ambit2.core.io

Class IteratingFilesWithHeaderReader<COLUMN>

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.IteratingFilesWithHeaderReader<COLUMN>

All Implemented Interfaces:

Closeable, AutoCloseable, Iterator, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.iterator.IIteratingChemObjectReader

Direct Known Subclasses:

IteratingDelimitedFileReaderComplexHeader, IteratingXLSReader

public abstract class IteratingFilesWithHeaderReader<COLUMN>
extends org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

Author:

Nina Jeliazkova

Nested Class Summary

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

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field and Description
static String	defaultSMILESHeader
protected ArrayList<COLUMN>	header
protected org.openscience.cdk.inchi.InChIGeneratorFactory	inchiFactory
protected int	inchiIndex
protected static Logger	logger
protected int	numberOfHeaderLines
String	optionalSMILESHeader
protected int	smilesIndex
protected SmilesParserWrapper	sp
protected long	timeout

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
IteratingFilesWithHeaderReader()

Method Summary

Modifier and Type	Method and Description
protected void	addHeaderColumn(String name)
protected abstract ArrayList<COLUMN>	createHeader()
protected abstract COLUMN	createPropertyByColumnName(String name)
protected COLUMN	getHeaderColumn(int index)
protected int	getNumberOfColumns()
int	getNumberOfHeaderLines()
String	getOptionalSMILESHeader()
protected abstract LiteratureEntry	getReference()
long	getTimeout()
protected boolean	isHeaderEmpty()
protected void	setHeaderColumn(int index, String name)
void	setNumberOfHeaderLines(int numberOfHeaderLines)
void	setOptionalSMILESHeader(String optionalSMILESHeader)
void	setTimeout(long timeout)
protected void	updateHeaderColumn(int index, COLUMN value)

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

accepts, handleError, handleError, handleError, handleError, remove, setErrorHandler, setReaderMode

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.IChemObjectReader

setReader, setReader

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

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

Methods inherited from interface java.util.Iterator

forEachRemaining, hasNext, next

Field Detail

logger

protected static Logger logger

sp

protected SmilesParserWrapper sp

inchiFactory

protected org.openscience.cdk.inchi.InChIGeneratorFactory inchiFactory

defaultSMILESHeader

public static final String defaultSMILESHeader

See Also:

Constant Field Values

header

protected ArrayList<COLUMN> header

smilesIndex

protected int smilesIndex

inchiIndex

protected int inchiIndex

timeout

protected long timeout

numberOfHeaderLines

protected int numberOfHeaderLines

optionalSMILESHeader

public String optionalSMILESHeader

Constructor Detail

IteratingFilesWithHeaderReader

public IteratingFilesWithHeaderReader()

Method Detail

getOptionalSMILESHeader

public String getOptionalSMILESHeader()

setOptionalSMILESHeader

public void setOptionalSMILESHeader(String optionalSMILESHeader)

getTimeout

public long getTimeout()

setTimeout

public void setTimeout(long timeout)

getNumberOfHeaderLines

public int getNumberOfHeaderLines()

setNumberOfHeaderLines

public void setNumberOfHeaderLines(int numberOfHeaderLines)

getReference

protected abstract LiteratureEntry getReference()

addHeaderColumn

protected void addHeaderColumn(String name)

setHeaderColumn

protected void setHeaderColumn(int index,
                               String name)

createPropertyByColumnName

protected abstract COLUMN createPropertyByColumnName(String name)

getHeaderColumn

protected COLUMN getHeaderColumn(int index)

updateHeaderColumn

protected void updateHeaderColumn(int index,
                                  COLUMN value)

getNumberOfColumns

protected int getNumberOfColumns()

isHeaderEmpty

protected boolean isHeaderEmpty()

createHeader

protected abstract ArrayList<COLUMN> createHeader()