genoverse 3.2.0 → 4.0.1

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 (217) hide show
  1. package/.eslintrc.js +93 -162
  2. package/.github/workflows/test.yml +9 -10
  3. package/.github/workflows/update-gh-pages.yml +33 -0
  4. package/LICENSE.TXT +2 -2
  5. package/README.md +174 -3
  6. package/{i → assets}/sort_handle.png +0 -0
  7. package/babel.config.js +19 -0
  8. package/dist/129.css +334 -0
  9. package/dist/129.css.map +1 -0
  10. package/dist/129.genoverse.js +2 -0
  11. package/dist/129.genoverse.js.map +1 -0
  12. package/dist/15d98c18221c8bcb2334.ttf +0 -0
  13. package/dist/166.css +2 -0
  14. package/dist/166.genoverse.js +1 -0
  15. package/dist/216.css +20 -0
  16. package/dist/216.css.map +1 -0
  17. package/dist/232.css +114 -0
  18. package/dist/232.css.map +1 -0
  19. package/dist/232.genoverse.js +2 -0
  20. package/dist/232.genoverse.js.map +1 -0
  21. package/dist/2e659e443f3e98569e9f.png +0 -0
  22. package/dist/394.css +114 -0
  23. package/dist/394.css.map +1 -0
  24. package/dist/394.genoverse.js +2 -0
  25. package/dist/394.genoverse.js.map +1 -0
  26. package/dist/469.css +24 -0
  27. package/dist/469.css.map +1 -0
  28. package/dist/469.genoverse.js +2 -0
  29. package/dist/469.genoverse.js.map +1 -0
  30. package/dist/4896d4b04430cc3dfb06.woff2 +0 -0
  31. package/dist/530.css +39 -0
  32. package/dist/530.css.map +1 -0
  33. package/dist/530.genoverse.js +2 -0
  34. package/dist/530.genoverse.js.map +1 -0
  35. package/dist/547.css +469 -0
  36. package/dist/547.css.map +1 -0
  37. package/dist/547.genoverse.js +1 -0
  38. package/dist/729.css +315 -0
  39. package/dist/729.css.map +1 -0
  40. package/dist/79da213423ac0def2058.ttf +0 -0
  41. package/dist/804.genoverse.js +2 -0
  42. package/dist/804.genoverse.js.map +1 -0
  43. package/dist/842.genoverse.js +2 -0
  44. package/dist/842.genoverse.js.map +1 -0
  45. package/dist/893.genoverse.js +2 -0
  46. package/dist/893.genoverse.js.map +1 -0
  47. package/dist/949.css +315 -0
  48. package/dist/949.css.map +1 -0
  49. package/dist/949.genoverse.js +2 -0
  50. package/dist/949.genoverse.js.map +1 -0
  51. package/dist/952.css +315 -0
  52. package/dist/952.css.map +1 -0
  53. package/dist/952.genoverse.js +2 -0
  54. package/dist/952.genoverse.js.map +1 -0
  55. package/dist/d79c2ec96ab9ff1161a2.woff2 +0 -0
  56. package/dist/genoverse.js +2 -0
  57. package/dist/genoverse.js.map +1 -0
  58. package/index.html +13 -14
  59. package/jest.config.js +5 -0
  60. package/jest.setup.js +13 -0
  61. package/package.json +29 -12
  62. package/{css → src/css}/controlPanel.css +0 -0
  63. package/{css → src/css}/fileDrop.css +0 -0
  64. package/src/css/fontawesome.css +3 -0
  65. package/{css → src/css}/fullscreen.css +0 -0
  66. package/{css → src/css}/genoverse.css +1 -1
  67. package/{css → src/css}/karyotype.css +2 -0
  68. package/{css → src/css}/resizer.css +0 -0
  69. package/{css → src/css}/tooltips.css +0 -0
  70. package/{css → src/css}/trackControls.css +0 -0
  71. package/src/js/Genoverse.js +1747 -0
  72. package/{js → src/js}/Track/Controller/Sequence.js +6 -4
  73. package/src/js/Track/Controller/Stranded.js +83 -0
  74. package/{js → src/js}/Track/Controller.js +201 -160
  75. package/src/js/Track/Model/File/BAM.js +47 -0
  76. package/src/js/Track/Model/File/BED.js +122 -0
  77. package/src/js/Track/Model/File/GFF.js +42 -0
  78. package/src/js/Track/Model/File/VCF.js +109 -0
  79. package/src/js/Track/Model/File/WIG.js +82 -0
  80. package/src/js/Track/Model/File.js +36 -0
  81. package/src/js/Track/Model/Gene/Ensembl.js +24 -0
  82. package/{js → src/js}/Track/Model/Gene.js +3 -1
  83. package/src/js/Track/Model/Sequence/Ensembl.js +6 -0
  84. package/{js → src/js}/Track/Model/Sequence/Fasta.js +24 -17
  85. package/{js → src/js}/Track/Model/Sequence.js +10 -7
  86. package/{js → src/js}/Track/Model/SequenceVariation.js +17 -11
  87. package/{js → src/js}/Track/Model/Stranded.js +11 -8
  88. package/src/js/Track/Model/Transcript/Ensembl.js +73 -0
  89. package/{js → src/js}/Track/Model/Transcript.js +3 -1
  90. package/{js → src/js}/Track/Model.js +125 -93
  91. package/{js → src/js}/Track/View/Gene/Ensembl.js +6 -4
  92. package/src/js/Track/View/Gene.js +8 -0
  93. package/{js → src/js}/Track/View/Sequence.js +18 -22
  94. package/src/js/Track/View/SequenceVariation.js +117 -0
  95. package/src/js/Track/View/Transcript/Ensembl.js +17 -0
  96. package/src/js/Track/View/Transcript.js +32 -0
  97. package/{js → src/js}/Track/View.js +200 -159
  98. package/{js → src/js}/Track/library/Chromosome.js +18 -13
  99. package/src/js/Track/library/File/BAM.js +34 -0
  100. package/src/js/Track/library/File/BED.js +27 -0
  101. package/src/js/Track/library/File/BIGBED.js +51 -0
  102. package/src/js/Track/library/File/BIGWIG.js +54 -0
  103. package/src/js/Track/library/File/GFF.js +10 -0
  104. package/{js → src/js}/Track/library/File/VCF.js +29 -22
  105. package/src/js/Track/library/File/WIG.js +8 -0
  106. package/{js → src/js}/Track/library/File.js +4 -2
  107. package/src/js/Track/library/Gene.js +44 -0
  108. package/src/js/Track/library/Graph/Bar.js +263 -0
  109. package/src/js/Track/library/Graph/Line.js +335 -0
  110. package/{js → src/js}/Track/library/Graph.js +137 -114
  111. package/{js → src/js}/Track/library/HighlightRegion.js +118 -93
  112. package/src/js/Track/library/Legend.js +258 -0
  113. package/{js → src/js}/Track/library/Scalebar.js +69 -49
