@molgenis/vip-report-template 2.7.2 → 3.0.0-beta2

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 (591) hide show
  1. package/.eslintignore +4 -0
  2. package/.eslintrc.js +16 -22
  3. package/.gitattributes +1 -0
  4. package/.husky/pre-commit +4 -0
  5. package/.prettierignore +4 -0
  6. package/.prettierrc.json +3 -0
  7. package/.travis.yml +14 -11
  8. package/README.md +7 -29
  9. package/index.html +12 -0
  10. package/package.json +42 -55
  11. package/src/Api.ts +12 -0
  12. package/src/App.tsx +101 -0
  13. package/src/__tests__/decisionTreeUtils.test.ts +75 -0
  14. package/src/__tests__/field.test.ts +107 -0
  15. package/src/__tests__/query.test.ts +156 -0
  16. package/src/__tests__/sortUtils.test.ts +83 -0
  17. package/src/__tests__/utils.test.ts +24 -0
  18. package/src/__tests__/viewUtils.test.ts +125 -0
  19. package/src/assets/sass/main.scss +113 -0
  20. package/src/components/Abbr.tsx +20 -0
  21. package/src/components/Anchor.tsx +12 -0
  22. package/src/components/Breadcrumb.tsx +33 -0
  23. package/src/components/Checkbox.tsx +32 -0
  24. package/src/components/ConsequenceTable.tsx +38 -0
  25. package/src/components/DatasetDropdown.tsx +48 -0
  26. package/src/components/Error.tsx +9 -0
  27. package/src/components/FieldHeader.tsx +26 -0
  28. package/src/components/GenomeBrowser.tsx +114 -0
  29. package/src/components/InfoCollapsablePane.tsx +68 -0
  30. package/src/components/Loader.tsx +5 -0
  31. package/src/components/SampleTable.tsx +118 -0
  32. package/src/components/SearchBox.tsx +44 -0
  33. package/src/components/Sort.tsx +58 -0
  34. package/src/components/VariantInfoNestedTable.tsx +117 -0
  35. package/src/components/VariantInfoTable.tsx +30 -0
  36. package/src/components/VariantSampleTable.tsx +56 -0
  37. package/src/components/VariantTable.tsx +71 -0
  38. package/src/components/VariantsSampleTable.tsx +87 -0
  39. package/src/components/VariantsTable.tsx +135 -0
  40. package/src/components/VcfHeaderRow.tsx +15 -0
  41. package/src/components/filter/Filter.tsx +37 -0
  42. package/src/components/filter/FilterCategorical.tsx +66 -0
  43. package/src/components/filter/FilterIntegerDp.tsx +24 -0
  44. package/src/components/filter/FilterIntegerVid.tsx +28 -0
  45. package/src/components/filter/FilterIntegerVim.tsx +24 -0
  46. package/src/components/filter/Filters.tsx +30 -0
  47. package/src/components/filter/InfoFilter.tsx +36 -0
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  49. package/src/components/filter/SampleFilters.tsx +44 -0
  50. package/src/components/filter/SamplesFilters.tsx +31 -0
  51. package/src/components/record/Allele.tsx +38 -0
  52. package/src/components/record/AlleleBreakend.tsx +5 -0
  53. package/src/components/record/AlleleMissing.tsx +5 -0
  54. package/src/components/record/AlleleNucs.tsx +49 -0
  55. package/src/components/record/AlleleSymbolic.tsx +5 -0
  56. package/src/components/record/Alt.tsx +17 -0
  57. package/src/components/record/Chrom.tsx +5 -0
  58. package/src/components/record/Filter.tsx +9 -0
  59. package/src/components/record/Format.tsx +31 -0
  60. package/src/components/record/Id.tsx +9 -0
  61. package/src/components/record/Info.tsx +53 -0
  62. package/src/components/record/Pager.tsx +64 -0
  63. package/src/components/record/Pos.tsx +5 -0
  64. package/src/components/record/Qual.tsx +5 -0
  65. package/src/components/record/RecordDownload.tsx +36 -0
  66. package/src/components/record/Ref.tsx +6 -0
  67. package/src/components/record/field/Field.tsx +20 -0
  68. package/src/components/record/field/FieldMultipleValue.tsx +22 -0
  69. package/src/components/record/field/FieldSingleValue.tsx +35 -0
  70. package/src/components/record/field/FieldValueCharacter.tsx +11 -0
  71. package/src/components/record/field/FieldValueFlag.tsx +11 -0
  72. package/src/components/record/field/FieldValueFloat.tsx +17 -0
  73. package/src/components/record/field/FieldValueInteger.tsx +11 -0
  74. package/src/components/record/field/FieldValueString.tsx +14 -0
  75. package/src/components/record/format/GenotypeField.tsx +63 -0
  76. package/src/components/record/info/ClinVar.tsx +37 -0
  77. package/src/components/record/info/Consequence.tsx +19 -0
  78. package/src/components/record/info/Gene.tsx +11 -0
  79. package/src/components/record/info/GnomAD.tsx +29 -0
  80. package/src/components/record/info/Hgvs.tsx +18 -0
  81. package/src/components/record/info/HpoTerm.tsx +12 -0
  82. package/src/components/record/info/PubMed.tsx +19 -0
  83. package/src/components/tree/DecisionTreeBoolMultiQuery.tsx +21 -0
  84. package/src/components/tree/DecisionTreeBoolQuery.tsx +22 -0
  85. package/src/components/tree/DecisionTreeNode.tsx +64 -0
  86. package/src/components/tree/DecisionTreeNodeBool.tsx +35 -0
  87. package/src/components/tree/DecisionTreeNodeBoolMulti.tsx +32 -0
  88. package/src/components/tree/DecisionTreeNodeCategorical.tsx +32 -0
  89. package/src/components/tree/DecisionTreeNodeExists.tsx +25 -0
  90. package/src/components/tree/DecisionTreeNodeLeaf.tsx +6 -0
  91. package/src/components/tree/DecisionTreeOutcomeNode.tsx +11 -0
  92. package/src/components/tree/DecisionTreePath.tsx +27 -0
  93. package/src/igv.d.ts +4 -1
  94. package/src/index.tsx +40 -0
  95. package/src/mocks/GRCh37/alignment.bam.blob +0 -0
  96. package/src/mocks/GRCh37/decisionTree.json +354 -0
  97. package/src/mocks/GRCh37/fasta/1-10042288-10042788.fasta.gz.blob +0 -0
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  133. package/src/mocks/GRCh37/fasta/Y-2655391-2655891.fasta.gz.blob +0 -0
  134. package/src/mocks/GRCh37/genes.txt.gz.blob +0 -0
