trace_visualization 0.0.1

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Files changed (38) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +17 -0
  3. data/Gemfile +6 -0
  4. data/LICENSE +339 -0
  5. data/LICENSE.txt +22 -0
  6. data/README.md +4 -0
  7. data/Rakefile +1 -0
  8. data/lib/trace_visualization/bwt.rb +32 -0
  9. data/lib/trace_visualization/bwt.rbold +32 -0
  10. data/lib/trace_visualization/data/irepetition.rb +49 -0
  11. data/lib/trace_visualization/data/repetition.rb +101 -0
  12. data/lib/trace_visualization/generators.rb +53 -0
  13. data/lib/trace_visualization/longest_common_prefix.rb +34 -0
  14. data/lib/trace_visualization/mapping.rb +120 -0
  15. data/lib/trace_visualization/reorder.rb +25 -0
  16. data/lib/trace_visualization/repetitions.rb +66 -0
  17. data/lib/trace_visualization/repetitions_concatenation.rb +134 -0
  18. data/lib/trace_visualization/repetitions_context.rb +18 -0
  19. data/lib/trace_visualization/repetitions_incrementation.rb +81 -0
  20. data/lib/trace_visualization/repetitions_psy.rb +83 -0
  21. data/lib/trace_visualization/suffix_array.rb +203 -0
  22. data/lib/trace_visualization/utils.rb +47 -0
  23. data/lib/trace_visualization/version.rb +3 -0
  24. data/lib/trace_visualization/visualization/console_color_print.rb +32 -0
  25. data/lib/trace_visualization.rb +10 -0
  26. data/spec/bwt_spec.rb +47 -0
  27. data/spec/generators_spec.rb +30 -0
  28. data/spec/longest_common_prefix_spec.rb +29 -0
  29. data/spec/mapping_spec.rb +67 -0
  30. data/spec/reorder_spec.rb +42 -0
  31. data/spec/repetitions_concatenation_spec.rb +58 -0
  32. data/spec/repetitions_incrementation_spec.rb +88 -0
  33. data/spec/repetitions_psy_spec.rb +39 -0
  34. data/spec/repetitions_spec.rb +18 -0
  35. data/spec/spec_helper.rb +19 -0
  36. data/spec/suffix_array_spec.rb +68 -0
  37. data/trace_visualization.gemspec +35 -0
  38. metadata +204 -0
@@ -0,0 +1,39 @@
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+ require 'trace_visualization'
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+ require 'trace_visualization/repetitions_psy'
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+ require 'trace_visualization/suffix_array'
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+ require 'trace_visualization/longest_common_prefix'
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+ require 'trace_visualization/bwt'
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+ require 'trace_visualization/mapping'
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+
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+ describe TraceVisualization::Repetitions do
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+ it 'simple test PSY1' do
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+ TraceVisualization::Repetitions.psy1("aaabbbcccaaacccbbb", 3, false).should eq [
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+ {:lcp=>3, :i=>0, :j=>1},
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+ {:lcp=>3, :i=>8, :j=>9},
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+ {:lcp=>3, :i=>16, :j=>17}
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+ ]
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+ end
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+
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+ it 'simple test PSY1 with mapping' do
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+ str = "aaa[123]aaa"
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+ arr = TraceVisualization::Mapping.parse(str)
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+
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+ TraceVisualization::Repetitions.psy1(arr, 3, false).should eq [{:lcp=>3, :i=>2, :j=>3}]
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+ end
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+
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+ it 'test decode PSY1' do
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+ str = "aaa[123]xyz[654]aaa[123]" # <---> "aaaXxyzYaaaX"
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+ arr = TraceVisualization::Mapping.parse(str)
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+
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+ rs = TraceVisualization::Repetitions.psy1(arr, 3)
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+
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+ rs.size.should eq 1
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+ rs[0].length.should eq 4
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+ rs[0].left_positions.should eq [0, 8]
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+
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+ length = rs[0].length
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+ position = rs[0].left_positions[0]
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+
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+ TraceVisualization::Mapping.restore(arr[position ... position + length]).should eq "aaa[123]"
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+ end
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+ end
@@ -0,0 +1,18 @@
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+ require 'trace_visualization/repetitions'
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+ require 'trace_visualization/generators'
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+
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+ describe TraceVisualization::Repetitions do
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+ context 'naive implementation' do
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+ it 'strict repetitions for fibonacci string f6' do
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+ f6 = TraceVisualization::Generators::Fibonacci.str(6)
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+
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+ TraceVisualization::Repetitions.naive(f6, 1).should eq([[1, 3, 4, 6, 8, 9, 11, 12], [2, 5, 7, 10, 13]])
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+ TraceVisualization::Repetitions.naive(f6, 2).should eq([[1, 4, 6, 9, 12], [2, 5, 7, 10], [3, 8, 11]])
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+ TraceVisualization::Repetitions.naive(f6, 3).should eq([[1, 4, 6, 9], [2, 7, 10], [3, 8, 11]])
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+ TraceVisualization::Repetitions.naive(f6, 4).should eq([[1, 6, 9], [2, 7, 10], [3, 8]])
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+ TraceVisualization::Repetitions.naive(f6, 5).should eq([[1, 6, 9], [2, 7]])
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+ TraceVisualization::Repetitions.naive(f6, 6).should eq([[1, 6]])
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+ TraceVisualization::Repetitions.naive(f6, 7).should eq([])
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+ end
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+ end
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+ end
@@ -0,0 +1,19 @@
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+ # This file was generated by the `rspec --init` command. Conventionally, all
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+ # specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
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+ # Require this file using `require "spec_helper"` to ensure that it is only
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+ # loaded once.
