMapRange(MapRange) - Method in class jadex.swing.sequence.HorizontalMiniMapCartoon
Set the full maprange
setGeneRenderer(GeneRenderer) - Method in class jadex.swing.sequence.SequenceDisplay
Set gene renderer.
setHelpAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set help action
setHelpMenu() - Method in class jadex.swing.classView.MapViewContainerMenuBar
Set up the help menu.
setIndex_comsunjavaswingJLabel__MethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the setIndex(javax.swing.JLabel[]) method descriptor.
setIndex_int_comsunjavaswingJLabelMethodDescriptor() - Method in class jadex.swing.IndexSelectorBeanInfo
Gets the setIndex(int, javax.swing.JLabel) method descriptor.
setIndex(int, JLabel) - Method in class jadex.swing.IndexSelector
Set the index at specified position.
setIndex(JLabel[]) - Method in class jadex.swing.IndexSelector
Set all 26 JLabels
setIndexSelector1Index_comsunjavaswingJLabel__MethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the setIndexSelector1Index(javax.swing.JLabel[]) method descriptor.
setIndexSelector1Index_int_comsunjavaswingJLabelMethodDescriptor() - Method in class jadex.swing.ClassDisplayerBeanInfo
Gets the setIndexSelector1Index(int, javax.swing.JLabel) method descriptor.
setIndexSelector1Index(int, JLabel) - Method in class jadex.swing.ClassDisplayer
Method generated to support the promotion of the indexSelector1Index attribute.
setIndexSelector1Index(JLabel[]) - Method in class jadex.swing.ClassDisplayer
Method generated to support the promotion of the indexSelector1Index attribute.
setInterval() - Method in class jadex.swing.classView.MapView
Create the intervalContainer.
setInterval(Object[][]) - Method in class jadex.swing.classView.MapView
Set up the data and create the intervalContainer.
setIsClone(boolean) - Method in class jadex.swing.map.LocusUI
Set this LocusUI as a CloneUI
setJButton1Enabled(boolean) - Method in class jadex.swing.ProgressPanel
Method generated to support the promotion of the CancellEnabled attribute.
setJLabelAll(JLabel) - Method in class jadex.swing.ClassDisplayer
 
setKnobs(Knob, Knob) - Method in class jadex.swing.map.DisplayControl
set knobs in this display: Assume all display have knobs.
setLabelAll(JLabel) - Method in class jadex.swing.ClassDisplayerModel
Set the JLabel, LabelAll.
setLabels(int, JLabel) - Method in class jadex.swing.ClassDisplayerModel
Set a specific JLabel at index index.
setLabels(JLabel[]) - Method in class jadex.swing.ClassDisplayerModel
Set all 26 JLabels.
setLayoutModel(SequenceLayoutModel) - Method in class jadex.swing.sequence.SequenceDisplay
Set the layoutModel
setLeftMapScale(boolean) - Method in class jadex.swing.classView.MapViewContainer
create the left mapscale.
setLetterList_comsunjavaswingJLabel__MethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setLetterList(javax.swing.JLabel[]) method descriptor.
setLetterList_javautilVectorMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setLetterList(java.util.Vector) method descriptor.
setLetterList(JLabel[]) - Method in class jadex.swing.ClassListModel
 
