@sjcrh/proteinpaint-client 2.63.0 → 2.63.2

package/dist/{app-f91922b4.js → app-71453429.js}

@@ -1 +1 @@
-function e(e,t){if(t===void 0)t={};var n=t.insertAt;if(!e||typeof document==="undefined"){return}var o=document.head||document.getElementsByTagName("head")[0];var i=document.createElement("style");i.type="text/css";if(n==="top"){if(o.firstChild){o.insertBefore(i,o.firstChild)}else{o.appendChild(i)}}else{o.appendChild(i)}if(i.styleSheet){i.styleSheet.cssText=e}else{i.appendChild(document.createTextNode(e))}}var t='\n/**\n * Render the `main` element consistently in IE.\n */\n\n.sja_root_holder main, .sja_menu_div main, .sja_pane main {\n  display: block;\n}\n\n/**\n * Correct the font size and margin on `h1` elements within `section` and\n * `article` contexts in Chrome, Firefox, and Safari.\n */\n\n.sja_root_holder h1, .sja_menu_div h1, .sja_pane h1 {\n  font-size: 2em;\n  margin: 0.67em 0;\n}\n\n/* Grouping content\n   ========================================================================== */\n\n/**\n * 1. Add the correct box sizing in Firefox.\n * 2. Show the overflow in Edge and IE.\n */\n\n.sja_root_holder hr, .sja_menu_div hr, .sja_pane hr {\n  box-sizing: content-box; /* 1 */\n  height: 0; /* 1 */\n  overflow: visible; /* 2 */\n}\n\n/**\n * 1. Correct the inheritance and scaling of font size in all browsers.\n * 2. Correct the odd `em` font sizing in all browsers.\n */\n\n.sja_root_holder pre, .sja_menu_div pre, .sja_pane pre {\n  font-family: monospace, monospace; /* 1 */\n  font-size: 1em; /* 2 */\n}\n\n/* Text-level semantics\n   ========================================================================== */\n\n/**\n * Remove the gray background on active links in IE 10.\n */\n\n.sja_root_holder a, .sja_menu_div a, .sja_pane a {\n  background-color: transparent;\n}\n\n/**\n * 1. Remove the bottom border in Chrome 57-\n * 2. Add the correct text decoration in Chrome, Edge, IE, Opera, and Safari.\n */\n\n.sja_root_holder abbr[title], .sja_menu_div abbr[title], .sja_pane abbr[title] {\n  border-bottom: none; /* 1 */\n  text-decoration: underline; /* 2 */\n  text-decoration: underline dotted; /* 2 */\n}\n\n/**\n * Add the correct font weight in Chrome, Edge, and Safari.\n */\n\n.sja_root_holder b, .sja_menu_div b, .sja_pane b,\n.sja_root_holder strong, .sja_menu_div strong, .sja_pane strong {\n  font-weight: bolder;\n}\n\n/**\n * 1. Correct the inheritance and scaling of font size in all browsers.\n * 2. Correct the odd `em` font sizing in all browsers.\n */\n\n.sja_root_holder code, .sja_menu_div code, .sja_pane code,\n.sja_root_holder kbd, .sja_menu_div kbd, .sja_pane kbd,\n.sja_root_holder samp, .sja_menu_div samp, .sja_pane samp {\n  font-family: monospace, monospace; /* 1 */\n  font-size: 1em; /* 2 */\n}\n\n/**\n * Add the correct font size in all browsers.\n */\n\n.sja_root_holder small, .sja_menu_div small, .sja_pane small {\n  font-size: 80%;\n}\n\n/**\n * Prevent `sub` and `sup` elements from affecting the line height in\n * all browsers.\n */\n\n.sja_root_holder sub, .sja_menu_div sub, .sja_pane sub,\n.sja_root_holder sup, .sja_menu_div sup, .sja_pane sup {\n  font-size: 75%;\n  line-height: 0;\n  position: relative;\n  vertical-align: baseline;\n}\n\n.sja_root_holder sub, .sja_menu_div sub, .sja_pane sub {\n  bottom: -0.25em;\n}\n\n.sja_root_holder sup, .sja_menu_div sup, .sja_pane sup {\n  top: -0.5em;\n}\n\n/* Embedded content\n   ========================================================================== */\n\n/**\n * Remove the border on images inside links in IE 10.\n */\n\n.sja_root_holder img, .sja_menu_div img, .sja_pane img {\n  border-style: none;\n}\n\n/* Forms\n   ========================================================================== */\n\n/**\n * 1. Change the font styles in all browsers.