Uses of Class
compbio.engine.client.CommandBuilder

Packages that use CommandBuilder

Package	Description
compbio.engine.client
compbio.runner.conservation
compbio.runner.disorder
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)

Uses of CommandBuilder in compbio.engine.client

Fields in compbio.engine.client declared as CommandBuilder

Modifier and Type	Field and Description
protected CommandBuilder<T>	SkeletalExecutable.cbuilder This has to allow duplicate parameters as different options may have the same value e.g.
private CommandBuilder<?>	RunConfiguration.parameters Parameters

Methods in compbio.engine.client that return CommandBuilder

Modifier and Type	Method and Description
CommandBuilder<T>	ConfExecutable.getParameters()
CommandBuilder<?>	RunConfiguration.getParameters()
CommandBuilder<T>	ConfiguredExecutable.getParameters()
CommandBuilder<T>	SkeletalExecutable.getParameters(Executable.ExecProvider provider)
CommandBuilder<T>	ConfExecutable.getParameters(Executable.ExecProvider provider)
CommandBuilder<T>	Executable.getParameters(Executable.ExecProvider provider)
static <T> CommandBuilder<T>	CommandBuilder.newCommandBuilder(java.util.List<? extends Option<T>> arguments, java.lang.String nameValueSeparator) This produces the same result as getCommands method.

Methods in compbio.engine.client with parameters of type CommandBuilder

Modifier and Type	Method and Description
void	RunConfiguration.setParameters(CommandBuilder<?> parameters)

Uses of CommandBuilder in compbio.runner.conservation

Methods in compbio.runner.conservation that return CommandBuilder

Modifier and Type	Method and Description
CommandBuilder<AACon>	AACon.getParameters(Executable.ExecProvider provider)

Uses of CommandBuilder in compbio.runner.disorder

Methods in compbio.runner.disorder that return CommandBuilder

Modifier and Type	Method and Description
CommandBuilder<Jronn>	Jronn.getParameters(Executable.ExecProvider provider)

Uses of CommandBuilder in compbio.runner.msa

Methods in compbio.runner.msa that return CommandBuilder

Modifier and Type	Method and Description
CommandBuilder<Tcoffee>	Tcoffee.getParameters(Executable.ExecProvider provider)
CommandBuilder<ClustalO>	ClustalO.getParameters(Executable.ExecProvider provider)