  114. package/{js → src/js}/Track/library/Scaleline.js +29 -27
  115. package/src/js/Track/library/Static.js +82 -0
  116. package/{js → src/js}/Track/library/dbSNP.js +47 -50
  117. package/src/js/Track.js +651 -0
  118. package/{js → src/js}/genomes/grch37.js +52 -52
  119. package/{js → src/js}/genomes/grch38.js +52 -52
  120. package/src/js/lib/BWReader.js +562 -0
  121. package/src/js/lib/VCFReader.js +296 -0
  122. package/src/js/lib/dalliance/bam.js +517 -0
  123. package/src/js/lib/dalliance/bin.js +317 -0
  124. package/src/js/lib/dalliance/jszlib-inflate.js +2159 -0
  125. package/src/js/lib/dalliance/lh3utils.js +105 -0
  126. package/src/js/lib/dalliance/sha1.js +334 -0
  127. package/src/js/lib/import-tracks.js +42 -0
  128. package/{js/lib → src/js/lib/jquery-plugins}/jquery.mousehold.js +0 -0
  129. package/{js/lib → src/js/lib/jquery-plugins}/jquery.mousewheel.js +0 -0
  130. package/{js/lib → src/js/lib/jquery-plugins}/jquery.tipsy.js +0 -0
  131. package/src/js/lib/jquery.js +26 -0
  132. package/src/js/lib/polyfills.js +11 -0
  133. package/src/js/lib/wrap-functions.js +88 -0
  134. package/src/js/plugins/controlPanel.js +388 -0
  135. package/src/js/plugins/fileDrop.js +81 -0
  136. package/src/js/plugins/focusRegion.js +13 -0
  137. package/{js → src/js}/plugins/fullscreen.js +18 -14
  138. package/{js → src/js}/plugins/karyotype.js +51 -45
  139. package/src/js/plugins/resizer.js +52 -0
  140. package/{js → src/js}/plugins/tooltips.js +31 -29
  141. package/src/js/plugins/trackControls.js +159 -0
  142. package/test/View/render-legends.test.js +1 -1
  143. package/test/change-width.test.js +71 -0
  144. package/test/create-and-destroy.test.js +2 -2
  145. package/test/track-ordering.test.js +3 -2
  146. package/test/track_config/config-settings.test.js +1 -1
  147. package/test/utils.js +4 -2
  148. package/webpack.config.js +103 -34
  149. package/css/font-awesome.css +0 -3
  150. package/expanded.html +0 -120
  151. package/fontawesome/css/fontawesome.min.css +0 -5
  152. package/fontawesome/css/regular.min.css +0 -5
  153. package/fontawesome/css/solid.min.css +0 -5
  154. package/fontawesome/webfonts/fa-brands-400.ttf +0 -0
  155. package/fontawesome/webfonts/fa-brands-400.woff +0 -0
  156. package/fontawesome/webfonts/fa-brands-400.woff2 +0 -0
  157. package/fontawesome/webfonts/fa-regular-400.ttf +0 -0
  158. package/fontawesome/webfonts/fa-regular-400.woff +0 -0
  159. package/fontawesome/webfonts/fa-regular-400.woff2 +0 -0
  160. package/fontawesome/webfonts/fa-solid-900.ttf +0 -0
  161. package/fontawesome/webfonts/fa-solid-900.woff +0 -0
  162. package/fontawesome/webfonts/fa-solid-900.woff2 +0 -0
  163. package/help.pdf +0 -0
  164. package/index.js +0 -83
  165. package/js/Genoverse.js +0 -1681
  166. package/js/Track/Controller/Stranded.js +0 -73
  167. package/js/Track/Model/File/BAM.js +0 -44
  168. package/js/Track/Model/File/BED.js +0 -116
  169. package/js/Track/Model/File/GFF.js +0 -40
  170. package/js/Track/Model/File/VCF.js +0 -101
  171. package/js/Track/Model/File/WIG.js +0 -67
  172. package/js/Track/Model/File.js +0 -36
  173. package/js/Track/Model/Gene/Ensembl.js +0 -22
  174. package/js/Track/Model/Sequence/Ensembl.js +0 -4
  175. package/js/Track/Model/Transcript/Ensembl.js +0 -67
  176. package/js/Track/View/Gene.js +0 -6
  177. package/js/Track/View/Sequence/Variation.js +0 -115
  178. package/js/Track/View/Transcript/Ensembl.js +0 -12
  179. package/js/Track/View/Transcript.js +0 -28
  180. package/js/Track/library/File/BAM.js +0 -30
  181. package/js/Track/library/File/BED.js +0 -24
  182. package/js/Track/library/File/BIGBED.js +0 -47
  183. package/js/Track/library/File/BIGWIG.js +0 -52
  184. package/js/Track/library/File/GFF.js +0 -9
  185. package/js/Track/library/File/WIG.js +0 -5
  186. package/js/Track/library/Gene.js +0 -37
  187. package/js/Track/library/Graph/Bar.js +0 -235
  188. package/js/Track/library/Graph/Line.js +0 -296
  189. package/js/Track/library/Legend.js +0 -224
  190. package/js/Track/library/Static.js +0 -78
  191. package/js/Track.js +0 -632
  192. package/js/genoverse.min.js +0 -2
  193. package/js/genoverse.min.js.map +0 -1
  194. package/js/lib/BWReader.js +0 -578
  195. package/js/lib/Base.js +0 -145
  196. package/js/lib/VCFReader.js +0 -286
  197. package/js/lib/dalliance/js/bam.js +0 -494
  198. package/js/lib/dalliance/js/bin.js +0 -185
  199. package/js/lib/dalliance/js/das.js +0 -749
  200. package/js/lib/dalliance/js/utils.js +0 -370
  201. package/js/lib/dalliance-lib.js +0 -3594
  202. package/js/lib/dalliance-lib.min.js +0 -68
  203. package/js/lib/jDataView.js +0 -2
  204. package/js/lib/jParser.js +0 -192
  205. package/js/lib/jquery-ui.js +0 -8
  206. package/js/lib/jquery.js +0 -2
  207. package/js/lib/rtree.js +0 -1
  208. package/js/plugins/controlPanel.js +0 -395
  209. package/js/plugins/fileDrop.js +0 -62
  210. package/js/plugins/focusRegion.js +0 -12
  211. package/js/plugins/resizer.js +0 -45
  212. package/js/plugins/trackControls.js +0 -143
  213. package/utils/expandedTemplate.html +0 -46
  214. package/utils/git-hooks/post-commit +0 -9
  215. package/utils/git-hooks/pre-commit +0 -7
  216. package/utils/git-hooks/setup +0 -6
  217. package/utils/makeExpanded.js +0 -19
package/dist/216.css.map ADDED
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package/dist/232.css ADDED
