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. |