ambit2.core.io
Class RandomAccessSDFReader

java.lang.Object
  org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
      ambit2.core.io.RandomAccessReader
          ambit2.core.io.RandomAccessSDFReader

All Implemented Interfaces:

ambit2.base.interfaces.IRandomAccessChemObjectReader, java.lang.Runnable, java.util.Iterator, java.util.ListIterator, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.iterator.IIteratingChemObjectReader

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.

Field Summary

Fields inherited from class ambit2.core.io.RandomAccessReader

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

Constructor Summary

RandomAccessSDFReader(java.io.File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder)

RandomAccessSDFReader(java.io.File file, org.openscience.cdk.interfaces.IChemObjectBuilder builder, org.openscience.cdk.io.listener.IReaderListener listener)

Method Summary

org.openscience.cdk.io.IChemObjectReader	createChemObjectReader()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
protected boolean	isRecordEnd(java.lang.String line)
java.lang.Object	readContent(java.lang.String buffer, int length)

Methods inherited from class ambit2.core.io.RandomAccessReader

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

Methods inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

accepts, fireFrameRead, fireIOSettingQuestion, getIOSettings, remove

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.ListIterator

remove

Constructor Detail

RandomAccessSDFReader

public RandomAccessSDFReader(java.io.File file,
                             org.openscience.cdk.interfaces.IChemObjectBuilder builder)
                      throws java.io.IOException

Parameters:

file -

builder -

Throws:

java.io.IOException

RandomAccessSDFReader

public RandomAccessSDFReader(java.io.File file,
                             org.openscience.cdk.interfaces.IChemObjectBuilder builder,
                             org.openscience.cdk.io.listener.IReaderListener listener)
                      throws java.io.IOException

Throws:

java.io.IOException

Method Detail

createChemObjectReader

public org.openscience.cdk.io.IChemObjectReader createChemObjectReader()

Specified by:

createChemObjectReader in class RandomAccessReader

isRecordEnd

protected boolean isRecordEnd(java.lang.String line)

Specified by:

isRecordEnd in class RandomAccessReader

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()

readContent

public java.lang.Object readContent(java.lang.String buffer,
                                    int length)
                             throws org.openscience.cdk.exception.CDKException

Overrides:

readContent in class RandomAccessReader

Throws:

org.openscience.cdk.exception.CDKException