Uses of Class
compbio.runner.msa.Muscle

Packages that use Muscle

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

Uses of Muscle in compbio.runner.msa

Methods in compbio.runner.msa that return Muscle

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

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

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

Uses of Muscle in compbio.ws.server

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

Modifier and Type	Field and Description
private static LimitsManager<Muscle>	MuscleWS.limitMan
private static RunnerConfig<Muscle>	MuscleWS.muscleOptions
private static PresetManager<Muscle>	MuscleWS.musclePresets

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

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

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

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