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+ #
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+ # See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
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+ RSpec.configure do |config|
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+ config.treat_symbols_as_metadata_keys_with_true_values = true
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+ config.run_all_when_everything_filtered = true
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+ config.filter_run :focus
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+
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+ # Run specs in random order to surface order dependencies. If you find an
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+ # order dependency and want to debug it, you can fix the order by providing
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+ # the seed, which is printed after each run.
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+ # --seed 1234
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+ config.order = 'random'
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+
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+ config.mock_with :rr
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+ end
@@ -0,0 +1,68 @@
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+ require 'trace_visualization/suffix_array'
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+ require 'trace_visualization/mapping'
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+
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+ describe TraceVisualization::SuffixArray do
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+
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+ context ".naive" do
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+ it "should return suffix array" do
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+ TraceVisualization::SuffixArray.naive("abaabaab").should eq([5, 2, 6, 3, 0, 7, 4, 1])
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+ TraceVisualization::SuffixArray.naive("abracadabra").should eq([10, 7, 0, 3, 5, 8, 1, 4, 6, 9, 2])
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+ end
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+
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+ it "should correct process mapped string" do
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+ str = "abc[123]def[456]ghi"
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+ arr = TraceVisualization::Mapping.parse(str)
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+
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+ TraceVisualization::SuffixArray.naive(arr).should eq([0, 1, 2, 4, 5, 6, 8, 9, 10, 3, 7])
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+ end
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+ end
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+
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+ context ".radix_pass" do
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+ it "do stable radix sort" do
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+ str = [3, 3, 2, 1, 5, 5, 4]
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+ a = [0, 1, 2, 3, 4, 5, 6]
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+ n = a.length
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+ b = Array.new(n)
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+
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+ TraceVisualization::SuffixArray.radix_pass(a, b, str, n, 10)
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+
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+ b.should eq([3, 2, 0, 1, 6, 4, 5])
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+ end
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+ end
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+
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+ context ".effective_linear" do
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+ it "should return suffix array for linear time (native function)" do
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+ s = [3, 3, 2, 1, 5, 5, 4, 0, 0, 0]
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+ n = s.length - 3 # exclude last 3 zeros
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+ alphabet_size = 10
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+ suffix_array = Array.new(n + 3, 0)
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+
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+ TraceVisualization::SuffixArray.effective_linear(s, suffix_array, n, alphabet_size)
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+
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+ suffix_array.should eq([3, 2, 1, 0, 6, 5, 4, 0, 0, 0])
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+ end
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+ end
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+
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+ context ".effective" do
