toxTree.io.batch
Class ChemObjectBatchProcessing
java.lang.Object
java.util.Observable
toxTree.io.batch.BatchProcessing
toxTree.io.batch.ChemObjectBatchProcessing
- All Implemented Interfaces:
- java.io.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
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 |
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 |
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 java.lang.String[] extensions
extensions_descr
public static final transient java.lang.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
ChemObjectBatchProcessing
public ChemObjectBatchProcessing()
ChemObjectBatchProcessing
public ChemObjectBatchProcessing(java.lang.String input,
java.lang.String output)
throws BatchProcessingException
- Parameters:
input
- Input file nameoutput
- Output file name
- Throws:
BatchProcessingException
ChemObjectBatchProcessing
public ChemObjectBatchProcessing(java.io.File input,
java.io.File output)
throws BatchProcessingException
- Parameters:
input
- Input Fileoutput
- Output File
- Throws:
BatchProcessingException
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()
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