trace_visualization 0.0.3 → 0.0.5

data/trace_visualization.gemspec

@@ -25,8 +25,8 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'bundler', '~> 1.3'
   spec.add_development_dependency 'rake'
   
-  spec.add_development_dependency 'redcarpet', '~> 1.17'
-  spec.add_development_dependency 'yard', '~> 0.7.5'
+  spec.add_development_dependency 'redcarpet'
+  spec.add_development_dependency 'yard', "~> 0.8.7.3"
   
   spec.add_development_dependency 'rspec-core', '~> 2.0'
   spec.add_development_dependency 'rspec-expectations', '~> 2.0'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trace_visualization
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.5
 platform: ruby
 authors:
 - Sergey
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-09 00:00:00.000000000 Z
+date: 2013-12-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -42,30 +42,30 @@ dependencies:
   name: redcarpet
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: '1.17'
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: '1.17'
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.5
+        version: 0.8.7.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.7.5
+        version: 0.8.7.3
 - !ruby/object:Gem::Dependency
   name: rspec-core
   requirement: !ruby/object:Gem::Requirement
@@ -137,12 +137,14 @@ files:
 - Rakefile
 - bin/trace_visualization
 - lib/trace_visualization.rb
+- lib/trace_visualization/algorithm.rb
 - lib/trace_visualization/assert.rb
 - lib/trace_visualization/bwt.rb
 - lib/trace_visualization/bwt.rbold
 - lib/trace_visualization/data/irepetition.rb
-- lib/trace_visualization/data/lexeme.rb
 - lib/trace_visualization/data/repetition.rb
+- lib/trace_visualization/data/sorted_array.rb
+- lib/trace_visualization/data/token.rb
 - lib/trace_visualization/generators.rb
 - lib/trace_visualization/lexeme_overlap_filter.rb
 - lib/trace_visualization/longest_common_prefix.rb
@@ -150,8 +152,10 @@ files:
 - lib/trace_visualization/profile.rb
 - lib/trace_visualization/reorder.rb
 - lib/trace_visualization/repetitions.rb
-- lib/trace_visualization/repetitions_concatenation.rb
-- lib/trace_visualization/repetitions_context.rb
+- lib/trace_visualization/repetitions/concatenation.rb
+- lib/trace_visualization/repetitions/context.rb
+- lib/trace_visualization/repetitions/filter.rb
+- lib/trace_visualization/repetitions/incrementation.rb
 - lib/trace_visualization/repetitions_incrementation.rb
 - lib/trace_visualization/repetitions_psy.rb
 - lib/trace_visualization/repetitions_score.rb
@@ -159,19 +163,24 @@ files:
 - lib/trace_visualization/utils.rb
 - lib/trace_visualization/version.rb
 - lib/trace_visualization/visualization/console_color_print.rb
+- spec/algorithm_spec.rb
 - spec/bwt_spec.rb
+- spec/data/sorted_array_spec.rb
 - spec/generators_spec.rb
 - spec/lexeme_overlap_filter_spec.rb
 - spec/longest_common_prefix_spec.rb
 - spec/mapping_spec.rb
 - spec/reorder_spec.rb
-- spec/repetitions_concatenation_spec.rb
+- spec/repetitions/concatenation_spec.rb
+- spec/repetitions/filter_spec.rb
+- spec/repetitions/incrementation_spec.rb
 - spec/repetitions_incrementation_spec.rb
 - spec/repetitions_psy_spec.rb
 - spec/repetitions_spec.rb
 - spec/spec_helper.rb
 - spec/suffix_array_spec.rb
 - spec/utils_spec.rb
+- spec/visualization/console_color_print_spec.rb
 - trace_visualization.gemspec
 homepage: ''
 licenses:
@@ -198,17 +207,22 @@ signing_key:
 specification_version: 4
 summary: Software for smart trace visualization
 test_files:
+- spec/algorithm_spec.rb
 - spec/bwt_spec.rb
+- spec/data/sorted_array_spec.rb
 - spec/generators_spec.rb
 - spec/lexeme_overlap_filter_spec.rb
 - spec/longest_common_prefix_spec.rb
 - spec/mapping_spec.rb
 - spec/reorder_spec.rb
-- spec/repetitions_concatenation_spec.rb
+- spec/repetitions/concatenation_spec.rb
+- spec/repetitions/filter_spec.rb
+- spec/repetitions/incrementation_spec.rb
 - spec/repetitions_incrementation_spec.rb
 - spec/repetitions_psy_spec.rb
 - spec/repetitions_spec.rb
 - spec/spec_helper.rb
 - spec/suffix_array_spec.rb
 - spec/utils_spec.rb
+- spec/visualization/console_color_print_spec.rb
 has_rdoc: 

