class BioInterchange::Phylogenetics::TreeSet
A phylogenetic tree set that can contain multiple phylogenetic trees.
Public Class Methods
new()
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Create a new instance of a tree set. A tree set can contain multiple phylogenetic trees.
# File lib/biointerchange/phylogenetics/tree_set.rb, line 9 def initialize # Trees are stored as the keys of a hash map to increase performance: @set = {} end
Public Instance Methods
add(tree)
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Add a tree to the tree set.
tree
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BioRuby tree instance that is added to the contents of this tree set
# File lib/biointerchange/phylogenetics/tree_set.rb, line 39 def add(tree) @set[tree] = true end
contents()
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Returns the contents of the tree set.
# File lib/biointerchange/phylogenetics/tree_set.rb, line 15 def contents @set.keys end
date()
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If a date was provided, then this method returns its value.
# File lib/biointerchange/phylogenetics/tree_set.rb, line 20 def date @date end
prune()
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Removes all features from the set, but keeps additional data (e.g., the date).
# File lib/biointerchange/phylogenetics/tree_set.rb, line 44 def prune @set.clear end
set_date(date)
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Sets a date that is associated with the trees in this model (e.g., annotation date, creation date, etc.).
date
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an instance of Date that is associated with all trees in the model
# File lib/biointerchange/phylogenetics/tree_set.rb, line 27 def set_date(date) @date = date end
uri()
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Returns an URI for this particular tree set, which is a not necessarily globally unique SHA1 hash.
# File lib/biointerchange/phylogenetics/tree_set.rb, line 32 def uri "biointerchange://phylogenetics/treeset/self/#{Digest::SHA1.hexdigest(Time.now.to_s)}" end