info.bioinfweb.jphyloio.formats.xml

Class AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventReader<P>

info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader<P>

All Implemented Interfaces:

JPhyloIOXMLEventReader, JPhyloIOEventReader, JPhyloIOFormatSpecificObject, ReadWriteConstants

Direct Known Subclasses:

NeXMLEventReader, PDEEventReader, PhyloXMLEventReader, XTGEventReader

public abstract class AbstractXMLEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>
extends AbstractEventReader<P>
implements JPhyloIOXMLEventReader

Implements shared functionality for reading XML formats.

Since:

0.0.0

Author:

Ben Stöver, Sarah Wiechers

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	INTERNAL_USE_NAMESPACE
static javax.xml.namespace.QName	TAG_PARENT_OF_ROOT

Fields inherited from interface info.bioinfweb.jphyloio.ReadWriteConstants

ATTRIBUTE_STRING_KEY, ATTRIBUTES_NAMESPACE_FOLDER, DATA_TYPE_NAMESPACE_FOLDER, DATA_TYPE_SIMPLE_VALUE_LIST, DEFAULT_CHAR_SET_ID_PREFIX, DEFAULT_CHARACTER_DEFINITION_ID_PREFIX, DEFAULT_EDGE_ID_PREFIX, DEFAULT_GENERAL_ID_PREFIX, DEFAULT_MATRIX_ID_PREFIX, DEFAULT_MAX_COMMENT_LENGTH, DEFAULT_MAX_TOKENS_TO_READ, DEFAULT_META_ID_PREFIX, DEFAULT_NETWORK_ID_PREFIX, DEFAULT_NODE_EDGE_SET_ID_PREFIX, DEFAULT_NODE_ID_PREFIX, DEFAULT_OTU_ID_PREFIX, DEFAULT_OTU_LIST_ID_PREFIX, DEFAULT_OTU_SET_ID_PREFIX, DEFAULT_SEQUENCE_ID_PREFIX, DEFAULT_SEQUENCE_SET_ID_PREFIX, DEFAULT_TOKEN_DEFINITION_ID_PREFIX, DEFAULT_TOKEN_SET_ID_PREFIX, DEFAULT_TREE_ID_PREFIX, DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX, DEFAULT_TREE_NETWORK_SET_ID_PREFIX, JPHYLOIO_ATTRIBUTES_NAMESPACE, JPHYLOIO_ATTRIBUTES_PREFIX, JPHYLOIO_DATA_TYPE_NAMESPACE, JPHYLOIO_DATA_TYPE_PREFIX, JPHYLOIO_FORMATS_NAMESPACE_PREFIX, JPHYLOIO_GENERAL_NAMESPACE, JPHYLOIO_NAMESPACE_PREFIX, JPHYLOIO_PREDICATE_NAMESPACE, JPHYLOIO_PREDICATE_PREFIX, PREDICATE_CHARACTER_COUNT, PREDICATE_EDGE_LENGTH, PREDICATE_EDGE_SOURCE_NODE, PREDICATE_EDGE_TARGET_NODE, PREDICATE_HAS_CUSTOM_XML, PREDICATE_HAS_LITERAL_METADATA, PREDICATE_HAS_RESOURCE_METADATA, PREDICATE_IS_CROSSLINK, PREDICATE_NAMESPACE_FOLDER, PREDICATE_PART_SEPERATOR, PREDICATE_SEQUENCE_COUNT, RESERVED_ID_PREFIX

Constructor Summary

Constructors

Constructor and Description
AbstractXMLEventReader(java.io.File file, ReadWriteParameterMap parameters)
AbstractXMLEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
AbstractXMLEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)
AbstractXMLEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)

Method Summary

Modifier and Type	Method and Description
void	close() Closes the underlying document source (usually a stream).
MetaXMLEventReader	createMetaXMLEventReader() Creates a new XMLEventReader that allows to read events of XML content of literal metadata from this JPhyloIO event reader instance through that interface.
MetaXMLStreamReader	createMetaXMLStreamReader() Creates a XMLStreamReader that allows to read events of XML content of literal metadata from this JPhyloIO event reader instance through that interface.
protected P	createStreamDataProvider() This method is called in the constructor of AbstractEventReader to initialize the stream data provider that will be returned by AbstractEventReader.getStreamDataProvider().
protected abstract void	fillMap()
protected XMLElementReader<P>	getElementReader(javax.xml.namespace.QName parentTag, javax.xml.namespace.QName elementTag, int eventType)
protected java.util.Map<XMLElementReaderKey,XMLElementReader<P>>	getElementReaderMap()
protected java.util.Stack<javax.xml.namespace.QName>	getEncounteredTags()
javax.xml.namespace.NamespaceContext	getNamespaceContext() Returns the currently valid namespace context object or null, if the root element was not yet read.
javax.xml.stream.XMLEventReader	getXMLReader()
protected boolean	isAllowDefaultNamespace()
javax.xml.namespace.QName	parseQName(java.lang.String curie, javax.xml.stream.events.StartElement element)
protected void	putElementReader(XMLElementReaderKey key, XMLElementReader<P> reader)
protected void	readNextEvent() Method to be implemented be inherited classes that adds at least one additional event (determined from the underlying data source) to the event queue.

