info.bioinfweb.jphyloio.formats.phyloxml

Class PhyloXMLColorTranslator

java.lang.Object

info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator<java.awt.Color>

info.bioinfweb.jphyloio.formats.phyloxml.PhyloXMLColorTranslator

All Implemented Interfaces:

PhyloXMLConstants, ObjectTranslator<java.awt.Color>

public class PhyloXMLColorTranslator
extends AbstractObjectTranslator<java.awt.Color>
implements PhyloXMLConstants

Object translator between Color and the PhyloXML complex type BranchColor.

Since:

0.0.0

Author:

Sarah Wiechers, Ben Stöver

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

Constructor Summary

Constructors

Constructor and Description
PhyloXMLColorTranslator()

Method Summary

Modifier and Type	Method and Description
java.lang.Class<java.awt.Color>	getObjectClass() Returns the Java class of object instances created by this translator.
boolean	hasStringRepresentation() Determines whether the objects handled by this instance have a simple string representation or need a more complex XML representation.
java.lang.String	javaToRepresentation(java.lang.Object object, WriterStreamDataProvider<?> streamDataProvider) Converts the specified Java object to its string representation.
java.awt.Color	readXMLRepresentation(javax.xml.stream.XMLEventReader reader, ReaderStreamDataProvider<?> streamDataProvider) Tries to create a new instance of the handled object type from the data provided by the specified XML reader.
java.awt.Color	representationToJava(java.lang.String representation, ReaderStreamDataProvider<?> streamDataProvider) Converts the specified string representation to a new instance of the according Java object.
void	writeXMLRepresentation(javax.xml.stream.XMLStreamWriter writer, java.lang.Object object, WriterStreamDataProvider<?> streamDataProvider) Writes the XML representation of the specified object into the specified XML writer.

Methods inherited from class info.bioinfweb.jphyloio.objecttranslation.implementations.AbstractObjectTranslator

equals, hashCode

Methods inherited from class java.lang.Object

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

Constructor Detail

PhyloXMLColorTranslator

public PhyloXMLColorTranslator()

Method Detail

getObjectClass

public java.lang.Class<java.awt.Color> getObjectClass()

Description copied from interface: ObjectTranslator

Returns the Java class of object instances created by this translator.

Note that ObjectTranslator.javaToRepresentation(Object, WriterStreamDataProvider) and ObjectTranslator.writeXMLRepresentation(XMLStreamWriter, Object, WriterStreamDataProvider) may also accept instances of other classes. This is independent from the return value here.

Specified by:

getObjectClass in interface ObjectTranslator<java.awt.Color>

Returns:

the class of the handled objects

hasStringRepresentation

public boolean hasStringRepresentation()

Description copied from interface: ObjectTranslator

Determines whether the objects handled by this instance have a simple string representation or need a more complex XML representation.

Instances that return false here will throw an UnsupportedOperationException, if ObjectTranslator.javaToRepresentation(Object, WriterStreamDataProvider) is called.

Specified by:

hasStringRepresentation in interface ObjectTranslator<java.awt.Color>

Returns:

true if handled objects have a simple string representation or false if XML is necessary to represent the handled objects

javaToRepresentation

public java.lang.String javaToRepresentation(java.lang.Object object,
                                             WriterStreamDataProvider<?> streamDataProvider)
                                      throws java.lang.UnsupportedOperationException,
                                             java.lang.ClassCastException

Description copied from interface: ObjectTranslator

Converts the specified Java object to its string representation.

Specified by:

javaToRepresentation in interface ObjectTranslator<java.awt.Color>

Parameters:

object - the object to be translated

streamDataProvider - TODO

Returns:

the string representation of the object

Throws:

java.lang.UnsupportedOperationException - if objects handled by this instance can only be represented as XML

java.lang.ClassCastException - if the specified object is not an instance of the supported class or does not implement the supported interface

See Also:

ObjectTranslator.hasStringRepresentation()

writeXMLRepresentation

public void writeXMLRepresentation(javax.xml.stream.XMLStreamWriter writer,
                                   java.lang.Object object,
                                   WriterStreamDataProvider<?> streamDataProvider)
                            throws java.io.IOException,
                                   javax.xml.stream.XMLStreamException

Description copied from interface: ObjectTranslator

Writes the XML representation of the specified object into the specified XML writer.

Specified by:

writeXMLRepresentation in interface ObjectTranslator<java.awt.Color>

Parameters:

writer - the writer to be used to write the XML representation

object - the object to be converted

streamDataProvider - TODO

Throws:

java.io.IOException - if an I/O error occurs while trying to write to the specified writer

javax.xml.stream.XMLStreamException - if an XML stream exception occurs while trying to write to the specified writer

representationToJava

public java.awt.Color representationToJava(java.lang.String representation,
                                           ReaderStreamDataProvider<?> streamDataProvider)
                                    throws InvalidObjectSourceDataException,
                                           java.lang.UnsupportedOperationException

Description copied from interface: ObjectTranslator

Converts the specified string representation to a new instance of the according Java object.

If #getClass() returns an interface for this instance, the concrete class of the returned object may depend on the representation.

Specified by:

representationToJava in interface ObjectTranslator<java.awt.Color>

Parameters:

representation - the string representation of the object to be created

streamDataProvider - the stream data provider of the calling reader (Maybe null. Some translators will use it to gain additional status information required for translating, e.g. prefix to namespace mapping for creating QNames.)

Returns:

the new object

Throws:

InvalidObjectSourceDataException - if the specified string representation cannot be parsed to a supported object

java.lang.UnsupportedOperationException - if objects handled by this instance can only be represented as XML

readXMLRepresentation

public java.awt.Color readXMLRepresentation(javax.xml.stream.XMLEventReader reader,
                                            ReaderStreamDataProvider<?> streamDataProvider)
                                     throws java.io.IOException,
                                            javax.xml.stream.XMLStreamException,
                                            InvalidObjectSourceDataException

Description copied from interface: ObjectTranslator

Tries to create a new instance of the handled object type from the data provided by the specified XML reader.

This method will start reading from the current position of the reader and read only as far as necessary to collect all data for the new object. Therefore the reader should be positioned before the start tag, that represents the object and will read until the according end tag was consumed. If the supported objects have a simple string representation, the reader should be positioned in front of the according characters.

If this

Specified by:

readXMLRepresentation in interface ObjectTranslator<java.awt.Color>

Parameters:

reader - the XML reader providing the data to create a new object

streamDataProvider - TODO

Returns:

the new object

Throws:

java.io.IOException - if an I/O error occurs while trying to read from the specified reader

javax.xml.stream.XMLStreamException - if an XML stream exception occurs while trying to read from the specified reader

InvalidObjectSourceDataException - if an unexpected XML event was encountered or an XML event has unexpected contents