genoverse 3.2.0

package/.eslintrc.js

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+const noRestrictedProperies = require('eslint-config-airbnb-base/rules/best-practices').rules['no-restricted-properties'].filter(
+  rule => !(
+    // Disable options which force code that doesn't work in IE11
+    (rule.object === 'Math'   && rule.property === 'pow')  ||
+    (rule.object === 'window' && rule.property === 'isNaN')
+  )
+);
+
+module.exports = {
+  env: {
+    browser : true,
+    jquery  : true
+  },
+  extends : [
+    'airbnb-base',
+  ],
+  globals: {
+    Base         : true,
+    Genoverse    : true,
+    RTree        : true,
+    dallianceLib : true,
+    VCFReader    : true,
+    BWReader     : true
+  },
+  ignorePatterns: [
+    '.eslintrc.js',
+    'node_modules',
+    'index.js',
+    '**/*.min.js',
+    'js/lib/**/*.js'
+  ],
+  overrides: [
+    {
+      files : [ 'js/**/*.js' ],
+      plugins : [ 'es' ],
+      extends : [
+        'airbnb-base',
+        'plugin:es/no-new-in-es2018',
+        'plugin:es/no-new-in-es2017',
+        'plugin:es/no-new-in-es2016',
+        'plugin:es/no-new-in-es2015'
+      ],
+      parserOptions: {
+        parser      : 'espree',
+        ecmaVersion : 5,
+        sourceType  : 'script'
+      },
+      rules: {
+        'linebreak-style'       : [ 'error', 'unix' ],
+        'comma-dangle'          : [ 'error', 'never' ],
+        'quotes'                : [ 'warn', 'single', { avoidEscape: true }], // be more permissive than airbnb - allow 'double quotes containing 'singles''
+        'object-shorthand'      : [ 'error', 'never' ],
+        'array-bracket-spacing' : [ 'warn', 'always', {
+          objectsInArrays : false,
+          arraysInArrays  : false
+        }],
+        'object-curly-newline': [ 'error', {
+          ObjectExpression : { multiline: true, consistent: true },
+          ObjectPattern    : { multiline: true, consistent: true }
+        }],
+        'key-spacing': [ 'error', {
+          singleLine : { beforeColon: false, afterColon: true },
+          multiLine  : { beforeColon: false, afterColon: true },
+          align      : { beforeColon: true,  afterColon: true, on: 'colon' },
+        }],
+        'quote-props'                         : 'off',
+        'no-multi-spaces'                     : 'off',
+        'prefer-destructuring'                : 'off',
+        'no-prototype-builtins'               : 'off',
+        'no-nested-ternary'                   : 'off',
+        'no-plusplus'                         : 'off',
+        'template-curly-spacing'              : 'off',
+        'no-var'                              : 'off',
+        'one-var'                             : 'off',
+        'one-var-declaration-per-line'        : 'off',
+        'vars-on-top'                         : 'off',
+        'func-names'                          : 'off',
+        'prefer-arrow-callback'               : 'off',
+        'prefer-spread'                       : 'off',
+        'prefer-template'                     : 'off',
+        'prefer-rest-params'                  : 'off',
+        'no-param-reassign'                   : 'off',
+        'no-multi-assign'                     : 'off',
+        'no-underscore-dangle'                : 'off',
+        'no-empty'                            : 'off',
+        'switch-colon-spacing'                : 'off',
+        'max-len'                             : 'off',
+        'no-continue'                         : 'off',
+        'consistent-return'                   : 'off',
+        'operator-linebreak'                  : 'off',
+        'guard-for-in'                        : 'off',
+        'no-restricted-syntax'                : 'off',
+        'no-restricted-globals'               : 'off',
+        'function-paren-newline'              : 'off',
+        'no-fallthrough'                      : 'off',
+        'no-bitwise'                          : 'off',
+        'no-cond-assign'                      : 'off',
+        'no-new'                              : 'off',
+        'newline-per-chained-call'            : 'off',
+        'prefer-exponentiation-operator'      : 'off',
