public abstract class JannovarAnnotationCommandLineParser extends Object
Modifier and Type | Field and Description |
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protected org.apache.commons.cli.Options |
helpOptions
option to catch the help option if set
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protected org.apache.commons.cli.Options |
options
options representation for the Apache commons command line parser
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protected org.apache.commons.cli.DefaultParser |
parser
the Apache commons command line parser
|
Constructor and Description |
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JannovarAnnotationCommandLineParser()
Calls initializeParser().
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Modifier and Type | Method and Description |
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protected void |
initializeParser()
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abstract JannovarOptions |
parse(String[] argv)
Parse command line arguments and return
JannovarOptions . |
protected abstract void |
printHelp() |
protected void |
printHelpIfOptionIsSet(org.apache.commons.cli.CommandLine cmd) |
protected org.apache.commons.cli.Options options
protected org.apache.commons.cli.Options helpOptions
protected org.apache.commons.cli.DefaultParser parser
public JannovarAnnotationCommandLineParser()
protected void initializeParser()
protected void printHelpIfOptionIsSet(org.apache.commons.cli.CommandLine cmd) throws HelpRequestedException
HelpRequestedException
public abstract JannovarOptions parse(String[] argv) throws org.apache.commons.cli.ParseException, HelpRequestedException
JannovarOptions
.argv
- arguments to parseorg.apache.commons.cli.ParseException
- on problems with the argumentsHelpRequestedException
protected abstract void printHelp()
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