ambit2.core.external
Class ShellSDFoutput<INPUT>

java.lang.Object
  ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule>
      ambit2.core.external.ShellSDFoutput<INPUT>

All Implemented Interfaces:

ambit2.base.interfaces.IProcessor<INPUT,org.openscience.cdk.interfaces.IMolecule>, java.io.Serializable

Direct Known Subclasses:

OpenBabelShell

public abstract class ShellSDFoutput<INPUT>
extends ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule>

See Also:

Serialized Form

Field Summary

protected boolean

readOutput

Fields inherited from class ambit2.base.external.CommandShell

enabled, executables, exitCode, inputFile, logger, os_LINUX, os_MAC, os_WINDOWS, os_WINDOWSVISTA, outputFile, prefix, runAsync

Constructor Summary

ShellSDFoutput()

Method Summary

protected void	initialize()
boolean	isReadOutput()
protected org.openscience.cdk.interfaces.IMolecule	parseOutput(java.lang.String path, INPUT mol)
void	setReadOutput(boolean readOutput)

Methods inherited from class ambit2.base.external.CommandShell

addExecutable, addExecutable, addExecutableLinux, addExecutableMac, addExecutableWin, exitCodeOK, getExecutable, getExecutable, getExitCode, getID, getInputFile, getOutputFile, getPath, isEnabled, prepareInput, process, runShell, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, transform_input, transform, transform

Methods inherited from class java.lang.Object

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

Field Detail

readOutput

protected boolean readOutput

Constructor Detail

ShellSDFoutput

public ShellSDFoutput()
               throws ambit2.base.external.ShellException

Throws:

ambit2.base.external.ShellException

Method Detail

initialize

protected void initialize()
                   throws ambit2.base.external.ShellException

Overrides:

initialize in class ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule>

Throws:

ambit2.base.external.ShellException

parseOutput

protected org.openscience.cdk.interfaces.IMolecule parseOutput(java.lang.String path,
                                                               INPUT mol)
                                                        throws ambit2.base.external.ShellException

Specified by:

parseOutput in class ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule>

Throws:

ambit2.base.external.ShellException

isReadOutput

public boolean isReadOutput()

setReadOutput

public void setReadOutput(boolean readOutput)