+        'no-restricted-properties'            : noRestrictedProperies
+      }
+    },
+    {
+      files : [ '**/*.js' ],
+      excludedFiles: 'js/**/*.js',
+      env   : {
+        es6: true,
+      },
+      plugins : [ 'align-assignments' ],
+      globals : {
+        jest       : true,
+        describe   : true,
+        it         : true,
+        expect     : true,
+        fail       : true,
+        beforeAll  : true,
+        afterAll   : true,
+        afterEach  : true,
+        beforeEach : true,
+      },
+      rules: {
+        'align-assignments/align-assignments' : [ 'error', { requiresOnly: false }],
+        'padding-line-between-statements'     : [
+          'error', ...[
+            [ '*', [ 'multiline-block-like', 'return', 'break', 'export', 'throw', 'cjs-export' ]],
+            [ '*', [ 'cjs-import', 'import', 'const', 'let', 'var' ]],
+            [[ 'multiline-block-like', 'return', 'break', 'export', 'throw', 'cjs-export' ], '*' ],
+            [[ 'cjs-import', 'import', 'const', 'let', 'var' ], '*' ],
+            [ 'cjs-import',       'cjs-import', 'any' ],
+            [ 'import',           'import', 'any' ],
+            [ 'singleline-const', 'const', 'any' ],
+            [ 'singleline-let',   'let', 'any' ],
+            [ 'singleline-var',   'var', 'any' ],
+            [ 'expression',       'expression', 'any' ],
+          ].map(
+            ([ prev, next = '*', blankLine = 'always' ]) => ({ prev, next, blankLine })
+          ),
+        ],
+        'max-len'                    : 'off',
+        'no-multi-spaces'            : 'off',
+        'no-multi-assign'            : 'off',
+        'no-nested-ternary'          : 'off',
+        'no-prototype-builtins'      : 'off',
+        'no-plusplus'                : 'off',
+        'operator-linebreak'         : 'off',
+        'prefer-destructuring'       : 'off',
+        'quote-props'                : 'off',
+        'template-curly-spacing'     : 'off',
+        'yoda'                       : 'off',
+        'no-underscore-dangle'       : 'off',
+        'newline-per-chained-call'   : 'off',
+        'default-param-last'         : 'off',
+        'no-promise-executor-return' : 'off',
+        'no-continue'                : 'off',
+        'no-fallthrough'             : 'off',
+        'no-bitwise'                 : 'off',
+        'func-names'                 : 'off',
+        'no-param-reassign'          : 'off',
+
+        'array-bracket-spacing' : [ 'warn', 'always', { objectsInArrays: false, arraysInArrays: false }],
+        'quotes'                : [ 'warn', 'single', { avoidEscape: true }],
+
+        'arrow-parens'                   : [ 'error', 'as-needed', { requireForBlockBody: true }],
+        'function-paren-newline'         : [ 'error', 'consistent' ],
+        'function-call-argument-newline' : [ 'error', 'consistent' ],
+        'linebreak-style'                : [ 'error', 'unix' ],
+        'object-shorthand'               : [ 'error', 'consistent' ],
+
+        'comma-dangle': [ 'error', {
+          arrays    : 'always-multiline',
+          objects   : 'always-multiline',
+          imports   : 'always-multiline',
+          exports   : 'always-multiline',
+          functions : 'never',
+        }],
+        'key-spacing': [ 'error', {
+          singleLine : { beforeColon: false, afterColon: true },
+          multiLine  : { beforeColon: false, afterColon: true },
+          align      : { beforeColon: true,  afterColon: true, on: 'colon' },
+        }],
+        'object-curly-newline': [ 'error', {
+          ObjectExpression : { multiline: true, consistent: true },
+          ObjectPattern    : { multiline: true, consistent: true },
+        }],
+        'import/no-extraneous-dependencies' : [ 'error' ],
+        'import/order'                      : [ 'error', {
+          alphabetize : { order: 'asc' },
+          groups      : [ 'builtin', 'external', 'internal', 'parent', 'sibling' ],
+        }],
+
+        'no-restricted-globals'    : [ 'error', 'event', 'isFinite' ],
+        'no-restricted-properties' : noRestrictedProperies,
+      }
+    },
+  ]
+};

