Class AbstractIdentificationParametersCli
java.lang.Object
com.compomics.cli.identification_parameters.AbstractIdentificationParametersCli
- All Implemented Interfaces:
Callable
- Direct Known Subclasses:
IdentificationParametersCLI
public abstract class AbstractIdentificationParametersCli extends Object implements Callable
This class serves as a base for the implementation of
IdentificationParametersCLI in specific tools. To make an
IdentificationParametersCLI extend this class and call initiate in the
constructor of your class.
- Author:
- Marc Vaudel, Harald Barsnes
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Constructor Summary
Constructors Constructor Description AbstractIdentificationParametersCli()
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Method Summary
Modifier and Type Method Description Object
call()
protected abstract void
createOptionsCLI(org.apache.commons.cli.Options options)
Provides the options left to the user.static String
getHeader()
IdentificationParametersCLI header message when printing the usage.protected abstract String
getJarFilePath()
Returns the path to the jar file.protected abstract String
getOptionsAsString()
Returns the options left to the user as a string.void
initiate(String[] args)
Initiates the IdentificationParametersCli.void
printEnzymes()
Prints the available enzymes.void
printModifications()
Prints the available modifications.
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Constructor Details
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AbstractIdentificationParametersCli
public AbstractIdentificationParametersCli()
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Method Details
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initiate
Initiates the IdentificationParametersCli.- Parameters:
args
- the command line arguments
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call
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printModifications
public void printModifications()Prints the available modifications. -
printEnzymes
public void printEnzymes()Prints the available enzymes. -
getJarFilePath
Returns the path to the jar file.- Returns:
- the path to the jar file
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createOptionsCLI
protected abstract void createOptionsCLI(org.apache.commons.cli.Options options)Provides the options left to the user.- Parameters:
options
- the options object where the options will be added
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getOptionsAsString
Returns the options left to the user as a string.- Returns:
- the options left to the user as a string
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getHeader
IdentificationParametersCLI header message when printing the usage.- Returns:
- the header message as a string
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