public class PhyloXMLSpecificPredicatesDataReceiver extends PhyloXMLMetaDataReceiver
This receiver does not fully validate the contents of the meta events. An InconsistentAdapterDataException
will be thrown if incorrect predicates are nested under a phylogeny, a node or an edge or if any predicate is nested
in an incorrect order. Which predicates are allowed in which order can be obtained from the documentation of PhyloXMLEventWriter
or the PhyloXML schema.
PhyloXMLEventWriter}
VALID_XSD_TYPES
APPLIES_TO_ANNOTATION, APPLIES_TO_CLADE, APPLIES_TO_NODE, APPLIES_TO_OTHER, APPLIES_TO_PARENT_BRANCH, APPLIES_TO_PHYLOGENY, ATTR_ABSENT_COUNT, ATTR_ALT_UNIT, ATTR_APPLIES_TO, ATTR_BRANCH_LENGTH, ATTR_BRANCH_LENGTH_UNIT, ATTR_COLLAPSE, ATTR_COMMENT, ATTR_CONFIDENCE, ATTR_DATATYPE, ATTR_DESC, ATTR_DISTANCE, ATTR_DOI, ATTR_EVIDENCE, ATTR_FROM, ATTR_GAINED_COUNT, ATTR_GEO_DATUM, ATTR_ID, ATTR_ID_PROVIDER, ATTR_ID_REF, ATTR_ID_REF_0, ATTR_ID_REF_1, ATTR_ID_SOURCE, ATTR_IS_ALIGNED, ATTR_LENGTH, ATTR_LOST_COUNT, ATTR_PRESENT_COUNT, ATTR_REF, ATTR_REROOTABLE, ATTR_ROOTED, ATTR_SOURCE, ATTR_STANDARD_DEVIATION, ATTR_TO, ATTR_TYPE, ATTR_UNIT, DATA_TYPE_BRANCH_COLOR, DATA_TYPE_EVENTTYPE, DATA_TYPE_RANK, DATA_TYPE_SEQUENCE_SYMBOL, DATA_TYPE_TAXONOMY_CODE, JPHYLOIO_PHYLOXML_NAMESPACE, PHYLOXML_DATA_TYPE_NAMESPACE, PHYLOXML_DEFAULT_PRE, PHYLOXML_FORMAT_NAME, PHYLOXML_NAMESPACE, PHYLOXML_PREDICATE_NAMESPACE, PHYLOXML_SCHEMA_LOCATION_URI, PREDICATE_ANNOTATION, PREDICATE_ANNOTATION_ATTR_EVIDENCE, PREDICATE_ANNOTATION_ATTR_REF, PREDICATE_ANNOTATION_ATTR_SOURCE, PREDICATE_ANNOTATION_ATTR_TYPE, PREDICATE_ANNOTATION_CONFIDENCE, PREDICATE_ANNOTATION_CONFIDENCE_ATTR_TYPE, PREDICATE_ANNOTATION_CONFIDENCE_VALUE, PREDICATE_ANNOTATION_DESC, PREDICATE_ANNOTATION_PROPERTY, PREDICATE_ANNOTATION_PROPERTY_ATTR_APPLIES_TO, PREDICATE_ANNOTATION_PROPERTY_ATTR_DATATYPE, PREDICATE_ANNOTATION_PROPERTY_ATTR_ID_REF, PREDICATE_ANNOTATION_PROPERTY_ATTR_UNIT, PREDICATE_ANNOTATION_URI, PREDICATE_ANNOTATION_URI_ATTR_DESC, PREDICATE_ANNOTATION_URI_ATTR_TYPE, PREDICATE_ANNOTATION_URI_VALUE, PREDICATE_ATTR_COLLAPSE, PREDICATE_ATTR_ID_SOURCE, PREDICATE_BINARY_CHARACTERS, PREDICATE_BINARY_CHARACTERS_ABSENT, PREDICATE_BINARY_CHARACTERS_ABSENT_BC, PREDICATE_BINARY_CHARACTERS_ATTR_ABSENT_COUNT, PREDICATE_BINARY_CHARACTERS_ATTR_GAINED_COUNT, PREDICATE_BINARY_CHARACTERS_ATTR_LOST_COUNT, PREDICATE_BINARY_CHARACTERS_ATTR_PRESENT_COUNT, PREDICATE_BINARY_CHARACTERS_ATTR_TYPE, PREDICATE_BINARY_CHARACTERS_GAINED, PREDICATE_BINARY_CHARACTERS_GAINED_BC, PREDICATE_BINARY_CHARACTERS_LOST, PREDICATE_BINARY_CHARACTERS_LOST_BC, PREDICATE_BINARY_CHARACTERS_PRESENT, PREDICATE_BINARY_CHARACTERS_PRESENT_BC, PREDICATE_CLADE_REL, PREDICATE_CLADE_REL_ATTR_DISTANCE, PREDICATE_CLADE_REL_ATTR_IDREF0, PREDICATE_CLADE_REL_ATTR_IDREF1, PREDICATE_CLADE_REL_ATTR_TYPE, PREDICATE_COLOR, PREDICATE_COLOR_ALPHA, PREDICATE_COLOR_BLUE, PREDICATE_COLOR_GREEN, PREDICATE_COLOR_RED, PREDICATE_CONFIDENCE, PREDICATE_CONFIDENCE_ATTR_STDDEV, PREDICATE_CONFIDENCE_ATTR_TYPE, PREDICATE_CONFIDENCE_VALUE, PREDICATE_DATE, PREDICATE_DATE_ATTR_UNIT, PREDICATE_DATE_DESC, PREDICATE_DATE_MAXIMUM, PREDICATE_DATE_MINIMUM, PREDICATE_DATE_VALUE, PREDICATE_DISTRIBUTION, PREDICATE_DISTRIBUTION_DESC, PREDICATE_DISTRIBUTION_POINT, PREDICATE_DISTRIBUTION_POINT_ALT, PREDICATE_DISTRIBUTION_POINT_ATTR_ALT_UNIT, PREDICATE_DISTRIBUTION_POINT_ATTR_GEODETIC_DATUM, PREDICATE_DISTRIBUTION_POINT_LAT, PREDICATE_DISTRIBUTION_POINT_LONG, PREDICATE_DISTRIBUTION_POLYGON, PREDICATE_DISTRIBUTION_POLYGON_POINT, PREDICATE_DISTRIBUTION_POLYGON_POINT_ALT, PREDICATE_DISTRIBUTION_POLYGON_POINT_ATTR_ALT_UNIT, PREDICATE_DISTRIBUTION_POLYGON_POINT_ATTR_GEODETIC_DATUM, PREDICATE_DISTRIBUTION_POLYGON_POINT_LAT, PREDICATE_DISTRIBUTION_POLYGON_POINT_LONG, PREDICATE_DOMAIN_ARCHITECTURE, PREDICATE_DOMAIN_ARCHITECTURE_ATTR_LENGTH, PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN, PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_CONFIDENCE, PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_FROM, PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_ID, PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_ATTR_TO, PREDICATE_DOMAIN_ARCHITECTURE_DOMAIN_VALUE, PREDICATE_EVENTS, PREDICATE_EVENTS_CONFIDENCE, PREDICATE_EVENTS_CONFIDENCE_ATTR_TYPE, PREDICATE_EVENTS_CONFIDENCE_VALUE, PREDICATE_EVENTS_DUPLICATIONS, PREDICATE_EVENTS_LOSSES, PREDICATE_EVENTS_SPECIATIONS, PREDICATE_EVENTS_TYPE, PREDICATE_NODE_ID, PREDICATE_NODE_ID_ATTR_PROVIDER, PREDICATE_NODE_ID_VALUE, PREDICATE_PHYLOGENY_ATTR_BRANCH_LENGTH_UNIT, PREDICATE_PHYLOGENY_ATTR_REROOTABLE, PREDICATE_PHYLOGENY_ATTR_TYPE, PREDICATE_PHYLOGENY_DATE, PREDICATE_PHYLOGENY_DESCRIPTION, PREDICATE_PHYLOGENY_ID, PREDICATE_PHYLOGENY_ID_ATTR_PROVIDER, PREDICATE_PHYLOGENY_ID_VALUE, PREDICATE_PROPERTY, PREDICATE_PROPERTY_ATTR_APPLIES_TO, PREDICATE_PROPERTY_ATTR_ID_REF, PREDICATE_PROPERTY_ATTR_UNIT, PREDICATE_REFERENCE, PREDICATE_REFERENCE_ATTR