  135. package/src/mocks/GRCh37/static.ts +192 -0
  136. package/src/mocks/GRCh37/vcf/family.vcf.blob +104 -0
  137. package/src/mocks/GRCh37/vcf/no_vep.vcf.blob +61 -0
  138. package/src/mocks/GRCh37/vcf/samples_0.vcf.blob +93 -0
  139. package/src/mocks/GRCh37/vcf/samples_1.vcf.blob +93 -0
  140. package/src/mocks/GRCh37/vcf/samples_100.vcf.blob +93 -0
  141. package/src/mocks/GRCh38/alignment.bam.blob +0 -0
  142. package/src/mocks/GRCh38/decisionTree.json +369 -0
  143. package/src/mocks/GRCh38/fasta/chr1-152548062-152548562.fasta.gz.blob +0 -0
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  177. package/src/mocks/static.ts +1636 -0
  178. package/src/mocks/utils.ts +16 -0
  179. package/src/store/index.tsx +169 -0
  180. package/src/utils/ApiUtils.ts +253 -0
  181. package/src/utils/decisionTreeUtils.ts +14 -0
  182. package/src/utils/field.ts +49 -0
  183. package/src/utils/query.ts +130 -0
  184. package/src/utils/sample.ts +5 -0
  185. package/src/utils/sortUtils.ts +65 -0
  186. package/src/utils/utils.ts +3 -0
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package/babel.config.js DELETED
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- module.exports = {
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- presets: ['@vue/cli-plugin-babel/preset']
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- };
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- module.exports = {
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- preset: '@vue/cli-plugin-unit-jest/presets/typescript-and-babel',
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- collectCoverage: true,
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- transformIgnorePatterns: ['node_modules/(?!(@molgenis|igv|d3*)|/)']
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- };
package/public/index.html DELETED
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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- <meta charset="utf-8">
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- <meta http-equiv="X-UA-Compatible" content="IE=edge">
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- <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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- <title>VCF Report</title>
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- <!-- blank embedded favicon -->
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- <link rel="icon" href="data:image/x-icon;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQEAYAAABPYyMiAAAABmJLR0T///////8JWPfcAAAACXBIWXMAAABIAAAASABGyWs+AAAAF0lEQVRIx2NgGAWjYBSMglEwCkbBSAcACBAAAeaR9cIAAAAASUVORK5CYII=" type="image/x-icon">
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- <script type="text/javascript">
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- window.onerror = msg => { alert(msg); };
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- window.onunhandledrejection = event => { alert('Uncaught (in promise) ' + event.reason); };
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- </script>
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- </head>
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- <body>
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- <div id="app"></div>
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- <!-- built files will be auto injected -->
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- </body>
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- </html>
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- sonar.organization=molgenis
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- sonar.projectKey=molgenis_vip-report-template
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- sonar.sourceEncoding=UTF-8
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- sonar.host.url=https://sonarcloud.io
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- sonar.javascript.lcov.reportPaths=coverage/lcov.info
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- sonar.exclusions=tests/**,src/i18n.ts,babel.config.js,jest.config.js,vue.config.js,src/main.ts,src/plugins/**,src/router/**,src/store/store.ts,src/mocks/**
package/src/App.vue DELETED
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- <template>
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- <div id="app">
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- <NavigationBar class="mb-3" />
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- <!--suppress HtmlUnknownBooleanAttribute -->
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- <b-container fluid>
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- <Alerts />
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- <router-view />
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- </b-container>
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- </div>
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- </template>
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-
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- <script lang="ts">
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- import { mapActions } from 'vuex';
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-
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- import Alerts from '@/components/Alerts.vue';
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- import NavigationBar from '@/components/NavigationBar.vue';
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- import Vue from 'vue';
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-
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- export default Vue.extend({
