ambit2.core.io
Class IteratingDelimitedFileReader

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

All Implemented Interfaces:

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

public class IteratingDelimitedFileReader
extends IteratingFilesWithHeaderReader
implements org.openscience.cdk.io.iterator.IIteratingChemObjectReader

Iterating reader for delimited files.

Field Summary

static java.lang.String	defaultSMILESHeader
protected DelimitedFileFormat	format
protected java.lang.Object[]	values

Fields inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

logger, numberOfHeaderLines, smilesIndex, sp, timeout

Constructor Summary

IteratingDelimitedFileReader(java.io.InputStream in)

IteratingDelimitedFileReader(java.io.InputStream in, DelimitedFileFormat format)

IteratingDelimitedFileReader(java.io.Reader in)

IteratingDelimitedFileReader(java.io.Reader in, DelimitedFileFormat format)

Method Summary

void	close()
void	extractRowKeyAndData(java.lang.String line) Extract values from a line
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
protected ambit2.base.data.LiteratureEntry	getReference()
boolean	hasNext()
java.lang.Object	next()
protected void	processHeader(java.io.BufferedReader in)
void	remove()
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, 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

accepts, addChemObjectIOListener, getIOSettings, removeChemObjectIOListener

Field Detail

defaultSMILESHeader

public static java.lang.String defaultSMILESHeader

format

protected DelimitedFileFormat format

values

protected java.lang.Object[] values

Constructor Detail

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(java.io.Reader in)

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(java.io.Reader in,
                                    DelimitedFileFormat format)

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(java.io.InputStream in)

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(java.io.InputStream in,
                                    DelimitedFileFormat format)

Method Detail

getReference

protected ambit2.base.data.LiteratureEntry getReference()

Specified by:

getReference in class IteratingFilesWithHeaderReader

getFormat

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

Specified by:

getFormat in interface org.openscience.cdk.io.IChemObjectIO

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator

next

public java.lang.Object next()

Specified by:

next in interface java.util.Iterator

close

public void close()
           throws java.io.IOException

Specified by:

close in interface org.openscience.cdk.io.IChemObjectIO

Throws:

java.io.IOException

remove

public void remove()

Specified by:

remove in interface java.util.Iterator

Overrides:

remove in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

processHeader

protected void processHeader(java.io.BufferedReader in)

extractRowKeyAndData

public void extractRowKeyAndData(java.lang.String line)

Extract values from a line

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object