\n * 2. Remove the margin in Firefox and Safari.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder input, .sja_menu_div input, .sja_pane input,\n.sja_root_holder optgroup, .sja_menu_div optgroup, .sja_pane optgroup,\n.sja_root_holder select, .sja_menu_div select, .sja_pane select,\n.sja_root_holder textarea, .sja_menu_div textarea, .sja_pane textarea {\n  font-family: inherit; /* 1 */\n  font-size: 100%; /* 1 */\n  line-height: 1.15; /* 1 */\n  margin: 0; /* 2 */\n}\n\n/**\n * Show the overflow in IE.\n * 1. Show the overflow in Edge.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder input  /* 1 */, .sja_menu_div input  /* 1 */, .sja_pane input  /* 1 */ {\n  overflow: visible;\n}\n\n/**\n * Remove the inheritance of text transform in Edge, Firefox, and IE.\n * 1. Remove the inheritance of text transform in Firefox.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder select  /* 1 */, .sja_menu_div select  /* 1 */, .sja_pane select  /* 1 */ {\n  text-transform: none;\n}\n\n/**\n * Correct the inability to style clickable types in iOS and Safari.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder [type="button"], .sja_menu_div [type="button"], .sja_pane [type="button"],\n.sja_root_holder [type="reset"], .sja_menu_div [type="reset"], .sja_pane [type="reset"],\n.sja_root_holder [type="submit"], .sja_menu_div [type="submit"], .sja_pane [type="submit"] {\n  -webkit-appearance: button;\n}\n\n/**\n * Remove the inner border and padding in Firefox.\n */\n\n.sja_root_holder button::-moz-focus-inner, .sja_menu_div button::-moz-focus-inner, .sja_pane button::-moz-focus-inner,\n.sja_root_holder [type="button"]::-moz-focus-inner, .sja_menu_div [type="button"]::-moz-focus-inner, .sja_pane [type="button"]::-moz-focus-inner,\n.sja_root_holder [type="reset"]::-moz-focus-inner, .sja_menu_div [type="reset"]::-moz-focus-inner, .sja_pane [type="reset"]::-moz-focus-inner,\n.sja_root_holder [type="submit"]::-moz-focus-inner, .sja_menu_div [type="submit"]::-moz-focus-inner, .sja_pane [type="submit"]::-moz-focus-inner {\n  border-style: none;\n  padding: 0;\n}\n\n/**\n * Restore the focus styles unset by the previous rule.\n */\n\n.sja_root_holder button:-moz-focusring, .sja_menu_div button:-moz-focusring, .sja_pane button:-moz-focusring,\n.sja_root_holder [type="button"]:-moz-focusring, .sja_menu_div [type="button"]:-moz-focusring, .sja_pane [type="button"]:-moz-focusring,\n.sja_root_holder [type="reset"]:-moz-focusring, .sja_menu_div [type="reset"]:-moz-focusring, .sja_pane [type="reset"]:-moz-focusring,\n.sja_root_holder [type="submit"]:-moz-focusring, .sja_menu_div [type="submit"]:-moz-focusring, .sja_pane [type="submit"]:-moz-focusring {\n  outline: 1px dotted ButtonText;\n}\n\n/**\n * Correct the padding in Firefox.\n */\n\n.sja_root_holder fieldset, .sja_menu_div fieldset, .sja_pane fieldset {\n  padding: 0.35em 0.75em 0.625em;\n}\n\n/**\n * 1. Correct the text wrapping in Edge and IE.\n * 2. Correct the color inheritance from `fieldset` elements in IE.\n * 3. Remove the padding so developers are not caught out when they zero out\n *    `fieldset` elements in all browsers.\n */\n\n.sja_root_holder legend, .sja_menu_div legend, .sja_pane legend {\n  box-sizing: border-box; /* 1 */\n  color: inherit; /* 2 */\n  display: table; /* 1 */\n  max-width: 100%; /* 1 */\n  padding: 0; /* 3 */\n  white-space: normal; /* 1 */\n}\n\n/**\n * Add the correct vertical alignment in Chrome, Firefox, and Opera.\n */\n\n.sja_root_holder progress, .sja_menu_div progress, .sja_pane progress {\n  vertical-align: baseline;\n}\n\n/**\n * Remove the default vertical scrollbar in IE 10+.\n */\n\n.sja_root_holder textarea, .sja_menu_div textarea, .sja_pane textarea {\n  overflow: auto;\n}\n\n/**\n * 1. Add the correct box sizing in IE 10.