ambit2.core.io
Class IteratingXLSReader

java.lang.Object
  org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
      ambit2.core.io.IteratingFilesWithHeaderReader
          ambit2.core.io.IteratingXLSReader

All Implemented Interfaces:

java.util.Iterator, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.iterator.IIteratingChemObjectReader

Direct Known Subclasses:

EurasBCFReader

public class IteratingXLSReader
extends IteratingFilesWithHeaderReader

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.

Field Summary

protected java.io.InputStream	input
protected java.util.Iterator	iterator
protected org.apache.poi.hssf.usermodel.HSSFSheet	sheet
protected org.apache.poi.hssf.usermodel.HSSFWorkbook	workbook

Fields inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

defaultSMILESHeader, logger, numberOfHeaderLines, smilesIndex, sp, timeout

Constructor Summary

IteratingXLSReader(java.io.InputStream input, int sheetIndex)

Method Summary

void	close()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
protected ambit2.base.data.LiteratureEntry	getReference()
boolean	hasNext()
java.lang.Object	next()
void	processHeader()
protected void	processHeader(org.apache.poi.hssf.usermodel.HSSFRow row)
protected void	processRow(org.openscience.cdk.interfaces.IAtomContainer mol)
java.lang.String	toString()

Methods inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

addHeaderColumn, getHeaderColumn, getNumberOfColumns, getNumberOfHeaderLines, getTimeout, isHeaderEmpty, setHeaderColumn, setNumberOfHeaderLines, setTimeout

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

accepts, addChemObjectIOListener, fireFrameRead, fireIOSettingQuestion, getIOSettings, remove, removeChemObjectIOListener

Methods inherited from class java.lang.Object

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

Field Detail

workbook

protected org.apache.poi.hssf.usermodel.HSSFWorkbook workbook

sheet

protected org.apache.poi.hssf.usermodel.HSSFSheet sheet

iterator

protected java.util.Iterator iterator

input

protected java.io.InputStream input

Constructor Detail

IteratingXLSReader

public IteratingXLSReader(java.io.InputStream input,
                          int sheetIndex)
                   throws ambit2.base.exceptions.AmbitIOException

Throws:

ambit2.base.exceptions.AmbitIOException

Method Detail

getReference

protected ambit2.base.data.LiteratureEntry getReference()

Specified by:

getReference in class IteratingFilesWithHeaderReader

processHeader

public void processHeader()

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException

hasNext

public boolean hasNext()

processRow

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

next

public java.lang.Object next()

processHeader

protected void processHeader(org.apache.poi.hssf.usermodel.HSSFRow row)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getFormat

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