compbio.metadata
Class Option<T>

java.lang.Object
  compbio.metadata.Option<T>

Type Parameters:

T - type of executable

All Implemented Interfaces:

Argument<T>

Direct Known Subclasses:

Parameter

public class Option<T>
extends java.lang.Object
implements Argument<T>

Command line option/flag or multiple exclusive options with no value. Example -protein, -dna, -auto

Version:

1.0 October 2009

Author:

pvtroshin

Constructor Summary

Option(java.lang.String name, java.lang.String description)

Method Summary

java.util.Set<java.lang.String>	addOptionNames(java.lang.String... value) Adds an option to the optionName list
boolean	equals(java.lang.Object obj)
java.lang.String	getDefaultValue() A default value of the option.
java.lang.String	getDescription() A long description of the Option
java.net.URL	getFurtherDetails() The URL where further details about the option can be found
java.lang.String	getName() Human readable name of the option
java.util.List<java.lang.String>	getOptionNames()
java.util.List<java.lang.String>	getPossibleValues() List of possible optionNames
int	hashCode()
boolean	isRequired() Flag that indicated that this option must be specified in the command line for an executable to run
void	setDefaultValue(java.lang.String defaultVal) Sets one of the values defined in optionList as default.
void	setDescription(java.lang.String description)
void	setFurtherDetails(java.net.URL furtherDetails)
void	setName(java.lang.String name)
void	setOptionNames(java.util.Set<java.lang.String> optionNames)
void	setRequired(boolean isRequired)
void	setValue(java.lang.String dValue) Set default values for the parameter or an option
java.lang.String	toCommand(java.lang.String nameValueSeparator) Convert the option to the command string.
java.lang.String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Option

public Option(java.lang.String name,
              java.lang.String description)

Method Detail

getName

public java.lang.String getName()

Human readable name of the option

Specified by:

getName in interface Argument<T>

setName

public void setName(java.lang.String name)

getDescription

public java.lang.String getDescription()

A long description of the Option

Specified by:

getDescription in interface Argument<T>

setDescription

public void setDescription(java.lang.String description)

getFurtherDetails

public java.net.URL getFurtherDetails()

The URL where further details about the option can be found

Specified by:

getFurtherDetails in interface Argument<T>

setFurtherDetails

public void setFurtherDetails(java.net.URL furtherDetails)

getDefaultValue

public java.lang.String getDefaultValue()

A default value of the option. Defaults to command line argument name e.g. -auto

Specified by:

getDefaultValue in interface Argument<T>

setDefaultValue

public void setDefaultValue(java.lang.String defaultVal)
                     throws WrongParameterException

Sets one of the values defined in optionList as default. Attempting set the value not listed there will result in WrongParameter exception

Parameters:

defaultVal -

Throws:

WrongParameterException - is thrown if the defaultValue is not found in optionList

isRequired

public boolean isRequired()

Flag that indicated that this option must be specified in the command line for an executable to run

Returns:

true is the option is required, false otherwise

setRequired

public void setRequired(boolean isRequired)

getOptionNames

public java.util.List<java.lang.String> getOptionNames()

Returns:

List of option names

setOptionNames

public void setOptionNames(java.util.Set<java.lang.String> optionNames)

addOptionNames

public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)

Adds an option to the optionName list

Parameters:

value -

Returns:

modified optionName list

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toCommand

public java.lang.String toCommand(java.lang.String nameValueSeparator)

Convert the option to the command string.

Returns:

If only one optionName is defined, than it is returned, if many option names are defined, then the defaultValue is returned. Option must have a default value if there are many optionNames to be valid.

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

getPossibleValues

public java.util.List<java.lang.String> getPossibleValues()

List of possible optionNames

Specified by:

getPossibleValues in interface Argument<T>

Returns:

List of values allowed for an Argument

setValue

public void setValue(java.lang.String dValue)
              throws WrongParameterException

Description copied from interface: Argument

Set default values for the parameter or an option

Specified by:

setValue in interface Argument<T>

Parameters:

dValue - the value to be set

Throws:

WrongParameterException - - when the value to be set is illegal. Wrong value for numeric parameter is the value defined outside it , for string type parameter, wrong value is the one which is not listed in possible values list

See Also:

ValueConstrain