Parameters.xml file.
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-- Version:
- - 1.0 October 2009
-- Author:
- - pvtroshin
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-Constructor Detail |
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-RunnerConfig
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-public RunnerConfig()
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-copyAndValidateRConfig
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-public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
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-getOptions
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-public List<Option<T>> getOptions()
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-- Returns the list of the Options supported by the executable of type T
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-- Returns:
- list of
Option supported by type T - See Also:
Option
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-addParameter
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-public void addParameter(Parameter<T> param)
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-- Adds parameter to the internal parameter list
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-- Parameters:
param - the Parameter to add- See Also:
Parameter
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-addOption
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-public void addOption(Option<T> option)
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-- Adds Option to the internal list of options
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-- Parameters:
option - the Option to add
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-getArguments
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-public List<Option<T>> getArguments()
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-- Returns list of
Parameter and Option supported by current
- runner
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-- Returns:
- list of
Option and Parameter supported by type T
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-getPrmSeparator
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-public String getPrmSeparator()
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-- Returns:
- name value separator character
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-setPrmSeparator
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-public void setPrmSeparator(String prmSeparator)
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-- Sets name value separator character
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-- Parameters:
prmSeparator - the separator char
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-setOptions
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-public void setOptions(List<Option<T>> parameters)
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-- Adds the list of options or parameters to the internal list of options
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-- Parameters:
parameters - the list of parameters to add
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-getRunnerClassName
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-public String getRunnerClassName()
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-- Returns:
- fully qualified class name for type T
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-setRunnerClassName
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-public void setRunnerClassName(String runnerClassName)
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-- Set the name of a runner class
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-- Parameters:
runnerClassName - the name of the executable wrapping class
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-setParameters
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-public void setParameters(List<Parameter<T>> parameters)
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-- Sets the list of parameters as internal list
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-- Parameters:
parameters - the list of parameters
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-getParameters
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-public List<Parameter<T>> getParameters()
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-- Returns the list of parameters supported executable of type T. Where
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Parameter is an Option with value.
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-- Returns:
- List of
Parameter supported by type T.
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-toString
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-public String toString()
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-- Overrides:
toString in class Object
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-equals
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-public boolean equals(Object obj)
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-- Overrides:
equals in class Object
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-getArgument
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-public Option<T> getArgument(String name)
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-- Returns the argument by its name if found, NULL otherwise. Where the
- Argument is a common interface for
Option and Parameter
- therefore this method can return either. If you need to retrieve the
- Option by its optionNames use @link
- getArgumentByOptionName(String) method. The
- difference between option name and optionName is explained by the
- following example:
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- Sequence type
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- --nuc - Assume the sequences are nucleotide.
- --amino - Assume the sequences are amino acid.
- --amino
- --nuc
- --auto
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- In the example, the "Sequence type" is a name whereas --amino, --nuc and
- --auto are all optionNames. This dichotomy only manifests in
- Option never in Parameters as the latter can
- only have single element
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-- Parameters:
name - the Parameter of Option name
-- Returns:
Argument
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-removeArgument
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-public boolean removeArgument(String name)
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-- Removes the argument
Argument if found. Where Argument is either
- Option or Parameter.
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-- Parameters:
name - of the argument
-- Returns:
- true if argument was removed, false otherwise
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-getArgumentByOptionName
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-public Option<T> getArgumentByOptionName(String optionName)
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-- Returns the argument by option name, NULL if the argument is not found
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-- Parameters:
optionName - - the optionName. This is not the same as an Option name.
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- For example:
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- Output sequences order
- --inputorder - Output order: same as input.
- --reorder - Output order: aligned. Default: same as input
- --inputorder
- --reorder
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- The name of the option in the example is
- "Output sequences order" whereas optionNames are
- "--inputorder" and "--reorder". If you need to retrieve the
- Option or Parameter by its names use
- getArgument(String) method
-- Returns:
- Option
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-removeArgumentByOptionName
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-public boolean removeArgumentByOptionName(String optionName)
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-- Removes the argument which can be a Parameter or an Option instance by
- the value in element of the runner configuration
- descriptor.
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-- Parameters:
optionName - the optionName of the option, do not confuse with the name!
-- Returns:
- true if argument with optionName exists and was removed, false
- otherwise
- See Also:
for destinctions
- between optionNames and the name of the Option
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-validate
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-public void validate()
- throws ValidationException
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-- Validate the value of the argument. Checks whether the argument value is
- in the valid values range.
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-- Throws:
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ValidationException - if any of the arguments found invalid which is when
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- Parameter value outside
ValueConstrain boundary
- - Parameter name is not listed in possible values
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compbio.metadata.RunnerConfig<T>
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