Package org.openscience.cdk.io.random

Class RandomAccessSDFReader

java.lang.Object

org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader

org.openscience.cdk.io.random.RandomAccessReader

org.openscience.cdk.io.random.RandomAccessSDFReader

All Implemented Interfaces:

Iterator<IChemObject>, ListIterator<IChemObject>, IRandomAccessChemObjectReader<IChemObject>

public class RandomAccessSDFReader
extends RandomAccessReader

Random access of SDF file. Doesn't load molecules in memory, uses prebuilt index and seeks to find the correct record offset.

Author:

Nina Jeliazkova <nina@acad.bg>

Source code:

main

Belongs to CDK module:

io

Field Summary

Fields inherited from class org.openscience.cdk.io.random.RandomAccessReader

b, builder, chemObjectReader, currentRecord, headerOptions, index, indexCreated, indexVersion, logger, raFile, records

Fields inherited from class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader

mode

Constructor Summary

Constructors

Constructor	Description
RandomAccessSDFReader(File file, IChemObjectBuilder builder)
RandomAccessSDFReader(File file, IChemObjectBuilder builder, IReaderListener listener)

Method Summary

Modifier and Type	Method	Description
boolean	accepts(Class<? extends IChemObject> classObject)
ISimpleChemObjectReader	createChemObjectReader()
IResourceFormat	getFormat()
protected boolean	isRecordEnd(String line)
protected IChemObject	processContent()	The reader is already set to read the record buffer.
void	remove()
void	setReader(InputStream reader)
void	setReader(Reader reader)

Methods inherited from class org.openscience.cdk.io.random.RandomAccessReader

add, addChemObjectIOListener, close, finalize, first, getChemObjectReader, getCurrentRecord, getIndexFile, hasNext, hasPrevious, isIndexCreated, last, loadIndex, makeIndex, next, nextIndex, previous, previousIndex, readContent, readRecord, removeChemObjectIOListener, resize, saveIndex, set, setChemObjectReader, setIndexCreated, size, toString

Methods inherited from class org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader

fireIOSettingQuestion, getIOSettings, setReaderMode

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

RandomAccessSDFReader

public RandomAccessSDFReader(File file,
                             IChemObjectBuilder builder)
                      throws IOException

Parameters:

file -

builder -

Throws:

IOException

RandomAccessSDFReader

public RandomAccessSDFReader(File file,
                             IChemObjectBuilder builder,
                             IReaderListener listener)
                      throws IOException

Throws:

IOException

Method Detail

createChemObjectReader

public ISimpleChemObjectReader createChemObjectReader()

Specified by:

createChemObjectReader in class RandomAccessReader

isRecordEnd

protected boolean isRecordEnd(String line)

Specified by:

isRecordEnd in class RandomAccessReader

getFormat

public IResourceFormat getFormat()

processContent

protected IChemObject processContent()
                              throws CDKException

Description copied from class: RandomAccessReader

The reader is already set to read the record buffer.

Overrides:

processContent in class RandomAccessReader

Returns:

the read IChemObject

Throws:

CDKException - an error occurred whilst reading the file

setReader

public void setReader(Reader reader)
               throws CDKException

Throws:

CDKException

setReader

public void setReader(InputStream reader)
               throws CDKException

Throws:

CDKException

accepts

public boolean accepts(Class<? extends IChemObject> classObject)

remove

public void remove()