+Uses of Class compbio.metadata.Option +

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+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.metadata	A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.

+ +

+ + + + + +
+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.
+ 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.
+ +

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.
+ `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
+ +

+ + + + + + + + + + + + + +
Methods in compbio.data.msa.jaxws that return types with arguments of type Option
+ java.util.List<Option> CustomAnalize.getOptions() + +
+
+ java.util.List<Option> CustomAlign.getOptions() + +
+
+ +

Methods in compbio.data.msa.jaxws that return types with arguments of type Option
+ `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
+ void CustomAnalize.setOptions(java.util.List<Option> options) + +
+
+ void CustomAlign.setOptions(java.util.List<Option> options) + +
+
+ +

Method parameters in compbio.data.msa.jaxws with type arguments of type Option
+ `void`	`CustomAnalize.setOptions(java.util.List<Option> options)` + + +
+ `void`	`CustomAlign.setOptions(java.util.List<Option> options)` + + +

+ + + + + +
+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.
+ +

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(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 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() + +
+          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 that return types with arguments of type Option
+ `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
+ void RunnerConfig.addOption(Option<T> option) + +
+ Adds Option to the internal list of options
+ +

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(java.util.List<Option<T>> parameters) + +
+ Adds the list of options or parameters to the internal list of options
+ +

Method parameters in compbio.metadata with type arguments of type Option
+ `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
WrongParameterException(Option<?> option) + +
+
+ +

Constructors in compbio.metadata with parameters of type Option
`WrongParameterException(Option<?> option)` + + +