info.bioinfweb.jphyloio.formats.nexml.receivers

Class AbstractNeXMLDataReceiverMixin

java.lang.Object

info.bioinfweb.jphyloio.formats.nexml.receivers.AbstractNeXMLDataReceiverMixin

All Implemented Interfaces:

NeXMLConstants

public class AbstractNeXMLDataReceiverMixin
extends java.lang.Object
implements NeXMLConstants

Provides a set of static methods to be used as static imports when needed across multiple NeXML data receivers. Since not all of these classes allow direct access to a NeXMLWriterStreamDataProvider, an instance of it is a parameter of the static methods instead of an instance of AbstractNeXMLDataReceiver.

Since:

0.0.0

Author:

Sarah Wiechers

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

Constructor Summary

Constructors

Constructor and Description
AbstractNeXMLDataReceiverMixin()

Method Summary

Modifier and Type	Method and Description
static void	checkLiteralContentMeta(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameters, LiteralMetadataContentEvent event)
static void	checkLiteralMeta(NeXMLWriterStreamDataProvider streamDataProvider, LiteralMetadataEvent event)
static void	checkResourceMeta(NeXMLWriterStreamDataProvider streamDataProvider, ResourceMetadataEvent event)
static void	handleComment(NeXMLWriterStreamDataProvider streamDataProvider, CommentEvent event)
static void	handleLiteralContentMeta(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameters, LiteralMetadataContentEvent event)
static void	handleLiteralMeta(NeXMLWriterStreamDataProvider streamDataProvider, LiteralMetadataEvent event)
static void	handleMetaEndEvent(NeXMLWriterStreamDataProvider streamDataProvider, JPhyloIOEvent event)
static void	handleResourceMeta(NeXMLWriterStreamDataProvider streamDataProvider, ResourceMetadataEvent event)

Methods inherited from class java.lang.Object

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

Constructor Detail

AbstractNeXMLDataReceiverMixin

public AbstractNeXMLDataReceiverMixin()

Method Detail

handleLiteralMeta

public static void handleLiteralMeta(NeXMLWriterStreamDataProvider streamDataProvider,
                                     LiteralMetadataEvent event)
                              throws javax.xml.stream.XMLStreamException,
                                     JPhyloIOWriterException

Throws:

javax.xml.stream.XMLStreamException

JPhyloIOWriterException

checkLiteralMeta

public static void checkLiteralMeta(NeXMLWriterStreamDataProvider streamDataProvider,
                                    LiteralMetadataEvent event)
                             throws javax.xml.stream.XMLStreamException,
                                    JPhyloIOWriterException

Throws:

javax.xml.stream.XMLStreamException

JPhyloIOWriterException

handleLiteralContentMeta

public static void handleLiteralContentMeta(NeXMLWriterStreamDataProvider streamDataProvider,
                                            ReadWriteParameterMap parameters,
                                            LiteralMetadataContentEvent event)
                                     throws javax.xml.stream.XMLStreamException,
                                            java.lang.ClassCastException,
                                            java.io.IOException

Throws:

javax.xml.stream.XMLStreamException

java.lang.ClassCastException

java.io.IOException

checkLiteralContentMeta

public static void checkLiteralContentMeta(NeXMLWriterStreamDataProvider streamDataProvider,
                                           ReadWriteParameterMap parameters,
                                           LiteralMetadataContentEvent event)
                                    throws javax.xml.stream.XMLStreamException

Throws:

javax.xml.stream.XMLStreamException

handleResourceMeta

public static void handleResourceMeta(NeXMLWriterStreamDataProvider streamDataProvider,
                                      ResourceMetadataEvent event)
                               throws java.lang.ClassCastException,
                                      javax.xml.stream.XMLStreamException,
                                      JPhyloIOWriterException

Throws:

java.lang.ClassCastException

javax.xml.stream.XMLStreamException

JPhyloIOWriterException

checkResourceMeta

public static void checkResourceMeta(NeXMLWriterStreamDataProvider streamDataProvider,
                                     ResourceMetadataEvent event)
                              throws java.io.IOException,
                                     javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleMetaEndEvent

public static void handleMetaEndEvent(NeXMLWriterStreamDataProvider streamDataProvider,
                                      JPhyloIOEvent event)
                               throws java.io.IOException,
                                      javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleComment

public static void handleComment(NeXMLWriterStreamDataProvider streamDataProvider,
                                 CommentEvent event)
                          throws java.lang.ClassCastException,
                                 javax.xml.stream.XMLStreamException

Throws:

java.lang.ClassCastException

javax.xml.stream.XMLStreamException