Package compbio.data.sequence

A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.

See: Description

Class Summary

Class	Description
Alignment	Multiple sequence alignment.
AlignmentMetadata	Alignment metadata e.g.
ClustalAlignmentUtil	Tools to read and write clustal formated files
FastaReader	Reads files with FASTA formatted sequences.
FastaSequence	A FASTA formatted sequence.
Range
RNAStructReader
RNAStructScoreManager
Score	A value class for AACon annotation results storage.
ScoreManager
ScoreManager.ScoreHolder
SequenceUtil	Utility class for operations on sequences

Enum Summary

Enum	Description
ConservationMethod	Enumeration listing of all the supported methods.
DisemblResult
DisorderMethod
GlobProtResult
IUPredResult
Program	The list of programmes that can produce alignments
RNAStructReader.AlifoldLine
RNAStructReader.AlifoldResult
RNAStructReader.RNAOut
SMERFSConstraints	Enumeration defining two constraints for SMERFS columns score calculation.

Exception Summary

Exception	Description
UnknownFileFormatException

Package compbio.data.sequence Description

A data model for multiple sequence alignment web services and utility methods that work on the objects of this model. Classes in this package have no dependencies to other sources in the project. They form a base layer of JAva Bioinformatics Analysis Web Services.

Version:

1.0 January 2010

Author:

Petr Troshin