setLetterList(JLabel, JLabel[]) - Method in class jadex.swing.ClassListModel
 
setLetterList(Vector) - Method in class jadex.swing.ClassListModel
 
setList_int_jadedbAceObjectMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setList(int, jade.db.AceObject) method descriptor.
setList_jadedbAceObject__MethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setList(jade.db.AceObject[]) method descriptor.
setLocus() - Method in class jadex.swing.classView.MapView
Set the Locus display.
setLocus(Object[][]) - Method in class jadex.swing.classView.MapView
Set the Locus display by using data from loci.
setLocusUI(LocusUI[]) - Method in class jadex.swing.map.LocusDisplay
loci will be shown by this method.
setLocusUI(LocusUI[]) - Method in class jadex.swing.map.LocusLayout
Set the showing loci.
setMainLoci(AceObject[]) - Method in class jadex.swing.map.MapCartoon
Deprecated. do not use this method. See LocusPanel.
setMap(MapRange) - Method in class jadex.swing.map.MapCartoon
An initilization method.
setMap(MapRange) - Method in class jadex.swing.map.MapControl
Set the total MapRange to be displayed.
setMap(String) - Method in class jadex.swing.sequence.Contig
Set the name of the Sequence_map this contig is in.
setMapCartoon(boolean) - Method in class jadex.swing.classView.MapViewContainer
create a mapcartoon.
setMapCartoon(MapCartoon) - Method in class jadex.swing.map.LocusShow
Deprecated. please see MapControl for the detail.
setMapControl(MapControl) - Method in class jadex.swing.classView.MapViewContainer
Set MapControl to coordinate all zooming activities.
setMapControl(MapControl) - Method in class jadex.swing.map.DisplayControl
MapControl is always the central controller.
setMapControl(MapControl) - Method in class jadex.swing.map.IntervalContainer
Set the mapcontrol for all intervalUI.
setMapControl(MapControl) - Method in class jadex.swing.map.IntervalPanel
Set the MapControl for this IntervalPanel.
setMapControl(MapControl) - Method in class jadex.swing.map.IntervalUI
Set the MapControl for this IntervalUI.
setMapControl(MapControl) - Method in class jadex.swing.map.MapCartoon
Set the MapControl as the central control to coordinate all zooming activites.
setMapControl(MapControl) - Method in class jadex.swing.map.RangeControlPanel
Set the central MapControl to coordinate all zooming activities.
setMapControl(MapControl) - Method in class jadex.swing.map.ZoomButtonControl
Set up the MapControl for all zooming buttons.
setMapMenuBar() - Method in class jadex.swing.classView.MapViewContainer
Create a default JMenuBar with MapMapMenubar.
setMapMenuBar(JMenuBar) - Method in class jadex.swing.classView.MapViewContainer
Create a JMenubar for this container.
setMapRange(MapRange) - Method in class jadex.swing.map.DisplayControl
MapRange is set by this control class.
setMapRange(MapRange) - Method in class jadex.swing.map.MapCartoon
Set the displayed MapRange.
setMapRange(MapRange) - Method in class jadex.swing.sequence.Clone
Set the MapRange of the clone.
setMapRange(MapRange) - Method in class jadex.swing.sequence.HorizontalMiniMapCartoon
Set the current maprange
setMapRange(MapRange) - Method in class jadex.swing.sequence.SequenceDisplay
Specify a maprange for this display
setMapRange(MapRange) - Method in class jadex.swing.sequence.SequenceLayoutModel
Set the displayed MapRange.
setMapView(SequenceMapView) - Method in class jadex.swing.sequence.CloneOpenFileAction
set SequenceMapView
setMarker() - Method in class jadex.swing.classView.MapView
Set the Marker Panel contents.
setMarker(LocusPanel) - Method in class jadex.swing.classView.MapViewContainer
create a marker panel from locus.
setMarker(MapPoint[]) - Method in class jadex.swing.map.MiniMapCartoon
Set the main marker for this MapCartoon.
setMarker(Object[][]) - Method in class jadex.swing.classView.MapView
Set the marker Panel contents by using data from Array loci.
setMaximum_intMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the setMaximum(int) method descriptor.
setMaximum(int) - Method in class jadex.swing.ProgressPanel
Maximum is used to hold the value of progressbar's maximum
setMessage_javalangStringMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the setMessage(java.lang.String) method descriptor.
setMessage(String) - Method in class jadex.swing.GeneticMapApplet
 
setMessage(String) - Method in class jadex.swing.ProgressPanel
Message is the string to be shown on the pane
setMessage(String) - Method in class jadex.swing.WelcomePane
Sets the message property (java.lang.String) value.
setModel(ClassDisplayerModel) - Method in class jadex.swing.ClassDisplayer
Set the ClassDisplayModel.
setModel(ClassListModel) - Method in class jadex.swing.ClassListDisplayer
Constructor
setModel(ClassListModel) - Method in class jadex.swing.ClassListMediator
 