_DOI, PREDICATE_REFERENCE_DESC, PREDICATE_REFERENCE_VALUE, PREDICATE_SEQ_REL, PREDICATE_SEQ_REL_ATTR_DISTANCE, PREDICATE_SEQ_REL_ATTR_IDREF0, PREDICATE_SEQ_REL_ATTR_IDREF1, PREDICATE_SEQ_REL_ATTR_TYPE, PREDICATE_SEQ_REL_CONFIDENCE, PREDICATE_SEQ_REL_CONFIDENCE_ATTR_TYPE, PREDICATE_SEQ_REL_CONFIDENCE_VALUE, PREDICATE_SEQUENCE, PREDICATE_SEQUENCE_ACCESSION, PREDICATE_SEQUENCE_ACCESSION_ATTR_COMMENT, PREDICATE_SEQUENCE_ACCESSION_ATTR_SOURCE, PREDICATE_SEQUENCE_ACCESSION_VALUE, PREDICATE_SEQUENCE_ATTR_ID_REF, PREDICATE_SEQUENCE_ATTR_TYPE, PREDICATE_SEQUENCE_CROSS_REFERENCES, PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION, PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_ATTR_COMMENT, PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_ATTR_SOURCE, PREDICATE_SEQUENCE_CROSS_REFERENCES_ACCESSION_VALUE, PREDICATE_SEQUENCE_GENE_NAME, PREDICATE_SEQUENCE_LOCATION, PREDICATE_SEQUENCE_MOL_SEQ, PREDICATE_SEQUENCE_MOL_SEQ_ATTR_IS_ALIGNED, PREDICATE_SEQUENCE_MOL_SEQ_VALUE, PREDICATE_SEQUENCE_NAME, PREDICATE_SEQUENCE_SYMBOL, PREDICATE_SEQUENCE_URI, PREDICATE_SEQUENCE_URI_ATTR_DESC, PREDICATE_SEQUENCE_URI_ATTR_TYPE, PREDICATE_SEQUENCE_URI_VALUE, PREDICATE_TAXONOMY, PREDICATE_TAXONOMY_AUTHORITY, PREDICATE_TAXONOMY_CODE, PREDICATE_TAXONOMY_COMMON_NAME, PREDICATE_TAXONOMY_ID, PREDICATE_TAXONOMY_ID_ATTR_PROVIDER, PREDICATE_TAXONOMY_ID_VALUE, PREDICATE_TAXONOMY_RANK, PREDICATE_TAXONOMY_SCIENTIFIC_NAME, PREDICATE_TAXONOMY_SYNONYM, PREDICATE_TAXONOMY_URI, PREDICATE_TAXONOMY_URI_ATTR_DESC, PREDICATE_TAXONOMY_URI_ATTR_TYPE, PREDICATE_TAXONOMY_URI_VALUE, PREDICATE_WIDTH, TAG_ABSENT, TAG_ACCESSION, TAG_ALPHA, TAG_ALT, TAG_ANNOTATION, TAG_AUTHORITY, TAG_BC, TAG_BINARY_CHARACTERS, TAG_BLUE, TAG_BRANCH_COLOR, TAG_BRANCH_LENGTH, TAG_BRANCH_WIDTH, TAG_CLADE, TAG_CLADE_RELATION, TAG_CODE, TAG_COMMON_NAME, TAG_CONFIDENCE, TAG_CROSS_REFERENCES, TAG_DATE, TAG_DESC, TAG_DESCRIPTION, TAG_DISTRIBUTION, TAG_DOMAIN, TAG_DOMAIN_ARCHITECTURE, TAG_DUPLICATIONS, TAG_EVENTS, TAG_GAINED, TAG_GENE_NAME, TAG_GREEN, TAG_ID, TAG_LAT, TAG_LOCATION, TAG_LONG, TAG_LOSSES, TAG_LOST, TAG_MAXIMUM, TAG_MINIMUM, TAG_MOL_SEQ, TAG_NAME, TAG_NODE_ID, TAG_PHYLOGENY, TAG_POINT, TAG_POLYGON, TAG_PRESENT, TAG_PROPERTY, TAG_RANK, TAG_RED, TAG_REFERENCE, TAG_ROOT, TAG_SCI_NAME, TAG_SEQUENCE, TAG_SEQUENCE_RELATION, TAG_SPECIATIONS, TAG_SYMBOL, TAG_SYNONYM, TAG_TAXONOMY, TAG_TYPE, TAG_URI, TAG_VALUE, TYPE_NETWORK_EDGE
Constructor and Description |
---|
