Uses of Class
compbio.runner.msa.Tcoffee

Packages that use Tcoffee

Package	Description
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

Modifier and Type	Method and Description
Tcoffee	Tcoffee.setInput(java.lang.String inFile)

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

Modifier and Type	Method and Description
CommandBuilder<Tcoffee>	Tcoffee.getParameters(Executable.ExecProvider provider)
java.lang.Class<Tcoffee>	Tcoffee.getType()

Uses of Tcoffee in compbio.ws.server

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

Modifier and Type	Field and Description
private static LimitsManager<Tcoffee>	TcoffeeWS.limitMan
private static RunnerConfig<Tcoffee>	TcoffeeWS.tcoffeeOptions
private static PresetManager<Tcoffee>	TcoffeeWS.tcoffeePresets

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

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

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

Modifier and Type	Method and Description
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)