ambit2.core.io

Class RawIteratingCSVReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.RawIteratingCSVReader

All Implemented Interfaces:

ICiteable, IRawReader<IStructureRecord>, Closeable, AutoCloseable, Iterator, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.iterator.IIteratingChemObjectReader

public class RawIteratingCSVReader
extends org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
implements IRawReader<IStructureRecord>, ICiteable

CSV parser implemented using CSVParser

Author:

nina

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 org.apache.commons.csv.CSVFormat	format
protected Iterator<org.apache.commons.csv.CSVRecord>	iterator
protected boolean	keeprawrecord
protected MoleculeReader	molReader
String	optionalInChIHeader
String	optionalInChIKeyHeader
String	optionalSMILESHeader
protected org.apache.commons.csv.CSVParser	parser
protected ILiteratureEntry	reference
protected IStructureRecord	structureRecord

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
RawIteratingCSVReader(InputStream in, org.apache.commons.csv.CSVFormat format)
RawIteratingCSVReader(InputStream in, DelimitedFileFormat format)
RawIteratingCSVReader(Reader in)
RawIteratingCSVReader(Reader in, org.apache.commons.csv.CSVFormat format)
RawIteratingCSVReader(Reader in, DelimitedFileFormat format)

Method Summary

Modifier and Type	Method and Description
void	close()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
String	getOptionalInChIHeader()
String	getOptionalInChIKeyHeader()
String	getOptionalSMILESHeader()
ILiteratureEntry	getReference()
boolean	hasNext()
boolean	isKeeprawrecord()
Object	next()
IStructureRecord	nextRecord()
void	setKeeprawrecord(boolean keeprawrecord)
void	setOptionalInChIHeader(String optionalInChIHeader)
void	setOptionalInChIKeyHeader(String optionalInChIKeyHeader)
void	setOptionalSMILESHeader(String optionalSMILESHeader)
void	setReader(InputStream in)
void	setReader(Reader reader)
void	setReference(ILiteratureEntry reference)
protected IStructureRecord	transform(org.apache.commons.csv.CSVRecord record)

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

handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

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

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

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Field Detail

parser

protected org.apache.commons.csv.CSVParser parser

iterator

protected Iterator<org.apache.commons.csv.CSVRecord> iterator

structureRecord

protected IStructureRecord structureRecord

format

protected org.apache.commons.csv.CSVFormat format

reference

protected ILiteratureEntry reference

molReader

protected MoleculeReader molReader

optionalSMILESHeader

public String optionalSMILESHeader

optionalInChIKeyHeader

public String optionalInChIKeyHeader

optionalInChIHeader

public String optionalInChIHeader

keeprawrecord

protected boolean keeprawrecord

Constructor Detail

RawIteratingCSVReader

public RawIteratingCSVReader(Reader in)
                      throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

RawIteratingCSVReader

public RawIteratingCSVReader(InputStream in,
                             DelimitedFileFormat format)
                      throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

RawIteratingCSVReader

public RawIteratingCSVReader(Reader in,
                             DelimitedFileFormat format)
                      throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

RawIteratingCSVReader

public RawIteratingCSVReader(InputStream in,
                             org.apache.commons.csv.CSVFormat format)
                      throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

RawIteratingCSVReader

public RawIteratingCSVReader(Reader in,
                             org.apache.commons.csv.CSVFormat format)
                      throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

Method Detail

isKeeprawrecord

public boolean isKeeprawrecord()

setKeeprawrecord

public void setKeeprawrecord(boolean keeprawrecord)

getOptionalInChIKeyHeader

public String getOptionalInChIKeyHeader()

setOptionalInChIKeyHeader

public void setOptionalInChIKeyHeader(String optionalInChIKeyHeader)

getOptionalInChIHeader

public String getOptionalInChIHeader()

setOptionalInChIHeader

public void setOptionalInChIHeader(String optionalInChIHeader)

getOptionalSMILESHeader

public String getOptionalSMILESHeader()

setOptionalSMILESHeader

public void setOptionalSMILESHeader(String optionalSMILESHeader)

setReader

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

Specified by:

setReader in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

setReader

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

Specified by:

setReader in interface org.openscience.cdk.io.IChemObjectReader

Throws:

org.openscience.cdk.exception.CDKException

getFormat

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

Specified by:

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

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

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

Throws:

IOException

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator

next

public Object next()

Specified by:

next in interface Iterator

setReference

public void setReference(ILiteratureEntry reference)

Specified by:

setReference in interface ICiteable

getReference

public ILiteratureEntry getReference()

Specified by:

getReference in interface ICiteable

nextRecord

public IStructureRecord nextRecord()

Specified by:

nextRecord in interface IRawReader<IStructureRecord>

transform

protected IStructureRecord transform(org.apache.commons.csv.CSVRecord record)