\n * 2. Remove the padding in IE 10.\n */\n\n.sja_root_holder [type="checkbox"], .sja_menu_div [type="checkbox"], .sja_pane [type="checkbox"],\n.sja_root_holder [type="radio"], .sja_menu_div [type="radio"], .sja_pane [type="radio"] {\n  box-sizing: border-box; /* 1 */\n  padding: 0; /* 2 */\n}\n\n/**\n * Correct the cursor style of increment and decrement buttons in Chrome.\n */\n\n.sja_root_holder [type="number"]::-webkit-inner-spin-button, .sja_menu_div [type="number"]::-webkit-inner-spin-button, .sja_pane [type="number"]::-webkit-inner-spin-button,\n.sja_root_holder [type="number"]::-webkit-outer-spin-button, .sja_menu_div [type="number"]::-webkit-outer-spin-button, .sja_pane [type="number"]::-webkit-outer-spin-button {\n  height: auto;\n}\n\n/**\n * 1. Correct the odd appearance in Chrome and Safari.\n * 2. Correct the outline style in Safari.\n */\n\n.sja_root_holder [type="search"], .sja_menu_div [type="search"], .sja_pane [type="search"] {\n  -webkit-appearance: textfield; /* 1 */\n  outline-offset: -2px; /* 2 */\n}\n\n/**\n * Remove the inner padding in Chrome and Safari on macOS.\n */\n\n.sja_root_holder [type="search"]::-webkit-search-decoration, .sja_menu_div [type="search"]::-webkit-search-decoration, .sja_pane [type="search"]::-webkit-search-decoration {\n  -webkit-appearance: none;\n}\n\n/**\n * 1. Correct the inability to style clickable types in iOS and Safari.\n * 2. Change font properties to `inherit` in Safari.\n */\n\n.sja_root_holder ::-webkit-file-upload-button, .sja_menu_div ::-webkit-file-upload-button, .sja_pane ::-webkit-file-upload-button {\n  -webkit-appearance: button; /* 1 */\n  font: inherit; /* 2 */\n}\n\n/* Interactive\n   ========================================================================== */\n\n/*\n * Add the correct display in Edge, IE 10+, and Firefox.\n */\n\n.sja_root_holder details, .sja_menu_div details, .sja_pane details {\n  display: block;\n}\n\n/*\n * Add the correct display in all browsers.\n */\n\n.sja_root_holder summary, .sja_menu_div summary, .sja_pane summary {\n  display: list-item;\n}\n\n/* Misc\n   ========================================================================== */\n\n/**\n * Add the correct display in IE 10+.\n */\n\n.sja_root_holder template, .sja_menu_div template, .sja_pane template {\n  display: none;\n}\n\n/**\n * Add the correct display in IE 10.\n */\n\n.sja_root_holder [hidden], .sja_menu_div [hidden], .sja_pane [hidden] {\n  display: none;\n}';e(t);var n="pre code.hljs{display:block;overflow-x:auto;padding:1em}code.hljs{padding:3px 5px}/*!\n  Theme: GitHub\n  Description: Light theme as seen on github.com\n  Author: github.com\n  Maintainer: @Hirse\n  Updated: 2021-05-15\n\n  Outdated base version: https://github.com/primer/github-syntax-light\n  Current colors taken from GitHub's CSS\n*/.hljs{color:#24292e;background:#fff}.hljs-doctag,.hljs-keyword,.hljs-meta .hljs-keyword,.hljs-template-tag,.hljs-template-variable,.hljs-type,.hljs-variable.language_{color:#d73a49}.hljs-title,.hljs-title.class_,.hljs-title.class_.inherited__,.hljs-title.function_{color:#6f42c1}.hljs-attr,.hljs-attribute,.hljs-literal,.hljs-meta,.hljs-number,.hljs-operator,.hljs-selector-attr,.hljs-selector-class,.hljs-selector-id,.hljs-variable{color:#005cc5}.hljs-meta .hljs-string,.hljs-regexp,.hljs-string{color:#032f62}.hljs-built_in,.hljs-symbol{color:#e36209}.hljs-code,.hljs-comment,.hljs-formula{color:#6a737d}.hljs-name,.hljs-quote,.hljs-selector-pseudo,.hljs-selector-tag{color:#22863a}.hljs-subst{color:#24292e}.hljs-section{color:#005cc5;font-weight:700}.hljs-bullet{color:#735c0f}.hljs-emphasis{color:#24292e;font-style:italic}.hljs-strong{color:#24292e;font-weight:700}.hljs-addition{color:#22863a;background-color:#f0fff4}.hljs-deletion{color:#b31d28;background-color:#ffeef0}";e(n);var