require 'maasha/seq/trim'
require 'narray'
-autoload :BackTrack, 'maasha/seq/backtrack.rb'
-autoload :Dynamic, 'maasha/seq/dynamic.rb'
-autoload :Homopolymer, 'maasha/seq/homopolymer.rb'
+autoload :BackTrack, 'maasha/seq/backtrack'
+autoload :Dynamic, 'maasha/seq/dynamic'
+autoload :Homopolymer, 'maasha/seq/homopolymer'
+autoload :Levenshtein, 'maasha/seq/levenshtein'
# Residue alphabets
DNA = %w[a t c g]
"GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
}
-
# Error class for all exceptions to do with Seq.
class SeqError < StandardError; end
# Method to determine the Hamming Distance between
# two Sequence objects (case insensitive).
- def hamming_distance(seq)
- self.seq.upcase.hamming_distance(seq.seq.upcase)
+ def hamming_distance(entry)
+ self.seq.upcase.hamming_distance(entry.seq.upcase)
+ end
+
+ # Method to determine the Edit Distance between
+ # two Sequence objects (case insensitive).
+ def edit_distance(entry)
+ Levenshtein.distance(self.seq, entry.seq)
end
# Method that generates a random sequence of a given length and type.
--- /dev/null
+#!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__), '..', '..')
+
+# Copyright (C) 2013 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'test/unit'
+require 'test/helper'
+require 'maasha/seq/levenshtein'
+
+class LevenshteinTest < Test::Unit::TestCase
+ test "Levenshtein.distance returns 0 with identical strings" do
+ assert_equal(0, Levenshtein.distance("atcg", "atcg"))
+ end
+
+ test "Levenshtein.distance returns s length if t is empty" do
+ assert_equal(4, Levenshtein.distance("atcg", ""))
+ end
+
+ test "Levenshtein.distance returns t length if s is empty" do
+ assert_equal(5, Levenshtein.distance("", "atcgn"))
+ end
+
+ test "Levenshtein.distance with mismatch only returns correctly" do
+ assert_equal(1, Levenshtein.distance("atcg", "atgg"))
+ end
+
+ test "Levenshtein.distance with ambiguity code returns correctly" do
+ assert_equal(0, Levenshtein.distance("atcg", "nnnn"))
+ end
+
+ test "Levenshtein.distance with insertion returns correctly" do
+ assert_equal(1, Levenshtein.distance("atcg", "attcg"))
+ end
+
+ test "Levenshtein.distance returns correctly" do
+ assert_equal(2, Levenshtein.distance("atcg", "tgncg"))
+ end
+end
+++ /dev/null
-#!/usr/bin/env ruby
-$:.unshift File.join(File.dirname(__FILE__), '..', '..')
-
-# Copyright (C) 2013 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This software is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'test/unit'
-require 'test/helper'
-require 'maasha/levenshtein'
-
-class LevenshteinTest < Test::Unit::TestCase
- test "Levenshtein.distance returns 0 with identical strings" do
- assert_equal(0, Levenshtein.distance("foo", "foo"))
- end
-
- test "Levenshtein.distance returns s length if t is empty" do
- assert_equal(3, Levenshtein.distance("foo", ""))
- end
-
- test "Levenshtein.distance returns t length if s is empty" do
- assert_equal(5, Levenshtein.distance("", "fobar"))
- end
-
- test "Levenshtein.distance with mismatch only returns correctly" do
- assert_equal(1, Levenshtein.distance("foo", "fox"))
- end
-
- test "Levenshtein.distance returns correctly" do
- assert_equal(3, Levenshtein.distance("kitten", "sitting"))
- assert_equal(3, Levenshtein.distance("Saturday", "Sunday"))
- end
-end
assert_equal("UAGCuagc", @entry.complement!.seq)
end
-
- test "#hamming distance returns correctly" do
+ test "#hamming_distance returns correctly" do
seq1 = Seq.new("test1", "ATCG")
seq2 = Seq.new("test2", "atgg")
assert_equal(1, seq1.hamming_distance(seq2))
end
+ test "#edit_distance returns correctly" do
+ seq1 = Seq.new("test1", "ATCG")
+ seq2 = Seq.new("test2", "tgncg")
+ assert_equal(2, seq1.edit_distance(seq2))
+ end
+
test "#generate with length < 1 raises" do
assert_raise(SeqError) { @entry.generate(-10, :dna) }
assert_raise(SeqError) { @entry.generate(0, :dna) }