Uses of Class
compbio.runner.msa.Muscle

Packages that use Muscle

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

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

java.lang.Class<Muscle>

Muscle.getType()

Uses of Muscle in compbio.ws.server

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

Limit<Muscle>	MuscleWS.getLimit(java.lang.String presetName)
LimitsManager<Muscle>	MuscleWS.getLimits()
PresetManager<Muscle>	MuscleWS.getPresets()
RunnerConfig<Muscle>	MuscleWS.getRunnerOptions()

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

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)