data/lib/trace_visualization/repetitions_concatenation.rb

@@ -1,134 +0,0 @@
-require 'trace_visualization'
-
-module TraceVisualization
-  module RepetitionsConcatenation
-
-    def self.process(rs, k, context, options = {})
-      opts = {
-        :positions_min_size => 3
-      }.merge options
-  
-      result = []
-  
-      useful_cnt = 0
-
-      pairs_cnt = {}
-      context.rs_by_line.each do |item|
-        for i in 0 ... item.size
-          for j in i + 1 ... item.size
-            left, right = item[i][0], item[j][0]
-            delta = k - left.k - right.k
-
-            next if not concat_condition(left, right, delta, opts[:positions_min_size])
-
-            key = (left.id << 32) + right.id
-            val = (pairs_cnt[key] || 0) + 1
-            pairs_cnt[key] = val
-            next if val != opts[:positions_min_size]
-
-            lps, rps = process_common_positions(left, right, delta, context)
-      
-            if lps.size >= opts[:positions_min_size]
-              result << create_repetition(left, right, delta, lps, rps)
-            end
-      
-            useful_cnt += 1        
-          end
-        end
-      end
-  
-      options[:counter] << [k, useful_cnt] if options[:counter]
-  
-      puts "Total: #{rs.size ** 2} #{useful_cnt} #{result.size}"
-  
-      process_new_repetitions(result)
-  
-      rs.concat(result)
-    end
-
-    def self.process_new_repetitions(rs, context)
-      TraceVisualization::Utils.rs_by_line(rs, context.lines_pos, context.rs_by_line)
-    end
-
-    def self.process_full_search(rs, k, context, options = {})
-      opts = {
-        :positions_min_size => 3
-      }.merge options
-  
-      result = []
-  
-      useful_cnt = 0
-
-      for left in rs
-        for right in rs
-          delta = k - left.k - right.k
-          next if not concat_condition(left, right, delta, opts[:positions_min_size])
-      
-          # @@processed_path.add(key(left, right, delta))  
-      
-          lps, rps = process_common_positions(left, right, delta, context)
-      
-          if lps.size >= opts[:positions_min_size]
-            result << create_repetition(left, right, delta, lps, rps)
-          end
-      
-          useful_cnt += 1
-        end
-      end
-
-      puts "Total: #{rs.size ** 2} #{useful_cnt} #{result.size}"
-  
-      rs.concat(result)
-    end
-
-    def self.delete_repetition(r, context)
-      r.lines.each do |line|
-        context.rs_by_line[line].delete_if { |item| item[0] == r }
-      end
-    end
-
-    def self.concat_condition(left, right, delta, positions_min_size)
-      delta >= 0 && left.id != right.id && 
-        left.positions_size  >= positions_min_size && 
-        right.positions_size >= positions_min_size
-    end
-
-    # *Attention* Position arrays are modified in place which can lead to side 
-    # effects. Don't send left == right!
-    def self.process_common_positions(left, right, delta, context)
-      lr_pos = left.left_positions
-      lr_pos.collect! { |pos| pos + left.length + delta }
-
-      rr_pos = right.left_positions
-  
-      cpr = lr_pos & rr_pos
-      cpl = cpr.collect { |pos| pos - left.length - delta }
-  
-      idx = 0
-      while idx < cpr.size
-        if context.str[cpl[idx] + left.length ... cpr[idx]].scan(TraceVisualization::FORBIDDEN_CHARS).size != 0
-          cpr.delete_at(idx)
-          cpl.delete_at(idx)
-        else
-          idx += 1
-        end
-      end
-
-      lr_pos.collect! { |lpos| lpos - left.length - delta }
-      
-      [cpl, cpr]
-    end
-
-    def self.create_repetition(left, right, delta, lps, rps)
-      r = left.class.new(left.length + right.length + delta, lps, rps)
-
-      r.k          = left.k + right.k + delta
-      r.pcount     = left.pcount + right.pcount
-      r.left       = left
-      r.right      = right
-      r.strict_ids = left.strict_ids + right.strict_ids
-
-      r
-    end
-  end
-end

data/lib/trace_visualization/repetitions_context.rb

@@ -1,18 +0,0 @@
-require 'trace_visualization/utils'
-
-module TraceVisualization
-  module Repetitions
-    class Context
-      attr_accessor :str, :lines_pos, :rs_by_line
-      
-      def initialize(str, rs)
-        @str        = str
-        @lines_pos  = TraceVisualization::Utils.lines_pos(str)
-        @rs_by_line = Array.new(@lines_pos.size) { [] }
-    
-        TraceVisualization::Utils.rs_by_line(rs, @lines_pos, @rs_by_line)
-      end
-      
-    end
-  end
-end

data/spec/repetitions_concatenation_spec.rb

@@ -1,64 +0,0 @@
-require 'trace_visualization/repetitions_concatenation'
-require 'trace_visualization/repetitions_context'
-require 'trace_visualization/data/repetition'
-
-describe TraceVisualization::RepetitionsConcatenation do
-  it "process common positions" do
-    str = "aaaxbbbyaaazbbbvaaawbbb"
-
-    mapping = TraceVisualization::Mapping.init do
-      default_tokens
-    end
-
-    mapping.process { from_string(str) }
-
-    context = TraceVisualization::Repetitions::Context.new(mapping, [])
-    
-    lpos = [0, 8, 16]
-    rpos = [4, 12, 20]
-    ppos = [[0, 4], [8, 12], [16, 20]]
-    
-    left  = TraceVisualization::Data::Repetition.new(3, lpos)
-    right = TraceVisualization::Data::Repetition.new(3, rpos)
-    
-    cpl, cpr = TraceVisualization::RepetitionsConcatenation.process_common_positions(left, right, 1, context)
-
-    left.left_positions.should  eq cpl
-    right.left_positions.should eq cpr
-
-    lpos.should eq left.left_positions
-    rpos.should eq right.left_positions
-  end
-  
-  it "don't concatenate repetitions through forbidden chars" do
-    str = <<EOF
-aaa
-bbb
-aaa
-bbb
-EOF
-    context = TraceVisualization::Repetitions::Context.new(str, [])
-      
-    lpos, rpos = [0, 8], [4, 12]
-    left  = TraceVisualization::Data::Repetition.new(3, lpos)
-    right = TraceVisualization::Data::Repetition.new(3, rpos)      
-    
-    cpl, cpr = TraceVisualization::RepetitionsConcatenation.process_common_positions(left, right, 1, context)
-      
-    cpl.should eq []
-    cpr.should eq []
-    
-    #
-    str.gsub!(TraceVisualization::FORBIDDEN_CHARS, "x")
-    context = TraceVisualization::Repetitions::Context.new(str, [])
-      
-    lpos, rpos = [0, 8], [4, 12]
-    left  = TraceVisualization::Data::Repetition.new(3, lpos)
-    right = TraceVisualization::Data::Repetition.new(3, rpos)      
-    
-    cpl, cpr = TraceVisualization::RepetitionsConcatenation.process_common_positions(left, right, 1, context)
-    
-    cpl.should eq [0, 8]
-    cpr.should eq [4, 12]    
-  end
-end