o="/*\n    see client/generateScopedCss.js on how to generate style-normalize-*.css\n\n    also see a TODO comment in client/src/app.js, of dynamically importing\n    style-normalize-unscoped.css only if it's known to not conflict in\n    the embedder portal\n*/\n/* directly import these in src/app.js so that they will be processed as CSSStyleSheet\n@import './style-normalize-scoped.css';\n@import 'highlight.js/styles/github.css';\n*/\n/*\nhtml {\n    height:100%;\n}\nbody {\n    min-height:100%;\n}\ntable {\n    font-size:1em;\n    border-spacing:1px;\n    border-collapse:separate;\n}\n*/\n/*\n    !!! NOTE !!!\n    FireFox does not support the @scope (selector) syntax\n    that can enclose all affected rules inside a nested block,\n    so for now, will need to prepend the .sja_root_holder scope for each selector\n*/\n/***************************************\nCSS properties that are not covered \nby normalize.css are covered here\n\n!!! make sure to scope to sja_root_holder\n****************************************/\n.sja_root_holder h2 {\n    margin-block-start: 0.83em;\n    margin-block-end: 0.83em;\n}\n/***************************************\n    tag-based styles\n\n  prevent embedder styles from overriding\n  the styles within pp-controlled divs\n****************************************/\n/* use default browser styles within pp-controlled divs */\n/* using the !important flag:\n- this flag is used to override conflicting styles\n- this flag will override both embedder styling and inline styling\n- it is not necessary to use this flag to prevent embedder styles from overriding pp styles, because specifying styles within pp-specific classes will usually prevent this issue\n- the only time when it is necessary to use this flag is when (1) the conflicting styling also has an !important flag or (2) the conflicting styling is also specified in this same file\n*/\n.sja_root_holder {\n    /*background-color: #fff;*/\n}\n.sja_root_holder,\n.sja_menu_div,\n.sja_pane {\n    all: initial;\n    /* block inheritance for all properties */\n}\n.sja_root_holder table,\n.sja_menu_div table,\n.sja_pane table {\n    border-collapse: separate;\n    border-spacing: 2px;\n}\n.sja_root_holder svg {\n    display: inline-block;\n}\n/*\n    override the thicker button border\n    that results when a button's \n    border-radius: 0 which seems to override\n    all associated styles of \n    -webkit-appearance: button;\n*/\n.sja_root_holder button,\n.sja_menu_div button,\n.sja_pane button {\n    padding: 2px 3px;\n    border-width: 1px;\n    border-style: solid;\n    border-radius: 3px;\n    box-shadow: inset 0 0 0 99999px rgba(255, 255, 255, 0.3);\n    font-family: Arial;\n    color: black;\n    background-color: buttonface;\n    border-color: buttonborder;\n}\n.sja_root_holder button:disabled,\n.sja_menu_div button:disabled,\n.sja_pane button:disabled {\n    background-color: rgba(239, 239, 239, 0.3);\n    color: rgba(16, 16, 16, 0.3);\n    border-color: rgba(118, 118, 118, 0.3);\n}\n.sja_root_holder button:hover,\n.sja_menu_div button:hover,\n.sja_pane button:hover {\n    box-shadow: none;\n}\n.sja_root_holder label,\n.sja_menu_div label,\n.sja_pane label {\n    margin-bottom: 0;\n}\n.sja_root_holder a,\n.sja_menu_div a,\n.sja_pane a,\n.linkText {\n    color: rgb(0, 0, 238);\n    cursor: pointer;\n    text-decoration: underline;\n}\n.sja_root_holder input,\n.sja_menu_div input,\n.sja_pane input {\n    padding: 1px 3px;\n    margin:  2px 5px;\n    border:  1px solid #ccc;\n}\n.sja_root_holder select,\n.sja_menu_div select,\n.sja_pane select {\n    padding: 1px 3px;\n    padding-right: 30px; /* padding between text and arrow */\n    