Uses of Class
compbio.runner.msa.ClustalO

Packages that use ClustalO

Package	Description
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)
compbio.ws.server

Uses of ClustalO in compbio.runner.msa

Methods in compbio.runner.msa that return ClustalO

Modifier and Type	Method and Description
ClustalO	ClustalO.setInput(java.lang.String inFile)
ClustalO	ClustalO.setOutput(java.lang.String outFile)

Methods in compbio.runner.msa that return types with arguments of type ClustalO

Modifier and Type	Method and Description
CommandBuilder<ClustalO>	ClustalO.getParameters(Executable.ExecProvider provider)
java.lang.Class<ClustalO>	ClustalO.getType()

Uses of ClustalO in compbio.ws.server

Fields in compbio.ws.server with type parameters of type ClustalO

Modifier and Type	Field and Description
private static RunnerConfig<ClustalO>	ClustalOWS.clustalOptions
private static PresetManager<ClustalO>	ClustalOWS.clustalPresets
private static LimitsManager<ClustalO>	ClustalOWS.limitMan

Methods in compbio.ws.server that return types with arguments of type ClustalO

Modifier and Type	Method and Description
Limit<ClustalO>	ClustalOWS.getLimit(java.lang.String presetName)
LimitsManager<ClustalO>	ClustalOWS.getLimits()
PresetManager<ClustalO>	ClustalOWS.getPresets()
RunnerConfig<ClustalO>	ClustalOWS.getRunnerOptions()
(package private) ConfiguredExecutable<ClustalO>	ClustalOWS.init(java.util.List<FastaSequence> dataSet)

Method parameters in compbio.ws.server with type arguments of type ClustalO

Modifier and Type	Method and Description
java.lang.String	ClustalOWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalO>> options)
java.lang.String	ClustalOWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<ClustalO> preset)