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.