setModel(DisplayModel) - Method in class jadex.swing.map.DisplayControl
DisplayModel can be set: A property of this class
setModel(DisplayModel) - Method in class jadex.swing.map.LocusShow
Set the display DataModel.
setModel(DisplayModel) - Method in class jadex.swing.map.LocusDisplay
set locus model, which is the data class of locus display.
setModel(SequenceModel) - Method in class jadex.swing.sequence.SequenceDisplay
Set the sequence model.
setMouseAt(long) - Method in class jadex.swing.sequence.SequenceDisplay
Set the mouseAt position in bp unit
setMouseAt(long) - Method in class jadex.swing.sequence.SequenceLayoutModel
Set current mouse position in bp unit
setMouseInName(String) - Method in class jadex.swing.map.LocusDisplay
Set the name for lightening up label and line when mouse is in.
setMouseInName(String) - Method in class jadex.swing.map.LocusLayout
Set the name of the LocusUI where mouse is in.
setMouseInName(String) - Method in interface jadex.swing.map.MapPointDisplay
Record the name of the MapPoint where the mouse is in.
setMouseInName(String) - Method in class jadex.swing.sequence.CloneDisplay
Set the name in which the mouse is in.
setMoveLeftAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set moveLeft action.
setMoveRightAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set the moveRight action.
setMultiSelected(boolean) - Method in class jadex.swing.sequence.SequenceSelectionEvent
Set if there are more than one selected sequences.
setName_javalangStringMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setName(java.lang.String) method descriptor.
setName(String) - Method in class jadex.swing.classView.SequenceMapView
Implement name as a property of this class.
setName(String) - Method in class jadex.swing.map.AbstractMapPoint
Set the name of this MapPoint.
setName(String) - Method in class jadex.swing.map.IntervalUI
Set the name of this intervalUI.
setName(String) - Method in class jadex.swing.map.Locus
 
setName(String) - Method in class jadex.swing.map.LocusUI
Set the name for this display.
setName(String) - Method in interface jadex.swing.map.MapPoint
Set the name of the mappoint.
setName(String) - Method in class jadex.swing.sequence.AceDBCloneFetcher
Set the name of the Sequence_map to be displayed.
setName(String) - Method in class jadex.swing.sequence.Clone
Set the name of the clone.
setName(String) - Method in class jadex.swing.sequence.CloneUI
Set the name of the clone.
setName(String) - Method in class jadex.swing.sequence.Contig
Set the name of the contig.
setName(String) - Method in class jadex.swing.ClassListDisplayer
 
setName(String) - Method in class jadex.xml.SequenceMapXMLDump
Get and set the chromosome name
setNameLayout(LocusLayout) - Method in class jadex.swing.map.LocusDisplay
Set the Layout for the name labels for LocusUI.
setNameLayout(LocusLayout) - Method in class jadex.swing.sequence.CloneDisplay
Set the nameLayout.
setNameLayout(String) - Method in class jadex.swing.map.LocusDisplay
Set up a NameLayout by their names.
setNameLayout(String) - Method in interface jadex.swing.map.MapPointDisplay
Set the name layout by layout name.
setNameLayout(String) - Method in class jadex.swing.sequence.CloneDisplay
Set the name layout by layout name.
setNames(Vector) - Method in class jadex.swing.AceDBFrame
Sets the names property (java.util.Vector) value.
setObject(AceObject) - Method in class jadex.swing.classView.ClassView
Set the AceObject to be displayed by this ClassView.
setObject(AceObject) - Method in class jadex.swing.classView.DumpClassView
Set the AceObject to be displayed.
setObject(AceObject) - Method in class jadex.swing.classView.MapView
Set the AceObject to be displayed.
setObject(AceObject) - Method in class jadex.swing.classView.SequenceMapView
aceobject is implemented as a property of this class
setObject(AceObject) - Method in class jadex.swing.classView.SequenceView
AceObject will not be supported anymore.
setObject(AceObject) - Method in class jadex.swing.classView.TreeClassView
Set the AceObject to be displayed.
setPageBox(int) - Method in class jadex.swing.ClassListDisplayer
 
