Uses of Class
compbio.runner.msa.Mafft

Packages that use Mafft

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

Uses of Mafft in compbio.runner.msa

Methods in compbio.runner.msa that return Mafft

Modifier and Type	Method and Description
Mafft	Mafft.addParameters(java.util.List<java.lang.String> parameters) Mafft input must always be the last parameter!
Mafft	Mafft.setInput(java.lang.String inFile)

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

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

Uses of Mafft in compbio.ws.server

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

Modifier and Type	Field and Description
private static LimitsManager<Mafft>	MafftWS.limitMan
private static RunnerConfig<Mafft>	MafftWS.mafftOptions
private static PresetManager<Mafft>	MafftWS.mafftPresets

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

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

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

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