info.bioinfweb.jphyloio.formats.nexml.receivers

Class NeXMLCollectSequenceDataReceiver

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver<P>

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver<NeXMLWriterStreamDataProvider>

info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver

info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLCollectSequenceDataReceiver

All Implemented Interfaces:

JPhyloIOEventReceiver, NeXMLConstants

public class NeXMLCollectSequenceDataReceiver
extends NeXMLHandleSequenceDataReceiver

Receiver that collects information about the sequence tokens contained in a document.

It is checked if the document contains tokens with additional information attached (labels or metadata) (and therefore cells tags will have to be written to the document later on) and which CharacterStateSetType these tokens indicate.

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
NeXMLCollectSequenceDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens)

Method Summary

Modifier and Type	Method and Description
protected void	handleLiteralContentMeta(LiteralMetadataContentEvent event)
protected void	handleLiteralMetaStart(LiteralMetadataEvent event)
protected void	handleResourceMetaStart(ResourceMetadataEvent event)
protected void	handleToken(java.lang.String token, java.lang.String label)

Methods inherited from class info.bioinfweb.jphyloio.formats.nexml.receivers.NeXMLHandleSequenceDataReceiver

doAdd, getTokenIndex, handleTokenEnd, isNestedUnderSingleToken, setNestedUnderSingleToken, setTokenIndex

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver

isLongTokens

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver

add, addIgnoredComments, addIgnoredLiteralMetadata, addIgnoredResourceMetadata, addIgnoreLogMessage, didIgnoreComments, didIgnoreLiteralMetadata, didIgnoreMetadata, didIgnoreResourceMetadata, getIgnoredComments, getIgnoredLiteralMetadata, getIgnoredMetadata, getIgnoredResourceMetadata, getLogger, getParameterMap, getParentEvent, getParentEvents, getStreamDataProvider, handleComment, handleMetaEndEvent, isInComment

Methods inherited from class java.lang.Object

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

Constructor Detail

NeXMLCollectSequenceDataReceiver

public NeXMLCollectSequenceDataReceiver(NeXMLWriterStreamDataProvider streamDataProvider,
                                        ReadWriteParameterMap parameterMap,
                                        boolean longTokens)

Method Detail

handleResourceMetaStart

protected void handleResourceMetaStart(ResourceMetadataEvent event)
                                throws java.io.IOException,
                                       javax.xml.stream.XMLStreamException

Overrides:

handleResourceMetaStart in class BasicEventReceiver<NeXMLWriterStreamDataProvider>

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleLiteralMetaStart

protected void handleLiteralMetaStart(LiteralMetadataEvent event)
                               throws java.io.IOException,
                                      javax.xml.stream.XMLStreamException

Overrides:

handleLiteralMetaStart in class BasicEventReceiver<NeXMLWriterStreamDataProvider>

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleLiteralContentMeta

protected void handleLiteralContentMeta(LiteralMetadataContentEvent event)
                                 throws java.io.IOException,
                                        javax.xml.stream.XMLStreamException

Overrides:

handleLiteralContentMeta in class BasicEventReceiver<NeXMLWriterStreamDataProvider>

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

handleToken

protected void handleToken(java.lang.String token,
                           java.lang.String label)
                    throws JPhyloIOWriterException

Specified by:

handleToken in class AbstractSequenceContentReceiver<NeXMLWriterStreamDataProvider>

Throws:

JPhyloIOWriterException