bio-nexml

  doc = Bio::NeXML::Parser.new( "trees.xml" )
  nexml = doc.parse
  nexml.class #Bio::NeXML::Nexml

  # Parse a test file. This will give us Bio::NeXML::Otus,
  # Bio::NeXML::Trees, and Bio::NeXML::Characters object.
  doc1 = Bio::NeXML::Parser.new 'test.xml'
  nexml = doc1.parse
  doc1.close

  # Create a Writer object,
  writer = Bio::NeXML::Writer.new

  # add otus, trees and characters to it,
  writer << nexml.otus
  writer << nexml.trees
  writer << nexml.characters

  # save it.
  writer.save 'sample.xml'

  # Create an otus object with a child otu element
  taxa1 = Bio::NeXML::Otus.new 'taxa1', 'A taxa block'
  o1 = Bio::NeXML::Otu.new 'o1', 'A taxon'
  taxa1 << o1

  # Obtain the raw NeXML representation of the otus object created
  writer = Bio::NeXML::Writer.new
  writer.serialize_otus( taxa1 ).to_s
  # => "<otus label=\"A taxa block\" id=\"taxa1\">\n  <otu label=\"A taxon\" id=\"o1\"/>\n</otus>"

  #get a hash of otus objects indexed with 'id'
  nexml.otus_set

  #get an array of otus objects
  nexml.otus

  #get an otus by id
  taxa1 = nexml.get_otus_by_id "taxa1"

  #iterate over each otus object
  nexml.each_otus do |taxa|
    puts taxa.id
    puts taxa.label
  end

  #characters
  nexml.trees_set #return a hash of trees object indexed with 'id'
  nexml.trees #return an array of trees objects.

  #iterate over each trees object
  nexml.each_trees do |trees|
    puts trees.id
    puts trees.label
  end

  #find a trees by id
  trees1 = nexml.get_trees_by_id 'trees1'

  # characters
  nexml.characters_set #return a hash of characters object indexed with 'id'
  nexml.characters #return an array of characters object

  #iterate over each characters object
  nexml.each_characters do |ch|
    puts ch.id
    puts ch.label
  end

  #find a characters object by id
  characters = nexml.get_characters_by_id 'chars1'

  #get the id of otus
  taxa1.id # "taxa1"

  #get the label of otus
  taxa1.label # "Primary taxa block"

  #get a hash of child otu objects indexed with id
  taxa1.otu_set

  #get an array of child otu objects
  taxa1.otus

  #get an otu object by id
  #get_otu_by_id is an alias of []
  t1 = taxa1[ 't1' ]

  #add an otu object to otus
  t1.add_otu( otu_object )
  #to add more than one otu object at a time use << or otus= method
  t1 << [otu_object1, otu_object2]
  t1.otus = otu_object1, otu_object2

  #or iterate over each otu object
  #each_otu is an alias for each
  taxa1.each do |taxon|
    puts taxon.id
    puts taxon.label
  end

  #check if an otu with given id belongs to an otus or not
  #include? and has? are alias for has_otu?
  taxa1.has_otu? 't2' # => true
  taxa1.has? 't8' # => false

  #an otus object in enumerable
  taxa1.map &:id # => array of otu ids
  taxa1.select {|t| t.class == "Lemurs" } #maybe in future

  #get an otu's id
  t1.id # => "t1"

  #get an otu's label
  t1.label # => "Homo sapiens"

  trees1.class #Bio::NeXML::Trees

  #get the taxa block to which the trees is linked to
  trees1.otus #returns an otus object

  trees1.tree_set #return a hash or tree objects indexed with 'id'
  tress1.trees #return an arrayof trees object

  #iterate over each tree object
  trees1.each_tree do |t|
    puts t.id
    puts t.label
  end

