info.bioinfweb.jphyloio.formats.nexml.elementreader

Class AbstractNeXMLElementReader

java.lang.Object

info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader<NeXMLReaderStreamDataProvider>

info.bioinfweb.jphyloio.formats.nexml.elementreader.AbstractNeXMLElementReader

All Implemented Interfaces:

NeXMLConstants, XMLElementReader<NeXMLReaderStreamDataProvider>, ReadWriteConstants

Direct Known Subclasses:

AbstractSetElementReader, NeXMLMetaEndElementReader, NeXMLMetaStartElementReader, NeXMLSetEndElementReader

public abstract class AbstractNeXMLElementReader
extends AbstractXMLElementReader<NeXMLReaderStreamDataProvider>
implements XMLElementReader<NeXMLReaderStreamDataProvider>, NeXMLConstants, ReadWriteConstants

Processes a NeXML tag without any of its subelements.

Methods provided in this class are commonly used by different element readers.

Author:

Sarah Wiechers

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	AbstractNeXMLElementReader.LabeledIDEventInformation Contains information about a LabeledIDEvent.
protected static class	AbstractNeXMLElementReader.OTUorOTUsEventInformation Contains information about a LinkedLabeledIDEvent.

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.formats.nexml.NeXMLConstants

ATTR_ABOUT, ATTR_CELL_SET_LINKED_IDS, ATTR_CHAR_SET_LINKED_IDS, ATTR_CODON_POSITION, ATTR_CONTENT, ATTR_DATATYPE, ATTR_GENERATOR, ATTR_HREF, ATTR_ID, ATTR_LABEL, ATTR_LENGTH, ATTR_NODE_EDGE_SET_LINKED_EDGE_IDS, ATTR_NODE_EDGE_SET_LINKED_NODE_IDS, ATTR_NODE_EDGE_SET_LINKED_ROOTEDGE_IDS, ATTR_OTU_SET_LINKED_IDS, ATTR_OTUS, ATTR_PROPERTY, ATTR_REL, ATTR_ROOT, ATTR_SEQUENCE_SET_LINKED_IDS, ATTR_SINGLE_CHAR_LINK, ATTR_SINGLE_OTU_LINK, ATTR_SINGLE_STATE_LINK, ATTR_SOURCE, ATTR_STATE_SET_LINKED_IDS, ATTR_STATES, ATTR_SYMBOL, ATTR_TARGET, ATTR_TOKENS, ATTR_TREE_SET_LINKED_NETWORK_IDS, ATTR_TREE_SET_LINKED_TREE_IDS, ATTR_VERSION, ATTR_XSI_TYPE, DEFAULT_TOKEN_DEFINITION_SET_ID_PREFIX, NEXML_DEFAULT_NAMESPACE_PREFIX, NEXML_FORMAT_NAME, NEXML_NAMESPACE, NEXML_NAMESPACE_PREFIX, NEXML_PREDICATE_NAMESPACE, NEXML_VERSION, PREDICATE_CHAR_ATTR_CODON_POSITION, PREDICATE_CHAR_ATTR_TOKENS, PREDICATE_FORMAT, PREDICATE_MATRIX, PREDICATE_ORIGINAL_LABEL, PREDICATE_ORIGINAL_TOKEN_NAME, TAG_CELL, TAG_CHAR, TAG_CHARACTERS, TAG_EDGE, TAG_FORMAT, TAG_MATRIX, TAG_MEMBER, TAG_META, TAG_NETWORK, TAG_NODE, TAG_OTU, TAG_OTUS, TAG_POLYMORPHIC, TAG_ROOT, TAG_ROOTEDGE, TAG_ROW, TAG_SEQ, TAG_SET, TAG_STATE, TAG_STATES, TAG_TREE, TAG_TREES, TAG_UNCERTAIN, TYPE_CONTIN_CELLS, TYPE_CONTIN_SEQ, TYPE_DNA_CELLS, TYPE_DNA_SEQS, TYPE_FLOAT_NETWORK, TYPE_FLOAT_TREE, TYPE_INT_NETWORK, TYPE_INT_TREE, TYPE_LITERAL_META, TYPE_PROTEIN_CELLS, TYPE_PROTEIN_SEQS, TYPE_RESOURCE_META, TYPE_RESTRICTION_CELLS, TYPE_RESTRICTION_SEQS, TYPE_RNA_CELLS, TYPE_RNA_SEQS, TYPE_STANDARD_CELLS, TYPE_STANDARD_SEQ, UNDEFINED_OTU_ID_PREFIX, UNDEFINED_OTU_LABEL, UNDEFINED_OTUS_ID_PREFIX, UNDEFINED_OTUS_LABEL

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
AbstractNeXMLElementReader()

