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| -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)
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-- Align a list of sequences with options. |
-
- String |
-SequenceAnnotation.customAnalize(List<FastaSequence> sequences,
- List<Option<T>> options)
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-- 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()
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-- |
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- List<Option> |
-CustomAlign.getOptions()
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-- |
-
- -
| 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)
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-- |
-
| -Uses of Option in compbio.engine.client | -
|---|
- -
| Method parameters in compbio.engine.client with type arguments of type Option | -||
|---|---|---|
-static
- |
-CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments,
- String nameValueSeparator)
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-- 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)
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-- 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)
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-- |
-|
| -Uses of Option in compbio.runner | -
|---|
- -
| Methods in compbio.runner that return types with arguments of type Option | -|
|---|---|
- List<Option<?>> |
-OptionCombinator.getAllOptions()
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-- |
-
- -
| 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
- |
-WSUtil.getCommands(List<Option<T>> options,
- String keyValueSeparator)
-
-- |
-|
-
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