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls {
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+ display: block;
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+ white-space: nowrap;
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+ position: relative;
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+ background: rgba(0, 0, 0, 0.5);
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+ border-radius: 0 0 0 2px;
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+ color: white;
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+ float: right;
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+ text-align: right;
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+ font-family: Verdana;
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+ font-size: 12px;
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+ font-weight: bold;
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+ padding: 5px 0;
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+ z-index: 5;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls:hover {
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+ background: rgba(0, 0, 0, 0.7);
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls .gv-track-controls-container {
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+ display: none;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls.gv-maximized .gv-track-controls-container {
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+ display: inline-block;
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+ border-right: 1px solid white;
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+ padding-right: 5px;
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+ text-align: center;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls .gv-track-controls-container > * {
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+ display: inline-block;
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+ min-width: 20px;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a {
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+ color: white;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a:hover {
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+ text-decoration: underline;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.far:hover,
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.fas:hover {
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+ text-decoration: none;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container:hover > div.gv-track-controls {
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+ display: block;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-track-controls-toggle {
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+ padding-left: 5px;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls.gv-maximized a.gv-track-controls-toggle {
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+ padding: 0 5px 0 10px;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-track-controls-toggle .far,
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-track-controls-toggle .fas {
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+ margin-right: 5px;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls:not(.gv-maximized) a.gv-track-controls-toggle > :last-child,
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls.gv-maximized a.gv-track-controls-toggle > :first-child {
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+ display: none;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle {
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+ position: relative;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle .fa-sort-up,
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle .fa-sort-down,
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort {
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+ display: none;
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+ }
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+
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort-up,
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort-down {
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+ display: inline-block;
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+ position: absolute;
86
+ left: 6px;
87
+ top: -4px;
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+ }
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls a.gv-height-toggle.gv-auto-height .fa-sort-down {
90
+ top: -15px;
91
+ }
92
+
93
+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls select,
94
+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls input,
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+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls button,
96
+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls textarea {
97
+ color: #333;
98
+ font-weight: normal;
99
+ }
100
+
101
+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls select {
102
+ margin: 0 5px;
103
+ }
104
+
105
+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls label {
106
+ margin: 0 0 0 5px;
107
+ }
108
+
109
+ .gv-track-controls-plugin .gv-track-container div.gv-track-controls .gv-track-controls-container > :first-child:not(select):not(label) {
110
+ margin-left: 5px;
111
+ }
112
+
113
+
114
+ /*# sourceMappingURL=232.css.map*/
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package/dist/232.genoverse.js ADDED
