Uses of Class
compbio.metadata.RunnerConfig

Packages that use RunnerConfig

Package	Description
compbio.data.msa	Web Service interfaces for JAva Bioinformatics Analysis Web Services.
compbio.data.msa.jaxws
compbio.engine.client
compbio.metadata	A meta-data model for multiple sequence alignment web services Classes in this package have no dependencies to other sources in the project.
compbio.runner	Utilities commonly used by all runners.
compbio.ws.client	A command line client and web services testing client for JAva Bioinformatics Analysis Web Services.
compbio.ws.server

Uses of RunnerConfig in compbio.data.msa

Methods in compbio.data.msa that return RunnerConfig

Modifier and Type	Method and Description
RunnerConfig<T>	Metadata.getRunnerOptions() Get options supported by a web service

Uses of RunnerConfig in compbio.data.msa.jaxws

Fields in compbio.data.msa.jaxws declared as RunnerConfig

Modifier and Type	Field and Description
private RunnerConfig	GetRunnerOptionsResponse._return

Methods in compbio.data.msa.jaxws that return RunnerConfig

Modifier and Type	Method and Description
RunnerConfig	GetRunnerOptionsResponse.getReturn()

Methods in compbio.data.msa.jaxws with parameters of type RunnerConfig

Modifier and Type	Method and Description
void	GetRunnerOptionsResponse.setReturn(RunnerConfig _return)

Uses of RunnerConfig in compbio.engine.client

Methods in compbio.engine.client that return RunnerConfig

Modifier and Type	Method and Description
static <V> RunnerConfig<V>	ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)

Uses of RunnerConfig in compbio.metadata

Methods in compbio.metadata that return RunnerConfig

Modifier and Type	Method and Description
RunnerConfig<T>	RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf)

Methods in compbio.metadata with parameters of type RunnerConfig

Modifier and Type	Method and Description
RunnerConfig<T>	RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf)
(package private) Argument<T>	PresetManager.getArgument(RunnerConfig<T> options, java.lang.String optionName)
java.util.List<Option<T>>	Preset.getArguments(RunnerConfig<T> rconfig) Converts list of options as String to type Option
void	PresetManager.validate(RunnerConfig<T> options) Checks whether preset option and parameter are defined in RunnerConfig object.

Uses of RunnerConfig in compbio.runner

Fields in compbio.runner declared as RunnerConfig

Modifier and Type	Field and Description
private RunnerConfig<? extends Executable<?>>	OptionCombinator.rconfig

Methods in compbio.runner that return RunnerConfig

Modifier and Type	Method and Description
static <T> RunnerConfig<T>	Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)
static <T> RunnerConfig<T>	RunnerUtil.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)

Methods in compbio.runner with parameters of type RunnerConfig

Modifier and Type	Method and Description
static java.util.List<java.lang.String>	OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, RunnerConfig<? extends Executable<?>> rconfig)

Constructors in compbio.runner with parameters of type RunnerConfig

Constructor and Description
OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)

Uses of RunnerConfig in compbio.ws.client

Methods in compbio.ws.client with parameters of type RunnerConfig

Modifier and Type	Method and Description
(package private) static <T> java.util.List<Option<T>>	MetadataHelper.processParameters(java.util.List<java.lang.String> params, RunnerConfig<T> options) Converts options supplied via parameters file into Option objects

Uses of RunnerConfig in compbio.ws.server

Fields in compbio.ws.server declared as RunnerConfig

Modifier and Type	Field and Description
private RunnerConfig<T>	GenericMetadataService.aaconOptions
private static RunnerConfig<ClustalO>	ClustalOWS.clustalOptions
private static RunnerConfig<ClustalW>	ClustalWS.clustalOptions
private static RunnerConfig<GLprobs>	GLprobsWS.GLprobsOptions
private static RunnerConfig<Mafft>	MafftWS.mafftOptions
private static RunnerConfig<MSAprobs>	MSAprobsWS.MSAprobsOptions
private static RunnerConfig<Muscle>	MuscleWS.muscleOptions
private static RunnerConfig<Probcons>	ProbconsWS.probconsOptions
private static RunnerConfig<Tcoffee>	TcoffeeWS.tcoffeeOptions

Methods in compbio.ws.server that return RunnerConfig

Modifier and Type	Method and Description
RunnerConfig<T>	GenericMetadataService.getRunnerOptions()
RunnerConfig<GLprobs>	GLprobsWS.getRunnerOptions()
RunnerConfig<Mafft>	MafftWS.getRunnerOptions()
RunnerConfig<ClustalO>	ClustalOWS.getRunnerOptions()
RunnerConfig<MSAprobs>	MSAprobsWS.getRunnerOptions()
RunnerConfig<Muscle>	MuscleWS.getRunnerOptions()
RunnerConfig<ClustalW>	ClustalWS.getRunnerOptions()
RunnerConfig<Tcoffee>	TcoffeeWS.getRunnerOptions()
RunnerConfig<Probcons>	ProbconsWS.getRunnerOptions()