setPanel(JPanel) - Method in class jadex.swing.ClassListDisplayer
Comment
setPanel(MapZoom) - Method in class jadex.swing.map.ZoomPopupMenu
Set the zoomable.
setPMap(MapRange) - Method in class jadex.swing.sequence.Clone
Set the PMap of the clone if any.
setPMap(MapRange) - Method in class jadex.swing.sequence.Contig
 
setPopup(JPopupMenu) - Method in class jadex.swing.map.IntervalContainer
Set up a JOpoupMenu.
setPopup(JPopupMenu) - Method in class jadex.swing.map.LocusShow
A JPopup menu can be added.
setPopup(JPopupMenu) - Method in class jadex.swing.map.LocusDisplay
Set up a JPopupMenu for controlling this locus display.
setPopup(JPopupMenu) - Method in class jadex.swing.sequence.SequenceDisplay
Set up a popup menu
setPosition(float) - Method in class jadex.swing.map.AbstractMapPoint
Set the position of this MapPoint.
setPosition(float) - Method in class jadex.swing.map.Locus
 
setPosition(float) - Method in class jadex.swing.map.LocusUI
Set the position of the Locus.
setPosition(float) - Method in interface jadex.swing.map.MapPoint
Set the position of the MapPoint.
setPosition(float) - Method in class jadex.swing.sequence.Clone
Set the position of the clone.
setRange(MapRange) - Method in class jadex.swing.map.IntervalPanel
Set the displaying MapRange.
setRange(MapRange) - Method in class jadex.swing.map.LocusDisplay
Set up the displaying MapRange.
setRange(MapRange) - Method in class jadex.swing.map.LocusPanel
Set the dispplaying maprange.
setRange(MapRange) - Method in class jadex.swing.map.MapControl
Setter for property range.
setRange(MapRange) - Method in interface jadex.swing.map.MapPointDisplay
Set the MapRange to be displayed.
setRange(MapRange) - Method in class jadex.swing.map.MapScale
Setter for property range.
setRange(MapRange) - Method in class jadex.swing.map.MapScale1
Set the displayed MapRange.
setRange(MapRange) - Method in class jadex.swing.map.MiniMapCartoon
Set the displayed MapRange.
setRange(MapRange) - Method in class jadex.swing.sequence.CloneDisplay
Set the current maprange.
setRange(MapRange) - Method in class jadex.swing.sequence.HorizontalMapScale
Set the property of range
setRangeControl(boolean) - Method in class jadex.swing.classView.MapViewContainer
create a range control panel.
setRenderer(SequenceRenderer) - Method in class jadex.swing.sequence.SequenceDisplay
Set the sequence renderer.
setResetAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set Reset Action
setRightMapScale(boolean) - Method in class jadex.swing.classView.MapViewContainer
create the right mapscale.
setRootElement(Element) - Method in class jadex.swing.sequence.SequenceTreeDisplay
Set root element of the xml document to be displayed.
setSearchAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set the Search Action
setSelected(boolean) - Method in class jadex.swing.sequence.SequenceSelectionEvent
Set if this is used in selection.
setSelectedElement(Element) - Method in class jadex.swing.sequence.SequenceSelectionModel
Set a selected Sequence element.
setSelectedElements(List) - Method in class jadex.swing.sequence.SequenceSelectionModel
Set a list of selected elements.
setSelectedSequence(Element) - Method in class jadex.swing.sequence.SequenceDisplay
Set one and only one selected Sequence element.
setSelectedSequences(List) - Method in class jadex.swing.sequence.SequenceDisplay
Set a list of selected sequence elements.
setSelection(List) - Method in class jadex.swing.sequence.SequenceSelectionModel
This method will not fire a SequneceSelectionEvent, and is for fine control of display.
setSelectionModel(SequenceSelectionModel) - Method in class jadex.swing.sequence.SequenceDisplay
Set the selection model
setSequence(Element) - Method in class jadex.swing.sequence.SequenceElementTableView
Set the Sequence elmenet to be displayed.
setSequence(Element) - Method in interface jadex.swing.sequence.SequenceElementView
Set the Sequence element to be displayed.
setSequence(Element) - Method in class jadex.swing.sequence.SequenceSelectionEvent
Set the selected sequence.
setSequence(Element) - Method in class jadex.swing.sequence.SequenceTreeNode
Set the wrapped sequence element.
setSequence(String) - Method in class jadex.swing.classView.SequenceView
Set the name of the chromosome to be displayed.
setSequence(String, String) - Method in class jadex.swing.sequence.SequenceViewApplet
Set the chromsome name and display it on the display
setSequenceDisplay(SequenceDisplay) - Method in class jadex.swing.sequence.SequenceActions
Set the SequenceDisplay for all Actions.
setSequenceFetcher(SequenceFetcher) - Method in class jadex.swing.sequence.SequenceViewFactory
Set the sequence fetcher, i.e., data source, to be displayed
setSequences(List) - Method in class jadex.swing.sequence.SequenceSelectionEvent
For multiselecton, set the selected sequences.
setShowNames(LocusUI[]) - Method in class jadex.swing.sequence.CloneDisplay
Names will be shown in this range.
setShowNumber(int) - Method in class jadex.swing.map.DisplayControl
Showing mappoint with the total number of number.
setSmallIcon() - Method in class jadex.swing.sequence.SequenceActions
Use small icons
setSource(InputStream) - Method in class jadex.swing.sequence.SequenceXMLFetcher
Create a xml document based on an input stream.
setSource(InputStream, String) - Method in class jadex.swing.sequence.SequenceXMLFetcher
Overloaded method to set the source of xml.
setStart(float) - Method in class jadex.swing.map.IntervalUI
Set the start value.
setStart(long) - Method in class jadex.swing.map.MapRange
Set the start value.
setStartF(float) - Method in class jadex.swing.map.MapRange
Set the start value in float.
setStartingLabel_comsunjavaswingJLabelMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setStartingLabel(javax.swing.JLabel) method descriptor.
setStartingLabel(JLabel) - Method in class jadex.swing.ClassListModel
 
