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Brainstorming on design of node element.

Bio::PhyloXML::PhyloXMLNode

attributes inherited from Bio::Tree::Node

• bootstrap
• bootstrap_string
• ec_number
• name
• scientific_name
• taxonomy_id

new attributes:
[CZ: of course, extending Bio::Tree::Node has many advantages, but it also creates a number of awkward redundancies; for example bootstrap vs. Confidence, scientific name, taxonomy_id vs. Taxonomy]

[DJ: i agree to CZ. Then It looks like its better to have a class which matches closely phyloxml structure and have a method which returns Bio::Tree::Node, thus allowing people still run existing code, but having data in a new format. Also it will simplify the phyloxml writer. ]

• id_source
• confidence [] (hash of values? where keys are confidence tag type attribute values (confidence, probability etc) ) [CZ: hash might not be ideal, a small object with type and value might be better — could have two or more confidence value of equal type] (DJ: agreed)

• color
• node_id
• taxonomy [] (Taxonomy class inherited from general Bio::Taxonomy class)
• sequence [] (Bio::Sequence object)
• events (design class for this)
  • type
  • duplications
  • speciations
  • losses
  • confidence
• binary_characters (design class for this) [CZ: this is probably the least important element — implement only if enough time]
• distribution []
  • desc
  • point []
  • polygon []
• date
• reference []
  • doi
  • desc
• property []

General Bio::Taxonomy class

• code (I guess its swiss-prot specific)
• scientific_name
• common_name []
• rank
• ? authority
• ? aliases []

Taxonomy class inherited from General Bio::Taxonomy class

additional attributes:

• id
• uri

Bio::PhyloXMLTree

inherited from Bio::Tree:

• options
• root

new attributes

• rooted (boolean)
• rerootable (boolean)
• branch_length_unit
• type
• name
• id
• description
• date
• confidence []
• clade_relation []
• sequence_relation []
• property []