ambit2.vega

Class VegaShell

java.lang.Object

ambit2.base.external.CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

ambit2.dragon.AbstractDescriptorShell

ambit2.vega.VegaShell

All Implemented Interfaces:

Serializable, net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

public class VegaShell
extends AbstractDescriptorShell

Launches VEGA as external executable

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected String	config
protected String[]	inFile
static String	JAVA_BIN
static String	JAVA_EXE
static String	JAVA_HOME
protected String[]	outFile
static String	VEGA_HOME

Fields inherited from class ambit2.base.external.CommandShell

enabled, executables, exitCode, inputFile, logger, os_FreeBSD, os_LINUX, os_LINUX64, os_MAC, os_WINDOWS, os_WINDOWS7, os_WINDOWSVISTA, outputFile, prefix, runAsync, workFolder

Constructor Summary

Constructors

Constructor and Description
VegaShell()
VegaShell(String config)

Method Summary

Modifier and Type	Method and Description
List<Property>	createProperties()
protected String	getConfig()
protected String	getHome()
protected String	getHomeDir(File file)
Map<String,Property>	getProperties()
protected void	initialize()
protected Map<String,Property>	loadProperties()
protected org.openscience.cdk.interfaces.IAtomContainer	parseOutput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Does nothing, override with smth meaningfull
protected List<String>	prepareInput(String path, org.openscience.cdk.interfaces.IAtomContainer mol) Returns empty string, override with smth meaningfull
org.openscience.cdk.interfaces.IAtomContainer	process(org.openscience.cdk.interfaces.IAtomContainer target)
org.openscience.cdk.interfaces.IAtomContainer	runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
protected void	setConfig(String config)
String	toString()
protected org.openscience.cdk.interfaces.IAtomContainer	transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class ambit2.dragon.AbstractDescriptorShell

canApply, getPath, transform

Methods inherited from class ambit2.base.external.CommandShell

addExecutable, addExecutable, addExecutableFreeBSD, addExecutableLinux, addExecutableLinux64, addExecutableMac, addExecutableWin, close, exitCodeOK, getExecutable, getExecutable, getExitCode, getHomeFromConfig, getID, getInputFile, getMsgemptymolecule, getOutputFile, getWorkFolder, isEnabled, open, parseOutput, processStdOut, runShell, setEnabled, setExitCode, setInputFile, setOutputFile, setWorkFolder, transform

Methods inherited from class java.lang.Object

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

Field Detail

config

protected String config

JAVA_EXE

public static final String JAVA_EXE

See Also:

Constant Field Values

VEGA_HOME

public static final String VEGA_HOME

See Also:

Constant Field Values

JAVA_HOME

public static final String JAVA_HOME

See Also:

Constant Field Values

JAVA_BIN

public static final String JAVA_BIN

See Also:

Constant Field Values

inFile

protected String[] inFile

outFile

protected String[] outFile

Constructor Detail

VegaShell

public VegaShell()
          throws ShellException

Throws:

ShellException

VegaShell

public VegaShell(String config)
          throws ShellException

Throws:

ShellException

Method Detail

getConfig

protected String getConfig()

setConfig

protected void setConfig(String config)

loadProperties

protected Map<String,Property> loadProperties()

getProperties

public Map<String,Property> getProperties()

getHomeDir

protected String getHomeDir(File file)

Overrides:

getHomeDir in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

getHome

protected String getHome()
                  throws ShellException

Specified by:

getHome in class AbstractDescriptorShell

Throws:

ShellException

prepareInput

protected List<String> prepareInput(String path,
                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                             throws ShellException

Description copied from class: CommandShell

Returns empty string, override with smth meaningfull

Overrides:

prepareInput in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Returns:

list of command line parameters (exe name excluded) to be passed to the executable

Throws:

ShellException

initialize

protected void initialize()
                   throws ShellException

Overrides:

initialize in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

transform_input

protected org.openscience.cdk.interfaces.IAtomContainer transform_input(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                                 throws ShellException

Overrides:

transform_input in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

parseOutput

protected org.openscience.cdk.interfaces.IAtomContainer parseOutput(String path,
                                                                    org.openscience.cdk.interfaces.IAtomContainer mol)
                                                             throws ShellException

Description copied from class: CommandShell

Does nothing, override with smth meaningfull

Specified by:

parseOutput in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

ShellException

toString

public String toString()

Overrides:

toString in class Object

runShell

public org.openscience.cdk.interfaces.IAtomContainer runShell(org.openscience.cdk.interfaces.IAtomContainer mol)
                                                       throws ShellException

Overrides:

runShell in class AbstractDescriptorShell

Throws:

ShellException

process

public org.openscience.cdk.interfaces.IAtomContainer process(org.openscience.cdk.interfaces.IAtomContainer target)
                                                      throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Overrides:

process in class CommandShell<org.openscience.cdk.interfaces.IAtomContainer,org.openscience.cdk.interfaces.IAtomContainer>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

createProperties

public List<Property> createProperties()
                                throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException