trace_visualization 0.0.1

checksums.yaml

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+SHA512:
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data/.gitignore

@@ -0,0 +1,17 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

@@ -0,0 +1,6 @@
+source 'https://rubygems.org'
+
+ruby "2.0.0"
+
+# Specify your gem's dependencies in trace_visualization.gemspec
+gemspec

data/LICENSE

@@ -0,0 +1,339 @@
+GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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+    RubyGem for smart trace visualization
+    Copyright (C) 2013  Sergey
+
+    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
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+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2013 TODO: Write your name
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,4 @@
+trace_visualization
+===================
+
+RubyGem for smart trace visualization

data/Rakefile

@@ -0,0 +1 @@
+require "bundler/gem_tasks"

data/lib/trace_visualization/bwt.rb

@@ -0,0 +1,32 @@
+=begin
+The Burrows–Wheeler transform (BWT, also called block-sorting compression), is 
+an algorithm used in data compression techniques such as bzip2. When a character 
+string is transformed by the BWT, none of its characters change value. The 
+transformation permutes the order of the characters. If the original string had 
+several substrings that occurred often, then the transformed string will have 
+several places where a single character is repeated multiple times in a row. 
+This is useful for compression, since it tends to be easy to compress a string 
+that has runs of repeated characters by techniques such as move-to-front 
+transform and run-length encoding.
+
+The transform is done by sorting all rotations of the text in lexicographic 
+order, then taking the last column. For example, the text "^BANANA|" is 
+transformed into "BNN^AA|A".
+=end
+
+module TraceVisualization
+  module BurrowsWheelerTransform
+    
+    def self.naive(str)
+      (0 ... str.length).collect{ |i| (str * 2)[i, str.length]}.sort.map{|x| x[-1]}
+    end
+    
+    # Attention! This implementation work correctly only when the string ends 
+    # with TERMINATION_CHAR that greater of all possible chars in the
+    # lexicographical order
+    def self.bwt(str, sa, n)
+  		Array.new(n) { |i| str[sa[i] - 1] }		
+    end
+    
+  end
+end

data/lib/trace_visualization/bwt.rbold

@@ -0,0 +1,32 @@
+=begin
+The Burrows–Wheeler transform (BWT, also called block-sorting compression), is 
+an algorithm used in data compression techniques such as bzip2. When a character 
+string is transformed by the BWT, none of its characters change value. The 
+transformation permutes the order of the characters. If the original string had 
+several substrings that occurred often, then the transformed string will have 
+several places where a single character is repeated multiple times in a row. 
+This is useful for compression, since it tends to be easy to compress a string 
+that has runs of repeated characters by techniques such as move-to-front 
+transform and run-length encoding.
+
+The transform is done by sorting all rotations of the text in lexicographic 
+order, then taking the last column. For example, the text "^BANANA|" is 
+transformed into "BNN^AA|A".
+=end
+
+module Travis
+  module BurrowsWheelerTransform
+    
+    def self.naive(str)
+      (0 ... str.length).collect{ |i| (str * 2)[i, str.length]}.sort.map{|x| x[-1]}
+    end
+    
+    # Attention! This implementation work correctly only when the string ends 
+    # with TERMINATION_CHAR that greater of all possible chars in the
+    # lexicographical order
+    def self.bwt(str, sa, n)
+  		Array.new(n) { |i| str[sa[i] - 1] }		
+    end
+    
+  end
+end

data/lib/trace_visualization/data/irepetition.rb

@@ -0,0 +1,49 @@
+# Interface for Repetition 
+module IRepetition
+  def positions_size; end
+  
+  def get_id; end
+  def get_left_pos(idx);     end
+  def get_right_pos(idx);    end
+  def set_left_pos(idx,val); end
+  
+  def left_positions(); end
+  def right_positions(); end
+  
+  def equal_positions?(r); end
+  
+  def left_length; end
+  def right_length; end
+  
+  def strict_length; end
+end
+
+class RepetitionBase
+  include IRepetition
+  
+  attr_accessor :length
+  
+  # Left and right repeatition involved in merge
+  attr_accessor :left, :right
+  
+  attr_accessor :k
+
+  attr_accessor :lines
+
+  def initialize
+    @lines = []
+  end
+  
+  def left_length
+    @left  != nil ? @left.length  : @length
+  end
+  
+  def right_length
+    @right != nil ? @right.length : @length
+  end
+  
+  # Length of strict repetitions involved in the repetition
+  def strict_length
+    @length - @k
+  end
+end

data/lib/trace_visualization/data/repetition.rb

@@ -0,0 +1,101 @@
+$LOAD_PATH.unshift(File.expand_path('../', __FILE__))
+require 'irepetition'
+
+module TraceVisualization
+  module Data
+    class Repetition < RepetitionBase
+      @@sequence = 0
+  
+      attr_accessor :score
+      attr_accessor :pcount
+      attr_reader :left_positions, :right_positions
+      attr_reader :id
+      attr_accessor :strict_ids
+  
+      def to_s
+        "Repetition ##{self.id}: score = #{@score}, k = #{@k}, " + 
+        "length = #{@length}, " + 
+        "positions.size = #{@left_positions.size}, " + 
+        "left_positions = #{@left_positions}, " +
+        "right_positions = #{@right_positions}, " +
+        "strict_ids = #{@strict_ids}, " + 
+        "lines = #{lines}, " +
+        "left = #{@left != nil ? @left.id : 'nil'}, " +
+        "right = #{@right != nil ? @right.id : 'nil'}"
+      end
+  
+      def initialize(length, left_positions, right_positions = nil)
+        super()
+    
+        @k = 0
+        @pcount = 1
+        @length = length
+    
+        @left_positions  = left_positions
+        @right_positions = right_positions 
+    
+        @id = (@@sequence += 1)
+        @strict_ids = [@id]
+        @lines = []
+      end
+  
+      def positions_size
+        @left_positions.size
+      end
+  
+      def get_left_pos(idx)
+        @left_positions[idx]
+      end
+  
+      def set_left_pos(idx, val)
+        @left_positions[idx] = val
+      end
+  
+      def get_right_pos(idx)
+        @right_positions != nil ? @right_positions[idx] : -1
+      end
+  
+      def equal_positions?(r)
+        @left_positions == r.left_positions && 
+        @right_positions == r.right_positions
+      end
+  
+      # Build positions for hl print:
+      #   [
+      #     [[pos, len], [], ... ],
+      #     [[pos, len], [], ... ],
+      #     ...  
+      #   ]
+      def build_positions
+        result = []
+    
+        @left_positions.each do |lpos|
+          result << build_positions_for_repeat(lpos)
+        end
+    
+        result 
+      end
+  
+      #-------------------------------------------------------------------------
+      #   [[pos, len], [], ... ]
+      def build_positions_for_repeat(pos)
+        result = []
+
+        for i in 0 ... positions_size
+          lpos, rpos = get_left_pos(i), get_right_pos(i)
+          if lpos == pos
+            if @k == 0
+              result += [[lpos, left_length()]]
+            else
+              result += left.build_positions_for_repeat(lpos)
+              result += right.build_positions_for_repeat(rpos)
+            end
+          end
+        end
+    
+        result
+      end
+    end
+  end # module Data
+end # module TraceVisualization
+

data/lib/trace_visualization/generators.rb

@@ -0,0 +1,53 @@
+module TraceVisualization
+  module Generators
+    module Thue
+
+      # (2,3)-avoidance string (cube-free string on a binary alphabet)
+      # Strings contain many repetitions!
+      def self.str_2_3(n)
+        return "a" if n == 0
+        x = str_2_3(n - 1)
+    
+        x + invert(x)
+      end
+  
+      # (3,2)-avoidance string (square-free strings on a ternary alphabet).
+      # Strings contain no repetitions at all!
+      def self.str_3_2(n)
+        x = "a"
+        n.times do 
+          y = ""
+          x.each_char do |c|
+            case c
+            when 'a'
+              y += "abcab"
+            when 'b'
+              y += "acabcb"
+            when 'c'
+              y += "acbcacb"
+            end
+          end
+          x = y
+        end
+        x
+      end
+  
+      def self.invert(x)
+        str = ""
+        x.each_char { |c| str += (c == 'a' ? 'b' : 'a') }
+        str    
+      end
+    end
+
+    module Fibonacci
+      def self.str(num)
+        a, b = "a", "b"
+        num.times do
+          a, b = a + b, a
+        end
+    
+        b
+      end
+    end
+  end
+end