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+ "use strict";(self.webpackChunkgenoverse=self.webpackChunkgenoverse||[]).push([[232],{4232:function(t,o,e){function a(t){return a="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t},a(t)}e.r(o);o.default={trackControls:function(){var t=this.jQuery,o=[t('<a title="More info" class="fas fa-question-circle">').on("click",(function(){var o,e,a,i=t(this).data("track"),r=i.prop("menus").filter(".gv-track-info");if(!r.length){var n=i.prop("info");r=i.prop("menus",i.prop("menus").add(i.browser.makeMenu((o={title:i.name},e="function"==typeof n?n.call(i):n||"",a="",e in o?Object.defineProperty(o,e,{value:a,enumerable:!0,configurable:!0,writable:!0}):o[e]=a,o)).addClass("gv-track-info")))}r.show().position({of:i.prop("container"),at:"center top",my:"center top",collision:"none"})})),t('\n <a class="gv-height-toggle">\n <i class="fas fa-sort"></i>\n <i class="fas fa-sort-down"></i>\n <i class="fas fa-sort-up"></i>\n </a>\n ').on({click:function(){var o,e=t(this).data("track");e.prop("autoHeight",!e.prop("autoHeight"))?(e.prop("heightBeforeToggle",e.prop("height")),o=e.prop("fullVisibleHeight")):o=e.prop("heightBeforeToggle")||e.prop("initialHeight"),t(this).trigger("toggleState"),e.controller.resize(o,!0)},toggleState:function(){var o=t(this).data("track"),e=o.prop("autoHeight"),a=o.prop("resizer");this.title=e?"Set track to fixed height":"Set track to auto-adjust height",t(this)[e?"addClass":"removeClass"]("gv-auto-height"),a&&a[e?"hide":"show"]()}})],e=t('<a title="Remove track" class="far fa-trash-alt">').on("click",(function(){t(this).data("track").remove()})),i=t('\n <a class="gv-track-controls-toggle">\n <span><i class="fas fa-angle-double-left"></i><i class="fas fa-cog"></i></span>\n <span><i class="fas fa-angle-double-right"></i></span>\n </a>\n ').on("click",(function(){t(this).parent().toggleClass("gv-maximized")}));this.on({afterAddDomElements:function(){var r,n=this,s=this.prop("controls");if("off"!==s){var c=this.prop("defaultConfig"),l=(null===(r=this.browser.savedConfig)||void 0===r?void 0:r[this.prop("id")])||{};s=(s||[]).concat(o,!1===this.prop("removable")?[]:e),this.trackControls=t('<div class="gv-track-controls">').prependTo(this.container);var h=t('<div class="gv-track-controls-container">').appendTo(this.trackControls);s.forEach((function(o){var e;if(t.isPlainObject(o)&&o.type?(e=t("<".concat(o.type,">")).data("control",o.name),(o.options||[]).forEach((function(t){return e.append('<option value="'.concat(t.value,'">').concat(t.text,"</option>"))}))):"string"==typeof o?e=t(o):"object"===a(o)&&o.constructor&&o instanceof t&&(e=o.clone(!0)),e.data("track",n.track).appendTo(h),e.is("select")){var i=e.data("control");e.find("option[value=".concat(l[i]||c[i]||"all","]")).attr("selected",!0).end().change((function(){t(this).data("track").setConfig(t(this).data("control"),this.value)}))}})),this.prop("heightToggler",h.children(".gv-height-toggle").trigger("toggleState"));var p=i.clone(!0).data("track",this.track).appendTo(this.trackControls);p.trigger("click"),this.minLabelHeight=Math.max(this.minLabelHeight,this.trackControls.outerHeight(!0)+this.prop("margin")),p.trigger("click")}},afterResize:function(){this.trackControls&&this.trackControls[this.prop("height")<this.trackControls.outerHeight(!0)?"hide":"show"]()},afterResetHeight:function(){var t=this.prop("heightToggler");!0===this.prop("resizable")&&t&&(t[this.prop("autoHeight")?"addClass":"removeClass"]("gv-auto-height"),t.trigger("toggleState"))},afterSetMVC:function(){var t=this.prop("heightToggler");t&&t.trigger("toggleState")[!0===this.prop("resizable")?"removeClass":"addClass"]("gv-hide")}},"tracks")}}}}]);
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'Set track to fixed height' : 'Set track to auto-adjust height';\n\n jQuery(this)[autoHeight ? 'addClass' : 'removeClass']('gv-auto-height');\n\n if (resizer) {\n resizer[autoHeight ? 'hide' : 'show']();\n }\n },\n }),\n ];\n\n const remove = jQuery('<a title=\"Remove track\" class=\"far fa-trash-alt\">').on('click', function () {\n jQuery(this).data('track').remove();\n });\n\n const toggle = jQuery(`\n <a class=\"gv-track-controls-toggle\">\n <span><i class=\"fas fa-angle-double-left\"></i><i class=\"fas fa-cog\"></i></span>\n <span><i class=\"fas fa-angle-double-right\"></i></span>\n </a>\n `).on('click', function () {\n jQuery(this).parent().toggleClass('gv-maximized');\n });\n\n this.on({\n afterAddDomElements: function () {\n let controls = this.prop('controls');\n\n if (controls === 'off') {\n return;\n }\n\n const defaultConfig = this.prop('defaultConfig');\n const savedConfig = this.browser.savedConfig?.[this.prop('id')] || {};\n\n controls = (controls || []).concat(defaultControls, this.prop('removable') === false ? [] : remove);\n\n this.trackControls = jQuery('<div class=\"gv-track-controls\">').prependTo(this.container);\n\n const controlsContainer = jQuery('<div class=\"gv-track-controls-container\">').appendTo(this.trackControls);\n\n controls.forEach(\n (control) => {\n let el;\n\n if (jQuery.isPlainObject(control) && control.type) {\n el = jQuery(`<${control.type}>`).data('control', control.name);\n\n (control.options || []).forEach(\n option => el.append(`<option value=\"${option.value}\">${option.text}</option>`)\n );\n } else if (typeof control === 'string') {\n el = jQuery(control);\n } else if (typeof control === 'object' && control.constructor && control instanceof jQuery) {\n el = control.clone(true);\n }\n\n el.data('track', this.track).appendTo(controlsContainer);\n\n // TODO: other control types\n if (el.is('select')) {\n const prop = el.data('control');\n\n el.find(`option[value=${savedConfig[prop] || defaultConfig[prop] || 'all'}]`).attr('selected', true).end().change(function () {\n jQuery(this).data('track').setConfig(jQuery(this).data('control'), this.value);\n });\n }\n }\n );\n\n this.prop('heightToggler', controlsContainer.children('.gv-height-toggle').trigger('toggleState'));\n\n const toggler = toggle.clone(true).data('track', this.track).appendTo(this.trackControls);\n\n toggler.trigger('click');\n\n this.minLabelHeight = Math.max(this.minLabelHeight, this.trackControls.outerHeight(true) + this.prop('margin'));\n\n toggler.trigger('click');\n },\n afterResize: function () {\n if (this.trackControls) {\n this.trackControls[this.prop('height') < this.trackControls.outerHeight(true) ? 'hide' : 'show']();\n }\n },\n afterResetHeight: function () {\n const heightToggler = this.prop('heightToggler');\n\n if (this.prop('resizable') === true && heightToggler) {\n heightToggler[this.prop('autoHeight') ? 'addClass' : 'removeClass']('gv-auto-height');\n heightToggler.trigger('toggleState');\n }\n },\n afterSetMVC: function () {\n const heightToggler = this.prop('heightToggler');\n\n if (heightToggler) {\n heightToggler.trigger('toggleState')[this.prop('resizable') === true ? 'removeClass' : 'addClass']('gv-hide');\n }\n },\n }, 'tracks');\n};\n\nexport default { trackControls: plugin };\n"],"names":["trackControls","jQuery","this","defaultControls","on","track","data","menu","prop","filter","length","info","add","browser","makeMenu","title","name","call","addClass","show","position","of","at","my","collision","click","height","trigger","controller","resize","toggleState","autoHeight","resizer","remove","toggle","parent","toggleClass","afterAddDomElements","controls","defaultConfig","savedConfig","concat","prependTo","container","controlsContainer","appendTo","forEach","control","el","isPlainObject","type","options","option","append","value","text","constructor","clone","is","find","attr","end","change","setConfig","children","toggler","minLabelHeight","Math","max","outerHeight","afterResize","afterResetHeight","heightToggler","afterSetMVC"],"sourceRoot":""}
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+
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+ .tipsy-n .tipsy-arrow { top: 0px; left: 50%; margin-left: -5px; border-bottom-style: solid; border-top: none; border-left-color: transparent; border-right-color: transparent; }
16
+ .tipsy-nw .tipsy-arrow { top: 0; left: 10px; border-bottom-style: solid; border-top: none; border-left-color: transparent; border-right-color: transparent;}
17
+ .tipsy-ne .tipsy-arrow { top: 0; right: 10px; border-bottom-style: solid; border-top: none; border-left-color: transparent; border-right-color: transparent;}
18
+ .tipsy-s .tipsy-arrow { bottom: 0; left: 50%; margin-left: -5px; border-top-style: solid; border-bottom: none; border-left-color: transparent; border-right-color: transparent; }
19
+ .tipsy-sw .tipsy-arrow { bottom: 0; left: 10px; border-top-style: solid; border-bottom: none; border-left-color: transparent; border-right-color: transparent; }
20
+ .tipsy-se .tipsy-arrow { bottom: 0; right: 10px; border-top-style: solid; border-bottom: none; border-left-color: transparent; border-right-color: transparent; }
21
+ .tipsy-e .tipsy-arrow { right: 0; top: 50%; margin-top: -5px; border-left-style: solid; border-right: none; border-top-color: transparent; border-bottom-color: transparent; }
22
+ .tipsy-w .tipsy-arrow { left: 0; top: 50%; margin-top: -5px; border-right-style: solid; border-left: none; border-top-color: transparent; border-bottom-color: transparent; }
23
+
24
+ .gv-wrapper-tooltip { position: absolute; left: 50%; top: 60px; }
25
+
26
+ .genoverse .tooltip { z-index: 1000; }
27
+ .gv-karyotype-plugin .gv-karyotype-container {
28
+ height: 50px;
29
+ overflow: hidden;
30
+ box-shadow: inset 0 0 33px -7px rgba(24, 36, 56, 0.97);
31
+ border: 1px solid #000;
32
+ background-color: #FFF;
33
+ }
34
+
35
+ .gv-karyotype-plugin .gv-karyotype-container .gv-wrapper {
36
+ border: 0;
37
+ }
38
+
39
+ .gv-karyotype-plugin .gv-karyotype-container .gv-chromosome {
40
+ margin: 15px;
41
+ position: relative;
42
+ height: calc(100% - 30px);
43
+ }
44
+
45
+ .gv-karyotype-plugin .gv-karyotype-container .gv-image-container {
46
+ box-shadow: 0 0 33px -7px #CCC inset;
47
+ }
48
+
49
+ .gv-karyotype-plugin .gv-karyotype-container .gv-karyotype-viewpoint-wrapper {
50
+ position: relative;
51
+ height: 70%;
52
+ top: -85%;
53
+ margin: 0 15px;
54
+ }
55
+
56
+ .gv-karyotype-plugin .gv-karyotype-container .gv-karyotype-viewpoint {
57
+ background-color: rgba(222, 84, 35, 0.37);
58
+ border: 1px dashed #E6380D;
59
+ box-shadow: 0 0 3px 2px rgba(237, 237, 237, 0.4) inset, 0 0 4px 0 rgba(116, 116, 116, 0.7);
60
+ height: 100%;
61
+ position: absolute;
62
+ z-index: 50;
63
+ cursor: grab;
64
+ cursor: -moz-grab;
65
+ cursor: -webkit-grab;
66
+ }
67
+
68
+ .gv-karyotype-plugin .gv-karyotype-container .ui-resizable-e {
69
+ cursor: e-resize;
70
+ height: 100%;
71
+ right: -5px;
72
+ top: 0;
73
+ width: 7px;
74
+ }
75
+
76
+ .gv-karyotype-plugin .gv-karyotype-container .ui-resizable-w {
77
+ cursor: w-resize;
78
+ height: 100%;
79
+ left: -5px;
80
+ top: 0;
81
+ width: 7px;
82
+ }
83
+
84
