added requirement of RubyInline

[biopieces.git] / code_ruby / lib / maasha / backtrack.rb

diff --git a/code_ruby/lib/maasha/backtrack.rb b/code_ruby/lib/maasha/backtrack.rb
index 02eb047121e6c61680d89e8cde33f65b9a1811ce..f5e581b802df1da0d63b28f3e1c5703476fe7e90 100644 (file)
--- a/code_ruby/lib/maasha/backtrack.rb
+++ b/code_ruby/lib/maasha/backtrack.rb
@@ -56,7 +56,7 @@ module BackTrack
   # matches are returned in an Array of Match objects.
   def patscan(pattern, offset = 0, max_mismatches = 0, max_insertions = 0, max_deletions = 0)
     raise BackTrackError, "Bad pattern: #{pattern}" unless pattern.downcase =~ OK_PATTERN
-    raise BackTrackError, "offset: #{offset} out of range (0 ... #{self.length - 1})" unless (0 ... self.length).include? offset
+    raise BackTrackError, "offset: #{offset} out of range (0 ... #{self.length - 1})"        unless (0 ... self.length).include? offset
     raise BackTrackError, "max_mismatches: #{max_mismatches} out of range (0 .. #{MAX_MIS})" unless (0 .. MAX_MIS).include? max_mismatches
     raise BackTrackError, "max_insertions: #{max_insertions} out of range (0 .. #{MAX_INS})" unless (0 .. MAX_INS).include? max_insertions
     raise BackTrackError, "max_deletions: #{max_deletions} out of range (0 .. #{MAX_DEL})"   unless (0 .. MAX_DEL).include? max_deletions
@@ -83,10 +83,14 @@ module BackTrack
   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[(unsigned short) A] & bitmap[(unsigned short) 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 %{
       unsigned short bitmap[256] = {
           0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
@@ -108,7 +112,9 @@ module BackTrack
       };
     }
 
-    # ss is the start of the string, used only for reporting the match endpoints.
+    # Backtrack algorithm for matching a pattern (p) starting in a sequence (s) allowing for mm
+    # mismatches, ins insertions and del deletions. ss is the start of the sequence, used only for
+    # reporting the match endpoints.
     builder.prefix %{
       unsigned int backtrack(char* ss, char* s, char* p, int mm, int ins, int del)
       {
@@ -129,8 +135,8 @@ module BackTrack
       }
     }
  
-    # Find all occurrences of p starting at pos in s, with at most
-    # mm mismatches, ins insertions and del deletions.
+    # Find pattern (p) in a sequence (@seq) starting at pos, with at most mm mismatches, ins
+    # insertions and del deletions.
     builder.c %{
       static VALUE track(char* p, unsigned int pos, int mm, int ins, int del)
       {
@@ -165,6 +171,7 @@ module BackTrack
     }
   end
 
+  # Class containing match information.
   class Match
     attr_reader :pos, :length, :match