Uses of Class
compbio.data.sequence.Alignment

Packages that use Alignment

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.runner	Utilities commonly used by all runners.
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.ws.client	A command line client and web services testing client for JAva Bioinformatics Analysis Web Services.
compbio.ws.server

Uses of Alignment in compbio.data.msa

Methods in compbio.data.msa that return Alignment

Modifier and Type	Method and Description
Alignment	MsaWS.getResult(java.lang.String jobId) Return the result of the job.

Uses of Alignment in compbio.data.msa.jaxws

Fields in compbio.data.msa.jaxws declared as Alignment

Modifier and Type	Field and Description
private Alignment	GetResultResponse._return
private Alignment	PresetFold.alignment
private Alignment	Fold.alignment
private Alignment	CustomFold.alignment

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

Modifier and Type	Method and Description
Alignment	PresetFold.getAlignment()
Alignment	Fold.getAlignment()
Alignment	CustomFold.getAlignment()
Alignment	GetResultResponse.getReturn()

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

Modifier and Type	Method and Description
void	PresetFold.setAlignment(Alignment alignment)
void	Fold.setAlignment(Alignment alignment)
void	CustomFold.setAlignment(Alignment alignment)
void	GetResultResponse.setReturn(Alignment _return)

Uses of Alignment in compbio.data.sequence

Methods in compbio.data.sequence that return Alignment

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
static Alignment	Util.readClustalFile(java.lang.String workDirectory, java.lang.String clustFile)
static Alignment	RunnerUtil.readClustalFile(java.lang.String workDirectory, java.lang.String clustFile)

Uses of Alignment in compbio.runner.msa

Methods in compbio.runner.msa that return Alignment

Modifier and Type	Method and Description
Alignment	Probcons.getResults(java.lang.String workDirectory)
Alignment	Tcoffee.getResults(java.lang.String workDirectory)
Alignment	Mafft.getResults(java.lang.String workDirectory)
Alignment	Muscle.getResults(java.lang.String workDirectory)
Alignment	MSAprobs.getResults(java.lang.String workDirectory)
Alignment	ClustalO.getResults(java.lang.String workDirectory)
Alignment	ClustalW.getResults(java.lang.String workDirectory)
Alignment	GLprobs.getResults(java.lang.String workDirectory)

Uses of Alignment in compbio.ws.client

Methods in compbio.ws.client that return Alignment

Modifier and Type	Method and Description
(package private) static <T> Alignment	Jws2Client.align(java.io.File file, MsaWS<T> msaws, Preset<T> preset, java.util.List<Option<T>> customOptions) Align sequences from the file using MsaWS

Methods in compbio.ws.client with parameters of type Alignment

Modifier and Type	Method and Description
(package private) static void	IOHelper.writeOut(java.io.Writer writer, Alignment align) Outputs clustal formatted alignment into the file represented by the outStream

Uses of Alignment in compbio.ws.server

Methods in compbio.ws.server that return Alignment

Modifier and Type	Method and Description
Alignment	GLprobsWS.getResult(java.lang.String jobId)
Alignment	MafftWS.getResult(java.lang.String jobId)
Alignment	ClustalOWS.getResult(java.lang.String jobId)
Alignment	MSAprobsWS.getResult(java.lang.String jobId)
Alignment	MuscleWS.getResult(java.lang.String jobId)
Alignment	ClustalWS.getResult(java.lang.String jobId)
Alignment	TcoffeeWS.getResult(java.lang.String jobId)
Alignment	ProbconsWS.getResult(java.lang.String jobId)