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- components: {
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- Alerts,
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- NavigationBar
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- },
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- methods: {
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- ...mapActions(['validateRecords', 'validateSamples'])
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- },
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- async created() {
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- await this.validateRecords();
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- await this.validateSamples();
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- }
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- });
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- </script>
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-
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- <!--suppress CssUnusedSymbol -->
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- <style>
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- html {
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- font-size: 12px;
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- }
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-
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- .btn-xs {
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- padding: 0.125rem 0.375rem;
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- font-size: 0.75rem;
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- }
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-
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- td {
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- white-space: nowrap;
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- }
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-
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- td.compact {
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- padding: 0.25rem;
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- width: 0;
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- }
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-
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- td.input {
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- padding-top: 0rem;
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- padding-bottom: 0rem;
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- }
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-
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- .nuc {
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- width: 0.9rem;
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- display: inline-block;
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- text-align: center;
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- }
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-
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- .nuc-a {
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- background-color: #90ee90;
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- }
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-
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- .nuc-c {
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- background-color: #b0c4de;
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- }
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-
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- .nuc-t {
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- background-color: #eea2ad;
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- }
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-
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- .nuc-g {
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- background-color: #ffec8b;
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- }
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-
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- /* missing */
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- .nuc-m {
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- background-color: #e3e3e3;
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- }
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-
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- .modal-container {
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- overflow: auto;
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- }
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-
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- .nav-link {
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- word-break: break-all;
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- }
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-
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- .nav-vertical {
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- max-height: calc(100vh - 9rem);
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- overflow-y: auto;
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- flex-wrap: nowrap;
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- }
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-
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- .igv-root {
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- margin-left: 0;
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- margin-right: 0;
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- }
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-
