Package ffx.algorithms.commands
Class ForEachFile
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.ForEachFile
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>]
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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
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Constructor Summary
ConstructorsConstructorDescriptionForEachFile Constructor.ForEachFile
(FFXBinding binding) ForEachFile Constructor.ForEachFile
(String[] args) ForEachFile constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionReturns a List of all Potential objects associated with this script.run()
Execute this Command.Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand
destroyPotentials, getActiveAssemblies, getActiveAssembly, init, saveDirFile, setActiveAssembly, setBaseDir, updateTitle
Methods inherited from class ffx.utilities.FFXCommand
getCommand, helpString, listCommands, setBinding
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Constructor Details
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ForEachFile
public ForEachFile()ForEachFile Constructor. -
ForEachFile
ForEachFile Constructor.- Parameters:
binding
- The Binding to use.
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ForEachFile
ForEachFile constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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run
Execute this Command.- Overrides:
run
in classFFXCommand
- Returns:
- The current FFXCommand.
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getPotentials
Description copied from class:AlgorithmsCommand
Returns a List of all Potential objects associated with this script.- Overrides:
getPotentials
in classAlgorithmsCommand
- Returns:
- All Potentials. Sometimes empty, never null.
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