ambit2.core.io

Class FilesWithHeaderWriter

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

ambit2.core.io.FilesWithHeaderWriter

All Implemented Interfaces:

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

Direct Known Subclasses:

ArffWriter, DelimitedFileWriter, PDFWriter

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

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	addSMILEScolumn
static String	defaultSMILESHeader
protected ArrayList	header
protected static Logger	logger
protected int	smilesIndex
protected boolean	writingStarted

Constructor Summary

Constructors

Constructor and Description
FilesWithHeaderWriter()

Method Summary

Modifier and Type	Method and Description
ArrayList	getHeader()
boolean	isAddSMILEScolumn()
void	setAddSMILEScolumn(boolean addSMILEScolumn)
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
protected abstract void	writeHeader()

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, write

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

defaultSMILESHeader

public static String defaultSMILESHeader

header

protected ArrayList header

writingStarted

protected boolean writingStarted

smilesIndex

protected int smilesIndex

addSMILEScolumn

protected boolean addSMILEScolumn

Constructor Detail

FilesWithHeaderWriter

public FilesWithHeaderWriter()

Method Detail

isAddSMILEScolumn

public boolean isAddSMILEScolumn()

setAddSMILEScolumn

public void setAddSMILEScolumn(boolean addSMILEScolumn)

getHeader

public ArrayList getHeader()

Returns:

Returns the header.

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 -

writeHeader

protected abstract void writeHeader()
                             throws IOException

Throws:

IOException

setHeader

public void setHeader(ArrayList header)

Parameters:

header - The header to set.