setTabbedPane(JTabbedPane) - Method in class jadex.swing.CategoryTreeSelectionListener
Set the JTabbedPane
setTitle(String) - Method in class jadex.swing.classView.MapView
Set the JFrame's title.
setTotalBP(long) - Method in class jadex.swing.sequence.SequenceLayoutModel
By setting total bp of chromosome, the rel and offset should be calculated.
setTotalEntries_intMethodDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the setTotalEntries(int) method descriptor.
setTotalLengthF(float) - Method in class jadex.swing.map.MapCartoon
Set the total length of the chromosome in float.
setTotalLengthL(long) - Method in class jadex.swing.map.MapCartoon
Set the total length of the chromosome this cartoon represents.
setTotalLocus(MapPoint[]) - Method in class jadex.swing.map.LocusDisplay
Set the total loci in a specific range.
setTotalMapRange(MapRange) - Method in class jadex.swing.map.DisplayControl
Set the total maprange.
setUI(SequenceUI) - Method in class jadex.swing.sequence.SequenceDisplay
Set the SequenceUI.
setURL(String) - Method in class jadex.swing.map.LocusUI
Set URL for Locus or Clone information.
setValue_intMethodDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the setValue(int) method descriptor.
setValue(int) - Method in class jadex.swing.ProgressPanel
Current value of progressbar
setVerTicalPosition(float) - Method in class jadex.swing.util.Magnifier
Set the vertical position.
setView(JComponent) - Method in class jadex.swing.classView.ClassView
Set a JComponent for displaying the AceObject.
setView(JComponent) - Method in class jadex.swing.classView.DumpClassView
Set the JComponent for displaying the AceObject.
setView(JComponent) - Method in class jadex.swing.classView.MapView
Set the JComponent for displaying the AceObject.
setView(JComponent) - Method in class jadex.swing.classView.SequenceMapView
Set the JComponent displaying the AceObject.
setView(JComponent) - Method in class jadex.swing.classView.SequenceView
Do nothing.
setView(JComponent) - Method in class jadex.swing.classView.TreeClassView
Set the displaying JComponent.
setViewMenu() - Method in class jadex.swing.classView.MapViewContainerMenuBar
Set up the View Menu.
setZoom(Rectangle2D.Float) - Method in class jadex.swing.map.LocusDisplay
Set a rectangel for zooming.
setZoom(Rectangle2D.Float) - Method in class jadex.swing.sequence.CloneDisplay
Zoom range should be passed from magnifier to here.
setZoom(Rectangle2D.Float) - Method in class jadex.swing.util.TestPanel
 
