public abstract class JannovarCommand extends Object
Modifier and Type | Field and Description |
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protected com.google.common.collect.ImmutableList<String> |
args
command line arguments
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protected JannovarOptions |
options
Configuration to use for the command execution.
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protected int |
verbosity
Verbosity level: (0) quiet, (1) normal, (2) verbose, (3) very verbose
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Constructor and Description |
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JannovarCommand(String[] argv)
Initialize the JannovarCommand.
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Modifier and Type | Method and Description |
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protected abstract JannovarOptions |
parseCommandLine(String[] argv)
Function for parsing the command line.
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abstract void |
run()
Function for the execution of the command.
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protected JannovarOptions options
protected int verbosity
protected final com.google.common.collect.ImmutableList<String> args
public JannovarCommand(String[] argv) throws CommandLineParsingException, HelpRequestedException
argv
- command line arguments to useCommandLineParsingException
- on problems with the command lineHelpRequestedException
- if the user requested help through the command line parametersprotected abstract JannovarOptions parseCommandLine(String[] argv) throws CommandLineParsingException, HelpRequestedException
argv
- command line to parse, as in the program's main functionJannovarOptions
with the programs' configurationCommandLineParsingException
- on problems with the command lineHelpRequestedException
- when the user requested the help pagepublic abstract void run() throws JannovarException
JannovarException
- on problems executing the command.Copyright © 2016. All rights reserved.