Class: BioInterchange::Phylogenetics::TreeSet

Inherits:
Model
  • Object
show all
Defined in:
lib/biointerchange/phylogenetics/tree_set.rb

Overview

A phylogenetic tree set that can contain multiple phylogenetic trees.

Instance Method Summary collapse

Constructor Details

#initialize ⇒ TreeSet

Create a new instance of a tree set. A tree set can contain multiple phylogenetic trees.



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# 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

Instance Method Details

#add(tree) ⇒ Object

Add a tree to the tree set.

tree

BioRuby tree instance that is added to the contents of this tree set



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# File 'lib/biointerchange/phylogenetics/tree_set.rb', line 39

def add(tree)
  @set[tree] = true
end

#contents ⇒ Object

Returns the contents of the tree set.



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# File 'lib/biointerchange/phylogenetics/tree_set.rb', line 15

def contents
  @set.keys
end

#date ⇒ Object

If a date was provided, then this method returns its value.



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# File 'lib/biointerchange/phylogenetics/tree_set.rb', line 20

def date
  @date
end

#prune ⇒ Object

Removes all features from the set, but keeps additional data (e.g., the date).



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# File 'lib/biointerchange/phylogenetics/tree_set.rb', line 44

def prune
  @set.clear
end

#set_date(date) ⇒ Object

Sets a date that is associated with the trees in this model (e.g., annotation date, creation date, etc.).

date

an instance of Date that is associated with all trees in the model



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# File 'lib/biointerchange/phylogenetics/tree_set.rb', line 27

def set_date(date)
  @date = date
end

#uri ⇒ Object

Returns an URI for this particular tree set, which is a not necessarily globally unique SHA1 hash.



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# File 'lib/biointerchange/phylogenetics/tree_set.rb', line 32

def uri
  "biointerchange://phylogenetics/treeset/self/#{Digest::SHA1.hexdigest(Time.now.to_s)}"
end