ambit2.core.external
Class ShellSDFoutput<INPUT>

Package class diagram package ShellSDFoutput
java.lang.Object
  extended by ambit2.base.external.CommandShell<INPUT,org.openscience.cdk.interfaces.IMolecule>
      extended by 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)