+ .gv-karyotype-plugin .gv-karyotype-container .ui-resizable-handle {
85
+ display: block;
86
+ font-size: 0.1px;
87
+ position: absolute;
88
+ }
89
+
90
+ .gv-karyotype-plugin .gv-karyotype-container .gv-chromosome .gv-label-container {
91
+ background: transparent;
92
+ box-shadow: none;
93
+ border: none;
94
+ cursor: default;
95
+ width: auto;
96
+ }
97
+
98
+ .gv-karyotype-plugin .gv-karyotype-container .gv-chromosome .gv-label-container .gv-name {
99
+ color: #000;
100
+ float: none;
101
+ left: 0 !important;
102
+ margin: 0;
103
+ overflow: auto;
104
+ position: relative;
105
+ text-shadow: none;
106
+ width: 100%;
107
+ }
108
+
109
+ .gv-karyotype-plugin .gv-karyotype-container.gv-no-label .gv-wrapper {
110
+ margin-left: 0;
111
+ }
112
+
113
+
114
+ /*# sourceMappingURL=394.css.map*/
package/dist/394.css.map ADDED
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position: absolute; padding: 5px; z-index: 1000; }\n.tipsy-inner { background-color: #000; color: #FFF; max-width: 250px; padding: 5px 8px 4px 8px; text-align: center; font-family: Tahoma; font-size: 11px; }\n\n/* Rounded corners */\n.tipsy-inner { border-radius: 3px; -moz-border-radius: 3px; -webkit-border-radius: 3px; }\n\n.tipsy-arrow { position: absolute; width: 0; height: 0; line-height: 0; border: 5px dashed #000; }\n\n/* Rules to colour arrows */\n.tipsy-arrow-n { border-bottom-color: #000; }\n.tipsy-arrow-s { border-top-color: #000; }\n.tipsy-arrow-e { border-left-color: #000; }\n.tipsy-arrow-w { border-right-color: #000; }\n\n.tipsy-n .tipsy-arrow { top: 0px; left: 50%; margin-left: -5px; border-bottom-style: solid; border-top: none; border-left-color: transparent; border-right-color: transparent; }\n.tipsy-nw .tipsy-arrow { top: 0; left: 10px; border-bottom-style: solid; border-top: none; border-left-color: transparent; border-right-color: transparent;}\n.tipsy-ne .tipsy-arrow { top: 0; right: 10px; border-bottom-style: solid; border-top: none; border-left-color: transparent; border-right-color: transparent;}\n.tipsy-s .tipsy-arrow { bottom: 0; left: 50%; margin-left: -5px; border-top-style: solid; border-bottom: none; border-left-color: transparent; border-right-color: transparent; }\n.tipsy-sw .tipsy-arrow { bottom: 0; left: 10px; border-top-style: solid; border-bottom: none; border-left-color: transparent; border-right-color: transparent; }\n.tipsy-se .tipsy-arrow { bottom: 0; right: 10px; border-top-style: solid; border-bottom: none; border-left-color: transparent; border-right-color: transparent; }\n.tipsy-e .tipsy-arrow { right: 0; top: 50%; margin-top: -5px; border-left-style: solid; border-right: none; border-top-color: transparent; border-bottom-color: transparent; }\n.tipsy-w .tipsy-arrow { left: 0; top: 50%; margin-top: -5px; border-right-style: solid; border-left: none; border-top-color: transparent; border-bottom-color: transparent; }\n\n.gv-wrapper-tooltip { position: absolute; left: 50%; top: 60px; }\n\n.genoverse .tooltip { z-index: 1000; }","@import url('./tooltips.css');\n\n.gv-karyotype-plugin .gv-karyotype-container {\n height: 50px;\n overflow: hidden;\n box-shadow: inset 0 0 33px -7px rgba(24, 36, 56, 0.97);\n border: 1px solid #000;\n background-color: #FFF;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .gv-wrapper {\n border: 0;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .gv-chromosome {\n margin: 15px;\n position: relative;\n height: calc(100% - 30px);\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .gv-image-container {\n box-shadow: 0 0 33px -7px #CCC inset;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .gv-karyotype-viewpoint-wrapper {\n position: relative;\n height: 70%;\n top: -85%;\n margin: 0 15px;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .gv-karyotype-viewpoint {\n background-color: rgba(222, 84, 35, 0.37);\n border: 1px dashed #E6380D;\n box-shadow: 0 0 3px 2px rgba(237, 237, 237, 0.4) inset, 0 0 4px 0 rgba(116, 116, 116, 0.7);\n height: 100%;\n position: absolute;\n z-index: 50;\n cursor: grab;\n cursor: -moz-grab;\n cursor: -webkit-grab;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .ui-resizable-e {\n cursor: e-resize;\n height: 100%;\n right: -5px;\n top: 0;\n width: 7px;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .ui-resizable-w {\n cursor: w-resize;\n height: 100%;\n left: -5px;\n top: 0;\n width: 7px;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .ui-resizable-handle {\n display: block;\n font-size: 0.1px;\n position: absolute;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .gv-chromosome .gv-label-container {\n background: transparent;\n box-shadow: none;\n border: none;\n cursor: default;\n width: auto;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container .gv-chromosome .gv-label-container .gv-name {\n color: #000;\n float: none;\n left: 0 !important;\n margin: 0;\n overflow: auto;\n position: relative;\n text-shadow: none;\n width: 100%;\n}\n\n.gv-karyotype-plugin .gv-karyotype-container.gv-no-label .gv-wrapper {\n margin-left: 0;\n}\n"],"names":[],"sourceRoot":""}
package/dist/394.genoverse.js ADDED
@@ -0,0 +1,2 @@
1
