ambit2.core.io
Class RandomAccessReader

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

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

Direct Known Subclasses:

RandomAccessSDFReader

public abstract class RandomAccessReader
extends org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
implements ambit2.base.interfaces.IRandomAccessChemObjectReader, java.lang.Runnable

Random access to text files of compounds. First reads the file and builds an index in memory. The index stores offset, length and number of atoms of the molecule in that record. Subsequent access for a record N uses this index to seek the record and return the molecule. Useful for very big files.

Field Summary

protected byte[]	b
protected org.openscience.cdk.interfaces.IChemObjectBuilder	builder
protected org.openscience.cdk.io.IChemObjectReader	chemObjectReader
protected int	currentRecord
protected org.openscience.cdk.io.setting.IOSetting[]	headerOptions
protected long[][]	index
protected boolean	indexCreated
protected int	indexVersion
protected static org.openscience.cdk.tools.LoggingTool	logger
protected java.io.RandomAccessFile	raFile
protected int	records

Constructor Summary

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

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

Method Summary

void	add(java.lang.Object arg0)
void	addChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener listener)
void	close()
abstract org.openscience.cdk.io.IChemObjectReader	createChemObjectReader()
protected void	finalize()
java.lang.Object	first()
org.openscience.cdk.io.IChemObjectReader	getChemObjectReader()
int	getCurrentRecord()
static java.io.File	getIndexFile(java.lang.String filename)
int	getNumberOfRecords()
boolean	hasNext()
boolean	hasPrevious()
boolean	isIndexCreated()
protected abstract boolean	isRecordEnd(java.lang.String line)
java.lang.Object	last()
protected void	loadIndex(java.io.File file)
protected void	makeIndex()
java.lang.Object	next()
int	nextIndex()
java.lang.Object	previous()
int	previousIndex()
int	read(char[] cbuf, int off, int len)
java.lang.Object	readContent(java.lang.String buffer, int length)
java.lang.Object	readRecord(int record)
void	removeChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener listener)
protected long[][]	resize(long[][] index, int newLength)
void	run()
protected void	saveIndex(java.io.File file)
void	set(java.lang.Object arg0)
void	setChemObjectReader(org.openscience.cdk.io.IChemObjectReader chemObjectReader)
void	setIndexCreated(boolean indexCreated)
int	size()
java.lang.String	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

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

getFormat

Field Detail

logger

protected static org.openscience.cdk.tools.LoggingTool logger

raFile

protected java.io.RandomAccessFile raFile

headerOptions

protected org.openscience.cdk.io.setting.IOSetting[] headerOptions

chemObjectReader

protected org.openscience.cdk.io.IChemObjectReader chemObjectReader

indexVersion

protected int indexVersion

index

protected long[][] index

records

protected int records

currentRecord

protected int currentRecord

b

protected byte[] b

builder

protected org.openscience.cdk.interfaces.IChemObjectBuilder builder

indexCreated

protected boolean indexCreated

Constructor Detail

RandomAccessReader

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

Throws:

java.io.IOException

RandomAccessReader

public RandomAccessReader(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

finalize

protected void finalize()
                 throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable

readRecord

public java.lang.Object readRecord(int record)
                            throws java.lang.Exception

Specified by:

readRecord in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

Throws:

java.lang.Exception

readContent

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

Throws:

org.openscience.cdk.exception.CDKException

resize

protected long[][] resize(long[][] index,
                          int newLength)

isRecordEnd

protected abstract boolean isRecordEnd(java.lang.String line)

saveIndex

protected void saveIndex(java.io.File file)
                  throws java.lang.Exception

Throws:

java.lang.Exception

loadIndex

protected void loadIndex(java.io.File file)
                  throws java.lang.Exception

Throws:

java.lang.Exception

makeIndex

protected void makeIndex()
                  throws java.io.IOException

Throws:

java.io.IOException

getIndexFile

public static java.io.File getIndexFile(java.lang.String filename)

read

public int read(char[] cbuf,
                int off,
                int len)
         throws java.io.IOException

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface org.openscience.cdk.io.IChemObjectIO

Throws:

java.io.IOException

getChemObjectReader

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

createChemObjectReader

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

setChemObjectReader

public void setChemObjectReader(org.openscience.cdk.io.IChemObjectReader chemObjectReader)

getNumberOfRecords

public int getNumberOfRecords()

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator

Specified by:

hasNext in interface java.util.ListIterator

hasPrevious

public boolean hasPrevious()

Specified by:

hasPrevious in interface java.util.ListIterator

first

public java.lang.Object first()

Specified by:

first in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

last

public java.lang.Object last()

Specified by:

last in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

next

public java.lang.Object next()

Specified by:

next in interface java.util.Iterator

Specified by:

next in interface java.util.ListIterator

previous

public java.lang.Object previous()

Specified by:

previous in interface java.util.ListIterator

set

public void set(java.lang.Object arg0)

Specified by:

set in interface java.util.ListIterator

add

public void add(java.lang.Object arg0)

Specified by:

add in interface java.util.ListIterator

previousIndex

public int previousIndex()

Specified by:

previousIndex in interface java.util.ListIterator

nextIndex

public int nextIndex()

Specified by:

nextIndex in interface java.util.ListIterator

size

public int size()

Specified by:

size in interface ambit2.base.interfaces.IRandomAccessChemObjectReader

addChemObjectIOListener

public void addChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener listener)

Specified by:

addChemObjectIOListener in interface org.openscience.cdk.io.IChemObjectIO

Overrides:

addChemObjectIOListener in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

removeChemObjectIOListener

public void removeChemObjectIOListener(org.openscience.cdk.io.listener.IChemObjectIOListener listener)

Specified by:

removeChemObjectIOListener in interface org.openscience.cdk.io.IChemObjectIO

Overrides:

removeChemObjectIOListener in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

getCurrentRecord

public int getCurrentRecord()

isIndexCreated

public boolean isIndexCreated()

setIndexCreated

public void setIndexCreated(boolean indexCreated)

run

public void run()

Specified by:

run in interface java.lang.Runnable

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object