From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 17 Nov 2011 07:28:58 +0000 (+0000)
Subject: fixed ins/del reverse
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=f40fdc8f55be97c491ad5d2caba71bab5a970248;p=biopieces.git

fixed ins/del reverse

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1655 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/backtrack.rb b/code_ruby/lib/maasha/backtrack.rb
index acc5b8c..02eb047 100644
--- a/code_ruby/lib/maasha/backtrack.rb
+++ b/code_ruby/lib/maasha/backtrack.rb
@@ -22,7 +22,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'inline'
+require 'inline' # RubyInline
 
 # Error class for all exceptions to do with BackTrack.
 class BackTrackError < StandardError; end
@@ -30,8 +30,14 @@ class BackTrackError < StandardError; end
 # Module containing code to locate nucleotide patterns in sequences allowing for
 # ambiguity codes and a given maximum mismatches, insertions, and deletions. The
 # pattern match engine is based on a backtrack algorithm.
+# Insertions are nucleotides found in the pattern but not in the sequence.
+# Deletions are nucleotides found in the sequence but not in the pattern.
+# Algorithm based on code kindly provided by j_random_hacker @ Stackoverflow.
 module BackTrack
   OK_PATTERN = Regexp.new('^[flsycwphqrimtnkvadegu]+$')
+  MAX_MIS    = 5 # Maximum number of mismatches allowed
+  MAX_INS    = 5 # Maximum number of insertions allowed
+  MAX_DEL    = 5 # Maximum number of deletions allowed
 
   # ------------------------------------------------------------------------------
   #   str.scan(pattern[, max_mismatches [, max_insertions [,max_deletions]]])
@@ -44,10 +50,17 @@ module BackTrack
   # ------------------------------------------------------------------------------
   # Method to iterate through a sequence to locate pattern matches starting at a
   # given offset allowing for a maximum number of mismatches, insertions, and
-  # deletions. Matches found in block context return the Match object. Otherwise
+  # deletions. Insertions are nucleotides found in the pattern but not in the
+  # sequence. Deletions are nucleotides found in the sequence but not in the
+  # pattern. Matches found in block context return the Match object. Otherwise
   # 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, "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
+
     matches = []
 
     if block_given?
@@ -108,8 +121,8 @@ module BackTrack
           else
           {
               if (mm && *s && *p && (r = backtrack(ss, s + 1, p + 1, mm - 1, ins, del))) return r;
-              if (ins && *s &&      (r = backtrack(ss, s + 1, p, mm, ins - 1, del)))     return r;
-              if (del && *p &&      (r = backtrack(ss, s, p + 1, mm, ins, del - 1)))     return r;
+              if (ins && *p &&      (r = backtrack(ss, s, p + 1, mm, ins - 1, del)))     return r;
+              if (del && *s &&      (r = backtrack(ss, s + 1, p, mm, ins, del - 1)))     return r;
           }
 
           return 0;