package/.github/workflows/test.yml

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+name: test
+
+on:
+  push:
+    branches:
+      - gh-pages
+      - master
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [14.x]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: npm install and test
+      uses: actions/setup-node@v1
+      with:
+        node-version: ${{ matrix.node-version }}
+    - run: npm install
+    - run: npm test

package/LICENSE.TXT

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+Copyright (c) 2011 Genome Research Ltd.
+Author: Evgeny Bragin
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

package/README.md

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+# Genoverse [![Build Status](https://github.com/wtsi-web/Genoverse/actions/workflows/test.yml/badge.svg)](https://github.com/wtsi-web/Genoverse/actions)
+
+Genoverse is a portable, customizable, back-end independent JavaScript and HTML5 based genome browser which allows the user to explore data in a dynamic and interactive manner.
+
+Data is visualized in the browser, meaning Genoverse can be installed on any website and show data from a wide range of online or local sources.
+
+Genoverse works with a variety of formats, such as XML, JSON, BED, VCF, GFF, GFF3 or delimited text files, and can be customized to parse and display any data source as required.
+
+If you have any questions, please raise an issue at https://github.com/wtsi-web/Genoverse
+
+Example: https://wtsi-web.github.io/Genoverse/

package/css/controlPanel.css

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+.gv-control-panel-plugin table.gv {
+  position: relative;
+  margin-bottom: 30px;
+  border-collapse: separate;
+}
+
+.gv-control-panel-plugin table.gv td {
+  padding: 0;
+  color: white;
+  vertical-align: top;
+}
+
+.gv-control-panel-plugin .gv-panel {
+  height: 100%;
+  background-color: #5F8CB0;
+  border: 1px solid #1C5380;
+  box-shadow: 0 0 1px rgba(255, 255, 255, 0.4) inset, 0 1px 3px rgba(0, 0, 0, 0.1), -2px 0 2px rgba(0, 0, 0, 0.1);
+}
+
+.gv-control-panel-plugin .gv-panel div {
+  white-space: nowrap;
+}
+
+.gv-control-panel-plugin .gv-panel button {
+  background: none;
+  border: none;
+  border-bottom: 1px solid #1C5380;
+  color: #E2E9EF;
+  text-shadow: 0 1px 0 rgba(0, 0, 0, 0.75);
+  width: 30px;
+  height: 50px;
+  font-family: inherit;
+  font-size: 18px;
+  line-height: 20px;
+  padding: 2px;
+  margin: 0;
+}
+
+.gv-control-panel-plugin .gv-panel button:only-child {
+  width: 100%;
+}
+
+.gv-control-panel-plugin .gv-panel div.gv-button-set > button:not(:first-child) {
+  border-left: 1px solid #1C5380;
+}
+
+.gv-control-panel-plugin .gv-panel button.gv-button-large {
+  font-size: 25px;
+}
+
+.gv-control-panel-plugin .gv-panel div.gv-button-set:not(:first-child) > button {
+  box-shadow: 0 1px 1px rgba(255, 255, 255, 0.12) inset;
+}
+
+.gv-control-panel-plugin .gv-panel div.gv-button-set:last-child {
+  box-shadow: 0 1px 0 rgba(255, 255, 255, 0.12);
+}
+
+.gv-control-panel-plugin .gv-panel button:hover {
+  background-color: rgba(255, 255, 255, 0.1);
+  color: #FFFFFF;
+  cursor: pointer;
+}
+
+.gv-control-panel-plugin .gv-panel button:active,
+.gv-control-panel-plugin .gv-panel button.gv-active {
+  border-top: none;
+  background-color: rgba(6, 54, 95, 0.35);
+  box-shadow: 0 0 1px rgba(6, 54, 95, 0.8) inset !important;
+}
+
+.gv-control-panel-plugin .gv-panel-right {
+  background-image: -webkit-linear-gradient(left, #5F8CB0, #4A7496);
+  background-image: -moz-linear-gradient(left center, #5F8CB0, #4A7496);
+  border-radius: 0 5px 5px 0;
+  border-left: 0;
+}
+
+.gv-control-panel-plugin .gv-panel-right button.gv-wheel-zoom {
+  font-weight: bold;
+}
+
+.gv-control-panel-plugin .gv-panel-right button.gv-drag-select i {
+  border: 1px dashed #FFF;
+  padding: 0 5px;
+  box-shadow: 0px 0px 1px #FFF inset, 0px 1px 3px rgba(0, 0, 0, 0.1), 2px 2px rgba(0, 0, 0, 0.2);
+}
+
+.gv-control-panel-plugin .gv-panel-left {
+  background-image: -webkit-linear-gradient(right, #5F8CB0, #4A7496);
+  background-image: -moz-linear-gradient(right center, #5F8CB0, #4A7496);
+  border-radius: 5px 0 0 5px;
+  border-right: 0;
+}
+
+.gv-control-panel-plugin .gv-panel-left .gv-label-container {
+  border: 0;
+  box-shadow: none;
+  background: none;
+}
+
+.gv-control-panel-plugin td.gv-canvas-container {
+  border: 1px solid #000;
+}
+
+.gv-control-panel-plugin .gv-karyotype-container {
+  border-width: 0 0 1px!important;
+}
+
+.gv-control-panel-plugin .gv-canvas-container .gv-wrapper {
+  border: 0;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu {
+  top: 70px;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu .gv-close {
+  font-size: 20px;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu .gv-menu-content {
+  font-size: 13px;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu table {
+  margin: 0 0 10px;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu td {
+  padding: 5px 10px!important;
+  vertical-align: top;
+  width: 50%;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu tr:first-child td {
+  font-weight: bold;
+  white-space: nowrap;
+  padding: 5px 30px 5px 10px;
+  margin-bottom: 5px;
+  background: rgba(6, 54, 95, 0.35);
+  line-height: normal;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu tr:first-child td:last-child {
+  border-radius: 0 12px 0 0;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu tr td:first-child {
+  padding-right: 50px!important;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu .gv-current-tracks.ui-sortable {
+  cursor: move;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu .gv-current-tracks-instructions {
+  font-style: italic;
+  margin-bottom: 10px;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu .gv-remove-track,
+.gv-control-panel-plugin .gv-tracks-menu .gv-add-track {
+  font-size: 14px;
+  margin: 2px 5px 0 0;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu input {
+  margin-bottom: 10px;
+  width: 200px;
+}
+
+.gv-control-panel-plugin .gv-tracks-menu .gv-tracks-menu-reset {
+  font-style: italic;
+  margin-top: 10px;
+}
+
+.gv-control-panel-plugin .gv-tracks-library-category {
+  margin-bottom: 10px;
+}
+
+.gv-control-panel-plugin .gv-tracks-library-category:last-child {
+  margin-bottom: 0px;
+}
+
+.gv-control-panel-plugin .gv-tracks-library-category .gv-tracks-library-category-header {
+  font-weight: bold;
+}
+
+.gv-control-panel-plugin .gv-powered-by {
+  position: absolute;
+  right: 0;
+  bottom: -16px;
+  font-size: 10px;
+  color: black;
+}
+
+.gv-control-panel-plugin .gv-powered-by a {
+  font-weight: bold;
+}

