From 3ddd17e3d21f6b33ebe66fcf19d30bd79784032c Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 13 Jul 2012 14:43:11 +0000
Subject: [PATCH] fixed another bug in find orfs

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1872 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/align/pair.rb | 88 +++++++++++-------------------
 code_ruby/lib/maasha/seq.rb        |  2 +-
 2 files changed, 34 insertions(+), 56 deletions(-)

diff --git a/code_ruby/lib/maasha/align/pair.rb b/code_ruby/lib/maasha/align/pair.rb
index 45e9298..307197a 100644
--- a/code_ruby/lib/maasha/align/pair.rb
+++ b/code_ruby/lib/maasha/align/pair.rb
@@ -22,23 +22,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Extending Math module with a couple of useful methods.
-module Math
-  # Method for calculating the distance between a point and a line.
-  def self.dist_point2line(px, py, x1, y1, x2, y2)
-    a = (y2.to_f - y1) / (x2.to_f - x1)
-
-    b = y1 - a * x1
-
-    (a * px + b - py ).abs / Math.sqrt(a ** 2 + 1 )
-  end
-
-  # Method for calculating the distance between two points.
-  def self.dist_point2point(x1, y1, x2, y2)
-    Math.sqrt((x2 - x1) ** 2 + (y2 - y1) ** 2)
-  end
-end
-
 # Module with stuff to create a pairwise aligment.
 module PairAlign
   # Class for creating a pairwise alignment.
@@ -79,7 +62,13 @@ module PairAlign
         kmer /= 2
       end
 
-      matches = matches_select_by_score(matches, q_min, s_min, q_max, s_max)
+      matches_score(matches, q_min, s_min, q_max, s_max)
+
+#      matches.each { |m| puts m.to_s(q_seq) }
+
+      unless @matches.empty?
+        matches = matches.select { |match| match.score > 0 }
+      end
 
       if best_match = matches.pop
         @matches << best_match
@@ -116,48 +105,29 @@ module PairAlign
       new_matches
     end
 
-    # Method to select the best scoring matches and return these sorted
-    # according to score.
-    def matches_select_by_score(matches, q_min, s_min, q_max, s_max)
-      new_matches = []
-
+    def matches_score(matches, q_min, s_min, q_max, s_max)
       matches.each do |match|
-        score_length = match_score_by_length(match)
-        score_diag   = match_score_by_diagonal_dist(match, q_min, s_min, q_max, s_max)
-
-        match.score = score_length - score_diag
-
-        new_matches << match if match.score > 0
-      end
+        score_length = match.length
 
-      new_matches.sort_by! { |match| match.score }
+        min = (q_min - s_min).abs
+        max = ((q_max - q_min) - (s_max - s_min)).abs
+        beg = ((match.q_beg - q_min) - (match.s_beg - s_min)).abs
 
-      new_matches
-    end
-
-    # Method to calculate score based on match length.
-    def match_score_by_length(match)
-      match.length.to_f
-    end
+        if beg > (max - min) / 2
+          score_diag = max - min
+        else
+          score_diag = beg
+        end
 
-    # Method to calculate score based on the distance to the closest
-    # diagonal. The smaller the distance the better the score.
-    def match_score_by_diagonal_dist(match, q_min, s_min, q_max, s_max)
-      q_dim = q_max - q_min + 1
-      s_dim = s_max - s_min + 1
+#        puts "score_length: #{score_length}   score_diag: #{score_diag}     score: #{score_length - score_diag}"
 
-      if q_dim >= s_dim   # s_dim is the narrow end
-        beg_dist = Math.dist_point2line(match.q_beg, match.s_beg, q_min, s_min, q_min + s_dim, s_min + s_dim)
-        end_dist = Math.dist_point2line(match.q_beg, match.s_beg, q_max - s_dim, s_max - s_dim, q_max, s_max)
-      else
-        beg_dist = Math.dist_point2line(match.q_beg, match.s_beg, q_min, s_min, q_min + q_dim, s_min + q_dim)
-        end_dist = Math.dist_point2line(match.q_beg, match.s_beg, q_max - q_dim, s_max - q_dim, q_max, s_max)
+        match.score = score_length - score_diag
       end
 
-      min_dist = (beg_dist < end_dist) ? beg_dist : end_dist
-      min_dist.to_f
+      matches.sort_by! { |match| match.score }
     end
 
+
     # Method that finds all maximally expanded non-redundant matches shared
     # between two sequences inside a given search space.
     def matches_find(q_seq, s_seq, q_min, s_min, q_max, s_max, kmer)
@@ -267,17 +237,25 @@ module PairAlign
 
     # Method that insert gaps in sequences based on a list of matches and thus
     # creating an alignment.
-    # TODO check boundaries!
     def gaps_insert
       @matches.sort_by! { |m| m.q_beg }
 
       q_gaps = 0
       s_gaps = 0
 
-      @matches.each do |match|
-        diff = (q_gaps + match.q_beg) - (s_gaps + match.s_beg)
+      match = @matches.first
+      diff  = (q_gaps + match.q_beg) - (s_gaps + match.s_beg)
 
-        #pp "q_gaps #{q_gaps}   s_gaps #{s_gaps}   diff #{diff}"
+      if diff < 0
+        @q_entry.seq.insert(0, "-" * diff.abs)
+        q_gaps += diff.abs
+      elsif diff > 0
+        @s_entry.seq.insert(0, "-" * diff.abs)
+        s_gaps += diff.abs
+      end
+
+      @matches[1 .. -1].each do |match|
+        diff = (q_gaps + match.q_beg) - (s_gaps + match.s_beg)
 
         if diff < 0
           @q_entry.seq.insert(match.q_beg + q_gaps, "-" * diff.abs)
diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 62170b6..92d3398 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -536,7 +536,7 @@ class Seq
     if pick_longest
       orf_hash = {}
 
-      orfs.each { |orf| orf_hash[orf.last] = orf }
+      orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
 
       orfs = orf_hash.values
     end
-- 
2.39.2