Package ffx.algorithms.commands

Class ForEachFile

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.ForEachFile

public class ForEachFile
extends AlgorithmsCommand

Run an FFX command on a series of files. Parallel Java across nodes is supported.

Recursion through the directory structure is supported to a supplied level using the --recurse flag (0 only includes the current directory).

Files can be selected using a regular expression -- the default matches all files (".*").

To control placement of the variable file on the command line, the "FILE" string can be used. If present, it is replaced with the current file. If absent, the current file is last argument to the FFX command.
Usage:
ffxc ForEachFile [ForEachFile options] Command [Command options] <FILE> [<FILE2>]

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
ForEachFile()	ForEachFile Constructor.
ForEachFile(FFXBinding binding)	ForEachFile Constructor.
ForEachFile(String[] args)	ForEachFile 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.
ForEachFile	run()	Execute this Command.

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

ForEachFile

public ForEachFile()

ForEachFile Constructor.

ForEachFile

public ForEachFile(FFXBinding binding)

ForEachFile Constructor.

Parameters:

binding - The Binding to use.

ForEachFile

public ForEachFile(String[] args)

ForEachFile constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public ForEachFile run()

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.