  #get a tree object with its 'tree1'
  tree1 = trees1[ 'tree1' ]
  #or, with a conventional method call
  tree1 = trees1.get_tree_by_id 'tree1'
  #or, from a nexml object
  tree1 = nexml.get_tree_by_id 'tree1'

  tree1.class #Bio::NeXML::IntTree or Bio::NeXML::FloatTree

  #check if a tree belongs to a trees or not
  #pass it a tree id
  tree1.has_tree? 'tree1' #return true or false

  #get the number of treess
  trees1.number_of_trees

  trees1.network_set #return a hash or network objects indexed with 'id'
  tress1.networks #return an arrayof network objects

  #iterate over each network object
  trees1.each_network do |n|
    puts n.id
    puts n.label
  end

  #get a network object with its id
  network1 = trees1[ 'network1' ]
  #or, with a conventional method call
  network1 = trees1.get_network_by_id 'network1'
  #or, from a nexml object
  network1 = nexml.get_tree_by_id 'network1'

  network1.class #Bio::NeXML::IntTree or Bio::NeXML::FloatTree

  #check if a network belongs to a trees or not
  #pass it a network id
  trees1.has_network? 'network1' #return true or false

  #get the number of networks
  trees1.number_of_networks

  #iterate over both trees and networks
  trees1.each do |g|
    puts g.class
  end

  #find if a tree or a network belongs to a trees or not
  #include? is an alias for has?
  trees1.has? 'tree1' #return true or false

  #total number of trees and networks
  trees1.number_of_graphs

  node1 = tree.get_node_by_name "n3" #note name is same as id
  tree1.parents node1

  trees1.map &:id

  puts characters.class

  #get the taxa block to which the characters is linked to
  characters.otus #returns an otus object

  #get the child format element
  format = characters.format

  puts format.class

  #get the child matrix element
  matrix = characters.matrix

  puts matrix.class

  format.states_set #return a hash of states objects indexed with 'id'
  format.states #return an array of states object

  #iterate over each states object
  format.each_states do |states|
    puts states.id
    puts states.label
  end

  #get a states object by id
  states = format.get_states_by_id 'states1'

  #check if the states object with 'id' belongs to format or not
  format.has_states? 'states1'

  format.char_set #return a hash of char objects indexed with 'id'
  format.chars #return an array of char objects

  #iterate over each char object
  format.each_char do |char|
    puts char.id
    puts char.label
  end

  #get a char object by id
  char = format.get_char_by_id 'char1'

  #check if the char object with 'id' belongs to format or not
  format.has_char? 'char1'

  #get a states or a char object by id
  state = format[ 'states1' ]
  char = format[ 'char1' ]

  #check if a states or a char object with 'id' belongs to format or not
  format.has? 'states1'
  format.has? 'char1'

  #all objects, including char and states can be iterated over with each
  format.each do |obj|
    puts obj.class
  end

  #format is enumerable
  format.map &:id

  states.state_set #return a hash of state objects indexed with 'id'
  states.states #return an array of state objects

  #iterate over each state object
  states.each_state do |state|
    puts state.id
  end
  #or, use its alias each

  #get a state object by id
  state = states.get_state_by_id 'state1'
  #or, use hash notation
  state = states[ 'state1' ]

  #check if a state belongs to states or not
  states.has_state? 'state1'
  #or, use its alias has? and include?

  #get the symbol associated with the state
  state.symbol

  #find if the state is ambiguous
  state.ambiguous?

  #find the kind of ambiguity
  state.ambiguity

  #find if it is an uncertain state set
  state.uncertain?

  #find if it is a polymorphic state set
  state.polymorphic?

  #get the members of a state set as an array
  state.members

  #or iterate over each member
  state.each do |member|
    puts member.class #same as self
    puts member.id
  end

  #a state is Enumerable over its members
  state.select{ |member| member.id == "rna5" }

  #get the id
  char.id

  #get the label
  char.label

  #get the states object the char is linked to
  char.states

  #get the codon position for DnaChar and RnaChar objects
  char.codon