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+ it "should return suffix array for linear time (wrapper function)" do
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+ TraceVisualization::SuffixArray.effective("abaabaab").should eq(TraceVisualization::SuffixArray.naive("abaabaab"))
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+ TraceVisualization::SuffixArray.effective("abracadabra").should eq(TraceVisualization::SuffixArray.naive("abracadabra"))
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+ end
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+
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+ it "should correct process mapped string" do
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+ str = "abc[123]def[456]ghi"
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+ arr = TraceVisualization::Mapping.parse(str)
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+
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+ TraceVisualization::SuffixArray.effective(arr).should eq([0, 1, 2, 4, 5, 6, 8, 9, 10, 3, 7])
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+ end
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+
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+ it "bug with endless loop" do
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+ str = "127.0.0.1 user login\r\n127.0.0.1 user logout"
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+ arr = TraceVisualization::Mapping.parse(str)
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+
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+ sa = TraceVisualization::SuffixArray.effective(arr)
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+ end
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+
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+ end
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+
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+ end
@@ -0,0 +1,35 @@
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'trace_visualization/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "trace_visualization"
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+ spec.version = TraceVisualization::VERSION
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+ spec.authors = ["Sergey"]
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+ spec.email = ["mastedm@gmail.com"]
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+ spec.description = %q{
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+ Intelligent visualization of software traces
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+ }
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+ spec.summary = %q{
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+ Software for smart trace visualization
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+ }
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+ spec.homepage = ""
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+ spec.license = "MIT"
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+
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+ spec.files = `git ls-files`.split($/)
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+ spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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+ spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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+ spec.require_paths = ["lib"]
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+
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+ spec.add_development_dependency "bundler", "~> 1.3"
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+ spec.add_development_dependency "rake"
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+
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+ spec.add_development_dependency "redcarpet", "~> 1.17"
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+ spec.add_development_dependency "yard", "~> 0.7.5"
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+
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+ spec.add_development_dependency "rspec-core", "~> 2.0"
32
+ spec.add_development_dependency "rspec-expectations", "~> 2.0"
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+ spec.add_development_dependency "rspec-mocks"
34
+ spec.add_development_dependency "rr", "~> 1.0"
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+ end
metadata ADDED
@@ -0,0 +1,204 @@
1
+ --- !ruby/object:Gem::Specification
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+ name: trace_visualization
3
+ version: !ruby/object:Gem::Version
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+ version: 0.0.1
5
+ platform: ruby
6
+ authors:
7
+ - Sergey
8
+ autorequire:
9
+ bindir: bin
10
+ cert_chain: []
11
+ date: 2013-08-04 00:00:00.000000000 Z
12
+ dependencies:
13
+ - !ruby/object:Gem::Dependency
14
+ name: bundler
15
+ requirement: !ruby/object:Gem::Requirement
16
+ requirements:
17
+ - - ~>
18
+ - !ruby/object:Gem::Version
19
+ version: '1.3'
20
+ type: :development
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - ~>
25
+ - !ruby/object:Gem::Version
26
+ version: '1.3'
