Uses of Class
compbio.metadata.Option

Packages that use Option

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 Option in compbio.data.msa

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

Modifier and Type	Method and Description
java.lang.String	MsaWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options) Align a list of sequences with options.
java.lang.String	SequenceAnnotation.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options) Analyse the sequences according to custom settings defined in options list.

Uses of Option in compbio.data.msa.jaxws

Fields in compbio.data.msa.jaxws with type parameters of type Option

Modifier and Type	Field and Description
private java.util.List<Option>	CustomFold.options
private java.util.List<Option>	CustomAnalize.options
private java.util.List<Option>	CustomAlign.options

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

Modifier and Type	Method and Description
java.util.List<Option>	CustomFold.getOptions()
java.util.List<Option>	CustomAnalize.getOptions()
java.util.List<Option>	CustomAlign.getOptions()

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

Modifier and Type	Method and Description
void	CustomFold.setOptions(java.util.List<Option> options)
void	CustomAnalize.setOptions(java.util.List<Option> options)
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

Modifier and Type	Method and Description
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

Modifier and Type	Class and Description
class	Parameter<T> A single value containing an option supported by the web service e.g.

Fields in compbio.metadata with type parameters of type Option

Modifier and Type	Field and Description
(package private) java.util.List<Option<T>>	RunnerConfig.arguments
(package private) java.util.List<Option<T>>	RunnerConfig.options

Methods in compbio.metadata that return Option

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
java.util.List<Option<T>>	RunnerConfig.getArguments() Returns list of Parameter and Option supported by current runner
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() Returns the list of the Options supported by the executable of type T

Methods in compbio.metadata with parameters of type Option

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
void	RunnerConfig.setOptions(java.util.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

Constructor and Description
WrongParameterException(Option<?> option)

Uses of Option in compbio.runner

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

Modifier and Type	Method and Description
java.util.List<Option<?>>	OptionCombinator.getAllOptions()

Methods in compbio.runner with parameters of type Option

Modifier and Type	Method and Description
(package private) static java.lang.String	OptionCombinator.optionToCommandString(Option<?> option)

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

Modifier and Type	Method and Description
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.client

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

Modifier and Type	Method and Description
(package private) static <T> java.util.List<Option<T>>	MetadataHelper.getParametersList(Metadata<T> msaws) Returns a list of options supported by web service
(package private) static <T> java.util.List<Option<T>>	MetadataHelper.getParametersList(Metadata<T> msaws, java.lang.String host) Returns a list of options supported by web service
(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

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

Modifier and Type	Method and Description
(package private) static <T> Alignment	Jws2Client.align(java.io.File file, MsaWS<T> msaws, Preset<T> preset, java.util.List<Option<T>> customOptions) Align sequences from the file using MsaWS
(package private) static ScoreManager	AAConClient.analize(java.io.File file, SequenceAnnotation<AAConWS> wsproxy, Preset<AAConWS> preset, java.util.List<Option<AAConWS>> customOptions) Calculate conservation for sequences loaded from the file
(package private) static <T> ScoreManager	Jws2Client.analize(java.io.File file, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions) Calculate conservation for sequences loaded from the file
(package private) static <T> ScoreManager	Jws2Client.analize(java.util.List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions) Calculate conservation for sequences loaded from a FASTA record list structure
private <T> boolean	WSTester.testDefaultAnalyse(java.util.List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions)

Uses of Option in compbio.ws.server

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

Modifier and Type	Method and Description
java.lang.String	ClustalOWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalO>> options)
java.lang.String	ClustalWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<ClustalW>> options)
java.lang.String	GLprobsWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<GLprobs>> options)
java.lang.String	MafftWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<Mafft>> options)
java.lang.String	MSAprobsWS.customAlign(java.util.List<FastaSequence> sequences, java.util.List<Option<MSAprobs>> 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)
java.lang.String	AAConWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<AACon>> options)
java.lang.String	DisemblWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<Disembl>> options)
java.lang.String	GlobPlotWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<GlobPlot>> options)
java.lang.String	RNAalifoldWS.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<RNAalifold>> options)
java.lang.String	SequenceAnnotationService.customAnalize(java.util.List<FastaSequence> sequences, java.util.List<Option<T>> options)
static <T> java.util.List<java.lang.String>	WSUtil.getCommands(java.util.List<Option<T>> options, java.lang.String keyValueSeparator)