public class AnnotatePositionCommandLineParser extends JannovarAnnotationCommandLineParser
helpOptions, options, parser
Constructor and Description |
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AnnotatePositionCommandLineParser() |
Modifier and Type | Method and Description |
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protected void |
initializeParser()
|
JannovarOptions |
parse(String[] argv)
Parse command line arguments and return
JannovarOptions . |
void |
printHelp() |
printHelpIfOptionIsSet
public JannovarOptions parse(String[] argv) throws org.apache.commons.cli.ParseException, HelpRequestedException
JannovarAnnotationCommandLineParser
JannovarOptions
.parse
in class JannovarAnnotationCommandLineParser
argv
- arguments to parseorg.apache.commons.cli.ParseException
- on problems with the argumentsHelpRequestedException
protected void initializeParser()
JannovarAnnotationCommandLineParser
JannovarAnnotationCommandLineParser.parser
and JannovarAnnotationCommandLineParser.options
.
override to add more options to the parserinitializeParser
in class JannovarAnnotationCommandLineParser
public void printHelp()
printHelp
in class JannovarAnnotationCommandLineParser
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