package/css/fileDrop.css

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+.gv-file-drop {
+  position: absolute;
+  display: block;
+  background-color: rgba(255,255,255,0.7);
+  border: 10px dashed rgb(111,111,111);
+  border-radius: 11px;
+  z-index: 10;
+  right: 0;
+  bottom: 0;
+  top: 0;
+  left: 0;
+}
+
+.gv-file-drop-total-overlay {
+  display: block;
+  position: absolute;
+  top: 0;
+  left: 0;
+  height: 100%;
+  width: 100%;
+  z-index: 1000000;
+}

package/css/font-awesome.css

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+@import url(../fontawesome/css/fontawesome.min.css);
+@import url(../fontawesome/css/regular.min.css);
+@import url(../fontawesome/css/solid.min.css);

package/css/fullscreen.css

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+.genoverse.gv-fullscreen {
+  overflow-y: scroll;
+}
+
+.genoverse.gv-fullscreen table.gv {
+  background: #FFF;
+  margin-bottom: 0;
+}
+
+.genoverse.gv-fullscreen .gv-powered-by {
+  display: none;
+}
+
+.gv-control-panel-plugin .gv-panel-right .gv-fullscreen-button i {
+  width: 30px;
+  padding: 5px;
+  border: 1px solid #FFF;
+  box-shadow: 0px 0px 1px #FFF inset, 0px 1px 3px rgba(0, 0, 0, 0.1), 2px 2px rgba(0, 0, 0, 0.2);
+}