genoverse 3.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (148) hide show
  1. package/.eslintrc.js +197 -0
  2. package/.github/workflows/test.yml +24 -0
  3. package/LICENSE.TXT +24 -0
  4. package/README.md +11 -0
  5. package/css/controlPanel.css +200 -0
  6. package/css/fileDrop.css +22 -0
  7. package/css/font-awesome.css +3 -0
  8. package/css/fullscreen.css +19 -0
  9. package/css/genoverse.css +466 -0
  10. package/css/karyotype.css +85 -0
  11. package/css/resizer.css +36 -0
  12. package/css/tooltips.css +26 -0
  13. package/css/trackControls.css +111 -0
  14. package/expanded.html +120 -0
  15. package/fontawesome/css/fontawesome.min.css +5 -0
  16. package/fontawesome/css/regular.min.css +5 -0
  17. package/fontawesome/css/solid.min.css +5 -0
  18. package/fontawesome/webfonts/fa-brands-400.ttf +0 -0
  19. package/fontawesome/webfonts/fa-brands-400.woff +0 -0
  20. package/fontawesome/webfonts/fa-brands-400.woff2 +0 -0
  21. package/fontawesome/webfonts/fa-regular-400.ttf +0 -0
  22. package/fontawesome/webfonts/fa-regular-400.woff +0 -0
  23. package/fontawesome/webfonts/fa-regular-400.woff2 +0 -0
  24. package/fontawesome/webfonts/fa-solid-900.ttf +0 -0
  25. package/fontawesome/webfonts/fa-solid-900.woff +0 -0
  26. package/fontawesome/webfonts/fa-solid-900.woff2 +0 -0
  27. package/help.pdf +0 -0
  28. package/i/sort_handle.png +0 -0
  29. package/index.html +68 -0
  30. package/index.js +83 -0
  31. package/jest.config.js +4 -0
  32. package/js/Genoverse.js +1681 -0
  33. package/js/Track/Controller/Sequence.js +17 -0
  34. package/js/Track/Controller/Stranded.js +73 -0
  35. package/js/Track/Controller.js +620 -0
  36. package/js/Track/Model/File/BAM.js +44 -0
  37. package/js/Track/Model/File/BED.js +116 -0
  38. package/js/Track/Model/File/GFF.js +40 -0
  39. package/js/Track/Model/File/VCF.js +101 -0
  40. package/js/Track/Model/File/WIG.js +67 -0
  41. package/js/Track/Model/File.js +36 -0
  42. package/js/Track/Model/Gene/Ensembl.js +22 -0
  43. package/js/Track/Model/Gene.js +5 -0
  44. package/js/Track/Model/Sequence/Ensembl.js +4 -0
  45. package/js/Track/Model/Sequence/Fasta.js +60 -0
  46. package/js/Track/Model/Sequence.js +50 -0
  47. package/js/Track/Model/SequenceVariation.js +41 -0
  48. package/js/Track/Model/Stranded.js +28 -0
  49. package/js/Track/Model/Transcript/Ensembl.js +67 -0
  50. package/js/Track/Model/Transcript.js +5 -0
  51. package/js/Track/Model.js +303 -0
  52. package/js/Track/View/Gene/Ensembl.js +46 -0
  53. package/js/Track/View/Gene.js +6 -0
  54. package/js/Track/View/Sequence/Variation.js +115 -0
  55. package/js/Track/View/Sequence.js +63 -0
  56. package/js/Track/View/Transcript/Ensembl.js +12 -0
  57. package/js/Track/View/Transcript.js +28 -0
  58. package/js/Track/View.js +566 -0
  59. package/js/Track/library/Chromosome.js +145 -0
  60. package/js/Track/library/File/BAM.js +30 -0
  61. package/js/Track/library/File/BED.js +24 -0
  62. package/js/Track/library/File/BIGBED.js +47 -0
  63. package/js/Track/library/File/BIGWIG.js +52 -0
  64. package/js/Track/library/File/GFF.js +9 -0
  65. package/js/Track/library/File/VCF.js +71 -0
  66. package/js/Track/library/File/WIG.js +5 -0
  67. package/js/Track/library/File.js +10 -0
  68. package/js/Track/library/Gene.js +37 -0
  69. package/js/Track/library/Graph/Bar.js +235 -0
  70. package/js/Track/library/Graph/Line.js +296 -0
  71. package/js/Track/library/Graph.js +355 -0
  72. package/js/Track/library/HighlightRegion.js +292 -0
  73. package/js/Track/library/Legend.js +224 -0
  74. package/js/Track/library/Scalebar.js +227 -0
  75. package/js/Track/library/Scaleline.js +91 -0
  76. package/js/Track/library/Static.js +78 -0
  77. package/js/Track/library/dbSNP.js +142 -0
  78. package/js/Track.js +632 -0
  79. package/js/genomes/grch37.js +990 -0
  80. package/js/genomes/grch38.js +990 -0
  81. package/js/genoverse.min.js +2 -0
  82. package/js/genoverse.min.js.map +1 -0
  83. package/js/lib/BWReader.js +578 -0
  84. package/js/lib/Base.js +145 -0
  85. package/js/lib/VCFReader.js +286 -0
  86. package/js/lib/dalliance/js/bam.js +494 -0
  87. package/js/lib/dalliance/js/bin.js +185 -0
  88. package/js/lib/dalliance/js/das.js +749 -0
  89. package/js/lib/dalliance/js/utils.js +370 -0