+ "use strict";(self.webpackChunkgenoverse=self.webpackChunkgenoverse||[]).push([[394],{4394:function(t,e,i){i.r(e);var n=i(5337);e.default={karyotype:function(t){var e=this.jQuery;function i(){var i=e('<div class="gv-chromosome">'),s=e('<div class="gv-karyotype-container">').html(i).insertBefore(this.wrapper),a=this.assembly||this.genomeName,o="".concat(t.showAssembly&&a?"".concat(a,": "):"","Chr ").concat(this.chr);t.showAssembly&&a&&s.addClass("gv-show-assembly");var r=e('<div class="gv-chromosome"><ul class="gv-label-container"><li><span class="gv-name">'.concat(o,"</span></li></ul></div>")).appendTo(s),h=!1===t.karyotypeLabel?0:r.find(".gv-name").outerWidth(!0)+10;r.remove(),this.karyotype=new Genoverse({parent:this,container:i,width:i.width(),genome:this.genome,chr:this.chr,start:1,end:this.chromosomeSize,isStatic:!0,tracks:[n.default.extend({name:o,height:20,featureHeight:20,border:!1,legend:!1,unsortable:!0,click:function(t){var i=this.container.parent().offset().left,n=t.pageX-i,s=this.featurePositions.search({x:n,y:1,w:1,h:1})[0];if(s)if("mouseup"===t.type)this.browser.parent.isStatic||this.browser.parent.moveTo(s.chr,s.start,s.end,!0);else if(this.hoverFeature!==s&&!this.browser.hideTooltip){if(this.container.tipsy("hide"),s.label){var a=i+s.position[this.scale].start+s.position[this.scale].width/2;this.container.attr("title",s.label[0]).tipsy({trigger:"manual",container:"body"}).tipsy("show").data("tipsy").$tip.css("left",(function(){return a-e(this).width()/2}))}this.hoverFeature=s}},addUserEventHandlers:function(){var t=this;this.base(),this.container.on({mousemove:function(e){t.click(e)},mouseout:function(e){if(t.browser.viewPoint.is(e.relatedTarget)||t.browser.viewPoint.find(e.relatedTarget).length)return!0;t.container.tipsy("hide"),t.hoverFeature=!1}},".gv-image-container"),this.container.on("mousewheel",".gv-image-container, .gv-selector",(function(t){t.stopPropagation()}))},afterSetName:function(){this.label.css("lineHeight","".concat(this.label.height(),"px"))}})],addUserEventHandlers:function(){},afterInit:function(){this.updatePosition(),this.viewPoint.fadeIn()},afterAddTracks:function(){this.track=this.tracks[0]},afterAddDomElements:function(){var i=this,n=this.parent;function a(){i.hideTooltip=!0,i.track.prop("container").tipsy("hide")}function o(t,s){i.hideTooltip=!1;var a=i.chromosomeSize/i.width,o="resizestop"===t.type?e(this).data("ui-resizable").axis:void 0,r="e"===o?n.start:Math.max(Math.floor(s.position.left*a),1),h="w"===o?n.end:"dragstop"===t.type?r+n.length-1:Math.floor(s.helper.outerWidth(!0)*a)+r;r===n.start&&h===n.end||n.moveTo(i.chr,r,h,!0,"dragstop"===t.type)}!1===t.karyotypeLabel?(this.labelContainer.remove(),this.labelContainer=e(),s.addClass("gv-no-label")):this.labelContainer.width(h),this.viewPoint=e('<div class="gv-karyotype-viewpoint-wrapper"><div class="gv-karyotype-viewpoint"></div></div>').appendTo(s).css({left:h,width:this.width-h}).children().on({mousemove:function(t){i.track.controller.click(t)},mouseout:function(t){var n=e(t.relatedTarget);if(i.viewPoint.is(n)||i.viewPoint.find(n).length||"IMG"===n.prop("nodeName")&&n.parent().is(i.track.prop("imgContainers")[0]))return!0;i.track.prop("container").tipsy("hide"),i.track.prop("hoverFeature",!1)}}),n.isStatic||this.viewPoint.draggable({axis:"x",containment:this.wrapper,start:a,stop:o}).resizable({handles:"e, w",containment:"parent",start:a,stop:o,resize:function(t,e){e.element.css("left",Math.max(0,e.position.left)),e.position.left>0?e.element.width(Math.min(e.size.width,e.element.parent().width()-e.position.left)):e.element.width(e.size.width+e.position.left)}})},updatePosition:function(){var t=this.parent.start*this.scale,e=this.parent.end*this.scale-t;this.viewPoint.css({left:t,width:e})}}),!0!==this.loadedPlugins.controlPanel&&e('<li class="gv-unsortable">').height((function(t,e){return e+s.height()})).prependTo(this.labelContainer)}function s(){var t=this.karyotype.container.parent();this.karyotype.destroy(),t.remove(),i.call(this)}this.on({afterInit:i,afterSetRange:function(){this.karyotype&&this.karyotype.updatePosition()},afterSetWidth:s,afterMoveTo:function(t){this.karyotype&&this.karyotype.chr!==t&&s.call(this)}})}}}}]);
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+ //# sourceMappingURL=394.genoverse.js.map
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`${assemblyName}: ` : ''}Chr ${this.chr}`;\n\n if (pluginConf.showAssembly && assemblyName) {\n container.addClass('gv-show-assembly');\n }\n\n const measureWidth = jQuery(`<div class=\"gv-chromosome\"><ul class=\"gv-label-container\"><li><span class=\"gv-name\">${name}</span></li></ul></div>`).appendTo(container);\n const labelWidth = pluginConf.karyotypeLabel === false ? 0 : measureWidth.find('.gv-name').outerWidth(true) + 10;\n\n measureWidth.remove();\n\n this.karyotype = new Genoverse({\n parent : this,\n container : chromosome,\n width : chromosome.width(),\n genome : this.genome,\n chr : this.chr,\n start : 1,\n end : this.chromosomeSize,\n isStatic : true,\n tracks : [\n Chromosome.extend({\n name : name,\n height : 20,\n featureHeight : 20,\n border : false,\n legend : false,\n unsortable : true,\n\n click: function (e) {\n const offset = this.container.parent().offset().left;\n const x = e.pageX - offset;\n const f = this.featurePositions.search({ x: x, y: 1, w: 1, h: 1 })[0];\n\n if (f) {\n if (e.type === 'mouseup') {\n if (!this.browser.parent.isStatic) {\n this.browser.parent.moveTo(f.chr, f.start, f.end, true);\n }\n } else if (this.hoverFeature !== f && !this.browser.hideTooltip) {\n this.container.tipsy('hide');\n\n if (f.label) {\n const left = offset + f.position[this.scale].start + f.position[this.scale].width / 2;\n\n this.container.attr('title', f.label[0]).tipsy({ trigger: 'manual', container: 'body' }).tipsy('show').data('tipsy').