added align ruby lib

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1120 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/align.rb b/code_ruby/Maasha/lib/align.rb
new file mode 100644 (file)
index 0000000..5c0b9f5
--- /dev/null
+++ b/code_ruby/Maasha/lib/align.rb
@@ -0,0 +1,104 @@
+raise "Ruby 1.9 or later required" if RUBY_VERSION < "1.9"
+
+# Copyright (C) 2007-2010 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 Align
+  # Error class for all exceptions to do with matrix class.
+  class MatrixError < StandardError; end
+
+  class Matrix
+    attr_accessor :rows, :cols
+
+    def initialize(rows, cols)
+      @rows = rows
+      @cols = cols
+
+      raise MatrixError, "Bad rows value: #{rows}"    if rows <= 0
+      raise MatrixError, "Bad columns value: #{cols}" if cols <= 0
+
+      @matrix = matrix
+    end
+
+    def set(row, col)
+      raise MatrixError, "Bad row value: #{row}"    unless (0 ... @rows).include? row
+      raise MatrixError, "Bad column value: #{col}" unless (0 ... @cols).include? col
+
+      @matrix[@cols * row + col] = 1
+      @matrix
+    end
+
+    def to_s
+      rows = ""
+      (0 ... @rows).each do |row|
+        rows << @matrix[@cols * row, @cols].join(" ") + "\n"
+      end
+
+      rows
+    end
+
+    def slice(row_beg, row_end, col_beg, col_end)
+      raise MatrixError, "Bad row_beg value: #{row_beg}" unless (0 ... @rows).include? row_beg
+      raise MatrixError, "Bad col_beg value: #{col_beg}" unless (0 ... @cols).include? col_beg
+      raise MatrixError, "Bad row_end value: #{row_end}" unless (row_beg ... @rows).include? row_end
+      raise MatrixError, "Bad col_end value: #{col_end}" unless (col_beg ... @rows).include? col_end
+
+      new_rows  = row_end - row_beg + 1
+      new_cols  = col_end - col_beg + 1
+      submatrix = Matrix.new(new_rows, new_cols)
+
+      (0 ... @rows).each do |row|
+        (0 ... @cols).each do |col|
+          if set?(row, col)
+            if (0 ... new_rows).include? row - row_beg and (0 ... new_cols).include? col - col_beg
+              submatrix.set(row - row_beg, col - col_beg)
+            end
+          end
+        end
+      end
+
+      submatrix
+    end
+
+    private
+
+    def matrix
+      [0] * (@rows * @cols)
+    end
+
+    def set?(row, col)
+      if @matrix[@cols * row + col] == 0
+        return false
+      else
+        return true
+      end
+    end
+  end
+
+  # Error class for all exceptions to do with matrix class.
+  class AlignError < StandardError; end
+
+  class Align
+  end
+end