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Design of Classes

Bio::PhyloXML::Node

• id_source (string)
• name (string)
• confidences [] (Array of Confidence objects)
• width (float)
• color (Color object)
• node_id (string)
• taxonomies [] (Array of PhyloXML::Taxonomy objects inherited from general Bio::Taxonomy class)
• sequences [] (Array of PhyloXML::Sequence object)
• events (Events object)
• binary_characters (PhyloXML::BinaryCharacters class)
• distributions [] (Array of Distribution objects)
• date (PhyloXML::Date object)
• references [] (Reference object)
• properties [] (Array of Property objects)
• other [] (Array of PhyloXML::Other objects for holding any namespace data)

General Bio::Taxonomy class

• code (string)
• scientific_name (string)
• common_names [] (Array of Strings)
• rank (string)
• authority (string)
• synonyms [] (Array of strings)

Taxonomy class inherited from General Bio::Taxonomy class

additional attributes:

• taxonomy_id (Id object) (in xml file sis called ‘id’. taxonomy_id is used, since ‘id’ is reserved word in Ruby)
• uri (Uri object)
• id_source (string)
• other [] (Array of PhyloXML::Other objects)

Bio::PhyloXMLTree

inherited from Bio::Tree:

• options
• root

new attributes

• rooted (boolean)
• rerootable (boolean)
• branch_length_unit
• type (string)
• name (string)
• phylogeny_id (Id object) (in xml file corresponds to ‘id’ element)
• description (string)
• date (string) general date
• confidences [] (Confidence object)
• clade_relations [] (CladeRelation object)
• sequence_relations [] (SequenceRelation object)
• properties [] (Property object)
• other [] (PhyloXML::Other objects)

Confidence class

• type (string) required
• value (float)

Color class

• red (byte)
• green (byte)
• blue (byte)

Events class

• type (string)
• duplications (int)
• speciations (int)
• losses (int)
• confidence (Confidence object)

Distribution class

• desc (string)
• points [] (array of Point object)
• polygons [] (array of Polygon object)

Point class

• geodetic_datum (string)
• alt_unit (string)
• lat (float)
• long (float)
• alt (float)

Polygon class

• points [] (Point object)

Date class

• unit
• desc (string)
• value
• minimum
• maximum

Reference class

• doi (string)
• desc (string)

Property class

• ref (string)
• unit (string)
• value (string)
• datatype (string/ numeric constant?)
• applies_to (string / numeric constant?)
• id_ref (string)

CladeRelation class

• id_ref_0 (string)
• id_ref_1 (string)
• distance (int/float)
• type (string)
• confidence (Confidence object)

SequenceRelation class

• id_ref_0
• id_ref_1
• distance
• type (string)

ID class

• type
• value

PhyloXML::Sequence class

• type (string ) (values from rna, dna, protein)
• id_source (string)
• id_ref (string ?)
• symbol (string ?)
• accession (Accession object)
• name (string )
• location (string) (location of a sequence on a genome/chromosome)
• mol_seq (string)
• is_aligned (boolean)
• uri (Uri object)
• annotations [] (Array of Annotation objects)
• domain_architecture (DomainArchitecture object)
• other []

Accession class

• source (example: “UniProtKB”)
• value (example: “P17304”)

Uri class

• desc
• type
• uri

Annotation class

• ref (string)
• source (string)
• evidence (string)
• type (string)
• desc (string)
• confidence (Confidence object)
• properties [] (Array of Property objects)
• uri (Uri object

DomainArchitecture class

• length (int )
• domains [] (Array of ProteinDomain objects)

ProteinDomain class

• from (int)
• to (int)
• confidence (double) (for example, to store E-values)
• id (string)
• value (string)

BinaryCharacters

• type (string)
• gained_count (integer)
• lost_count (integer)
• present_count (integer)
• absent_count (integer)
• gained (array of strings)
• lost (array of strings)
• present ( array of strings)
• absent ( array of strings)