ambit2.core.io.bcf

Class EurasBCFReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.IteratingFilesWithHeaderReader<Property>

ambit2.core.io.IteratingXLSReader

ambit2.core.io.bcf.EurasBCFReader

All Implemented Interfaces:

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

public class EurasBCFReader
extends IteratingXLSReader

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 Hashtable<Double,LiteratureEntry>	references

Fields inherited from class ambit2.core.io.IteratingXLSReader

hssf, input, iterator, sheet, sheetIndex, 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
EurasBCFReader(InputStream input, int sheetIndex)

Method Summary

Modifier and Type	Method and Description
protected String	getAuthor(org.apache.poi.ss.usermodel.Row row)
protected LiteratureEntry	getCitation(org.apache.poi.ss.usermodel.Row row)
protected String	getIssue(org.apache.poi.ss.usermodel.Row row)
protected String	getJournal(org.apache.poi.ss.usermodel.Row row)
protected String	getPages(org.apache.poi.ss.usermodel.Row row)
protected String	getTitle(org.apache.poi.ss.usermodel.Row row)
protected int	getVolume(org.apache.poi.ss.usermodel.Row row)
protected int	getYear(org.apache.poi.ss.usermodel.Row row)
void	processHeader()
protected void	processRow(org.openscience.cdk.interfaces.IAtomContainer mol)
protected void	readReferences()

Methods inherited from class ambit2.core.io.IteratingXLSReader

close, createHeader, createPropertyByColumnName, getFormat, getReference, hasNext, next, processHeader, setReader, setReader, 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

references

protected Hashtable<Double,LiteratureEntry> references

Constructor Detail

EurasBCFReader

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

Throws:

org.openscience.cdk.exception.CDKException

Method Detail

readReferences

protected void readReferences()

getCitation

protected LiteratureEntry getCitation(org.apache.poi.ss.usermodel.Row row)

getAuthor

protected String getAuthor(org.apache.poi.ss.usermodel.Row row)

getTitle

protected String getTitle(org.apache.poi.ss.usermodel.Row row)

getJournal

protected String getJournal(org.apache.poi.ss.usermodel.Row row)

getYear

protected int getYear(org.apache.poi.ss.usermodel.Row row)

getVolume

protected int getVolume(org.apache.poi.ss.usermodel.Row row)

getIssue

protected String getIssue(org.apache.poi.ss.usermodel.Row row)

getPages

protected String getPages(org.apache.poi.ss.usermodel.Row row)

processHeader

public void processHeader()

Overrides:

processHeader in class IteratingXLSReader

processRow

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

Overrides:

processRow in class IteratingXLSReader