org.openscience.cdk.io.iterator
Class IteratingSMILESReader

java.lang.Object
  org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
      org.openscience.cdk.io.iterator.IteratingSMILESReader

All Implemented Interfaces:

Iterator, IChemObjectIO, IChemObjectReader, IIteratingChemObjectReader

@TestClass(value="org.openscience.cdk.io.iterator.IteratingSMILESReaderTest")
public class IteratingSMILESReader
extends DefaultIteratingChemObjectReader

Iterating SMILES file reader. It allows to iterate over all molecules in the SMILES file, without being read into memory all. Suitable for very large SMILES files. These SMILES files are expected to have one molecule on each line.

For parsing each SMILES it still uses the normal SMILESReader.

Author:

Egon Willighagen

See Also:

SMILESReader

Keywords:

file format, SMILES

Created on:

2004-12-16

Belongs to CDK module:

smiles

Source code:

HEAD

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

IChemObjectReader.Mode

Constructor Summary

IteratingSMILESReader(InputStream in)
Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream.

IteratingSMILESReader(InputStream in, IChemObjectBuilder builder)
Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.

IteratingSMILESReader(Reader in, IChemObjectBuilder builder)
Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.

Method Summary

void	close() Close the reader.
IResourceFormat	getFormat() Get the format for this reader.
boolean	hasNext() Checks whether there is another molecule to read.
IChemObject	next() Get the next molecule from the stream.
void	remove() File IO generally does not support removing of entries.
void	setReader(InputStream reader) Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader reader) Sets the Reader from which this ChemObjectReader should read the contents.

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

accepts, addChemObjectIOListener, getIOSettings, handleError, handleError, handleError, handleError, removeChemObjectIOListener, setErrorHandler, setReaderMode

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IteratingSMILESReader

@TestMethod(value="testSMILESFileWithNames")
public IteratingSMILESReader(Reader in,
                                             IChemObjectBuilder builder)

Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.

Parameters:

in - The Reader to read from

builder - The builder to use

See Also:

DefaultChemObjectBuilder, NoNotificationChemObjectBuilder

IteratingSMILESReader

@TestMethod(value="testSMILESFileWithNames")
public IteratingSMILESReader(InputStream in)

Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream. This method will use @link{DefaultChemObjectBuilder} to build the actual molecules

Parameters:

in - The InputStream to read from

IteratingSMILESReader

public IteratingSMILESReader(InputStream in,
                             IChemObjectBuilder builder)

Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.

Parameters:

in - The input stream

builder - The builder

Method Detail

getFormat

@TestMethod(value="testGetFormat")
public IResourceFormat getFormat()

Get the format for this reader.

Returns:

An instance of SMILESFormat

hasNext

@TestMethod(value="testSMILESFileWithNames,testSMILESFileWithSpacesAndTabs,testSMILESTitles,testSMILESFile")
public boolean hasNext()

Checks whether there is another molecule to read.

Returns:

true if there are molecules to read, false otherwise

next

@TestMethod(value="testSMILESFileWithNames,testSMILESFileWithSpacesAndTabs,testSMILESTitles,testSMILESFile")
public IChemObject next()

Get the next molecule from the stream.

Returns:

The next molecule

close

@TestMethod(value="testSMILESFileWithNames,testSMILESFileWithSpacesAndTabs,testClose")
public void close()
           throws IOException

Close the reader.

Throws:

IOException - if there is an error during closing

remove

@TestMethod(value="testRemove")
public void remove()

Description copied from class: DefaultIteratingChemObjectReader

File IO generally does not support removing of entries.

Specified by:

remove in interface Iterator

Overrides:

remove in class DefaultIteratingChemObjectReader

setReader

@TestMethod(value="testSetReader_Reader")
public void setReader(Reader reader)

Description copied from interface: IChemObjectReader

Sets the Reader from which this ChemObjectReader should read the contents.

setReader

@TestMethod(value="testSetReader1,testSetReader_InputStream")
public void setReader(InputStream reader)

Description copied from interface: IChemObjectReader

Sets the InputStream from which this ChemObjectReader should read the contents.