info.bioinfweb.jphyloio.formats.phyloxml

Class PhyloXMLWriterStreamDataProvider

java.lang.Object

info.bioinfweb.jphyloio.WriterStreamDataProvider<R>

info.bioinfweb.jphyloio.formats.xml.XMLWriterStreamDataProvider<PhyloXMLEventWriter>

info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLWriterStreamDataProvider

All Implemented Interfaces:

PhyloXMLConstants, PhyloXMLPrivateConstants

public class PhyloXMLWriterStreamDataProvider
extends XMLWriterStreamDataProvider<PhyloXMLEventWriter>
implements PhyloXMLConstants, PhyloXMLPrivateConstants

The XMLWriterStreamDataProvider used by PhyloXMLEventWriter.

Author:

Sarah Wiechers

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLConstants

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

Fields inherited from interface info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLPrivateConstants

IDENTIFIER_ANY_PREDICATE, IDENTIFIER_CUSTOM_XML, IDENTIFIER_EDGE, IDENTIFIER_NODE, IDENTIFIER_PHYLOGENY

Constructor Summary

Constructors

Constructor and Description
PhyloXMLWriterStreamDataProvider(PhyloXMLEventWriter eventWriter)

Method Summary

Modifier and Type	Method and Description
java.lang.String	getCurrentCladeIDSource()
java.util.Stack<java.lang.String>	getCustomXMLElements()
java.util.Set<java.lang.String>	getIdSources()
java.util.Map<java.lang.String,PhyloXMLMetaEventInfo>	getMetaEvents()
java.util.Set<java.lang.String>	getMetaIDs()
java.util.Map<java.lang.String,java.lang.String>	getNodeEventIDToIDSourceMap()
java.lang.String	getPhylogenyID()
java.lang.String	getPhylogenyIDProvider()
java.util.Map<javax.xml.namespace.QName,PhyloXMLPredicateInfo>	getPredicateInfoMap() This map is used by PhyloXMLSpecificPredicatesDataReceiver to translate meta events with certain predicates to PhyloXML tags.
boolean	hasTreeGroupMetadata()
boolean	isDocumentHasMetadata()
boolean	isDocumentHasPhylogeny()
void	setCurrentCladeIDSource(java.lang.String currentCladeIDSource)
void	setDocumentHasMetadata(boolean documentHasCustomXML)
void	setDocumentHasPhylogeny(boolean documentHasPhylogeny)
void	setPhylogenyID(java.lang.String phylogenyID)
void	setPhylogenyIDProvider(java.lang.String phylogenyIDProvider)
void	setTreeGroupHasMetadata(boolean treeGroupHasMetadata)

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

getCommentContent, getNamespacePrefixes, getWriter, isLiteralContentContinued, setLiteralContentIsContinued, setNamespacePrefix

Methods inherited from class info.bioinfweb.jphyloio.WriterStreamDataProvider

getEventWriter

Methods inherited from class java.lang.Object

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

Constructor Detail

PhyloXMLWriterStreamDataProvider

public PhyloXMLWriterStreamDataProvider(PhyloXMLEventWriter eventWriter)

Method Detail

getPredicateInfoMap

public java.util.Map<javax.xml.namespace.QName,PhyloXMLPredicateInfo> getPredicateInfoMap()

This map is used by PhyloXMLSpecificPredicatesDataReceiver to translate meta events with certain predicates to PhyloXML tags.

Returns:

a map containing information about the way a predicate shall be translated to a tag

getMetaEvents

public java.util.Map<java.lang.String,PhyloXMLMetaEventInfo> getMetaEvents()

getMetaIDs

public java.util.Set<java.lang.String> getMetaIDs()

isDocumentHasMetadata

public boolean isDocumentHasMetadata()

setDocumentHasMetadata

public void setDocumentHasMetadata(boolean documentHasCustomXML)

isDocumentHasPhylogeny

public boolean isDocumentHasPhylogeny()

setDocumentHasPhylogeny

public void setDocumentHasPhylogeny(boolean documentHasPhylogeny)

hasTreeGroupMetadata

public boolean hasTreeGroupMetadata()

setTreeGroupHasMetadata

public void setTreeGroupHasMetadata(boolean treeGroupHasMetadata)

getCustomXMLElements

public java.util.Stack<java.lang.String> getCustomXMLElements()

getPhylogenyIDProvider

public java.lang.String getPhylogenyIDProvider()

setPhylogenyIDProvider

public void setPhylogenyIDProvider(java.lang.String phylogenyIDProvider)

getPhylogenyID

public java.lang.String getPhylogenyID()

setPhylogenyID

public void setPhylogenyID(java.lang.String phylogenyID)

getCurrentCladeIDSource

public java.lang.String getCurrentCladeIDSource()

setCurrentCladeIDSource

public void setCurrentCladeIDSource(java.lang.String currentCladeIDSource)

getIdSources

public java.util.Set<java.lang.String> getIdSources()

getNodeEventIDToIDSourceMap

public java.util.Map<java.lang.String,java.lang.String> getNodeEventIDToIDSourceMap()