Class: Bio::BioAlignment::Alignment
- Inherits:
-
Object
- Object
- Bio::BioAlignment::Alignment
- Defined in:
- lib/bio-alignment/bioruby.rb,
lib/bio-alignment/alignment.rb
Instance Attribute Summary collapse
-
#sequences ⇒ Object
(also: #rows)
Returns the value of attribute sequences.
-
#tree ⇒ Object
readonly
Returns the value of attribute tree.
Instance Method Summary collapse
- #<<(seq) ⇒ Object
-
#[](index) ⇒ Object
Return a sequence by index.
-
#attach_tree(tree) ⇒ Object
extend BioAlignment with Tree functionality - this method adds a tree and pulls in the functionality of the Tree module.
-
#clone ⇒ Object
Return a deep cloned alignment.
- #each ⇒ Object
- #each_element ⇒ Object
- #find(name) ⇒ Object
-
#ids ⇒ Object
return an array of sequence ids.
-
#initialize(seqs = nil, ids = nil) ⇒ Alignment
constructor
Create alignment.
- #size ⇒ Object
- #to_bioruby_alignment ⇒ Object
- #to_s ⇒ Object
-
#tree_reduce(new_tree) ⇒ Object
Reduce an alignment, based on the new tree.
-
#update_each_element ⇒ Object
copy alignment and allow updating elements.
Methods included from Coerce
fetch_id, fetch_seq, fetch_seq_string, to_elements
Methods included from Columns
#clone_columns!, #columns, #columns_to_s, #columns_where, #num_columns
Methods included from Rows
Methods included from Pal2Nal
Constructor Details
#initialize(seqs = nil, ids = nil) ⇒ Alignment
Create alignment. seqs can be a list of sequences. If these are String types, they get converted to the library Sequence container
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# File 'lib/bio-alignment/alignment.rb', line 24 def initialize seqs = nil, ids = nil @sequences = [] if seqs num = 0 seqs.each_with_index do | seq, i | next if seq == nil or seq.to_s.strip == "" id = num id = ids[i] if ids and ids[i] @sequences << if seq.kind_of?(String) seq1 = Sequence.new(id,seq.strip) seq1 else seq end num += 1 end end end |
Instance Attribute Details
#sequences ⇒ Object Also known as: rows
Returns the value of attribute sequences.
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# File 'lib/bio-alignment/alignment.rb', line 18 def sequences @sequences end |
#tree ⇒ Object (readonly)
Returns the value of attribute tree.
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# File 'lib/bio-alignment/alignment.rb', line 19 def tree @tree end |
Instance Method Details
#<<(seq) ⇒ Object
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# File 'lib/bio-alignment/alignment.rb', line 60 def << seq @sequences << seq end |
#[](index) ⇒ Object
Return a sequence by index
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# File 'lib/bio-alignment/alignment.rb', line 56 def [] index rows[index] end |
#attach_tree(tree) ⇒ Object
extend BioAlignment with Tree functionality - this method adds a tree and pulls in the functionality of the Tree module. Returns the tree traverser
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# File 'lib/bio-alignment/alignment.rb', line 114 def attach_tree tree extend Tree @tree = Tree::init(tree,self) @tree end |
#clone ⇒ Object
Return a deep cloned alignment. This method clones sequences, and the state objects
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# File 'lib/bio-alignment/alignment.rb', line 98 def clone aln = super # clone the sequences aln.sequences = [] each do | seq | aln.sequences << seq.clone end aln.clone_columns! if @columns # clone the tree @tree = @tree.clone if @tree aln end |
#each ⇒ Object
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# File 'lib/bio-alignment/alignment.rb', line 64 def each rows.each { | seq | yield seq } self end |
#each_element ⇒ Object
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# File 'lib/bio-alignment/alignment.rb', line 69 def each_element each { |seq| seq.each { |e| yield e }} self end |
#find(name) ⇒ Object
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# File 'lib/bio-alignment/alignment.rb', line 74 def find name each do | seq | return seq if Coerce::fetch_id(seq) == name end raise "ERROR: Sequence not found by its name, looking for <#{name}>" end |
#ids ⇒ Object
return an array of sequence ids
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# File 'lib/bio-alignment/alignment.rb', line 47 def ids rows.map { |r| Coerce::fetch_id(r) } end |
#size ⇒ Object
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# File 'lib/bio-alignment/alignment.rb', line 51 def size rows.size end |
#to_bioruby_alignment ⇒ Object
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# File 'lib/bio-alignment/bioruby.rb', line 25 def to_bioruby_alignment Bio::Alignment.new(self) end |
#to_s ⇒ Object
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# File 'lib/bio-alignment/alignment.rb', line 88 def to_s res = "" res += "\t" + columns_to_s + "\n" if @columns # fetch each sequence in turn res += map{ |seq| Coerce::fetch_id(seq).to_s + "\t" + Coerce::fetch_seq_string(seq) }.join("\n") res end |
#tree_reduce(new_tree) ⇒ Object
Reduce an alignment, based on the new tree
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# File 'lib/bio-alignment/alignment.rb', line 121 def tree_reduce new_tree names = new_tree.map { | node | node.name }.compact # p names nrows = [] names.each do | name | nrows << find(name).clone end new_aln = Alignment.new(nrows) new_aln.attach_tree(new_tree.clone) new_aln end |
#update_each_element ⇒ Object
copy alignment and allow updating elements. Returns alignment.
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# File 'lib/bio-alignment/alignment.rb', line 82 def update_each_element aln = self.clone aln.each { |seq| seq.each_with_index { |e,i| seq.seq[i] = yield e }} aln end |