  90. package/js/lib/dalliance-lib.js +3594 -0
  91. package/js/lib/dalliance-lib.min.js +68 -0
  92. package/js/lib/jDataView.js +2 -0
  93. package/js/lib/jParser.js +192 -0
  94. package/js/lib/jquery-ui.js +8 -0
  95. package/js/lib/jquery.js +2 -0
  96. package/js/lib/jquery.mousehold.js +53 -0
  97. package/js/lib/jquery.mousewheel.js +84 -0
  98. package/js/lib/jquery.tipsy.js +258 -0
  99. package/js/lib/rtree.js +1 -0
  100. package/js/plugins/controlPanel.js +395 -0
  101. package/js/plugins/fileDrop.js +62 -0
  102. package/js/plugins/focusRegion.js +12 -0
  103. package/js/plugins/fullscreen.js +77 -0
  104. package/js/plugins/karyotype.js +210 -0
  105. package/js/plugins/resizer.js +45 -0
  106. package/js/plugins/tooltips.js +94 -0
  107. package/js/plugins/trackControls.js +143 -0
  108. package/package.json +43 -0
  109. package/test/View/__snapshots__/render-bar-graph.test.js.snap +111 -0
  110. package/test/View/__snapshots__/render-blocks.test.js.snap +105 -0
  111. package/test/View/__snapshots__/render-chromosome.test.js.snap +5 -0
  112. package/test/View/__snapshots__/render-highlights.test.js.snap +73 -0
  113. package/test/View/__snapshots__/render-insert-variants.test.js.snap +9 -0
  114. package/test/View/__snapshots__/render-labels.test.js.snap +241 -0
  115. package/test/View/__snapshots__/render-legends.test.js.snap +13 -0
  116. package/test/View/__snapshots__/render-line-graph.test.js.snap +349 -0
  117. package/test/View/__snapshots__/render-scalebar.test.js.snap +49 -0
  118. package/test/View/__snapshots__/render-scaleline.test.js.snap +31 -0
  119. package/test/View/__snapshots__/render-sequence.test.js.snap +23 -0
  120. package/test/View/__snapshots__/render-stranded.test.js.snap +5 -0
  121. package/test/View/__snapshots__/render-transcripts.test.js.snap +193 -0
  122. package/test/View/render-bar-graph.test.js +87 -0
  123. package/test/View/render-blocks.test.js +171 -0
  124. package/test/View/render-chromosome.test.js +40 -0
  125. package/test/View/render-highlights.test.js +67 -0
  126. package/test/View/render-insert-variants.test.js +11 -0
  127. package/test/View/render-labels.test.js +266 -0
  128. package/test/View/render-legends.test.js +31 -0
  129. package/test/View/render-line-graph.test.js +169 -0
  130. package/test/View/render-scalebar.test.js +36 -0
  131. package/test/View/render-scaleline.test.js +28 -0
  132. package/test/View/render-sequence.test.js +49 -0
  133. package/test/View/render-stranded.test.js +10 -0
  134. package/test/View/render-transcripts.test.js +165 -0
  135. package/test/create-and-destroy.test.js +63 -0
  136. package/test/track-ordering.test.js +514 -0
  137. package/test/track_config/__snapshots__/config-settings.test.js.snap +23 -0
  138. package/test/track_config/config-settings.test.js +321 -0
  139. package/test/track_config/zoom-level-settings.test.js +98 -0
  140. package/test/utils.js +80 -0
  141. package/utils/createGenome.js +52 -0
  142. package/utils/devServer.js +36 -0
  143. package/utils/expandedTemplate.html +46 -0
  144. package/utils/git-hooks/post-commit +9 -0
  145. package/utils/git-hooks/pre-commit +7 -0
  146. package/utils/git-hooks/setup +6 -0
  147. package/utils/makeExpanded.js +19 -0
  148. package/webpack.config.js +39 -0
@@ -0,0 +1,39 @@
1
+ const TerserPlugin = require('terser-webpack-plugin');
2
+ const webpack = require('webpack');
3
+
4
+ module.exports = {
5
+ mode : 'production',
6
+ entry : `${__dirname }/index.js`,
7
+ target : [ 'web', 'es5' ],
8
+ output : { filename: 'genoverse.min.js', path: `${__dirname }/js` },
9
+ devtool : 'source-map',
10
+ plugins : [
11
+ new webpack.ProvidePlugin({
12
+ $ : `${__dirname }/js/lib/jquery.js`,
13
+ jQuery : `${__dirname }/js/lib/jquery.js`,
14
+ }),
15
+ new webpack.DefinePlugin({
16
+ define: undefined, // Stop jquery-ui.js trying to do define(["jquery"]), which doesn't work if jquery isn't in node_modules
17
+ }),
18
+ ],
19
+ optimization: {
20
+ minimizer: [
21
+ new TerserPlugin({
22
+ extractComments : false,
23
+ parallel : true,
24
+ terserOptions : {
25
+ compress: {
26
+ keep_infinity: true,
27
+ },
28
+ output: {
29
+ comments: false,
30
+ },
31
+ },
32
+ }),
33
+ ],
34
+ },
35
+ performance: {
36
+ maxEntrypointSize : 400000,
37
+ maxAssetSize : 400000,
38
+ },
39
+ };