added math_aux.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1913 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/align/pair.rb b/code_ruby/lib/maasha/align/pair.rb
index 307197ad1dc6df82d324d6d87e7c82af778a25fb..72a5eae798262c7e4c276dd243ff22c7a70fa8cf 100644 (file)
--- a/code_ruby/lib/maasha/align/pair.rb
+++ b/code_ruby/lib/maasha/align/pair.rb
@@ -107,26 +107,34 @@ module PairAlign
 
     def matches_score(matches, q_min, s_min, q_max, s_max)
       matches.each do |match|
-        score_length = match.length
+        score_length = match_score_length(match)
+        score_diag   = match_score_diag(match, q_min, s_min, q_max, s_max)
+        score_corner = match_score_corner(match, q_min, s_min, q_max, s_max)
 
-        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
 
-        if beg > (max - min) / 2
-          score_diag = max - min
-        else
-          score_diag = beg
-        end
-
-#        puts "score_length: #{score_length}   score_diag: #{score_diag}     score: #{score_length - score_diag}"
-
-        match.score = score_length - score_diag
+        match.score = score_length - score_diag - score_corner
+        puts match
+        puts "score_length: #{score_length}   score_diag: #{score_diag}   score_corner: #{score_corner}  score: #{match.score}"
       end
 
       matches.sort_by! { |match| match.score }
     end
 
+    def match_score_length(match)
+      match.length
+    end
+
+    def match_score_diag(match, q_min, s_min, q_max, s_max)
+        dist1 = (match.q_beg - match.s_beg).abs
+        dist2 = ((match.q_end - match.q_end).abs - dist1).abs
+
+        dist1 < dist2 ? dist1 : dist2
+    end
+
+    def match_score_corner(match, q_min, s_min, q_max, s_max)
+      1
+    end
+
 
     # Method that finds all maximally expanded non-redundant matches shared
     # between two sequences inside a given search space.
@@ -158,7 +166,7 @@ module PairAlign
       matches
     end
 
-    # Method that indexes a seuquence within a given interval such that the
+    # Method that indexes a sequence within a given interval such that the
     # index contains all oligos of a given kmer size and the positions where
     # this oligo was located.
     def index_seq(seq, min, max, kmer)

diff --git a/code_ruby/lib/maasha/math_aux.rb b/code_ruby/lib/maasha/math_aux.rb
new file mode 100644 (file)
index 0000000..7ac4a47
--- /dev/null
+++ b/code_ruby/lib/maasha/math_aux.rb
@@ -0,0 +1,50 @@
+# Copyright (C) 2007-2012 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).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+module Math
+  # Class method to calculate the distance from at point to a line.
+  # The point and line are given as pairs of coordinates.
+  def self.dist_point2line(
+    px,  # point  x coordinate
+    py,  # point  y coordinate
+    x1,  # line 1 x coordinate
+    y1,  # line 1 y coordinate
+    x2,  # line 2 x coordinate
+    y2   # line 2 y coordinate
+  )
+
+    a = (y2 - y1).to_f / (x2 - x1).to_f
+    b = y1 - a * x1
+
+    (a * px + b - py).abs / Math.sqrt(a ** 2 + 1)
+  end
+
+
+  # Class method to calculate the distance between two points given
+  # as pairs of coordinates.
+  def self.dist_point2point(x1, y1, x2, y2)
+    Math.sqrt((x2.to_f - x1.to_f) ** 2 + (y2.to_f - y1.to_f) ** 2)
+  end
+end