+++ /dev/null
-# 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 'inline'
-
-# Class to calculate the Levenshtein distance between two
-# given strings.
-# http://en.wikipedia.org/wiki/Levenshtein_distance
-class Levenshtein
- BYTES_IN_INT = 4
-
- def self.distance(s, t)
- return 0 if s == t;
- return t.length if s.length == 0;
- return s.length if t.length == 0;
-
- v0 = "\0" * (t.length + 1) * BYTES_IN_INT
- v1 = "\0" * (t.length + 1) * BYTES_IN_INT
-
- l = self.new
- l.distance_C(s, t, s.length, t.length, v0, v1)
- end
-
- # >>>>>>>>>>>>>>> RubyInline C code <<<<<<<<<<<<<<<
-
- inline do |builder|
- builder.prefix %{
- unsigned int min(unsigned int a, unsigned int b, unsigned int c)
- {
- unsigned int m = a;
-
- if (m > b) m = b;
- if (m > c) m = c;
-
- return m;
- }
- }
-
- builder.c %{
- VALUE distance_C(
- VALUE _s, // string
- VALUE _t, // string
- VALUE _s_len, // string length
- VALUE _t_len, // string length
- VALUE _v0, // score vector
- VALUE _v1 // score vector
- )
- {
- char *s = (char *) StringValuePtr(_s);
- char *t = (char *) StringValuePtr(_t);
- unsigned int s_len = FIX2UINT(_s_len);
- unsigned int t_len = FIX2UINT(_t_len);
- unsigned int *v0 = (unsigned int *) StringValuePtr(_v0);
- unsigned int *v1 = (unsigned int *) StringValuePtr(_v1);
-
- unsigned int i = 0;
- unsigned int j = 0;
- unsigned int cost = 0;
-
- for (i = 0; i < t_len + 1; i++)
- v0[i] = i;
-
- for (i = 0; i < s_len; i++)
- {
- v1[0] = i + 1;
-
- for (j = 0; j < t_len; j++)
- {
- cost = (s[i] == t[j]) ? 0 : 1;
- v1[j + 1] = min(v1[j] + 1, v0[j + 1] + 1, v0[j] + cost);
- }
-
- for (j = 0; j < t_len + 1; j++)
- v0[j] = v1[j];
- }
-
- return UINT2NUM(v1[t_len]);
- }
- }
- end
-end
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__
--- /dev/null
+# 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 'inline'
+
+# Class to calculate the Levenshtein distance between two
+# given strings.
+# http://en.wikipedia.org/wiki/Levenshtein_distance
+class Levenshtein
+ BYTES_IN_INT = 4
+
+ def self.distance(s, t)
+ return 0 if s == t;
+ return t.length if s.length == 0;
+ return s.length if t.length == 0;
+
+ v0 = "\0" * (t.length + 1) * BYTES_IN_INT
+ v1 = "\0" * (t.length + 1) * BYTES_IN_INT
+
+ l = self.new
+ l.distance_C(s, t, s.length, t.length, v0, v1)
+ end
+
+ # >>>>>>>>>>>>>>> RubyInline C code <<<<<<<<<<<<<<<
+
+ inline do |builder|
+ # Macro for matching nucleotides including ambiguity codes.
+ builder.prefix %{
+ #define MATCH(A,B) ((bitmap[A] & bitmap[B]) != 0)
+ }
+
+ # Bitmap for matching nucleotides including ambiguity codes.
+ # For each value bits are set from the left: bit pos 1 for A,
+ # bit pos 2 for T, bit pos 3 for C, and bit pos 4 for G.
+ builder.prefix %{
+ char bitmap[256] = {
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
+ 0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
+ 0, 1,14, 4,11, 0, 0, 8, 7, 0, 0,10, 0, 5,15, 0,
+ 0, 0, 9,12, 2, 2,13, 3, 0, 6, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
+ };
+ }
+
+ builder.prefix %{
+ unsigned int min(unsigned int a, unsigned int b, unsigned int c)
+ {
+ unsigned int m = a;
+
+ if (m > b) m = b;
+ if (m > c) m = c;
+
+ return m;
+ }
+ }
+
+ builder.c %{
+ VALUE distance_C(
+ VALUE _s, // string
+ VALUE _t, // string
+ VALUE _s_len, // string length
+ VALUE _t_len, // string length
+ VALUE _v0, // score vector
+ VALUE _v1 // score vector
+ )
+ {
+ char *s = (char *) StringValuePtr(_s);
+ char *t = (char *) StringValuePtr(_t);
+ unsigned int s_len = FIX2UINT(_s_len);
+ unsigned int t_len = FIX2UINT(_t_len);
+ unsigned int *v0 = (unsigned int *) StringValuePtr(_v0);
+ unsigned int *v1 = (unsigned int *) StringValuePtr(_v1);
+
+ unsigned int i = 0;
+ unsigned int j = 0;
+ unsigned int cost = 0;
+
+ for (i = 0; i < t_len + 1; i++)
+ v0[i] = i;
+
+ for (i = 0; i < s_len; i++)
+ {
+ v1[0] = i + 1;
+
+ for (j = 0; j < t_len; j++)
+ {
+ cost = (MATCH(s[i], t[j])) ? 0 : 1;
+ v1[j + 1] = min(v1[j] + 1, v0[j + 1] + 1, v0[j] + cost);
+ }
+
+ for (j = 0; j < t_len + 1; j++)
+ v0[j] = v1[j];
+ }
+
+ return UINT2NUM(v1[t_len]);
+ }
+ }
+ end
+end
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__