$tip.css('left', function () { return left - jQuery(this).width() / 2; });\n }\n\n this.hoverFeature = f;\n }\n }\n },\n\n addUserEventHandlers: function () {\n const track = this;\n\n this.base();\n\n this.container.on({\n mousemove : (e) => { track.click(e); },\n mouseout : (e) => {\n if (track.browser.viewPoint.is(e.relatedTarget) || track.browser.viewPoint.find(e.relatedTarget).length) {\n return true;\n }\n\n track.container.tipsy('hide');\n track.hoverFeature = false;\n },\n }, '.gv-image-container');\n\n // Don't allow zooming in and out on the karyotype image\n this.container.on('mousewheel', '.gv-image-container, .gv-selector', (e) => {\n e.stopPropagation();\n });\n },\n\n afterSetName: function () {\n this.label.css('lineHeight', `${this.label.height()}px`);\n },\n }),\n ],\n\n addUserEventHandlers: () => {},\n\n afterInit: function () {\n this.updatePosition();\n this.viewPoint.fadeIn();\n },\n\n afterAddTracks: function () {\n this.track = this.tracks[0];\n },\n\n afterAddDomElements: function () {\n const karyotype = this;\n const parent = this.parent;\n\n function hideTooltip() {\n karyotype.hideTooltip = true;\n karyotype.track.prop('container').tipsy('hide');\n }\n\n function updateLocation(e, ui) {\n karyotype.hideTooltip = false;\n\n const scale = karyotype.chromosomeSize / karyotype.width;\n const axis = e.type === 'resizestop' ? jQuery(this).data('ui-resizable').axis : undefined;\n const start = axis === 'e' ? parent.start : Math.max(Math.floor(ui.position.left * scale), 1);\n const end = axis === 'w' ? parent.end : e.type === 'dragstop' ? start + parent.length - 1 : Math.floor(ui.helper.outerWidth(true) * scale) + start;\n\n if (start !== parent.start || end !== parent.end) {\n parent.moveTo(karyotype.chr, start, end, true, e.type === 'dragstop');\n }\n }\n\n if (pluginConf.karyotypeLabel === false) {\n this.labelContainer.remove();\n this.labelContainer = jQuery();\n container.addClass('gv-no-label');\n } else {\n this.labelContainer.width(labelWidth);\n }\n\n this.viewPoint = jQuery('<div class=\"gv-karyotype-viewpoint-wrapper\"><div class=\"gv-karyotype-viewpoint\"></div></div>').appendTo(container).css({\n left : labelWidth,\n width : this.width - labelWidth,\n }).children().on({\n mousemove : (e) => { karyotype.track.controller.click(e); },\n mouseout : (e) => {\n const el = jQuery(e.relatedTarget);\n\n if (karyotype.viewPoint.is(el) || karyotype.viewPoint.find(el).length || (el.prop('nodeName') === 'IMG' && el.parent().is(karyotype.track.prop('imgContainers')[0]))) {\n return true;\n }\n\n karyotype.track.prop('container').tipsy('hide');\n karyotype.track.prop('hoverFeature', false);\n },\n });\n\n if (!parent.isStatic) {\n this.viewPoint.draggable({\n axis : 'x',\n containment : this.wrapper,\n start : hideTooltip,\n stop : updateLocation,\n }).resizable({\n handles : 'e, w',\n containment : 'parent',\n start : hideTooltip,\n stop : updateLocation,\n resize : function (e, ui) {\n ui.element.css('left', Math.max(0, ui.position.left));\n\n if (ui.position.left > 0) {\n ui.element.width(Math.min(ui.size.width, ui.element.parent().width() - ui.position.left));\n } else {\n ui.element.width(ui.size.width + ui.position.left);\n }\n },\n });\n }\n },\n\n updatePosition: function () {\n const left = this.parent.start * this.scale;\n const width = (this.parent.end * this.scale) - left;\n\n this.viewPoint.css({ left: left, width: width });\n },\n });\n\n if (this.loadedPlugins.controlPanel !== true) {\n jQuery('<li class=\"gv-unsortable\">').height((i, h) => h + container.height()).prependTo(this.labelContainer);\n }\n }\n\n function recreateKaryotype() {\n const container = this.karyotype.container.parent();\n\n this.karyotype.destroy();\n container.remove();\n\n createKaryotype.call(this);\n }\n\n this.on({\n afterInit: createKaryotype,\n\n afterSetRange: function () {\n if (this.karyotype) {\n this.karyotype.updatePosition();\n }\n },\n\n afterSetWidth: recreateKaryotype,\n\n afterMoveTo: function (chr) {\n if (this.karyotype && this.karyotype.chr !== chr) {\n recreateKaryotype.call(this);\n }\n },\n });\n};\n\nexport default { karyotype: plugin };\n"],"names":["karyotype","pluginConf","jQuery","this","createKaryotype","chromosome","container","html","insertBefore","wrapper","assemblyName","assembly","genomeName","name","showAssembly","chr","addClass","measureWidth","appendTo","labelWidth","karyotypeLabel","find","outerWidth","remove","Genoverse","parent","width","genome","start","end","chromosomeSize","isStatic","tracks","Chromosome","height","featureHeight","border","legend","unsortable","click","e","offset","left","x","pageX","f","featurePositions","search","y","w","h","type","browser","moveTo","hoverFeature","hideTooltip","tipsy","label","position","scale","attr","trigger","data","$tip","css","addUserEventHandlers","track","base","on","mousemove","mouseout","viewPoint","is","relatedTarget","length","stopPropagation","afterSetName","afterInit","updatePosition","fadeIn","afterAddTracks","afterAddDomElements","prop","updateLocation","ui","axis","undefined","Math","max","floor","helper","labelContainer","children","controller","el","draggable","containment","stop","resizable","handles","resize","element","min","size","loadedPlugins","controlPanel","i","prependTo","recreateKaryotype","destroy","call","afterSetRange","afterSetWidth","afterMoveTo"],"sourceRoot":""}