Uses of Class
compbio.runner.msa.Mafft

Packages that use Mafft

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

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

java.lang.Class<Mafft>

Mafft.getType()

Uses of Mafft in compbio.ws.server

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

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

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

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)