Package org.emboss.jemboss.editor

Interface Summary

GroutAlignJFrameListener	GroutAlignJFrameListener.java Created: 10th June 2003
GroutGraphicSequenceCollectionListener	GroutGraphicSequenceCollectionListener.java Created: Thu Mar 13 14:42:13 2003

Class Summary

AlignApplet
AlignJFrame	Displays a grapical representation of a collection of sequences.
ColourJFrame	Colour pallette display and editor.
ColourMenu	Colour menu displayed in a popup menu from the colour display pallette (ColourJFrame).
ColourPanel	Colour panel for each individual residue in the pallette
Consensus	Calculate a consensus using the same method as 'cons' in the EMBOSS suite.
ConsensusOptions	Defines the options to be used in calculating a consensus
GraphicSequenceCollection	This class can be used to get a grapical representation of a collection of sequences.
GroutAlignJFrame	Displays a grapical representation of a collection of sequences.
GroutAlignJFrameEvent
GroutGraphicSequenceCollection	This class can be used to get a grapical representation of a collection of sequences.
GroutGraphicSequenceCollectionEvent
GroutSequence	Sequence object
GroutSequenceJPanel	Sequence panel for drawing a sequence or the sequence numbers
IDTableJFrame	Use to display the identical matches table for each pair of sequences
Matrix	Reads and hold a sequence scoring matrix
MatrixJFrame	Display a matrix and list of available scoring matrix files
Paste
PatternJFrame	Frame for searching for patterns in the sequences
PlotConsensus	Plot the average similarity.
PrettyPlotJFrame	JFrame to define the colour of residue if identical or a positive match.
PrintableJTable
PrintAlignment	Class for printing the alignment
PrintAlignmentImage	Print png/jpeg image and print preview.
Sequence	Sequence object
SequenceJPanel	Sequence panel for drawing a sequence or the sequence numbers
SequenceNameJButton	Draw sequence name toggle button
SequenceProperties	General sequence properties
SequenceReader	This class reads sequences in FASTA and MSF format.
SequenceSaver	This class saves sequences in FASTA format.