info.bioinfweb.jphyloio.formats.pde

Class PDEEventReader

java.lang.Object

info.bioinfweb.jphyloio.AbstractEventReader<P>

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

info.bioinfweb.jphyloio.formats.pde.PDEEventReader

All Implemented Interfaces:

PDEConstants, JPhyloIOXMLEventReader, JPhyloIOEventReader, JPhyloIOFormatSpecificObject, ReadWriteConstants

public class PDEEventReader
extends AbstractXMLEventReader<PDEReaderStreamDataProvider>
implements PDEConstants

Event reader for the PDE format used by the alignment editor PhyDE.

This reader supports reading sequence data and metadata as well as character sets from PDE files. Reading of taxon sets is not supported. Identifiers used to specify the number of missing characters at the start or end of a sequence are translated to the according number of missing symbols in SequenceTokensEvents. Token set events are fired with the CharacterStateSetType DNA or amino acid, according to the information in the file.

Sequence metadata of the types STRING and NUMBER is represented as LiteralMetadataEvents, data of the type FILE as ResourceMetadataEvents. The predicate is either ReadWriteConstants.PREDICATE_HAS_LITERAL_METADATA or ReadWriteConstants.PREDICATE_HAS_RESOURCE_METADATA. Char set attributes are represented by metaevents with predefined predicates according to the attribute.

Recognized parameters

• ReadWriteParameterNames.KEY_ALLOW_DEFAULT_NAMESPACE
• ReadWriteParameterNames.KEY_LOGGER

Since:

0.0.0

Author:

Sarah Wiechers, Ben Stöver

Field Summary

Fields inherited from class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader

INTERNAL_USE_NAMESPACE, TAG_PARENT_OF_ROOT

Fields inherited from interface info.bioinfweb.jphyloio.formats.pde.PDEConstants

AMINO_TYPE, ATTR_ALIGNMENT_LENGTH, ATTR_CHARSET_LABEL, ATTR_COLOR, ATTR_DATATYPE, ATTR_ID, ATTR_SEQUENCE_COUNT, ATTR_SEQUENCE_INDEX, ATTR_VERSION, ATTR_VISIBILITY, DNA_TYPE, FIRST_CUSTOM_META_ID, META_ID_ACCESS_NUMBER, META_ID_COMMENT, META_ID_LINKED_FILE, META_ID_SEQUENCE_LABEL, META_TYPE_FILE, META_TYPE_NUMBER, META_TYPE_STRING, PDE_FORMAT_NAME, PDE_NAMESPACE_PREFIX, PDE_PREDICATE_NAMESPACE, PREDICATE_ACCESS_NUMBER, PREDICATE_CHARSET_COLOR, PREDICATE_CHARSET_VISIBILITY, PREDICATE_COMMENT, PREDICATE_DESCRIPTION, PREDICATE_LINKED_FILE, SEQUENCE_END, TAG_ALIGNMENT, TAG_BLOCK, TAG_CHARSET, TAG_CHARSETS, TAG_DESCRIPTION, TAG_HEADER, TAG_MATRIX, TAG_META_TYPE_DEFINITIONS, TAG_ROOT, TAG_SEQUENCE_INFORMATION, TAG_SEQUENCE_META_INFORMATION, UNKNOWN_CHARS

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
PDEEventReader(java.io.File file, ReadWriteParameterMap parameters)
PDEEventReader(java.io.InputStream stream, ReadWriteParameterMap parameters)
PDEEventReader(java.io.Reader reader, ReadWriteParameterMap parameters)
PDEEventReader(javax.xml.stream.XMLEventReader xmlReader, ReadWriteParameterMap parameters)

Method Summary

Modifier and Type	Method and Description
protected PDEReaderStreamDataProvider	createStreamDataProvider() This method is called in the constructor of AbstractEventReader to initialize the stream data provider that will be returned by AbstractEventReader.getStreamDataProvider().
protected void	fillMap()
java.lang.String	getFormatID() Returns a string ID uniquely identifying the target format of this instance.

Methods inherited from class info.bioinfweb.jphyloio.formats.xml.AbstractXMLEventReader

close, createMetaXMLEventReader, createMetaXMLStreamReader, getElementReader, getElementReaderMap, getEncounteredTags, getNamespaceContext, getXMLReader, isAllowDefaultNamespace, parseQName, putElementReader, readNextEvent

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

Constructor Detail

PDEEventReader

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

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

PDEEventReader

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

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

PDEEventReader

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

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

PDEEventReader

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

Method Detail

getFormatID

public java.lang.String getFormatID()

Description copied from interface: JPhyloIOFormatSpecificObject

Returns a string ID uniquely identifying the target format of this instance. Additional information on the format can be retrieved by passing the returned ID to JPhyloIOReaderWriterFactory.getFormatInfo(String).

Third party developers that create readers or writers for additional formats must make sure to use a globally unique format ID. It is strongly recommended to use owned reverse domain names for this (e.g. org.example.additionalformat).

Specified by:

getFormatID in interface JPhyloIOFormatSpecificObject

Returns:

the ID of the target format of this instance

See Also:

JPhyloIOReaderWriterFactory.getFormatInfo(String)

fillMap

protected void fillMap()

Specified by:

fillMap in class AbstractXMLEventReader<PDEReaderStreamDataProvider>

createStreamDataProvider

protected PDEReaderStreamDataProvider 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 AbstractXMLEventReader<PDEReaderStreamDataProvider>

Returns:

the stream data provider to be used with this instance