ambit2.core.io

Class FileWithHeaderWriter

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

ambit2.core.io.FileWithHeaderWriter

All Implemented Interfaces:

Closeable, AutoCloseable, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectWriter

Direct Known Subclasses:

XLSFileWriter

public abstract class FileWithHeaderWriter
extends org.openscience.cdk.io.DefaultChemObjectWriter

Field Summary

Fields

Modifier and Type	Field and Description
static String	defaultSMILESHeader
protected ambit2.core.io.Header	header
protected static Logger	logger
protected org.openscience.cdk.smiles.SmilesGenerator	sg
protected int	smilesIndex
protected boolean	writingStarted

Constructor Summary

Constructors

Constructor and Description
FileWithHeaderWriter()

Method Summary

Modifier and Type	Method and Description
ambit2.core.io.Header	getHeader()
void	setHeader(ArrayList header)
void	setHeader(Map properties) Creates header from Hashtable keys Used for default header - created from properties of the first molecule written
void	write(org.openscience.cdk.interfaces.IChemObject object)
protected abstract void	writeHeader()
abstract void	writeMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)
void	writeSetOfMolecules(org.openscience.cdk.interfaces.IAtomContainerSet som)

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

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

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

setWriter, setWriter

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

accepts, addChemObjectIOListener, addSetting, addSettings, close, getFormat, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Field Detail

logger

protected static Logger logger

header

protected ambit2.core.io.Header header

smilesIndex

protected int smilesIndex

sg

protected org.openscience.cdk.smiles.SmilesGenerator sg

defaultSMILESHeader

public static String defaultSMILESHeader

writingStarted

protected boolean writingStarted

Constructor Detail

FileWithHeaderWriter

public FileWithHeaderWriter()

Method Detail

write

public void write(org.openscience.cdk.interfaces.IChemObject object)
           throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

writeHeader

protected abstract void writeHeader()
                             throws IOException

Throws:

IOException

getHeader

public ambit2.core.io.Header getHeader()

Returns:

Returns the header.

setHeader

public void setHeader(ArrayList header)

Parameters:

header - The header to set.

setHeader

public void setHeader(Map properties)

Creates header from Hashtable keys Used for default header - created from properties of the first molecule written

Parameters:

properties -

writeMolecule

public abstract void writeMolecule(org.openscience.cdk.interfaces.IAtomContainer molecule)

writeSetOfMolecules

public void writeSetOfMolecules(org.openscience.cdk.interfaces.IAtomContainerSet som)