background-size: auto;\n    background-position: right;\n    border: 1px solid #ccc;\n}\n.sja_root_holder textarea,\n.sja_menu_div textarea,\n.sja_pane textarea {\n    padding: 2px;\n}\n.sja_root_holder input[type=\"search\"].tree_search {\n    -webkit-appearance: searchfield;\n}\n.sja_root_holder ul {\n    display: block;\n    list-style-type: disc;\n    margin-block-start: 1em;\n    margin-block-end: 1em;\n    margin-inline-start: 0px;\n    margin-inline-end: 0px;\n    padding-inline-start: 40px;\n}\n.sja_root_holder ul ul {\n    list-style-type: circle;\n}\n.sja_root_holder li {\n    display: list-item;\n    text-align: -webkit-match-parent;\n}\n/*************************\n    class-specific styles\n*************************/\n.sja_errorbar {\n    position: relative;\n    padding: 5px 50px 5px 10px;\n    background-color: rgba(200, 0, 0, .1);\n    color: rgba(190, 0, 0, .5);\n    border: solid 1px rgba(200, 0, 0, .2);\n    /*border-width: 1px 0px;*/\n}\n.sja_errorbar>:nth-child(2) {\n    position: absolute;\n    padding: 5px 10px;\n    cursor: default;\n    top: 0px;\n    right: 10px;\n}\n.sja_inset_a {\n    background-color: #ebedeb;\n    box-shadow: inset 0px 0px 14px 0px #858585;\n    padding: 5px 10px;\n}\n.sja_menu,\n.sja_menu_persist,\n.sja_tooltip {\n    position: absolute;\n    background-color: white;\n    font-family: Arial;\n    z-index: 1000;\n}\n/* /client/src/app.js start */\n.sja_menuoption {\n    color: black;\n    padding: 5px 10px;\n    cursor: default;\n    background-color: #f2f2f2;\n    margin: 1px;\n    border-radius: 5px;\n}\n.sja_menuoption_not_interactive {\n    padding: 5px 10px;\n    cursor: default;\n    margin: 1px;\n}\n.sja_sharp_border {\n    border-radius: 0px;\n}\n.sja_menuoption:hover {\n    background-color: #e6e6e6\n}\n.sja_menuoption:active {\n    color: #cc0000;\n    background-color: #FCE2E1;\n}\n/* /client/src/app.js end */\n.sja_filter_tag_btn {\n    display: inline-block;\n    color: black;\n    padding: 5px 8px;\n    background-color: #cfe2f3;\n    cursor: default;\n}\n/* .sja_filter_tag_btn:hover { opacity: 0.8; cursor:default} */\n.sja_filter_tag_btn:active {\n    color: #cc0000;\n    opacity: 0.6;\n}\n.ts_pill:hover,\n.tvs_pill:hover {\n    opacity: 0.8;\n    cursor: default\n}\n.sjpp_apply_btn {\n    background-color: #d0e0e3;\n    border-radius: 13px !important; \n    padding: 7px 15px !important;\n    border: 0px !important;\n}\n.sjpp_delete_btn,\n.remove_btn {\n    background-color: #f4cccc;\n}\n.ts_summary_btn {\n    background-color: #d9d2e9;\n}\n/* mostly for table tr */\n.sja_clb {\n    padding: 5px 10px;\n    cursor: default;\n}\n.sja_clb:hover {\n    background: #ffff99;\n}\n.sja_clb:active {\n    background: #ffcc99;\n}\n.sja_clb_selected {\n    padding: 5px 10px;\n    cursor: default;\n    background: #FAF0C8;\n    border-bottom: solid 2px #E3CA64;\n}\n.sja_clb_selected:hover {\n    background: #FCE68B\n}\n.sja_clb_selected:active {\n    background: #ffcc99\n}\n/* table tr, gray highlight */\n.sja_clb_gray {\n    padding: 5px 10px;\n    cursor: default;\n}\n.sja_clb_gray:hover {\n    background-color: #f1f1f1;\n}\n.sja_clb_gray:active {\n    background-color: #ffffcc;\n}\n.sja_hideable_legend {\n    cursor: default;\n}\n.sja_hideable_legend:hover {\n    background: #ffff99;\n}\n.sja_legend_more_btn {\n    padding: 3px;\n    text-align: center;\n    font-size: 0.7em;\n    opacity: 0.5;\n    cursor: default;\n}\n.sja_legend_more_btn:hover {\n    text-decoration: underline;\n}\n/* text only */\n.sja_clbtext2 {\n    cursor: default;\n    text-decoration: none;\n}\n.sja_clbtext2:hover {\n    text-decoration: underline;\n}\n.sja_clbtext2:active {\n    fill: #CC0000;\n    color: #CC0000;\n}\n.sja_clbtext {\n    cursor: default;\n    color: black;\n    