Uses of Class
compbio.engine.client.CommandBuilder

Packages that use CommandBuilder

compbio.engine.client	Classes and interfaces representing an input for engines.
compbio.runner	Utilities commonly used by all runners.
compbio.runner._impl
compbio.runner.msa	Wrappers for native executables for multiple sequence alignment (msa)

Uses of CommandBuilder in compbio.engine.client

Methods in compbio.engine.client that return CommandBuilder

CommandBuilder<T>	ConfiguredExecutable.getParameters()
CommandBuilder<T>	ConfExecutable.getParameters()
CommandBuilder<?>	RunConfiguration.getParameters()
CommandBuilder<T>	SkeletalExecutable.getParameters(Executable.ExecProvider provider)
CommandBuilder<T>	Executable.getParameters(Executable.ExecProvider provider)
CommandBuilder<T>	ConfExecutable.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

void	RunConfiguration.setParameters(CommandBuilder<?> parameters)

Uses of CommandBuilder in compbio.runner

Methods in compbio.runner that return CommandBuilder

CommandBuilder<_SkeletalCommandBuilder>

_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider)

Uses of CommandBuilder in compbio.runner._impl

Methods in compbio.runner._impl that return CommandBuilder

CommandBuilder<NetNglyc>

NetNglyc.getParameters(Executable.ExecProvider provider)

Uses of CommandBuilder in compbio.runner.msa

Methods in compbio.runner.msa that return CommandBuilder

CommandBuilder<Tcoffee>

Tcoffee.getParameters(Executable.ExecProvider provider)