Uses of Class
compbio.runner.msa.ClustalW

Packages that use ClustalW

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

Uses of ClustalW in compbio.runner.msa

Methods in compbio.runner.msa that return ClustalW

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

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

Modifier and Type	Method and Description
java.lang.Class<ClustalW>	ClustalW.getType()

Uses of ClustalW in compbio.ws.server

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

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

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

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

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

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