Uses of Class
compbio.metadata.Option

Packages that use Option

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.server

Uses of Option in compbio.data.msa

Method parameters in compbio.data.msa with type arguments of type Option

String	MsaWS.customAlign(List<FastaSequence> sequences, List<Option<T>> options) Align a list of sequences with options.
String	SequenceAnnotation.customAnalize(List<FastaSequence> sequences, List<Option<T>> options) Analyse the sequences according to custom settings defined in options list.

Uses of Option in compbio.data.msa.jaxws

Methods in compbio.data.msa.jaxws that return types with arguments of type Option

List<Option>	CustomAnalize.getOptions()
List<Option>	CustomAlign.getOptions()

Method parameters in compbio.data.msa.jaxws with type arguments of type Option

void	CustomAnalize.setOptions(List<Option> options)
void	CustomAlign.setOptions(List<Option> options)

Uses of Option in compbio.engine.client

Method parameters in compbio.engine.client with type arguments of type Option

static <T> CommandBuilder<T>

CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments, String nameValueSeparator) This produces the same result as getCommands method.

Uses of Option in compbio.metadata

Subclasses of Option in compbio.metadata

class

Parameter<T> A single value containing an option supported by the web service e.g.

Methods in compbio.metadata that return Option

Option<T>	RunnerConfig.getArgument(String name) Returns the argument by its name if found, NULL otherwise.
Option<T>	RunnerConfig.getArgumentByOptionName(String optionName) Returns the argument by option name, NULL if the argument is not found

Methods in compbio.metadata that return types with arguments of type Option

List<Option<T>>	RunnerConfig.getArguments() Returns list of Parameter and Option supported by current runner
List<Option<T>>	Preset.getArguments(RunnerConfig<T> rconfig) Converts list of options as String to type Option
List<Option<T>>	RunnerConfig.getOptions() Returns the list of the Options supported by the executable of type T

Methods in compbio.metadata with parameters of type Option

void	RunnerConfig.addOption(Option<T> option) Adds Option to the internal list of options

Method parameters in compbio.metadata with type arguments of type Option

void	RunnerConfig.setOptions(List<Option<T>> parameters) Adds the list of options or parameters to the internal list of options

Constructors in compbio.metadata with parameters of type Option

WrongParameterException(Option<?> option)

Uses of Option in compbio.runner

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

List<Option<?>>

OptionCombinator.getAllOptions()

Method parameters in compbio.runner with type arguments of type Option

List<String>	OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments)
static List<String>	OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments, RunnerConfig<? extends Executable<?>> rconfig)
List<String>	OptionCombinator.optionsToCommandString(List<Option<?>> options)

Uses of Option in compbio.ws.server

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

String	ClustalOWS.customAlign(List<FastaSequence> sequences, List<Option<ClustalO>> options)
String	ClustalWS.customAlign(List<FastaSequence> sequences, List<Option<ClustalW>> options)
String	MafftWS.customAlign(List<FastaSequence> sequences, List<Option<Mafft>> options)
String	MuscleWS.customAlign(List<FastaSequence> sequences, List<Option<Muscle>> options)
String	ProbconsWS.customAlign(List<FastaSequence> sequences, List<Option<Probcons>> options)
String	_MsaService.customAlign(List<FastaSequence> sequences, List<Option<T>> options)
String	TcoffeeWS.customAlign(List<FastaSequence> sequences, List<Option<Tcoffee>> options)
String	DisemblWS.customAnalize(List<FastaSequence> sequences, List<Option<Disembl>> options)
String	GlobPlotWS.customAnalize(List<FastaSequence> sequences, List<Option<GlobPlot>> options)
String	SequenceAnnotationService.customAnalize(List<FastaSequence> sequences, List<Option<T>> options)
static <T> List<String>	WSUtil.getCommands(List<Option<T>> options, String keyValueSeparator)