ambit2.core.io

Class ToXMLReaderSimple

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.ToXMLReaderSimple

All Implemented Interfaces:

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

public class ToXMLReaderSimple
extends org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
implements IRawReader<IStructureRecord>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	ToXMLReaderSimple.toxml_attributes
protected static class	ToXMLReaderSimple.toxml_names
protected static class	ToXMLReaderSimple.toxml_quantity_types
protected static class	ToXMLReaderSimple.toxml_tags
protected static class	ToXMLReaderSimple.toxml_tags_level1 toxml.xsd 3.0.8

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 Stack<String[]>	attributes
protected Stack<Hashtable<String,Integer>>	branches
protected int	compounds
protected Hashtable<Dictionary,Integer>	dictionary
protected Property	inchiProperty
protected static Logger	logger
protected Stack<Property>	properties
protected XMLStreamReader	reader
protected IStructureRecord	record
protected int	recordCount
protected int	study
protected Hashtable<String,Integer>	tagCount
protected Stack<String>	tags
protected int	test
protected String	tmpValue
protected String	URI

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
ToXMLReaderSimple(InputStream in)

Method Summary

Modifier and Type	Method and Description
void	close()
protected boolean	endRecord(String tag, Integer tag_num, String parentTag, String path, String value)
Hashtable<Dictionary,Integer>	getDictionary()
protected String	getDotPath()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
boolean	hasNext()
protected boolean	newRecord(String tag, Integer tag_num, String parentTag, String path)
Object	next()
IStructureRecord	nextRecord()
protected void	processItem(String key, String value, boolean leaf)
protected String[]	readAttributes()
protected void	setProperty(Property key, Object value)
void	setReader(InputStream in)
void	setReader(Reader in)

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

compounds

protected int compounds

URI

protected final String URI

See Also:

Constant Field Values

study

protected int study

test

protected int test

inchiProperty

protected Property inchiProperty

dictionary

protected Hashtable<Dictionary,Integer> dictionary

tagCount

protected Hashtable<String,Integer> tagCount

record

protected IStructureRecord record

reader

protected XMLStreamReader reader

tmpValue

protected String tmpValue

recordCount

protected int recordCount

tags

protected Stack<String> tags

properties

protected Stack<Property> properties

attributes

protected Stack<String[]> attributes

branches

protected Stack<Hashtable<String,Integer>> branches

Constructor Detail

ToXMLReaderSimple

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

Throws:

org.openscience.cdk.exception.CDKException

Method Detail

getDictionary

public Hashtable<Dictionary,Integer> getDictionary()

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

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

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

processItem

protected void processItem(String key,
                           String value,
                           boolean leaf)

newRecord

protected boolean newRecord(String tag,
                            Integer tag_num,
                            String parentTag,
                            String path)

endRecord

protected boolean endRecord(String tag,
                            Integer tag_num,
                            String parentTag,
                            String path,
                            String value)

setProperty

protected void setProperty(Property key,
                           Object value)

getDotPath

protected String getDotPath()

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator

readAttributes

protected String[] readAttributes()

nextRecord

public IStructureRecord nextRecord()

Specified by:

nextRecord in interface IRawReader<IStructureRecord>

getFormat

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

Specified by:

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

next

public Object next()

Specified by:

next in interface Iterator