fill: black;\n    border-bottom: solid 1px transparent;\n}\n.sja_clbtext:hover {\n    color: #631318;\n    fill: #631318;\n    border-color: black;\n}\n.sja_clbtext:active {\n    color: #CC0000;\n    border-color: #cc0000;\n    fill: #cc0000;\n}\n.sja_clbtextbold {\n    cursor: default;\n    color: black;\n    fill: black;\n    font-weight: normal;\n}\n.sja_clbtextbold:hover {\n    color: #631318;\n    fill: #631318;\n    font-weight: bold;\n}\n.sja_clbtextbold:active {\n    color: #CC0000;\n    fill: #cc0000;\n    font-weight: bold;\n}\n.sja_opaque6 {\n    opacity: .6;\n    cursor: default;\n}\n.sja_opaque6:hover {\n    opacity: .9;\n}\n.sja_opaque8 {\n    opacity: .8;\n    cursor: default;\n}\n.sja_opaque8:hover {\n    opacity: 1;\n}\n.sja_simpletable tr td {\n    border-bottom: solid 1px #ededed;\n}\n.sja_mcdot {\n    cursor: default;\n    border-radius: 8px;\n    padding: 1px 2px;\n    margin-right: 1px;\n    color: white;\n    font-size: .8em;\n}\n.sja_variantpagesnv {\n    cursor: default;\n    display: inline-block;\n    border-radius: 3px;\n    padding: 3px 10px;\n    margin-right: 2px;\n    color: white;\n    background-color: #0099FF;\n    opacity: .6;\n}\n.sja_variantpagesnv:hover {\n    opacity: 1;\n}\n.sja_variantpagesnv:active {\n    background-color: #3366FF;\n}\n.sja_selectsample {\n    cursor: default;\n    display: inline-block;\n    border-radius: 2px;\n    border: solid 1px #545454;\n    padding: 3px 10px;\n    margin-right: 2px;\n    color: #545454;\n    background-color: white;\n    font-size: .8em;\n}\n.sja_selectsample:hover {\n    background-color: #f1f1f1;\n}\n.sja_selectsample:active {\n    background-color: #F2E1E3;\n}\n.sja_pane {\n    position: absolute;\n    /*border:solid 1px #ccc;\n    */\n    box-shadow: 0px 2px 4px 1px #999;\n    background-color: white;\n}\n.sja_pane>:first-child {\n    padding-right: 10px;\n    cursor: move;\n    background-color: #f0f0f0;\n}\n.sja_pane>:nth-child(2) {\n    padding: 0px 10px 10px 10px;\n    font-family: Arial;\n}\n.sja_cursor_hmove {\n    cursor: ew-resize;\n}\n.sja_svgtext {\n    cursor: default;\n    fill-opacity: .8\n}\n.sja_svgtext2 {\n    cursor: default;\n    fill: black;\n}\n.sja_svgtext2:hover {\n    fill: #B30000\n}\n.sja_clb5 {\n    /* tree button */\n    cursor: default;\n    display: inline-block;\n    border: solid 1px #006600;\n    color: #006600;\n    background-color: white;\n    margin-left: 6px;\n    padding: 0px 4px;\n    font-size: 80%;\n}\n.sja_clb5:hover {\n    background-color: #006600;\n    color: white;\n}\n.sja_clb5:active {\n    background-color: #009900;\n}\n.sja_clb2 {\n    color: black;\n    font-family: Courier;\n    display: inline-block;\n    padding: 1px 5px;\n    cursor: default;\n}\n.sja_clb2:hover {\n    background-color: #ffff99;\n}\n.sja_clb2:active {\n    background-color: #ccff99;\n}\n.sja_clbb {\n    /* highlight border */\n    border: solid 1px transparent;\n    cursor: default;\n}\n.sja_clbb:hover {\n    border-color: #ccc;\n}\n.sja_clbbox {\n    cursor: default;\n    padding: 2px 5px;\n    color: white;\n    font-size: .7em;\n    font-weight: normal;\n}\n.sja_clbbox:hover {\n    font-weight: bold;\n}\n.sja_tr {\n    cursor: default;\n    background-color: #f1f1f1;\n}\n.sja_tr:hover {\n    background-color: white;\n}\n.sja_tr:active {\n    background-color: #ffffcc;\n}\n.sja_tr2 {\n    cursor: default;\n}\n.sja_tr2:hover {\n    background-color: #ffffcc;\n}\n.sja_tr2:active {\n    background-color: #ffff00;\n}\n.sja_aa_disclabel {\n    cursor: default;\n}\n.sja_aa_discnum {\n    cursor: default;\n    text-rendering: geometricPrecision;\n}\n.sja_aa_skkick:hover {\n    stroke: #858585;\n}\n.sja_aa_disckick:hover {\n    stroke-opacity: 1;\n}\n.sja_menuoption_y {\n    display: inline-block;\n    