reverted backtrack.rb to 2006 prior to struct version

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2017 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/seq/backtrack.rb b/code_ruby/lib/maasha/seq/backtrack.rb
index 1de8b6cad4da8c70450b7c347e8a0de22b30403d..088b596a1e4e1e52784a5bdfeb67920d1fe2ea48 100644 (file)
--- a/code_ruby/lib/maasha/seq/backtrack.rb
+++ b/code_ruby/lib/maasha/seq/backtrack.rb
@@ -64,18 +64,16 @@ module BackTrack
 
     matches = []
 
-    while result = track_C(self.seq, self.length, pattern, offset, max_mismatches, max_insertions, max_deletions)
-      pos, length, mis, ins, del = result
-
-      match = Match.new(pos, length, mis, ins, del, self.seq[pos ... pos + length])
-
-      if block_given?
-        yield match
-      else
-        matches << match
+    if block_given?
+      while result = track_C(self.seq, self.length, pattern, offset, max_mismatches, max_insertions, max_deletions)
+        yield Match.new(result.first, result.last, self.seq[result.first ... result.first + result.last])
+        offset = result.first + 1
+      end
+    else
+      while result = track_C(self.seq, self.length, pattern, offset, max_mismatches, max_insertions, max_deletions)
+        matches << Match.new(result.first, result.last, self.seq[result.first ... result.first + result.last])
+        offset = result.first + 1
       end
-
-      offset = match.pos + 1
     end
 
     return matches.empty? ? nil : matches unless block_given?
@@ -84,22 +82,13 @@ module BackTrack
   private
 
   inline do |builder|
+    builder.add_static "id_seq", 'rb_intern("@seq")', "ID"
+
     # Macro for matching nucleotides including ambiguity codes.
     builder.prefix %{
       #define MATCH(A,B) ((bitmap[A] & bitmap[B]) != 0)
     }
 
-    # Defining a struct for returning match information.
-    builder.prefix %{
-      typedef struct 
-      {
-        unsigned int end;
-        unsigned int mis;
-        unsigned int ins;
-        unsigned int del;
-      } match;
-    }
-
     # 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.
@@ -128,38 +117,29 @@ module BackTrack
     # mismatches, ins insertions and del deletions. ss is the start of the sequence, used only for
     # reporting the match endpoints.
     builder.prefix %{
-      match* backtrack(
-        char         *ss,   // Sequence start
-        char         *s,    // Sequence
-        char         *p,    // Pattern
-        unsigned int  mis,  // Max mismatches
-        unsigned int  ins,  // Max insertions
-        unsigned int  del,  // Max deletions
-        int state           // 1 deletion, -1 insertion, 0 match or mismatch
+      unsigned int backtrack(
+        char *ss,   // Sequence start
+        char *s,    // Sequence
+        char *p,    // Pattern
+        int   mis,  // Max mismatches
+        int   ins,  // Max insertions
+        int   del   // Max deletions
       )
       {
-        match found = {0, 0, 0, 0};
-        match *f = &found;
+        unsigned int r = 0;
 
         while (*s && MATCH(*s, *p)) ++s, ++p;    // OK to always match longest segment
 
         if (!*p)
-        {
-          f->end = (unsigned int) (s - ss);
-          f->mis = mis;
-          f->ins = ins;
-          f->del = del;
-
-          return f;
-        }
+          return (unsigned int) (s - ss);
         else
         {
-          if (mis && *s && *p            && (f = backtrack(ss, s + 1, p + 1, mis - 1, ins, del, 0))) return f;
-          if (ins && *p && (state != 1)  && (f = backtrack(ss, s, p + 1, mis, ins - 1, del, -1)))    return f;
-          if (del && *s && (state != -1) && (f = backtrack(ss, s + 1, p, mis, ins, del - 1, 1)))     return f;
+          if (mis && *s && *p && (r = backtrack(ss, s + 1, p + 1, mis - 1, ins, del))) return r;
+          if (ins && *p &&       (r = backtrack(ss, s, p + 1, mis, ins - 1, del)))     return r;
+          if (del && *s &&       (r = backtrack(ss, s + 1, p, mis, ins, del - 1)))     return r;
         }
 