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- .btn-link {
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- padding: 0;
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- }
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-
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- textarea {
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- font-family: monospace;
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- }
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-
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- /* below bootstrap zindex-dropdown:1000 */
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- .igv-ui-popover {
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- z-index: 999;
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- }
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-
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- /* Decision tree styling */
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- .tree-node {
120
- fill: #6c757d;
121
- }
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-
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- .tree-exit-node {
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- fill: #007bff;
125
- }
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-
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- .tree-exit-node-label {
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- fill: #fff;
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- }
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-
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- .tree-node-label {
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- fill: #fff;
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- }
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-
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- .tree-edge-label {
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- fill: #000;
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- }
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-
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- .d3-tree-visualisation {
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- font-size: 0.8rem;
141
- }
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- .d3-tree-visualisation > svg {
143
- border-color: #000;
144
- border-style: solid;
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- border-width: thin;
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- display: block;
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- margin: auto;
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- }
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- </style>
package/src/components/Alerts.vue DELETED
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- <template>
2
- <div v-if="alerts.length > 0">
3
- <b-alert
4
- v-for="(alert, index) in alerts"
5
- :key="index"
6
- show
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- dismissible
8
- :variant="alert.type"
9
- @dismissed="removeAlert(alert)"
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- >
11
- {{ $t(alert.messageId, alert.messageArgs) }}
12
- </b-alert>
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- </div>
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- </template>
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-
16
- <script lang="ts">
17
- import Vue from 'vue';
18
- import { mapActions, mapState } from 'vuex';
19
-
20
- export default Vue.extend({
21
- computed: {
22
- ...mapState(['alerts'])
23
- },
24
- methods: {
25
- ...mapActions(['removeAlert'])
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- }
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- });
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- </script>
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- <template>
2
- <span>
3
- <span v-if="allele === null || allele === undefined" :class="getNucClasses('m')">?</span>
4
- <span
5
- v-else-if="
6
- (allele.startsWith('<') && allele.endsWith('>')) || allele.indexOf(']') !== -1 || allele.indexOf('[') !== -1
7
- "
8
- >{{ allele }}</span
9
- >
10
- <span v-else v-for="(nuc, index) in nucs" :key="index" :class="getNucClasses(nuc)">{{ nuc }}</span>
11
- </span>
12
- </template>
13
-
14
- <script lang="ts">
15
- import Vue from 'vue';
16
-
17
- export default Vue.extend({
18
- props: {
19
- allele: String,
20
- abbreviate: {
21
- type: Boolean,
22
- default: true
23
- }
24
- },
25
- computed: {
26
- nucs() {
27
- let nucleotides = this.allele.split('');
28
- if (this.abbreviate && nucleotides.length > 4) {
29
- const lastNuc = nucleotides[nucleotides.length - 1];
30
- nucleotides = nucleotides.slice(0, 2);
31
- nucleotides.push('\u2026'); // ellipsis
32
- nucleotides.push(lastNuc);
33
- }
34
- return nucleotides;
35
- }
36
- },
37
- methods: {
38
- getNucClasses(base: string): { [key: string]: boolean } {
39
- const classes: { [key: string]: boolean } = { nuc: true };
40
- // ellipsis
41
- if (base !== '*' && base !== '\u2026') {
42
- classes['nuc-' + base.toLocaleLowerCase()] = true;
43
- }
44
- return classes;
45
- }
46
- }
47
- });
48
- </script>
package/src/components/Anchor.vue DELETED
@@ -1,16 +0,0 @@
1
- <template>
2
- <a :href="href" target="_blank" rel="noopener noreferrer nofollow">
3
- {{ text }}
4
- </a>
5
- </template>
6
-
7
- <script lang="ts">
8
- import Vue, { PropType } from 'vue';
9
-
10
- export default Vue.extend({
11
- props: {
12
- href: String as PropType<string>,
13
- text: [String, Number, Boolean] as PropType<string | number | boolean>
14
- }
15
- });
16
- </script>