Uses of Class
compbio.runner.msa.Tcoffee

Packages that use Tcoffee

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

Uses of Tcoffee in compbio.runner.msa

Methods in compbio.runner.msa that return Tcoffee

Tcoffee

Tcoffee.setInput(java.lang.String inFile)

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

CommandBuilder<Tcoffee>	Tcoffee.getParameters(Executable.ExecProvider provider)
java.lang.Class<Tcoffee>	Tcoffee.getType()

Uses of Tcoffee in compbio.ws.server

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

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

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

java.lang.String	TcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Tcoffee>> options)
java.lang.String	TcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, Preset<Tcoffee> preset)