Methods inherited from class info.bioinfweb.jphyloio.AbstractEventReader

addEventListener, fireEvent, getCurrentEventCollection, getIDManager, getLastNonCommentEvent, getParameters, getParentInformation, getPreviousEvent, getSequenceTokensEventManager, getStreamDataProvider, getUpcomingEvents, hasNextEvent, hasSpecialEventCollection, isBeforeFirstAccess, next, nextOfType, peek, removeEventListener, resetCurrentEventCollection, setCurrentEventCollection

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.jphyloio.JPhyloIOEventReader

addEventListener, getLastNonCommentEvent, getParentInformation, getPreviousEvent, hasNextEvent, next, nextOfType, peek, removeEventListener

Methods inherited from interface info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject

getFormatID

Field Detail

INTERNAL_USE_NAMESPACE

public static final java.lang.String INTERNAL_USE_NAMESPACE

See Also:

Constant Field Values

TAG_PARENT_OF_ROOT

public static final javax.xml.namespace.QName TAG_PARENT_OF_ROOT

Constructor Detail

AbstractXMLEventReader

public AbstractXMLEventReader(java.io.File file,
                              ReadWriteParameterMap parameters)
                       throws java.io.IOException,
                              javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

AbstractXMLEventReader

public AbstractXMLEventReader(java.io.InputStream stream,
                              ReadWriteParameterMap parameters)
                       throws java.io.IOException,
                              javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

AbstractXMLEventReader

public AbstractXMLEventReader(javax.xml.stream.XMLEventReader xmlReader,
                              ReadWriteParameterMap parameters)

AbstractXMLEventReader

public AbstractXMLEventReader(java.io.Reader reader,
                              ReadWriteParameterMap parameters)
                       throws java.io.IOException,
                              javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

Method Detail

isAllowDefaultNamespace

protected boolean isAllowDefaultNamespace()

putElementReader

protected void putElementReader(XMLElementReaderKey key,
                                XMLElementReader<P> reader)

fillMap

protected abstract void fillMap()

readNextEvent

protected void readNextEvent()
                      throws java.io.IOException

Description copied from class: AbstractEventReader

Method to be implemented be inherited classes that adds at least one additional event (determined from the underlying data source) to the event queue.

Specified by:

readNextEvent in class AbstractEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>

Throws:

java.io.IOException

getElementReader

protected XMLElementReader<P> getElementReader(javax.xml.namespace.QName parentTag,
                                               javax.xml.namespace.QName elementTag,
                                               int eventType)

parseQName

public javax.xml.namespace.QName parseQName(java.lang.String curie,
                                            javax.xml.stream.events.StartElement element)
                                     throws JPhyloIOReaderException

Throws:

JPhyloIOReaderException

createStreamDataProvider

protected P createStreamDataProvider()

Description copied from class: AbstractEventReader

This method is called in the constructor of AbstractEventReader to initialize the stream data provider that will be returned by AbstractEventReader.getStreamDataProvider(). Inherit classes that use their own stream data provider implementation should overwrite this method.

This default implementation creates a new instance of ReaderStreamDataProvider.

Overrides:

createStreamDataProvider in class AbstractEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>

Returns:

the stream data provider to be used with this instance

getXMLReader

public javax.xml.stream.XMLEventReader getXMLReader()

getEncounteredTags

protected java.util.Stack<javax.xml.namespace.QName> getEncounteredTags()

getElementReaderMap

protected java.util.Map<XMLElementReaderKey,XMLElementReader<P>> getElementReaderMap()

getNamespaceContext

public javax.xml.namespace.NamespaceContext getNamespaceContext()

Returns the currently valid namespace context object or null, if the root element was not yet read.

Specified by:

getNamespaceContext in interface JPhyloIOXMLEventReader

Returns:

the currently valid namespace context or null

createMetaXMLEventReader

public MetaXMLEventReader createMetaXMLEventReader()
                                            throws java.lang.IllegalStateException

Description copied from interface: JPhyloIOXMLEventReader

Creates a new XMLEventReader that allows to read events of XML content of literal metadata from this JPhyloIO event reader instance through that interface. Instances can be created any time, while this instance is located inside a literal metadata subsequence with the LiteralContentSequenceType.XML, but not outside of such a sequence.

In principle this method may be called multiple times within the same literal metadata event subsequence, which would result in having multiple XML event reader instances delegating to the same JPhyloIO reader, although that is not recommended for performance reasons.

Specified by:

createMetaXMLEventReader in interface JPhyloIOXMLEventReader

Returns:

the new reader instance

Throws:

java.lang.IllegalStateException - if no reader can be created at the current position (outside of a literal metadata event subsequence with type LiteralContentSequenceType.XML)

createMetaXMLStreamReader

public MetaXMLStreamReader createMetaXMLStreamReader()
                                              throws java.lang.IllegalStateException

Description copied from interface: JPhyloIOXMLEventReader

Creates a XMLStreamReader that allows to read events of XML content of literal metadata from this JPhyloIO event reader instance through that interface. Instances can be created any time, while this instance is located inside a literal metadata subsequence with the LiteralContentSequenceType.XML, but not outside of such a sequence.

In principle this method may be called multiple times within the same literal metadata event subsequence, which would result in having multiple XML event reader instances delegating to the same JPhyloIO reader, although that is not recommended for performance reasons.

Specified by:

createMetaXMLStreamReader in interface JPhyloIOXMLEventReader

Returns:

the new reader instance

Throws:

java.lang.IllegalStateException - if no reader can be created at the current position (outside of a literal metadata event subsequence with type LiteralContentSequenceType.XML)

close

public void close()
           throws java.io.IOException

Description copied from interface: JPhyloIOEventReader

Closes the underlying document source (usually a stream).

Specified by:

close in interface JPhyloIOEventReader

Overrides:

close in class AbstractEventReader<P extends XMLReaderStreamDataProvider<? extends AbstractXMLEventReader<P>>>

Throws:

java.io.IOException - Implementing classes might throw different types of exceptions if the stream cannot be closed properly