Package jadex.swing.sequence

Interface Summary
SequenceElementView This is the specificatio for individual Sequence element view.
SequenceFetcher This is the interface defining a specification for fetching data for SequenceView.
SequenceSelectionListener This is the EventListener all classes are interested in Sequence Selection should implement.
 

Class Summary
AceDBCloneFetcher This class is used to fetch SequenceMap information from AceDB directly for SequenceMap display.
Clone This wrapper class contains information about a clone.
CloneControl A subclass of DisplayControl to control CloneDisplay.
CloneDisplay This is the class used to show clones in the chromosome.
CloneFetcher This class is used to get clone data from a datasource, such as AceDB or local files.
CloneOpenFileAction This class is used to open a sequnece_map file.
CloneUI The vertical bar for representing the clone on the left to the chromosome line on the CloneDisplay.
Contig A wrapper class for Contig.
FileCloneFetcher This subclass of CloneFetcher is used to get clone information from local file systems.
GeneRenderer A customized JComponent for rendering gene structures in SequenceView.
HorizontalMapScale A horizonal mapscale to show bp position on the sequence map.
HorizontalMiniMapCartoon A minimapcartoon to show the position of the displaying region on the whole chromosome.
IndividualSequenceView This class is used to link sequence to the Wormbase, http://www.wormbase.org, in an applet or application.
RangeSpecifyDialog A customized JDialog to specify a MapRange for the SequenceView.
SequenceActions This is the central repository to handle all actions in the whole Sequence Display.
SequenceDisplay SequenceDisplay.java: Graphics Sequence display designed based on Swing MVC model and renderer method.
SequenceDisplayAndTreeAdapter An adapter to connect the selections of SequenceDisplay and SequenceTreeDisplay.
SequenceElementTableView This customized JPanel is used to display some more information for individual sequence element.
SequenceLayoutModel This class is used to transform bp coordinate on the chromosome to the graphics coordinate, and the zoom and some layout processing.
SequenceMapApplet This applet is used to launch the Sequnce_map View in an applet.
SequenceModel This is the data model for SequenceDisplay.
SequenceRenderer This customized JPanel is used for rendering the Sequence elemnet in the SequenceDisplay.
SequenceSelectionEvent A sequence selection event object.
SequenceSelectionModel This class processes and stores selections of sequnce on the sequence display.
SequenceTreeDisplay Display a sequence in a JTree based on an xml document or element.
SequenceTreeNode A customized TreeNode used in SequenceTreeDisplay by using JDOM element.
SequenceUI A customized ComponentUI for processing SequenceDispay activities.
SequenceViewApplet The applet for displaying a SequenceView in the browser.
SequenceViewFactory This class is used to set up all GUIs for Sequence View in a JFrame or JApplet.
SequenceXMLFetcher A subclass SequenceFetcher to get data from a XML document.