org.openscience.cdk.io.random

Class RandomAccessReader

java.lang.Object

org.openscience.cdk.io.random.DefaultRandomAccessChemObjectReader

org.openscience.cdk.io.random.RandomAccessReader

All Implemented Interfaces:

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

Direct Known Subclasses:

RandomAccessSDFReader

public abstract class RandomAccessReader
extends DefaultRandomAccessChemObjectReader
implements IRandomAccessChemObjectReader<IChemObject>

Random access to text files of compounds. Reads the file as a text and builds an index file, if the index file doesn't already exist. The index stores offset, length and a third field reserved for future use. Subsequent access for a record N uses this index to seek the record and return the molecule. Useful for very big files.

Author:

Nina Jeliazkova <nina@acad.bg>

Source code:

master

Belongs to CDK module:

io

Field Summary

Fields

Modifier and Type	Field and Description
protected byte[]	b
protected IChemObjectBuilder	builder
protected ISimpleChemObjectReader	chemObjectReader
protected int	currentRecord
protected IOSetting[]	headerOptions
protected long[][]	index
protected boolean	indexCreated
protected int	indexVersion
protected static ILoggingTool	logger
protected RandomAccessFile	raFile
protected int	records

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

mode

Constructor Summary

Constructors

Constructor and Description
RandomAccessReader(File file, IChemObjectBuilder builder) Reads the file and builds an index file, if the index file doesn't already exist.
RandomAccessReader(File file, IChemObjectBuilder builder, IReaderListener listener) Reads the file and builds an index file, if the index file doesn't already exist.

Method Summary

Modifier and Type	Method and Description
void	add(IChemObject arg0)
void	addChemObjectIOListener(IChemObjectIOListener listener)
void	close()
abstract ISimpleChemObjectReader	createChemObjectReader()
protected void	finalize()
IChemObject	first()
IChemObjectReader	getChemObjectReader()
int	getCurrentRecord()
static File	getIndexFile(String filename) Opens the file index file _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.
boolean	hasNext()
boolean	hasPrevious()
boolean	isIndexCreated()
protected abstract boolean	isRecordEnd(String line)
IChemObject	last()
protected void	loadIndex(File file)
protected void	makeIndex() The index file getIndexFile(String) is loaded, if already exists, or created a new.
IChemObject	next()
int	nextIndex()
IChemObject	previous()
int	previousIndex()
protected IChemObject	processContent() The reader is already set to read the record buffer.
protected String	readContent(int record) Reads the record text content into a String.
IChemObject	readRecord(int record) Returns the object at given record No.
void	removeChemObjectIOListener(IChemObjectIOListener listener)
protected long[][]	resize(long[][] index, int newLength)
protected void	saveIndex(File file)
void	set(IChemObject arg0)
void	setChemObjectReader(ISimpleChemObjectReader chemObjectReader)
void	setIndexCreated(boolean indexCreated)
int	size()
String	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.ListIterator

remove

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

logger

protected static ILoggingTool logger

raFile

protected RandomAccessFile raFile

headerOptions

protected IOSetting[] headerOptions

chemObjectReader

protected ISimpleChemObjectReader chemObjectReader

indexVersion

protected int indexVersion

index

protected long[][] index

records

protected int records

currentRecord

protected int currentRecord

b

protected byte[] b

builder

protected IChemObjectBuilder builder

indexCreated

protected boolean indexCreated

Constructor Detail

RandomAccessReader

public RandomAccessReader(File file,
                          IChemObjectBuilder builder)
                   throws IOException

Reads the file and builds an index file, if the index file doesn't already exist.

Parameters:

file - the file object containing the molecules to be indexed

builder - a chem object builder

Throws:

IOException - if there is an error during reading

RandomAccessReader

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

Reads the file and builds an index file, if the index file doesn't already exist.

Parameters:

file - file the file object containg the molecules to be indexed

builder - builder a chem object builder

listener - listen for read event

Throws:

IOException - if there is an error during reading

Method Detail

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

readRecord

public IChemObject readRecord(int record)
                       throws Exception

Returns the object at given record No. Record numbers are zero-based!

Specified by:

readRecord in interface IRandomAccessChemObjectReader<IChemObject>

Throws:

Exception

readContent

protected String readContent(int record)
                      throws IOException,
                             CDKException

Reads the record text content into a String.

Parameters:

record - The record number

Returns:

A String representation of the record

Throws:

IOException - if error occurs during reading

CDKException - if the record number is invalid

processContent

protected IChemObject processContent()
                              throws CDKException

The reader is already set to read the record buffer.

Returns:

the read IChemObject

Throws:

CDKException - an error occurred whilst reading the file

resize

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

isRecordEnd

protected abstract boolean isRecordEnd(String line)

saveIndex

protected void saveIndex(File file)
                  throws Exception

Throws:

Exception

loadIndex

protected void loadIndex(File file)
                  throws Exception

Throws:

Exception

makeIndex

protected void makeIndex()
                  throws Exception

The index file getIndexFile(String) is loaded, if already exists, or created a new.

Throws:

Exception

getIndexFile

public static File getIndexFile(String filename)

Opens the file index file _cdk.index in a temporary folder, as specified by "java.io.tmpdir" property.

Parameters:

filename - the name of the file for which the index was generated

Returns:

a file object representing the index file

close

public void close()
           throws IOException

Throws:

IOException

getChemObjectReader

public IChemObjectReader getChemObjectReader()

createChemObjectReader

public abstract ISimpleChemObjectReader createChemObjectReader()

setChemObjectReader

public void setChemObjectReader(ISimpleChemObjectReader chemObjectReader)

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<IChemObject>

Specified by:

hasNext in interface ListIterator<IChemObject>

hasPrevious

public boolean hasPrevious()

Specified by:

hasPrevious in interface ListIterator<IChemObject>

first

public IChemObject first()

Specified by:

first in interface IRandomAccessChemObjectReader<IChemObject>

last

public IChemObject last()

Specified by:

last in interface IRandomAccessChemObjectReader<IChemObject>

next

public IChemObject next()

Specified by:

next in interface Iterator<IChemObject>

Specified by:

next in interface ListIterator<IChemObject>

previous

public IChemObject previous()

Specified by:

previous in interface ListIterator<IChemObject>

set

public void set(IChemObject arg0)

Specified by:

set in interface ListIterator<IChemObject>

add

public void add(IChemObject arg0)

Specified by:

add in interface ListIterator<IChemObject>

previousIndex

public int previousIndex()

Specified by:

previousIndex in interface ListIterator<IChemObject>

nextIndex

public int nextIndex()

Specified by:

nextIndex in interface ListIterator<IChemObject>

size

public int size()

Specified by:

size in interface IRandomAccessChemObjectReader<IChemObject>

addChemObjectIOListener

public void addChemObjectIOListener(IChemObjectIOListener listener)

Overrides:

addChemObjectIOListener in class DefaultRandomAccessChemObjectReader

removeChemObjectIOListener

public void removeChemObjectIOListener(IChemObjectIOListener listener)

Overrides:

removeChemObjectIOListener in class DefaultRandomAccessChemObjectReader

getCurrentRecord

public int getCurrentRecord()

isIndexCreated

public boolean isIndexCreated()

setIndexCreated

public void setIndexCreated(boolean indexCreated)

toString

public String toString()

Overrides:

toString in class Object