setZoom(Rectangle2D.Float) - Method in interface jadex.swing.util.Zoomable
Zoom range should be passed from magnifier to here.
setZoomable(Zoomable) - Method in class jadex.swing.util.Magnifier
Set the Zoomable for zooming.
setZoomAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set zoomAction
setZoomInAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set zoomINActin
setZoomOutAction(Action) - Method in class jadex.swing.sequence.SequenceActions
Set zoomOUtAction
show(AceObject) - Method in class jadex.swing.OpenFrames
Clients should call this method to display the individual AceObject.
show(String, String) - Method in class jadex.swing.OpenFrames
A overloaded method for displaying AceObjects in Applets.
showControlPanel(boolean) - Method in class jadex.swing.classView.MapViewContainer
Control if both MapCartoon and RangeControl should be displayed.
showFileMenu(boolean) - Method in class jadex.swing.classView.MapViewContainerMenuBar
Control if the File menu should be displayed.
showFullMenu(boolean) - Method in class jadex.swing.map.MapMenuBar
Control if view and help menu should be displayed.
showHelpMenu(boolean) - Method in class jadex.swing.classView.MapViewContainerMenuBar
Control if the Help Menu should be displayed or not.
showInterval(boolean) - Method in class jadex.swing.classView.MapView
Display intervalContainer or not.
showLeftScale(boolean) - Method in class jadex.swing.classView.MapView
Control if the Mapscale on the left should be displayed.
showLess() - Method in class jadex.swing.map.DisplayControl
Show less.
showLocator(boolean) - Method in class jadex.swing.classView.MapView
Control if the locator should be displayed.
showLocus(boolean) - Method in class jadex.swing.classView.MapView
Control if the Locus Panel should be displayed or not.
showMarker(boolean) - Method in class jadex.swing.classView.MapView
Control if the marker should be displayed.
showMore() - Method in class jadex.swing.map.DisplayControl
Show more.
showNumber - Variable in class jadex.swing.map.DisplayControl
 
showReset() - Method in class jadex.swing.map.DisplayControl
Show reset.
showRightScale(boolean) - Method in class jadex.swing.classView.MapView
Control if the MapScale on the right should be displayed.
showSequenceInDetail(String) - Static method in class jadex.swing.sequence.IndividualSequenceView
Show the detailed information for the Sequence objects.
showViewMenu(boolean) - Method in class jadex.swing.classView.MapViewContainerMenuBar
Control if the View Menu should be displayed or not.
sLoci - Variable in class jadex.swing.map.DisplayControl
 
SMART_LAYOUT - Static variable in class jadex.swing.map.DisplayPopup
 
SmartLocusLayout - class jadex.swing.map.SmartLocusLayout.
A subclass of locuslayout to implement a smart locus labelling method.
SmartLocusLayout(float, int, boolean, Color) - Constructor for class jadex.swing.map.SmartLocusLayout
The sole construcotr.
sort() - Method in class jadex.swing.map.DisplayModel
Sort all MapPoints.
sort(Comparator) - Method in class jadex.swing.map.DisplayModel
Sort all MapPoints by a specified comparator.
sort(List) - Method in class jadex.swing.map.DisplayModel
Sort a MapPoint list by using the default Comparator.
sort(MapPoint[]) - Method in class jadex.swing.map.DisplayModel
Sort a MapPoint array by using defalt comparator.
sort(MapPoint[], Comparator) - Method in class jadex.swing.map.DisplayModel
A utility for sorting a MapPoint array using a Comparator.
sortByError() - Method in class jadex.swing.map.DisplayModel
Sort all MapPoints by position errors.
sPoints - Variable in class jadex.swing.map.DisplayControl
 
start() - Method in class jadex.swing.sequence.SequenceViewApplet
Just a check method for monitoring the memory usage.
startingLabelPropertyDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the startingLabel property descriptor.
stop() - Method in class jadex.swing.sequence.SequenceViewApplet
 

T

TestPanel - class jadex.swing.util.TestPanel.
 
