toxTree.data

Class MoleculesIterator

java.lang.Object

toxTree.data.MoleculesIterator

All Implemented Interfaces:

Iterator, IMoleculesIterator

Direct Known Subclasses:

FilteredMoleculesIterator

public class MoleculesIterator
extends Object
implements IMoleculesIterator

Contains molecules

• loaded from a file,
• entered by SMILES SmilesEntryPanel
• entered by structure diagram editor toxTree.ui.molecule.JChemPaintDialog

Author:

Nina Jeliazkova Modified 2005-9-3

Field Summary

Fields

Modifier and Type	Field and Description
protected ListOfAtomContainers	containers
protected int	currentNo
protected String	filename
protected static Logger	logger
protected int	status

Fields inherited from interface toxTree.core.IMoleculesIterator

MSG_EMPTYFILE, MSG_ERRORONOPEN, MSG_ERRORONSAVE, MSG_OPENSUCCESS, MSG_SAVESUCCESS, MSG_UNSUPPORTEDFORMAT

Constructor Summary

Constructors

Constructor and Description
MoleculesIterator()

Method Summary

Modifier and Type	Method and Description
void	addMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
void	clear()
Object	first()
org.openscience.cdk.interfaces.IAtomContainer	getAtomContainer(int index)
protected ListOfAtomContainers	getContainers()
int	getCurrentNo()
String	getFilename()
org.openscience.cdk.interfaces.IAtomContainer	getMolecule()
org.openscience.cdk.interfaces.IAtomContainerSet	getMoleculeForEdit()
org.openscience.cdk.interfaces.IAtomContainer[]	getMolecules()
int	getMoleculesCount()
org.openscience.cdk.interfaces.IAtomContainerSet	getSetOfAtomContainers()
String	getStatus()
boolean	hasNext()
boolean	isReading()
boolean	isWriting()
Object	last()
Object	next()
List	openFile(File input)
Object	prev()
void	remove()
void	saveFile(File output)
org.openscience.cdk.interfaces.IAtomContainer	setCurrentNo(int record)
void	setDone(boolean success)
void	setMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setMolecules(List molecules)
void	setReading()
void	setWriting()
String	toString()
protected void	useIterativeReader(InputStream in)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

containers

protected ListOfAtomContainers containers

currentNo

protected int currentNo

logger

protected static transient Logger logger

status

protected int status

filename

protected String filename

Constructor Detail

MoleculesIterator

public MoleculesIterator()

Method Detail

remove

public void remove()

Specified by:

remove in interface Iterator

getAtomContainer

public org.openscience.cdk.interfaces.IAtomContainer getAtomContainer(int index)

Specified by:

getAtomContainer in interface IMoleculesIterator

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator

next

public Object next()

Specified by:

next in interface Iterator

getMolecules

public org.openscience.cdk.interfaces.IAtomContainer[] getMolecules()

Specified by:

getMolecules in interface IMoleculesIterator

Returns:

Returns the molecules.

setMolecules

public void setMolecules(List molecules)

Specified by:

setMolecules in interface IMoleculesIterator

Parameters:

molecules - The molecules to set.

getCurrentNo

public int getCurrentNo()

Specified by:

getCurrentNo in interface IMoleculesIterator

Returns:

Returns the currentNo.

clear

public void clear()

Specified by:

clear in interface IMoleculesIterator

prev

public Object prev()

Specified by:

prev in interface IMoleculesIterator

first

public Object first()

Specified by:

first in interface IMoleculesIterator

last

public Object last()

Specified by:

last in interface IMoleculesIterator

setCurrentNo

public org.openscience.cdk.interfaces.IAtomContainer setCurrentNo(int record)

Specified by:

setCurrentNo in interface IMoleculesIterator

getMolecule

public org.openscience.cdk.interfaces.IAtomContainer getMolecule()

Specified by:

getMolecule in interface IMoleculesIterator

Returns:

Returns the molecule.

getMoleculesCount

public int getMoleculesCount()

Specified by:

getMoleculesCount in interface IMoleculesIterator

addMolecule

public void addMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

addMolecule in interface IMoleculesIterator

setMolecule

public void setMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

setMolecule in interface IMoleculesIterator

useIterativeReader

protected void useIterativeReader(InputStream in)

openFile

public List openFile(File input)
              throws ToxTreeIOException

Specified by:

openFile in interface IMoleculesIterator

Throws:

ToxTreeIOException

saveFile

public void saveFile(File output)
              throws ToxTreeIOException

Specified by:

saveFile in interface IMoleculesIterator

Throws:

ToxTreeIOException

isReading

public boolean isReading()

Specified by:

isReading in interface IMoleculesIterator

isWriting

public boolean isWriting()

Specified by:

isWriting in interface IMoleculesIterator

getStatus

public String getStatus()

Specified by:

getStatus in interface IMoleculesIterator

setReading

public void setReading()

Specified by:

setReading in interface IMoleculesIterator

setWriting

public void setWriting()

Specified by:

setWriting in interface IMoleculesIterator

setDone

public void setDone(boolean success)

Specified by:

setDone in interface IMoleculesIterator

toString

public String toString()

Overrides:

toString in class Object

getSetOfAtomContainers

public org.openscience.cdk.interfaces.IAtomContainerSet getSetOfAtomContainers()

getMoleculeForEdit

public org.openscience.cdk.interfaces.IAtomContainerSet getMoleculeForEdit()
                                                                    throws Exception

Specified by:

getMoleculeForEdit in interface IMoleculesIterator

Throws:

Exception

getFilename

public String getFilename()

Specified by:

getFilename in interface IMoleculesIterator

getContainers

protected ListOfAtomContainers getContainers()