Uses of Class
compbio.metadata.Option

Packages that use Option

compbio.data.msa
compbio.data.msa.jaxws
compbio.engine.client	Classes and interfaces representing an input for engines.
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

java.lang.String

MsaWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options) Align a list of sequences with options.

Uses of Option in compbio.data.msa.jaxws

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

java.util.List<Option>

CustomAlign.getOptions()

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

void	CustomAlign.setOptions(java.util.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(java.util.List<? extends Option<T>> arguments, java.lang.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 option supported by the web service e.g.

Methods in compbio.metadata that return Option

Option<T>	RunnerConfig.getArgument(java.lang.String name) Returns the argument by its name if found, NULL otherwise
Option<T>	RunnerConfig.getArgumentByOptionName(java.lang.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

java.util.List<Option<T>>	RunnerConfig.getArguments()
java.util.List<Option<T>>	Preset.getArguments(RunnerConfig<T> rconfig) Converts list of options as String to type Option
java.util.List<Option<T>>	RunnerConfig.getOptions()

Methods in compbio.metadata with parameters of type Option

void	RunnerConfig.addOption(Option<T> option)

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

void	RunnerConfig.setOptions(java.util.List<Option<T>> parameters)

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

java.util.List<Option<?>>

OptionCombinator.getAllOptions()

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

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

Uses of Option in compbio.ws.server

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

java.lang.String	ClustalWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalW>> options)
java.lang.String	MafftWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Mafft>> options)
java.lang.String	MuscleWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Muscle>> options)
java.lang.String	ProbconsWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Probcons>> options)
java.lang.String	TcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Tcoffee>> options)
static <T> java.util.List<java.lang.String>	WSUtil.getCommands(java.util.List<Option<T>> options, java.lang.String keyValueSeparator)