-        return NULL;
+        return 0;
       }
     }
  
@@ -167,54 +147,39 @@ module BackTrack
     # insertions and del deletions.
     builder.c %{
       VALUE track_C(
-        VALUE _s,         // Sequence
-        VALUE _len,       // Sequence length
-        VALUE _p,         // Pattern
-        VALUE _pos,       // Start position
-        VALUE _max_mis,   // Maximum mismatches
-        VALUE _max_ins,   // Maximum insertions
-        VALUE _max_del    // Maximum deletions
+        VALUE _s,     // Sequence
+        VALUE _len,   // Sequence length
+        VALUE _p,     // Pattern
+        VALUE _pos,   // Start position
+        VALUE _mis,   // Maximum mismatches
+        VALUE _ins,   // Maximum insertions
+        VALUE _del    // Maximum deletions
       )
       {
-        char         *s       = StringValuePtr(_s);
-        char         *p       = StringValuePtr(_p);
-        unsigned int  len     = FIX2UINT(_len);
-        unsigned int  pos     = FIX2UINT(_pos);
-        unsigned int  max_mis = FIX2UINT(_max_mis);
-        unsigned int  max_ins = FIX2UINT(_max_ins);
-        unsigned int  max_del = FIX2UINT(_max_del);
-
-        char         *ss    = s;
-        match        *f     = NULL;
-        unsigned int  mbeg  = 0;
-        unsigned int  mlen  = 0;
-        unsigned int  mmis  = 0;
-        unsigned int  mins  = 0;
-        unsigned int  mdel  = 0;
-        int           state = 0;
-        VALUE         ary   = 0;
-
-        if (pos < len) // FIXME: pos < len - plen + 1
+        char         *s   = StringValuePtr(_s);
+        char         *p   = StringValuePtr(_p);
+        unsigned int  len = FIX2UINT(_len);
+        unsigned int  pos = FIX2UINT(_pos);
+        unsigned int  mis = FIX2UINT(_mis);
+        unsigned int  ins = FIX2UINT(_ins);
+        unsigned int  del = FIX2UINT(_del);
+
+        char         *ss = s;
+        unsigned int  e  = 0;
+        VALUE         tuple;
+
+        if (pos < len)
         {
           s += pos;
 
           while (*s)
           {
-            if ((f = backtrack(ss, s, p, max_mis, max_ins, max_del, state)))
+            if ((e = backtrack(ss, s, p, mis, ins, del)))
             {
-              mbeg = (s - ss);
-              mlen = f->end - mbeg;
-              mmis = max_mis - f->mis;
-              mins = max_ins - f->ins;
-              mdel = max_del - f->del;
-
-              ary = rb_ary_new();
-              rb_ary_push(ary, INT2FIX(mbeg));
-              rb_ary_push(ary, INT2FIX(mlen));
-              rb_ary_push(ary, INT2FIX(mmis));
-              rb_ary_push(ary, INT2FIX(mins));
-              rb_ary_push(ary, INT2FIX(mdel));
-              return ary;
+              tuple = rb_ary_new();
+              rb_ary_push(tuple, INT2FIX((int) (s - ss)));
+              rb_ary_push(tuple, INT2FIX((int) e - (s - ss)));
+              return tuple;
             }
 
             s++;
@@ -228,19 +193,16 @@ module BackTrack
 
   # Class containing match information.
   class Match
-    attr_reader :pos, :length, :mis, :ins, :del, :match
+    attr_reader :pos, :length, :match
 
-    def initialize(pos, length, mis, ins, del, match)
+    def initialize(pos, length, match)
       @pos    = pos
       @length = length
-      @mis    = mis
-      @ins    = ins
-      @del    = del
       @match  = match
     end
 
     def to_s
-      "#{@pos}:#{@length}:#{@mis}:#{@ins}:#{@del}:#{@match}"
+      "#{pos}:#{length}:#{match}"
     end
   end
 end