genevalidatorapp 1.4.12

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Files changed (72) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +24 -0
  3. data/.travis.yml +7 -0
  4. data/Gemfile +4 -0
  5. data/GeneValidatorApp.gemspec +50 -0
  6. data/LICENSE.txt +661 -0
  7. data/README.md +101 -0
  8. data/Rakefile +14 -0
  9. data/bin/genevalidatorapp +122 -0
  10. data/config.ru +3 -0
  11. data/lib/GeneValidatorApp.rb +321 -0
  12. data/lib/GeneValidatorApp/config.rb +86 -0
  13. data/lib/GeneValidatorApp/database.rb +114 -0
  14. data/lib/GeneValidatorApp/genevalidator.rb +241 -0
  15. data/lib/GeneValidatorApp/logger.rb +24 -0
  16. data/lib/GeneValidatorApp/version.rb +3 -0
  17. data/public/GeneValidator/.gitkeep +0 -0
  18. data/public/web_files/css/bootstrap.min.css +7 -0
  19. data/public/web_files/css/bootstrap1.min.css +7 -0
  20. data/public/web_files/css/custom.css +521 -0
  21. data/public/web_files/css/custom.min.css +3 -0
  22. data/public/web_files/css/font-awesome.min.css +4 -0
  23. data/public/web_files/fonts/FontAwesome.otf +0 -0
  24. data/public/web_files/fonts/fontawesome-webfont.eot +0 -0
  25. data/public/web_files/fonts/fontawesome-webfont.svg +504 -0
  26. data/public/web_files/fonts/fontawesome-webfont.ttf +0 -0
  27. data/public/web_files/fonts/fontawesome-webfont.woff +0 -0
  28. data/public/web_files/img/gene.png +0 -0
  29. data/public/web_files/js/bionode-seq.min.js +1 -0
  30. data/public/web_files/js/bootstrap.min.js +6 -0
  31. data/public/web_files/js/d3.v3.min.js +5 -0
  32. data/public/web_files/js/genevalidator.js +282 -0
  33. data/public/web_files/js/genevalidator.min.js +1 -0
  34. data/public/web_files/js/jquery.cookie.min.js +1 -0
  35. data/public/web_files/js/jquery.min.js +4 -0
  36. data/public/web_files/js/jquery.tablesorter.min.js +5 -0
  37. data/public/web_files/js/jquery.validate.min.js +4 -0
  38. data/public/web_files/js/plots.js +744 -0
  39. data/public/web_files/js/plots.min.js +1 -0
  40. data/spec/app_spec.rb +107 -0
  41. data/spec/database/funky_ids/funky_ids.fa +10 -0
  42. data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
  43. data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
  44. data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
  45. data/spec/database/funky_ids/funky_ids.fa.nsd +9 -0
  46. data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
  47. data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
  48. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +6449 -0
  49. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  50. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  51. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
  52. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +2378 -0
  53. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
  54. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  55. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +5486 -0
  56. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  57. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  58. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
  59. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +946 -0
  60. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
  61. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  62. data/spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa +148303 -0
  63. data/spec/database/without_parse_seqids/without_parse_seqids.fa +10 -0
  64. data/spec/database/without_parse_seqids/without_parse_seqids.fa.phr +0 -0
  65. data/spec/database/without_parse_seqids/without_parse_seqids.fa.pin +0 -0
  66. data/spec/database/without_parse_seqids/without_parse_seqids.fa.psq +0 -0
  67. data/spec/database_spec.rb +37 -0
  68. data/spec/empty_config.yml +0 -0
  69. data/views/500.slim +5 -0
  70. data/views/index.slim +66 -0
  71. data/views/layout.slim +85 -0
  72. metadata +337 -0

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