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Packages that use Option | |
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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 |
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Method parameters in compbio.data.msa with type arguments of type Option | |
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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 |
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Methods in compbio.data.msa.jaxws that return types with arguments of type Option | |
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List<Option> |
CustomAnalize.getOptions()
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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 | |
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void |
CustomAnalize.setOptions(List<Option> options)
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void |
CustomAlign.setOptions(List<Option> options)
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Uses of Option in compbio.engine.client |
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Method parameters in compbio.engine.client with type arguments of type Option | ||
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static
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CommandBuilder.newCommandBuilder(List<? extends Option<T>> arguments,
String nameValueSeparator)
This produces the same result as getCommands method. |
Uses of Option in compbio.metadata |
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Subclasses of Option in compbio.metadata | |
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class |
Parameter<T>
A single value containing an option supported by the web service e.g. |
Methods in compbio.metadata that return Option | |
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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 | |
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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 | |
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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 | |
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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 | |
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WrongParameterException(Option<?> option)
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Uses of Option in compbio.runner |
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Methods in compbio.runner that return types with arguments of type Option | |
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List<Option<?>> |
OptionCombinator.getAllOptions()
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Method parameters in compbio.runner with type arguments of type Option | |
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List<String> |
OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments)
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static List<String> |
OptionCombinator.argumentsToCommandString(List<? extends Option<?>> arguments,
RunnerConfig<? extends Executable<?>> rconfig)
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List<String> |
OptionCombinator.optionsToCommandString(List<Option<?>> options)
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Uses of Option in compbio.ws.server |
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