color: black;\n    padding: 2px 4px;\n    cursor: default;\n    background-color: #E6E5C5;\n    margin: 2px;\n}\n.sja_menuoption_y:hover {\n    background-color: #DEDCA9\n}\n.sja_menuoption_y:active {\n    background-color: #FFFF99\n}\n.sja_menuoption_r {\n    display: inline-block;\n    color: black;\n    padding: 2px 4px;\n    cursor: default;\n    background-color: #EDDDDE;\n    margin: 2px;\n}\n.sja_menuoption_r:hover {\n    background-color: #E8CFD1\n}\n.sja_menuoption_r:active {\n    background-color: #FCD9DD\n}\n.sja_error2 {\n    display: inline-block;\n    padding: 5px 50px 5px 10px;\n    margin: 10px 20px;\n    background-color: rgba(200, 0, 0, .5);\n    color: white;\n    border-radius: 6px;\n}\n.sja_paint {\n    position: relative;\n}\n.sja_paint>:first-child {}\n.sja_paint>:nth-child(2) {\n    position: absolute;\n    padding: 3px 6px;\n    cursor: default;\n    top: 10px;\n    right: 30px;\n    font-size: 80%;\n}\n.sja_tree_ul {\n    list-style-type: none;\n    padding-left: 25px;\n    line-height: 1.4;\n}\n.sja_input {\n    display: inline-block;\n    padding: 2px 6px;\n}\n.sja_bulkcell {\n    display: inline-block;\n    width: 3px;\n    height: 9px;\n    margin: 1px 1px 0px 0px;\n}\n.sja_tag {\n    display: inline-block;\n    margin-left: 10px;\n    padding: 1px 3px;\n    background-color: #858585;\n    color: white;\n    font-size: 80%;\n}\n.sja_bgbox {\n    cursor: default;\n    fill: yellow;\n    fill-opacity: 0;\n}\n.sja_bgbox:hover {\n    fill-opacity: .2;\n}\n.sja_diseasehm_search_item {\n    display: inline-block;\n    margin: 3px;\n    padding: 2px;\n}\n.sja_pulse {\n    animation: pulse .5s alternate infinite;\n}\n@keyframes pulse {\n    from {\n        opacity: .2;\n    }\n    to {\n        opacity: 1;\n    }\n}\n.sja_hm-edittool-table td {\n    padding: 0 2px;\n    cursor: pointer;\n    text-align: center;\n    font-size: 14px;\n}\n.sja_hm-edittool-table td:hover {\n    opacity: 1;\n    font-weight: 600;\n}\n.sja_tinylogo_head {\n    display: inline-block;\n    background-color: #858585;\n    color: white;\n    font-size: .6em;\n    padding: 1px 3px;\n}\n.sja_tinylogo_body {\n    display: inline-block;\n    margin-left: 10px;\n    background-color: #ededed;\n    font-size: .9em;\n    color: black;\n    padding: 1px 5px;\n}\n.sja_handle_green {\n    display: inline-block;\n    font-size: .9em;\n    padding: 3px 6px;\n    background-color: #f0f7f1;\n    color: #146E17;\n    cursor: default;\n}\n.sja_handle_green:hover {\n    background-color: #D5F0D8;\n}\n.sja_handle_green:active {\n    background-color: #BAD1BC;\n    color: black;\n}\n.sja_handle_red {\n    display: inline-block;\n    font-size: .9em;\n    padding: 3px 6px;\n    background-color: #F5EBEC;\n    color: #991F1F;\n    cursor: default;\n}\n.sja_handle_red:hover {\n    background-color: #F2D8DB;\n}\n.sja_handle_red:active {\n    background-color: #E3B1B7;\n    color: black;\n}\n.sja_btn {\n    -webkit-appearance: button;\n    -moz-appearance: button;\n    appearance: button;\n    text-decoration: none;\n    color: initial;\n}\n.sja_button {\n    display: inline-block;\n    background: white;\n    padding: 3px 5px;\n    border: solid 1px black;\n    opacity: .8;\n    cursor: default;\n}\n.sja_button:hover {\n    opacity: 1;\n}\n.sja_button_open {\n    display: inline-block;\n    background: #ddd;\n    padding: 3px 5px;\n    border: solid 1px black;\n    opacity: .8;\n    cursor: default;\n}\n.sja_button_open:hover {\n    opacity: 1;\n}\n.sja_button_fold {\n    display: inline-block;\n    background: #aaa;\n    color: white;\n    padding: 3px 5px;\n    border: solid 1px black;\n    opacity: .8;\n    cursor: default;\n}\n.sja_button_fold:hover {\n    opacity: 1;\n}\n.sja-termdb-config-row-label {\n    padding: 