sequenceserver 2.0.0.beta3 → 2.0.0.beta4

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Potentially problematic release.

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Files changed (87) hide show
  1. checksums.yaml +5 -5
  2. data/.eslintrc.json +36 -0
  3. data/.rubocop.yml +1 -1
  4. data/.travis.yml +53 -20
  5. data/AppImage/recipe.yml +15 -0
  6. data/AppImage/sequenceserver.desktop +8 -0
  7. data/AppImage/sequenceserver.png +0 -0
  8. data/AppImage/sequenceserver.sh +11 -0
  9. data/README.md +79 -46
  10. data/bin/sequenceserver +4 -4
  11. data/lib/sequenceserver/version.rb +1 -1
  12. data/package.json +2 -0
  13. data/public/css/grapher.css +3 -0
  14. data/public/css/sequenceserver.css +17 -6
  15. data/public/css/sequenceserver.min.css +3 -3
  16. data/public/js/circos.js +515 -491
  17. data/public/js/grapher.js +12 -6
  18. data/public/js/hits_overview.js +321 -308
  19. data/public/js/hsp.js +12 -7
  20. data/public/js/length_distribution.js +241 -234
  21. data/public/js/report.js +196 -174
  22. data/public/js/search.js +3 -3
  23. data/public/js/sequenceserver.js +9 -9
  24. data/public/js/utils.js +17 -10
  25. data/public/js/visualisation_helpers.js +77 -77
  26. data/public/sequenceserver-report.min.js +17 -17
  27. data/public/sequenceserver-search.min.js +1 -1
  28. data/public/vendor/github/nicgirault/circosJs@1.7.0/dist/circosJS.js +1 -5
  29. data/sequenceserver.gemspec +1 -2
  30. data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +13 -13
  31. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +555 -25
  32. data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +13 -13
  33. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +558 -24
  34. data/spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb +13 -13
  35. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +561 -26
  36. data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +13 -13
  37. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +561 -25
  38. data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +13 -13
  39. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +558 -24
  40. data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +13 -13
  41. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +559 -24
  42. data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +13 -13
  43. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +559 -28
  44. data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +13 -13
  45. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +559 -27
  46. data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +13 -13
  47. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +557 -25
  48. data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +13 -13
  49. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +219 -21
  50. data/spec/capybara_spec.rb +25 -28
  51. data/spec/download_helper.rb +6 -3
  52. data/spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt +6 -0
  53. data/spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt +6 -0
  54. data/spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt +30 -0
  55. data/spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt +6 -0
  56. data/spec/sequences/alignment-35_hits_diamond_blastp.txt +210 -0
  57. data/spec/sequences/alignment-35_hits_diamond_blastx.txt +210 -0
  58. data/spec/sequences/alignment-3_hits.txt +18 -0
  59. data/spec/sequences/alignment-40_hits_blastn.txt +246 -0
  60. data/spec/sequences/alignment-40_hits_blastp.txt +240 -0
  61. data/spec/sequences/alignment-40_hits_blastp_2.2.30.txt +240 -0
  62. data/spec/sequences/alignment-40_hits_blastx.txt +240 -0
  63. data/spec/sequences/alignment-40_hits_tblastn.txt +240 -0
  64. data/spec/sequences/alignment-40_hits_tblastn_2.2.30.txt +240 -0
  65. data/spec/sequences/alignment-40_hits_tblastx.txt +2664 -0
  66. data/spec/sequences/alignment-4_hits.txt +24 -0
  67. data/spec/sequences/alignment-4_hits_blastn.txt +24 -0
  68. data/spec/sequences/alignment-4_hits_blastp.txt +24 -0
  69. data/spec/sequences/alignment-4_hits_blastp_2.2.30.txt +24 -0
  70. data/spec/sequences/alignment-4_hits_blastx.txt +24 -0
  71. data/spec/sequences/alignment-4_hits_diamond_blastp.txt +24 -0
  72. data/spec/sequences/alignment-4_hits_diamond_blastx.txt +24 -0
  73. data/spec/sequences/alignment-4_hits_tblastn.txt +24 -0
  74. data/spec/sequences/alignment-4_hits_tblastn_2.2.30.txt +24 -0
  75. data/spec/sequences/alignment-4_hits_tblastx.txt +318 -0
  76. data/spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt +6 -0
  77. data/spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt +6 -0
  78. data/spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt +6 -0
  79. data/spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt +6 -0
  80. data/spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt +6 -0
  81. data/spec/spec_helper.rb +3 -3
  82. metadata +67 -57
  83. data/.eslintrc +0 -213
  84. data/Rakefile +0 -8
  85. data/spec/dotdir/blast_2.4.0/blastn/TBLASTN_XML_2.4.0.xml +0 -1181
  86. data/spec/dotdir/blast_2.5.0/blastn/BLASTN_LONG_XML_2.5.0.xml +0 -18813
  87. data/spec/import_spec_capybara_local.rb +0 -61

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