Uses of Class
compbio.data.sequence.Alignment

Packages that use Alignment

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.runner	Utilities commonly used by all runners.
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.ws.server

Uses of Alignment in compbio.data.msa

Methods in compbio.data.msa that return Alignment

Alignment

MsaWS.getResult(java.lang.String jobId) Return the result of the job.

Uses of Alignment in compbio.data.msa.jaxws

Methods in compbio.data.msa.jaxws that return Alignment

Alignment

GetResultResponse.getReturn()

Methods in compbio.data.msa.jaxws with parameters of type Alignment

void	GetResultResponse.setReturn(Alignment _return)

Uses of Alignment in compbio.data.sequence

Methods in compbio.data.sequence that return Alignment

static Alignment	ClustalAlignmentUtil.readClustalFile(java.io.File file)
static Alignment	ClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) Read Clustal formatted alignment.

Methods in compbio.data.sequence with parameters of type Alignment

static void

ClustalAlignmentUtil.writeClustalAlignment(java.io.Writer out, Alignment alignment) Write Clustal formatted alignment Limitations: does not record the consensus.

Uses of Alignment in compbio.runner

Methods in compbio.runner that return Alignment

static Alignment

Util.readClustalFile(java.lang.String workDirectory, java.lang.String clustFile)

Uses of Alignment in compbio.runner.msa

Methods in compbio.runner.msa that return Alignment

Alignment	Mafft.getResults(java.lang.String workDirectory)
Alignment	ClustalO.getResults(java.lang.String workDirectory)
Alignment	ClustalW.getResults(java.lang.String workDirectory)
Alignment	Probcons.getResults(java.lang.String workDirectory)
Alignment	Tcoffee.getResults(java.lang.String workDirectory)
Alignment	Muscle.getResults(java.lang.String workDirectory)

Uses of Alignment in compbio.ws.server

Methods in compbio.ws.server that return Alignment

Alignment	MafftWS.getResult(java.lang.String jobId)
Alignment	ClustalOWS.getResult(java.lang.String jobId)
Alignment	ProbconsWS.getResult(java.lang.String jobId)
Alignment	TcoffeeWS.getResult(java.lang.String jobId)
Alignment	ClustalWS.getResult(java.lang.String jobId)
Alignment	MuscleWS.getResult(java.lang.String jobId)