added new match.rb and tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2052 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/align/match.rb b/code_ruby/lib/maasha/align/match.rb
new file mode 100644 (file)
index 0000000..d6a8008
--- /dev/null
+++ b/code_ruby/lib/maasha/align/match.rb
@@ -0,0 +1,132 @@
+# Copyright (C) 2007-2013 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 'inline'
+
+# Class for describing a match between two sequences q and s.
+class Match
+  attr_accessor :q_beg, :s_beg, :length, :score
+
+  def initialize(q_beg, s_beg, length)
+    @q_beg  = q_beg
+    @s_beg  = s_beg
+    @length = length
+    @score  = 0.0
+  end
+
+  def q_end
+    @q_beg + @length - 1
+  end
+
+  def s_end
+    @s_beg + @length - 1
+  end
+
+  # Method to expand a match as far as possible to the left and right
+  # within a given search space.
+  def expand(q_seq, s_seq, q_space_beg, s_space_beg, q_space_end, s_space_end)
+    length = expand_left_C(q_seq, s_seq, @q_beg, @s_beg, q_space_beg, s_space_beg)
+    @length += length
+    @q_beg  -= length
+    @s_beg  -= length
+
+    length = expand_right_C(q_seq, s_seq, q_end, s_end, q_space_end, s_space_end)
+    @length += length
+
+    self
+  end
+
+  def to_s(seq = nil)
+    s = "q: #{@q_beg}, s: #{@s_beg}, l: #{@length}, s: #{@score}"
+    s << " #{seq[@q_beg .. q_end]}" if seq
+
+    s
+  end
+
+  private
+
+  inline do |builder|
+    # Method to expand a match as far as possible to the left within a given
+    # search space.
+    builder.c %{
+      VALUE expand_left_C(
+        VALUE _q_seq,
+        VALUE _s_seq,
+        VALUE _q_beg,
+        VALUE _s_beg,
+        VALUE _q_space_beg,
+        VALUE _s_space_beg
+      )
+      {
+        unsigned char *q_seq       = (unsigned char *) StringValuePtr(_q_seq);
+        unsigned char *s_seq       = (unsigned char *) StringValuePtr(_s_seq);
+        unsigned int   q_beg       = NUM2UINT(_q_beg);
+        unsigned int   s_beg       = NUM2UINT(_s_beg);
+        unsigned int   q_space_beg = NUM2UINT(_q_space_beg);
+        unsigned int   s_space_beg = NUM2UINT(_s_space_beg);
+
+        unsigned int   len = 0;
+
+        while (q_beg > q_space_beg && s_beg > s_space_beg && q_seq[q_beg - 1] == s_seq[s_beg - 1])
+        {
+          q_beg--;
+          s_beg--;
+          len++;
+        }
+
+        return UINT2NUM(len);
+      }
+    }
+
+    builder.c %{
+      VALUE expand_right_C(
+        VALUE _q_seq,
+        VALUE _s_seq,
+        VALUE _q_end,
+        VALUE _s_end,
+        VALUE _q_space_end,
+        VALUE _s_space_end
+      )
+      {
+        unsigned char *q_seq       = (unsigned char *) StringValuePtr(_q_seq);
+        unsigned char *s_seq       = (unsigned char *) StringValuePtr(_s_seq);
+        unsigned int   q_end       = NUM2UINT(_q_end);
+        unsigned int   s_end       = NUM2UINT(_s_end);
+        unsigned int   q_space_end = NUM2UINT(_q_space_end);
+        unsigned int   s_space_end = NUM2UINT(_s_space_end);
+
+        unsigned int   len = 0;
+      
+        while (q_end + 1 <= q_space_end && s_end + 1 <= s_space_end && q_seq[q_end + 1] == s_seq[s_end + 1])
+        {
+          q_end++;
+          s_end++;
+          len++;
+        }
+
+        return UINT2NUM(len);
+      }
+    }
+  end
+end