removing align.rb code

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1297 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/align.rb b/code_ruby/Maasha/lib/align.rb
index a494b4dd954611112e817f77c17938eb17be9707..e1e09e4fa551f65b2191f8e96c0920563acf4901 100644 (file)
--- a/code_ruby/Maasha/lib/align.rb
+++ b/code_ruby/Maasha/lib/align.rb
@@ -24,81 +24,3 @@ raise "Ruby 1.9 or later required" if RUBY_VERSION < "1.9"
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-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

diff --git a/code_ruby/Maasha/test/test_align.rb b/code_ruby/Maasha/test/test_align.rb
index b1abb1ba3618b567b4413b94dd735f939c945e3b..aae1947feb1080092ef637cf043a5eef6fa056ce 100755 (executable)
--- a/code_ruby/Maasha/test/test_align.rb
+++ b/code_ruby/Maasha/test/test_align.rb
@@ -29,102 +29,6 @@ require 'test/unit'
 require 'align'
 require 'pp'
 
-class MatrixTest < Test::Unit::TestCase
-  def test_Matrix_initialize_raise_on_bad_rows_value
-    [-2, 0].each do |val|
-      assert_raise(Align::MatrixError) { Align::Matrix.new(val, 2) }
-    end
-  end
-
-  def test_Matrix_initialize_raise_on_bad_cols_value
-    [-2, 0].each do |val|
-      assert_raise(Align::MatrixError) { Align::Matrix.new(2, val) }
-    end
-  end
-
-  def test_Matrix_initialize_dont_raise_on_ok_values
-    assert_nothing_raised { Align::Matrix.new(2, 2) }
-  end
-
-  def test_Matrix_set_raise_on_bad_row_value
-    matrix = Align::Matrix.new(2,3)
-    [-1, 2, 3].each do |row|
-      assert_raise(Align::MatrixError) { matrix.set(row, 2) }
-    end
-  end
-
-  def test_Matrix_set_raise_on_bad_col_value
-    matrix = Align::Matrix.new(2,3)
-    [-1, 3, 4].each do |col|
-      assert_raise(Align::MatrixError) { matrix.set(1, col) }
-    end
-  end
-  
-  def test_Matrix_set_dont_raise_on_ok_values
-    matrix = Align::Matrix.new(2,3)
-    (0 ... 2).each do |row|
-      (0 ... 3).each do |col|
-        matrix.set(row, col)
-      end
-    end
-  end
-
-  def test_Matrix_set_returns_corretly
-    matrix = Align::Matrix.new(2,3)
-    assert_equal([0, 0, 1, 0, 0, 0], matrix.set(0, 2))
-  end
-
-  def test_Matrix_to_s_returns_correctly
-    matrix = Align::Matrix.new(2,3)
-    matrix.set(0,0)
-    matrix.set(0,2)
-    matrix.set(1,0)
-    matrix.set(1,2)
-    assert_equal("1 0 1\n1 0 1\n", matrix.to_s)
-  end
-
-  def test_Matrix_slice_raise_on_bad_row_beg_values
-    matrix = Align::Matrix.new(4,4)
-    [-1, 4].each do |val|
-      assert_raise(Align::MatrixError) { matrix.slice(val, 1, 1, 1) }
-    end
-  end
-
-  def test_Matrix_slice_raise_on_bad_row_end_values
-    matrix = Align::Matrix.new(4,4)
-    [-1, 2, 4].each do |val|
-      assert_raise(Align::MatrixError) { matrix.slice(3, val, 1, 1) }
-    end
-  end
-
-  def test_Matrix_slice_raise_on_bad_col_beg_values
-    matrix = Align::Matrix.new(4,4)
-    [-1, 4].each do |val|
-      assert_raise(Align::MatrixError) { matrix.slice(1, 1, val, 1) }
-    end
-  end
-
-  def test_Matrix_slice_raise_on_bad_col_end_values
-    matrix = Align::Matrix.new(4,4)
-    [-1, 2, 4].each do |val|
-      assert_raise(Align::MatrixError) { matrix.slice(1, 1, 3, val) }
-    end
-  end
-
-  def test_Matrix_slice_dont_raise_on_ok_values
-    matrix = Align::Matrix.new(4,4)
-    (0 ... 4).each do |val|
-      assert_nothing_raised {matrix.slice(val, val, val, val) }
-    end
-  end
-
-  def test_Matrix_slice_returns_correctly
-    matrix = Align::Matrix.new(4,4)
-    matrix.set(1,1)
-    matrix.set(2,2)
-    assert_equal( "0 0\n0 1\n", matrix.slice(0, 1, 0, 1).to_s )
-    assert_equal( "1 0\n0 1\n", matrix.slice(1, 2, 1, 2).to_s )
-    assert_equal( "1 0\n0 0\n", matrix.slice(2, 3, 2, 3).to_s )
-  end
+class AlignTest < Test::Unit::TestCase
+  def test_
 end
-