PhyloXMLSpecificPredicatesDataReceiver(PhyloXMLWriterStreamDataProvider streamDataProvider,
ReadWriteParameterMap parameterMap,
PropertyOwner propertyOwner,
javax.xml.namespace.QName parentPredicate) |
Modifier and Type | Method and Description |
---|---|
protected void |
handleLiteralContentMeta(LiteralMetadataContentEvent event) |
protected void |
handleLiteralMetaStart(LiteralMetadataEvent event)
In this method LiteralMetadataEvents are processed.
|
protected void |
handleMetaEndEvent(JPhyloIOEvent event) |
protected void |
handleResourceMetaStart(ResourceMetadataEvent event) |
determineWriteMeta, getOriginalType, getPropertyOwner, hasSimpleContent, isWriteContent, processLiteralContent, writeCustomXMLTag, writePropertyTag
handleComment
add, addIgnoredComments, addIgnoredLiteralMetadata, addIgnoredResourceMetadata, addIgnoreLogMessage, didIgnoreComments, didIgnoreLiteralMetadata, didIgnoreMetadata, didIgnoreResourceMetadata, doAdd, getIgnoredComments, getIgnoredLiteralMetadata, getIgnoredMetadata, getIgnoredResourceMetadata, getLogger, getParameterMap, getParentEvent, getParentEvents, getStreamDataProvider, isInComment
public PhyloXMLSpecificPredicatesDataReceiver(PhyloXMLWriterStreamDataProvider streamDataProvider, ReadWriteParameterMap parameterMap, PropertyOwner propertyOwner, javax.xml.namespace.QName parentPredicate)
protected void handleLiteralMetaStart(LiteralMetadataEvent event) throws java.io.IOException, javax.xml.stream.XMLStreamException
InconsistentAdapterDataException
is thrown. It is not validated if the number of
child elements is correct (i. e. if they are present too often or not often enough).handleLiteralMetaStart
in class PhyloXMLMetaDataReceiver
java.io.IOException
javax.xml.stream.XMLStreamException
protected void handleLiteralContentMeta(LiteralMetadataContentEvent event) throws java.io.IOException, javax.xml.stream.XMLStreamException
handleLiteralContentMeta
in class PhyloXMLMetaDataReceiver
java.io.IOException
javax.xml.stream.XMLStreamException
protected void handleResourceMetaStart(ResourceMetadataEvent event) throws java.io.IOException, javax.xml.stream.XMLStreamException
handleResourceMetaStart
in class PhyloXMLMetaDataReceiver
java.io.IOException
javax.xml.stream.XMLStreamException
protected void handleMetaEndEvent(JPhyloIOEvent event) throws java.io.IOException, javax.xml.stream.XMLStreamException
handleMetaEndEvent
in class PhyloXMLMetaDataReceiver
java.io.IOException
javax.xml.stream.XMLStreamException