toxTree.io.batch

Class ChemObjectBatchProcessing

java.lang.Object

java.util.Observable

toxTree.io.batch.BatchProcessing

toxTree.io.batch.ChemObjectBatchProcessing

All Implemented Interfaces:

Serializable, IBatchProcessing

Direct Known Subclasses:

ToxTreeBatchProcessing

public class ChemObjectBatchProcessing
extends BatchProcessing

Implements batch processing of chemical files

Author:

Nina Jeliazkova Modified 2005-9-4

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.openscience.cdk.interfaces.IChemObject	chemObject
protected static int	CSV_INDEX
static String[]	extensions
static String[]	extensions_descr
protected org.openscience.cdk.io.iterator.IIteratingChemObjectReader	reader
protected static int	SDF_INDEX
protected static int	SMI_INDEX
protected static int	TXT_INDEX
protected org.openscience.cdk.io.IChemObjectWriter	writer

Fields inherited from class toxTree.io.batch.BatchProcessing

configFile, dateCreated, dateLastSaved, deleteConfigOnSuccess, inputFile, logger, MSG_CANTCREATEFILE, MSG_ERRORCOUNTING, MSG_ERRORSAVE, MSG_FILEDONOTEXISTS, MSG_OPEN, MSG_UNSUPPORTEDFORMAT, outputFile, saveStateFrequency, status, STATUS_ABORTED, STATUS_FINISHED, STATUS_NOTINITIALIZED, STATUS_NOTSTARTED, STATUS_PAUSED, STATUS_RUNNING, statusMsg, tmpDir

Constructor Summary

Constructors

Constructor and Description
ChemObjectBatchProcessing()
ChemObjectBatchProcessing(File input, File output)
ChemObjectBatchProcessing(String input, String output)

Method Summary

Modifier and Type	Method and Description
void	closeInputFile()
void	closeOutputFile()
void	createOutputFile() Creates ChemObjectWriter
protected org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getReader(FileState file, boolean monitor)
boolean	hasNextRecord()
void	openInputFile() Opens the input file as set by constructor and creates IteratingChemObjectReader
void	processRecord()
void	readRecord()
void	start()
void	writeRecord()

Methods inherited from class toxTree.io.batch.BatchProcessing

cancel, close, createConfigFile, equals, getConfigFile, getDateCreated, getDateLastProcessed, getInputFile, getOutputFile, getReadRecordsCount, getSaveStateFrequency, getStatus, getTempDir, getWrittenRecordsCount, isCancelled, isPaused, isRunning, isStatus, loadConfig, pause, saveConfig, saveConfig, setConfigFile, setSaveStateFrequency, setStatus, toString

Methods inherited from class java.util.Observable

addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged

Methods inherited from class java.lang.Object

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

Field Detail

reader

protected transient org.openscience.cdk.io.iterator.IIteratingChemObjectReader reader

writer

protected transient org.openscience.cdk.io.IChemObjectWriter writer

chemObject

protected transient org.openscience.cdk.interfaces.IChemObject chemObject

extensions

public static final transient String[] extensions

extensions_descr

public static final transient String[] extensions_descr

SDF_INDEX

protected static transient int SDF_INDEX

CSV_INDEX

protected static transient int CSV_INDEX

SMI_INDEX

protected static transient int SMI_INDEX

TXT_INDEX

protected static transient int TXT_INDEX

Constructor Detail

ChemObjectBatchProcessing

public ChemObjectBatchProcessing()

ChemObjectBatchProcessing

public ChemObjectBatchProcessing(String input,
                                 String output)
                          throws BatchProcessingException

Parameters:

input - Input file name

output - Output file name

Throws:

BatchProcessingException

ChemObjectBatchProcessing

public ChemObjectBatchProcessing(File input,
                                 File output)
                          throws BatchProcessingException

Parameters:

input - Input File

output - Output File

Throws:

BatchProcessingException

Method Detail

getReader

protected org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader(FileState file,
                                                                               boolean monitor)
                                                                        throws BatchProcessingException

Throws:

BatchProcessingException

openInputFile

public void openInputFile()
                   throws BatchProcessingException

Opens the input file as set by constructor and creates IteratingChemObjectReader

Specified by:

openInputFile in interface IBatchProcessing

Overrides:

openInputFile in class BatchProcessing

Throws:

BatchProcessingException

createOutputFile

public void createOutputFile()
                      throws BatchProcessingException

Creates ChemObjectWriter

Specified by:

createOutputFile in interface IBatchProcessing

Overrides:

createOutputFile in class BatchProcessing

Throws:

BatchProcessingException

start

public void start()
           throws BatchProcessingException

Specified by:

start in interface IBatchProcessing

Overrides:

start in class BatchProcessing

Throws:

BatchProcessingException

closeInputFile

public void closeInputFile()
                    throws BatchProcessingException

Throws:

BatchProcessingException

closeOutputFile

public void closeOutputFile()
                     throws BatchProcessingException

Throws:

BatchProcessingException

processRecord

public void processRecord()
                   throws BatchProcessingException

Throws:

BatchProcessingException

readRecord

public void readRecord()
                throws BatchProcessingException

Throws:

BatchProcessingException

writeRecord

public void writeRecord()
                 throws BatchProcessingException

Throws:

BatchProcessingException

hasNextRecord

public boolean hasNextRecord()