picard.cmdline

Class PicardCommandLine

java.lang.Object

picard.cmdline.PicardCommandLine

public class PicardCommandLine
extends java.lang.Object

This is the main class of Picard and is the way of executing individual command line programs. CommandLinePrograms are listed in a single command line interface based on the java package specified to instanceMain. If you want your own single command line program, extend this class and give instanceMain a new list of java packages in which to search for classes that extend CommandLineProgram.

Constructor Summary

Constructors

Constructor and Description
PicardCommandLine()

Method Summary

Modifier and Type	Method and Description
protected static java.util.List<java.lang.String>	getPackageList() The packages we wish to include in our command line
static CommandLineProgramProperties	getProgramProperty(java.lang.Class clazz)
protected int	instanceMain(java.lang.String[] args) For testing
protected int	instanceMain(java.lang.String[] args, java.util.List<java.lang.String> packageList, java.lang.String commandLineName) The main method.
static void	main(java.lang.String[] args) Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
static void	printUnknown(java.util.Set<java.lang.Class<?>> classes, java.lang.String command) When a command does not match any known command, searches for similar commands, using the same method as GIT

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PicardCommandLine

public PicardCommandLine()

Method Detail

getPackageList

protected static java.util.List<java.lang.String> getPackageList()

The packages we wish to include in our command line

instanceMain

protected int instanceMain(java.lang.String[] args,
                           java.util.List<java.lang.String> packageList,
                           java.lang.String commandLineName)

The main method. Give a list of java packages in which to search for classes that extend CommandLineProgram. Those will be included on the command line.

instanceMain

protected int instanceMain(java.lang.String[] args)

For testing

main

public static void main(java.lang.String[] args)

Override this if you want to include different java packages to search for classes that extend CommandLineProgram.

getProgramProperty

public static CommandLineProgramProperties getProgramProperty(java.lang.Class clazz)

printUnknown

public static void printUnknown(java.util.Set<java.lang.Class<?>> classes,
                                java.lang.String command)

When a command does not match any known command, searches for similar commands, using the same method as GIT