Method Summary

Modifier and Type	Method and Description
protected void	createIntervalEvents(NeXMLReaderStreamDataProvider streamDataProvider, java.lang.String[] charIDs) Creates a series of CharacterSetIntervalEvents from an array of IDs referencing CharacterDefinitionEvents and adds them to the current event collection.
protected AbstractNeXMLElementReader.LabeledIDEventInformation	getLabeledIDEventInformation(NeXMLReaderStreamDataProvider streamDataProvider, javax.xml.stream.events.StartElement element) Obtains information about the ID and label associated with a StartElement by reading its attributes.
protected AbstractNeXMLElementReader.OTUorOTUsEventInformation	getOTUorOTUsEventInformation(NeXMLReaderStreamDataProvider streamDataProvider, javax.xml.stream.events.StartElement element) Obtains information about the ID, label and linked OTU or OTU list associated with a StartElement by reading its attributes.
static CharacterSymbolMeaning	parseStateMeaning(java.lang.String symbol)
protected java.util.List<java.lang.String>	readSequence(NeXMLReaderStreamDataProvider streamDataProvider, java.lang.String sequence, TokenTranslationStrategy translateTokens) Parses a sequence string to a list of single tokens by using the provided TokenTranslationStrategy.

Methods inherited from class info.bioinfweb.jphyloio.formats.xml.elementreaders.AbstractXMLElementReader

readAttributes, readAttributes

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.formats.xml.elementreaders.XMLElementReader

readEvent

Constructor Detail

AbstractNeXMLElementReader

public AbstractNeXMLElementReader()

Method Detail

readSequence

protected java.util.List<java.lang.String> readSequence(NeXMLReaderStreamDataProvider streamDataProvider,
                                                        java.lang.String sequence,
                                                        TokenTranslationStrategy translateTokens)
                                                 throws JPhyloIOReaderException,
                                                        javax.xml.stream.XMLStreamException

Parses a sequence string to a list of single tokens by using the provided TokenTranslationStrategy.

The sequence may contain tokens longer than one character in case of continuous or standard data.

Parameters:

streamDataProvider - the stream data provider of the calling NeXMLEventReader

sequence - the sequence as a string of tokens

translateTokens - the TokenTranslationStrategy to be applied

Returns:

the list of tokens obtained from the sequence

Throws:

JPhyloIOReaderException

javax.xml.stream.XMLStreamException

createIntervalEvents

protected void createIntervalEvents(NeXMLReaderStreamDataProvider streamDataProvider,
                                    java.lang.String[] charIDs)
                             throws JPhyloIOReaderException,
                                    javax.xml.stream.XMLStreamException

Creates a series of CharacterSetIntervalEvents from an array of IDs referencing CharacterDefinitionEvents and adds them to the current event collection.

Parameters:

streamDataProvider - the stream data provider of the calling NeXMLEventReader

charIDs - an array of IDs referencing CharacterDefinitionEvents

Throws:

JPhyloIOReaderException

javax.xml.stream.XMLStreamException

getLabeledIDEventInformation

protected AbstractNeXMLElementReader.LabeledIDEventInformation getLabeledIDEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
                                                                                            javax.xml.stream.events.StartElement element)
                                                                                     throws JPhyloIOReaderException

Obtains information about the ID and label associated with a StartElement by reading its attributes.

If no ID can be found a default ID is created in case of NeXMLConstants.TAG_META and NeXMLConstants.TAG_CHAR. In all other cases an ID attribute needs to provide a valid ID or a JPhyloIOReaderException will be thrown.

Parameters:

streamDataProvider - the stream data provider of the calling NeXMLEventReader

element - the StartElement to obtain the information from

Returns:

the AbstractNeXMLElementReader.LabeledIDEventInformation containing information about the given StartElement

Throws:

JPhyloIOReaderException

getOTUorOTUsEventInformation

protected AbstractNeXMLElementReader.OTUorOTUsEventInformation getOTUorOTUsEventInformation(NeXMLReaderStreamDataProvider streamDataProvider,
                                                                                            javax.xml.stream.events.StartElement element)
                                                                                     throws JPhyloIOReaderException

Obtains information about the ID, label and linked OTU or OTU list associated with a StartElement by reading its attributes.

If no label is associated with this start element, the label of the linked element will be returned as a label. If the linked element does not have a label either, the elemnent's ID will can used as a label, depending on ReadWriteParameterNames.KEY_USE_OTU_LABEL.

Parameters:

streamDataProvider - the stream data provider of the calling NeXMLEventReader

element - the StartElement to obtain the information from

Returns:

the AbstractNeXMLElementReader.OTUorOTUsEventInformation containing information about the given StartElement

Throws:

JPhyloIOReaderException

parseStateMeaning

public static CharacterSymbolMeaning parseStateMeaning(java.lang.String symbol)