AbstractEditableSequence.java
This class provides trivial implementations of all of those methods
which can be defined in terms of the others of the EditableSequence
interface, and also ensures that the event handling occurs correctly
Created: Fri Mar 3 12:11:49 2000
AlignmentEventType.java
This class provides an enumerated type for the AlignmentEvent class
to pass around as an identifier
Created: Tue Feb 15 20:26:54 2000
CinemaAlignmentFrame.java
This class provides a basic CinemaAlignmentFrame which consists of
a JScrollPane, with an JAlignmentViewer in the middle,
JAlignmentButton panel down the right hand side and a
JAlignmentRuler across the bottom.
CinemaAnchorManager.java
This group takes care of the anchoring groups, and adding and
removing appropriate listeners to the main alignment viewer, and
then adding and removing gaps.
CinemaResources.java
The purpose of this class is to provide access to the resources
that cinema needs in a manner which is appropriate and simple both
during development time and after deployment.
CinemaStatusInformation.java
A utility class which provides what are hopefully useful status bar
information messages about what Cinema is currently showing.
ColorList.java
This class is similar to ColorGenerator, except that instead of
cycling through the colours it presents them as a list
Created: Thu Jun 8 17:37:23 2000
FastAlignmentViewerCellRenderer.java
Although the JAlignmentViewer provides a pluggable renderer
architecture with the AlignmentViewerCellRenderer it has been found
that this has a fairly disasterous effect on performance of the
viewer particularly with respect to scrolling, due to the large
number of method calls and events to render a cell.
IndividualElementColorMap.java
Allows a direct mapping between an element and a color; thereby
every element in a sequence type will have an associated color.
IntArrayList.java
This class provides something akin to the ArrayList class but with
all the methods typed as ints, which avoids the additional bloat of
having to create an object for every containined integer.
Even more less pointless contstructor
Takes a param to be used later as a parameter
for the method which will be called on what is proably
going to be the source.
JLayableScrollPane.java
You cant reset the layout manager on a scroll pane, due to what
appears to be a bug in the JScrollPane layout, at least not it you
want anything to appear on screen.
ModuleStorageStructure.java
Stores the module (if it exists), the context, the module
configuration object and the required modules for one module
identifier.
OptionHandler.java
Objects implementing this interface should record all of
Optionable object, storing and restoring their options
as necessary
Created: Mon Feb 01 18:10:52 1999
SequenceAlignmentPoint.java
Represents a point in an alignment, where X is the position in a
sequence, and Y is the index of the sequence in the alignment.
SequenceEventType.java
This class provides an enumerated type for the SequenceEvent class
to pass around as an identifier
Created: Tue Feb 15 20:10:48 2000