TestPanel() - Constructor for class jadex.swing.util.TestPanel
Creates new TestPanel
toString() - Method in class jadex.swing.map.MapRange
An handy print method.
toString() - Method in class jadex.swing.sequence.Clone
A overrode method for pretty-printing.
toString() - Method in class jadex.swing.sequence.Contig
For pretty-printing purpose.
toString() - Method in class jadex.swing.sequence.SequenceTreeNode
This method return the name of the sequence element.
toStringF() - Method in class jadex.swing.map.MapRange
Deprecated. use toString.
TOTAL_LIST_NUMBER - Static variable in class jadex.swing.ClassListDisplayer
 
totalBP - Variable in class jadex.swing.sequence.SequenceLayoutModel
 
totalEntriesPropertyDescriptor() - Method in class jadex.swing.ClassListModelBeanInfo
Gets the totalEntries property descriptor.
totalLayers - Variable in class jadex.swing.sequence.SequenceLayoutModel
 
tPoints - Variable in class jadex.swing.map.DisplayControl
 
transform(String, String, String) - Method in class jadex.xml.GeneTransform
 
TreeClassView - class jadex.swing.classView.TreeClassView.
This is a general usable TreeView of the AceObjects.
TreeClassView() - Constructor for class jadex.swing.classView.TreeClassView
Default constructor
TreeClassView(AceObject) - Constructor for class jadex.swing.classView.TreeClassView
An overloaded constructor.

U

uninstallDefaults() - Method in class jadex.swing.sequence.SequenceUI
 
uninstallListeners() - Method in class jadex.swing.sequence.SequenceUI
 
uninstallUI(JComponent) - Method in class jadex.swing.sequence.SequenceUI
removing all initializtion setting
UnknownPositionException - exception jadex.swing.map.UnknownPositionException.
An exception when the position is unknown.
UnknownPositionException() - Constructor for class jadex.swing.map.UnknownPositionException
Creates new UnknownPositionException without detail message.
UnknownPositionException(String) - Constructor for class jadex.swing.map.UnknownPositionException
Constructs an UnknownPositionException with the specified detail message.
updateProp() - Method in class jadex.swing.ViewSettingPanel
 
updateUI() - Method in class jadex.swing.map.DisplayControl
Update UI after search or desearch
updateUI() - Method in class jadex.swing.map.LocusControl
Show the data in LocusDisplay: points, little bars, and default names This is the central points controled by this LocusControl.
updateUI() - Method in class jadex.swing.sequence.CloneControl
Show the data in LocusDisplay: points, little bars, and default names This is the central points controled by this LocusControl.
updateUI() - Method in class jadex.swing.sequence.SequenceDisplay
Create and set SequenceUI for this SequenceDisplay.
UpKnob - class jadex.swing.map.UpKnob.
This Knob is used on the north end of the chromosome line in the MapView.
UpKnob() - Constructor for class jadex.swing.map.UpKnob
Default constructor.
UpKnob(DisplayControl) - Constructor for class jadex.swing.map.UpKnob
An overloaded constructor.

V

valueChanged(SequenceSelectionEvent) - Method in class jadex.swing.sequence.SequenceDisplayAndTreeAdapter
EventHandler for event fired by SequenceSelectionModel from SequenceDisplay
valueChanged(SequenceSelectionEvent) - Method in interface jadex.swing.sequence.SequenceSelectionListener
The only method a sequence selection listener should implement.
valueChanged(TreeSelectionEvent) - Method in class jadex.swing.sequence.SequenceDisplayAndTreeAdapter
EventHandler for event fired by JTree in SequenceTreeDisplay
valueChanged(TreeSelectionEvent) - Method in class jadex.swing.CategoryTreeSelectionListener
The actual selectionListener method to process the selection evenet in CategoryTree.
valuePropertyDescriptor() - Method in class jadex.swing.ProgressPanelBeanInfo
Gets the value property descriptor.
verticalZoom(int) - Method in class jadex.swing.map.IntervalContainer
No vertical zooming temporarily.
verticalZoom(int) - Method in interface jadex.swing.map.MapZoom
 
ViewSettingPanel - class jadex.swing.ViewSettingPanel.
 
