Uses of Package
compbio.data.sequence

Packages that use compbio.data.sequence

Package	Description
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
compbio.data.msa.jaxws
compbio.data.sequence	A data model for multiple sequence alignment web services and utility methods that work on the objects of this model.
compbio.engine
compbio.metadata	A meta-data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project.
compbio.runner	Utilities commonly used by all runners.
compbio.runner.conservation
compbio.runner.disorder
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.runner.structure
compbio.ws.client	A command line client and web services testing client for JAva Bioinformatics Analysis Web Services.
compbio.ws.server

Classes in compbio.data.sequence used by compbio.data.msa

Class and Description
Alignment Multiple sequence alignment.
FastaSequence A FASTA formatted sequence.
ScoreManager

Classes in compbio.data.sequence used by compbio.data.msa.jaxws

Class and Description
Alignment Multiple sequence alignment.
FastaSequence A FASTA formatted sequence.
ScoreManager

Classes in compbio.data.sequence used by compbio.data.sequence

Class and Description
Alignment Multiple sequence alignment.
AlignmentMetadata Alignment metadata e.g.
ConservationMethod Enumeration listing of all the supported methods.
DisemblResult
DisorderMethod
FastaSequence A FASTA formatted sequence.
GlobProtResult
IUPredResult
Program The list of programmes that can produce alignments
Range
RNAStructReader.AlifoldLine
RNAStructReader.AlifoldResult
RNAStructReader.RNAOut
RNAStructScoreManager
Score A value class for AACon annotation results storage.
ScoreManager
ScoreManager.ScoreHolder
SMERFSConstraints Enumeration defining two constraints for SMERFS columns score calculation.
UnknownFileFormatException

Classes in compbio.data.sequence used by compbio.engine

Class and Description
FastaSequence A FASTA formatted sequence.

Classes in compbio.data.sequence used by compbio.metadata

Class and Description
FastaSequence A FASTA formatted sequence.

Classes in compbio.data.sequence used by compbio.runner

Class and Description
Alignment Multiple sequence alignment.
FastaSequence A FASTA formatted sequence.
RNAStructScoreManager
Score A value class for AACon annotation results storage.
UnknownFileFormatException

Classes in compbio.data.sequence used by compbio.runner.conservation

Class and Description
ScoreManager

Classes in compbio.data.sequence used by compbio.runner.disorder

Class and Description
Score A value class for AACon annotation results storage.
ScoreManager

Classes in compbio.data.sequence used by compbio.runner.msa

Class and Description
Alignment Multiple sequence alignment.

Classes in compbio.data.sequence used by compbio.runner.structure

Class and Description
RNAStructScoreManager

Classes in compbio.data.sequence used by compbio.ws.client

Class and Description
Alignment Multiple sequence alignment.
FastaSequence A FASTA formatted sequence.
ScoreManager

Classes in compbio.data.sequence used by compbio.ws.server

Class and Description
Alignment Multiple sequence alignment.
FastaSequence A FASTA formatted sequence.
ScoreManager