ambit2.core.io

Class IteratingXLSReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.IteratingFilesWithHeaderReader<Property>

ambit2.core.io.IteratingXLSReader

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:

EurasBCFReader

public class IteratingXLSReader
extends IteratingFilesWithHeaderReader<Property>

Reads XLS files. This implementation loads the workbook in memory which is inefficient for big files. TODO find how to read it without loading into memory.

Author:

Nina Jeliazkova nina@acad.bg Modified Aug 31, 2006

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
protected boolean	hssf
protected InputStream	input
protected Iterator	iterator
protected org.apache.poi.ss.usermodel.Sheet	sheet
protected int	sheetIndex
protected org.apache.poi.ss.usermodel.Workbook	workbook

Fields inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

defaultSMILESHeader, header, inchiFactory, inchiIndex, logger, numberOfHeaderLines, optionalSMILESHeader, smilesIndex, sp, timeout

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
IteratingXLSReader(InputStream input, int sheetIndex)
IteratingXLSReader(InputStream input, Integer sheetIndex, Boolean hssf)

Method Summary

Modifier and Type	Method and Description
void	close()
protected ArrayList<Property>	createHeader()
protected Property	createPropertyByColumnName(String name)
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
protected LiteratureEntry	getReference()
boolean	hasNext()
Object	next()
void	processHeader()
protected void	processHeader(org.apache.poi.ss.usermodel.Row row)
protected void	processRow(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setReader(InputStream input)
void	setReader(Reader reader)
String	toString()

Methods inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

addHeaderColumn, getHeaderColumn, getNumberOfColumns, getNumberOfHeaderLines, getOptionalSMILESHeader, getTimeout, isHeaderEmpty, setHeaderColumn, setNumberOfHeaderLines, setOptionalSMILESHeader, setTimeout, updateHeaderColumn

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, wait, wait, wait

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

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

workbook

protected org.apache.poi.ss.usermodel.Workbook workbook

sheet

protected org.apache.poi.ss.usermodel.Sheet sheet

iterator

protected Iterator iterator

input

protected InputStream input

sheetIndex

protected int sheetIndex

hssf

protected boolean hssf

Constructor Detail

IteratingXLSReader

public IteratingXLSReader(InputStream input,
                          int sheetIndex)
                   throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

IteratingXLSReader

public IteratingXLSReader(InputStream input,
                          Integer sheetIndex,
                          Boolean hssf)
                   throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

Method Detail

createHeader

protected ArrayList<Property> createHeader()

Specified by:

createHeader in class IteratingFilesWithHeaderReader<Property>

createPropertyByColumnName

protected Property createPropertyByColumnName(String name)

Specified by:

createPropertyByColumnName in class IteratingFilesWithHeaderReader<Property>

setReader

public void setReader(InputStream input)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

setReader

public void setReader(Reader reader)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getReference

protected LiteratureEntry getReference()

Specified by:

getReference in class IteratingFilesWithHeaderReader<Property>

processHeader

public void processHeader()

close

public void close()
           throws IOException

Throws:

IOException

hasNext

public boolean hasNext()

processRow

protected void processRow(org.openscience.cdk.interfaces.IAtomContainer mol)

next

public Object next()

processHeader

protected void processHeader(org.apache.poi.ss.usermodel.Row row)

toString

public String toString()

Overrides:

toString in class Object

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()