27
+ - !ruby/object:Gem::Dependency
28
+ name: rake
29
+ requirement: !ruby/object:Gem::Requirement
30
+ requirements:
31
+ - - '>='
32
+ - !ruby/object:Gem::Version
33
+ version: '0'
34
+ type: :development
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - '>='
39
+ - !ruby/object:Gem::Version
40
+ version: '0'
41
+ - !ruby/object:Gem::Dependency
42
+ name: redcarpet
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - ~>
46
+ - !ruby/object:Gem::Version
47
+ version: '1.17'
48
+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - ~>
53
+ - !ruby/object:Gem::Version
54
+ version: '1.17'
55
+ - !ruby/object:Gem::Dependency
56
+ name: yard
57
+ requirement: !ruby/object:Gem::Requirement
58
+ requirements:
59
+ - - ~>
60
+ - !ruby/object:Gem::Version
61
+ version: 0.7.5
62
+ type: :development
63
+ prerelease: false
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - ~>
67
+ - !ruby/object:Gem::Version
68
+ version: 0.7.5
69
+ - !ruby/object:Gem::Dependency
70
+ name: rspec-core
71
+ requirement: !ruby/object:Gem::Requirement
72
+ requirements:
73
+ - - ~>
74
+ - !ruby/object:Gem::Version
75
+ version: '2.0'
76
+ type: :development
77
+ prerelease: false
78
+ version_requirements: !ruby/object:Gem::Requirement
79
+ requirements:
80
+ - - ~>
81
+ - !ruby/object:Gem::Version
82
+ version: '2.0'
83
+ - !ruby/object:Gem::Dependency
84
+ name: rspec-expectations
85
+ requirement: !ruby/object:Gem::Requirement
86
+ requirements:
87
+ - - ~>
88
+ - !ruby/object:Gem::Version
89
+ version: '2.0'
90
+ type: :development
91
+ prerelease: false
92
+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
94
+ - - ~>
95
+ - !ruby/object:Gem::Version
96
+ version: '2.0'
97
+ - !ruby/object:Gem::Dependency
98
+ name: rspec-mocks
99
+ requirement: !ruby/object:Gem::Requirement
100
+ requirements:
101
+ - - '>='
102
+ - !ruby/object:Gem::Version
103
+ version: '0'
104
+ type: :development
105
+ prerelease: false
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ requirements:
108
+ - - '>='
109
+ - !ruby/object:Gem::Version
110
+ version: '0'
111
+ - !ruby/object:Gem::Dependency
112
+ name: rr
113
+ requirement: !ruby/object:Gem::Requirement
114
+ requirements:
115
+ - - ~>
116
+ - !ruby/object:Gem::Version
117
+ version: '1.0'
118
+ type: :development
119
+ prerelease: false
120
+ version_requirements: !ruby/object:Gem::Requirement
121
+ requirements:
122
+ - - ~>
123
+ - !ruby/object:Gem::Version
124
+ version: '1.0'
125
+ description: "\n Intelligent visualization of software traces \n "
126
+ email:
127
+ - mastedm@gmail.com
128
+ executables: []
129
+ extensions: []
130
+ extra_rdoc_files: []
131
+ files:
132
+ - .gitignore
133
+ - Gemfile
134
+ - LICENSE
135
+ - LICENSE.txt
136
+ - README.md
137
+ - Rakefile
138
+ - lib/trace_visualization.rb
139
+ - lib/trace_visualization/bwt.rb
140
+ - lib/trace_visualization/bwt.rbold
141
+ - lib/trace_visualization/data/irepetition.rb
142
+ - lib/trace_visualization/data/repetition.rb
143
+ - lib/trace_visualization/generators.rb
144
+ - lib/trace_visualization/longest_common_prefix.rb
145
+ - lib/trace_visualization/mapping.rb
146
+ - lib/trace_visualization/reorder.rb
147
+ - lib/trace_visualization/repetitions.rb
148
+ - lib/trace_visualization/repetitions_concatenation.rb
149
+ - lib/trace_visualization/repetitions_context.rb
150
+ - lib/trace_visualization/repetitions_incrementation.rb
151
+ - lib/trace_visualization/repetitions_psy.rb
152
+ - lib/trace_visualization/suffix_array.rb
153
+ - lib/trace_visualization/utils.rb
154
+ - lib/trace_visualization/version.rb
155
+ - lib/trace_visualization/visualization/console_color_print.rb
156
+ - spec/bwt_spec.rb
157
+ - spec/generators_spec.rb
158
+ - spec/longest_common_prefix_spec.rb
159
+ - spec/mapping_spec.rb
160
+ - spec/reorder_spec.rb
161
+ - spec/repetitions_concatenation_spec.rb
162
+ - spec/repetitions_incrementation_spec.rb
163
+ - spec/repetitions_psy_spec.rb
164
+ - spec/repetitions_spec.rb
165
+ - spec/spec_helper.rb
166
+ - spec/suffix_array_spec.rb
167
+ - trace_visualization.gemspec
168
+ homepage: ''
169
+ licenses:
170
+ - MIT
171
+ metadata: {}
172
+ post_install_message:
173
+ rdoc_options: []
174
+ require_paths:
175
+ - lib
176
+ required_ruby_version: !ruby/object:Gem::Requirement
177
+ requirements:
178
+ - - '>='
179
+ - !ruby/object:Gem::Version
180
+ version: '0'
181
+ required_rubygems_version: !ruby/object:Gem::Requirement
182
+ requirements:
183
+ - - '>='
184
+ - !ruby/object:Gem::Version
185
+ version: '0'
186
+ requirements: []
187
+ rubyforge_project:
188
+ rubygems_version: 2.0.6
189
+ signing_key:
190
+ specification_version: 4
191
+ summary: Software for smart trace visualization
192
+ test_files:
193
+ - spec/bwt_spec.rb
194
+ - spec/generators_spec.rb
195
+ - spec/longest_common_prefix_spec.rb
196
+ - spec/mapping_spec.rb
197
+ - spec/reorder_spec.rb
198
+ - spec/repetitions_concatenation_spec.rb
199
+ - spec/repetitions_incrementation_spec.rb
200
+ - spec/repetitions_psy_spec.rb
201
+ - spec/repetitions_spec.rb
202
+ - spec/spec_helper.rb
203
+ - spec/suffix_array_spec.rb
204
+ has_rdoc: