Package ffx.algorithms.commands

Class SortArc

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.SortArc

public class SortArc
extends AlgorithmsCommand

The SortArc script sort Monte Carlo archive files by lambda value. It presently assumes that the number of files composing the first end of the window equals the number of files composing the other end.
Usage:
ffxc SortArc [options] <structures1> <structures2>

Field Summary

Fields inherited from class ffx.algorithms.cli.AlgorithmsCommand

activeAssembly, algorithmFunctions, algorithmListener, baseDir

Fields inherited from class ffx.utilities.FFXCommand

args, binding, color, help, logger, parseResult, version

Constructor Summary

Constructors

Constructor	Description
SortArc()	SortArc Constructor.
SortArc(FFXBinding binding)	SortArc Constructor.
SortArc(String[] args)	SortArc constructor that sets the command line arguments.

Method Summary

Modifier and Type	Method	Description
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
SortArc	run()	Execute this Command.
void	setProperties(org.apache.commons.configuration2.CompositeConfiguration additionalProps)	Sets an optional Configuration with additional properties.

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

destroyPotentials, getActiveAssemblies, getActiveAssembly, getPotentialsFromAssemblies, init, saveDirFile, setBaseDir, updateTitle

Methods inherited from class ffx.utilities.FFXCommand

getCommand, helpString, listCommands, setBinding

Methods inherited from class java.lang.Object

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

Constructor Details

SortArc

public SortArc()

SortArc Constructor.

SortArc

public SortArc(FFXBinding binding)

SortArc Constructor.

Parameters:

binding - The Binding to use.

SortArc

public SortArc(String[] args)

SortArc constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

setProperties

public void setProperties(org.apache.commons.configuration2.CompositeConfiguration additionalProps)

Sets an optional Configuration with additional properties.

Parameters:

additionalProps -

run

public SortArc run()

Description copied from class: FFXCommand

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getPotentials

public List<Potential> getPotentials()

Description copied from class: AlgorithmsCommand

Returns a List of all Potential objects associated with this script.

Overrides:

getPotentials in class AlgorithmsCommand

Returns:

All Potentials. Sometimes empty, never null.