ambit2.core.io

Class I5ReaderSimple

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.I5ReaderSimple

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 I5ReaderSimple
extends org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
implements IRawReader<IStructureRecord>, ICiteable

IUCLID5 .i5d files support http://iuclid.eu/ Reads ReferenceSubstances only. For a better support for .i5d and .i5z files use https://github.com/ideaconsult/i5 or compile ambit with Maven profile -P i5

Author:

nina

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	I5ReaderSimple.i5_refs_attr
protected static class	I5ReaderSimple.i5_tags

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	attachment
protected CASProcessor	casProcessor
static Property	casProperty
static Property	ecProperty
static String	I5_REFERENCE
static String	I5_URL
protected static Logger	logger
static Property	nameProperty
protected I5ReaderSimple.i5_tags	parentTag
protected XMLStreamReader	reader
protected IStructureRecord	record
protected ILiteratureEntry	reference
protected Property	registrationProperty
protected ArrayList<String>	synonyms
protected String	tmpValue

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
I5ReaderSimple(InputStream in)
I5ReaderSimple(InputStreamReader in)

Method Summary

Modifier and Type	Method and Description
void	close()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
ILiteratureEntry	getReference()
boolean	hasNext()
Object	next()
IStructureRecord	nextRecord()
void	parseDocument()
void	setReader(InputStream in)
void	setReader(Reader in)
void	setReference(ILiteratureEntry reference)

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

logger

protected static Logger logger

record

protected IStructureRecord record

reader

protected XMLStreamReader reader

synonyms

protected ArrayList<String> synonyms

tmpValue

protected String tmpValue

casProcessor

protected CASProcessor casProcessor

I5_URL

public static String I5_URL

I5_REFERENCE

public static String I5_REFERENCE

casProperty

public static Property casProperty

ecProperty

public static Property ecProperty

nameProperty

public static Property nameProperty

registrationProperty

protected Property registrationProperty

reference

protected ILiteratureEntry reference

attachment

protected boolean attachment

parentTag

protected I5ReaderSimple.i5_tags parentTag

Constructor Detail

I5ReaderSimple

public I5ReaderSimple(InputStreamReader in)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

I5ReaderSimple

public I5ReaderSimple(InputStream in)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

Method Detail

getReference

public ILiteratureEntry getReference()

Specified by:

getReference in interface ICiteable

setReference

public void setReference(ILiteratureEntry reference)

Specified by:

setReference in interface ICiteable

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

setReader

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

Specified by:

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

Throws:

org.openscience.cdk.exception.CDKException

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

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 Iterator

next

public Object next()

Specified by:

next in interface Iterator

nextRecord

public IStructureRecord nextRecord()

Specified by:

nextRecord in interface IRawReader<IStructureRecord>

parseDocument

public void parseDocument()
                   throws Exception

Throws:

Exception