ViewSettingPanel() - Constructor for class jadex.swing.ViewSettingPanel
Creates new form ViewSettingPanel

W

WelcomePane - class jadex.swing.WelcomePane.
A message panel to show some messages.
WelcomePane() - Constructor for class jadex.swing.WelcomePane
Constructor
WelcomePaneBeanInfo - class jadex.swing.WelcomePaneBeanInfo.
The bean information class for jadex.swing.WelcomePane.
WelcomePaneBeanInfo() - Constructor for class jadex.swing.WelcomePaneBeanInfo
 
windowActivated(WindowEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the WindowListener interface.
windowClosed(WindowEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the WindowListener interface.
windowClosing(WindowEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the WindowListener interface.
windowDeactivated(WindowEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the WindowListener interface.
windowDeiconified(WindowEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the WindowListener interface.
windowIconified(WindowEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the WindowListener interface.
windowOpened(WindowEvent) - Method in class jadex.swing.AceDBFrame
Method to handle events for the WindowListener interface.
WORMBASE - Static variable in class jadex.swing.classView.SequenceView
This is a URL address all XML files of chromosomes should be in.

X

XMLParserAndValidation - class jadex.xml.XMLParserAndValidation.
 
XMLParserAndValidation() - Constructor for class jadex.xml.XMLParserAndValidation
Creates new form XMLParserAndValidation
XMLParserDemo - class jadex.xml.XMLParserDemo.
 
XMLParserDemo() - Constructor for class jadex.xml.XMLParserDemo
Default constructor: use org.apache.xerces.parsers.SAXParser
XMLParserDemo(String) - Constructor for class jadex.xml.XMLParserDemo
Second constructor: use class name for get reader
XMLUtilities - class jadex.xml.XMLUtilities.
This is a utility class for processing XML files in Sequence View.
XMLUtilities() - Constructor for class jadex.xml.XMLUtilities
 
xPadding - Variable in class jadex.swing.sequence.SequenceLayoutModel
 

Y

yPadding - Variable in class jadex.swing.sequence.SequenceLayoutModel
 

Z

zipIt(String) - Method in class jadex.xml.SequenceMapXMLDump
A utility to zip the xml files
ZOOM_STEP - Variable in class jadex.swing.sequence.SequenceLayoutModel
 
zoom(MapRange) - Method in class jadex.swing.map.DisplayControl
Do zooming.
zoom(Rectangle) - Method in class jadex.swing.sequence.SequenceLayoutModel
Zoom in a specific rectangle
Zoomable - interface jadex.swing.util.Zoomable.
An interface all Zoomable display JPanel should be implemented.
ZoomButtonControl - class jadex.swing.map.ZoomButtonControl.
A customized JPanel holding all zooming buttons.
ZoomButtonControl() - Constructor for class jadex.swing.map.ZoomButtonControl
Default constructor.
ZoomButtonControl(MapControl) - Constructor for class jadex.swing.map.ZoomButtonControl
An overloaded constructor.
zoomIn() - Method in class jadex.swing.sequence.SequenceLayoutModel
Do zooming-in in the current range
zoomIn(int) - Method in class jadex.swing.map.MapRange
Zoom-in in the current range
zoomOut() - Method in class jadex.swing.sequence.SequenceLayoutModel
Do zooming-out in the current range
zoomOut(int) - Method in class jadex.swing.map.MapRange
Zoom-out the current range
ZoomPopupMenu - class jadex.swing.map.ZoomPopupMenu.
A customized JPopupMenu for zooming.
ZoomPopupMenu() - Constructor for class jadex.swing.map.ZoomPopupMenu
Creates new ZoomPopupMenu
ZoomPopupMenu(MapZoom, JFrame) - Constructor for class jadex.swing.map.ZoomPopupMenu
A overloaded constructor.

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