5px;\n    text-align: left;\n    vertical-align: middle;\n}\n.sjpp-controls-table {\n  margin-bottom: 10px;\n}\n.sjpp-controls-table > tr:hover {\n  /*font-weight: 600;*/\n  text-shadow:0px 0px 0.5px black;\n  background-color: rgba(239, 236, 149, 0.389);\n}\n.sja_edit_btn {\n    display: inline-block;\n    color: black;\n    background-color: #f2f2f2;\n    border-radius: 5px;\n    border: solid 1px #aaa;\n    padding: 5px 10px;\n    cursor: default;\n    margin: 1px;\n    font-size: 0.8em;\n    margin-left: 20px;\n}\n.sja_edit_btn:hover {\n    background-color: #e6e6e6\n}\n.sja_edit_btn:active {\n    color: #cc0000;\n    background-color: #FCE2E1;\n}\n/* App Drawer style */\n.sjpp-appdrawer-cols {\n    font-family: Verdana, Geneva, Tahoma, sans-serif;\n    font-weight: 500;\n    font-size: 17px;\n    text-align: left;\n    color: #324870;\n    margin: 10px 10px 0px 10px;\n}\n.sjpp-track, .sjpp-track li {\n    display: grid !important;\n    grid-template-columns: 2fr 4fr 40px;\n    grid-template-areas: 'image header' 'image blurb';\n    gap: 5px;\n}\n.sjpp-app-drawer-card,\n.sjpp-track {\n    background-color: white;\n    max-width: 400px;\n    /* min-width: 320px; */\n    border-radius: 5px;\n    padding: 0px;\n    align-items: center;\n    justify-items: left;\n    box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);\n    -webkit-transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n    transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n}\n.sjpp-app-drawer-card::after,\n.sjpp-track::after {\n    content: \"\";\n    border-radius: 8px;\n    position: absolute;\n    z-index: -1;\n    top: 0;\n    left: 0;\n    width: 100%;\n    height: 100%;\n    box-shadow: 0 5px 15px rgba(0, 0, 0, 0.3);\n    opacity: 0;\n    -webkit-transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n    transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n}\n.sjpp-app-drawer-card:hover,\n.sjpp-track:hover {\n    -webkit-transform: scale(1, 1);\n    transform: scale(1, 1);\n}\n.sjpp-app-drawer-card:hover::after,\n.sjpp-track:hover::after {\n    opacity: 1;\n}\n.sjpp-track-image {\n    grid-area: image;\n    width: 75px;\n    height: 75px;\n    align-self: start;\n    justify-self: start;\n}\n.sjpp-track-image img {\n    width: 100%;\n    height: 100%;\n    object-fit: cover;\n    border-radius: 5px 0px 0px 5px;\n}\n.sjpp-app-drawer-card-ribbon{\n    grid-area: image;\n    overflow: hidden;\n    width: 100%;\n    height: 100%;\n}\n.sjpp-app-drawer-card-ribbon::before,\n.sjpp-app-drawer-card-ribbon::after {\n  position: relative;\n  z-index: -1;\n  content: '';\n  display: block;\n  border-top-color: transparent;\n  border-left-color: transparent;\n}\n.sjpp-app-drawer-card-ribbon span {\n  position: relative;\n  display: block;\n  width: 100%;\n  padding: 1px 0;\n  border-color: transparent transparent transparent darkgray;\n  box-shadow: 0 2px 7.5px rgba(0, 0, 0, 0.3);\n  opacity: 1;\n  font-family: 'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif;\n  transform: rotate(-45deg);\n}\n.sjpp-app-drawer-card-ribbon::before {\n    top: 0;\n    right: 0;\n}\n.sjpp-app-drawer-card-ribbon::after {\n    bottom: 0;\n    left: 0;\n}\n.sjpp-track-h {\n    grid-area: header;\n    font-family: 'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif;\n    margin-left: 5px;\n    padding: 0px;\n}\n.sjpp-track-blurb {\n    grid-area: blurb;\n    font-size: 13px;\n    font-weight: 300;\n    margin-left: 5px;\n    justify-content: center;\n    font-style: oblique;\n    color: #403f3f;\n}\n/* client/src/block.js start */\n.sjpp-active-tiny-button {\n\tdisplay: inline-block;\n\tbackground-color: #1C5E86;\n\tfont-size: .8em;\n\tcolor: white;\n\tpadding: 1px 5px;\n\tmargin-right: 5px;\n\tborder-radius: 4px;\n}\n.sjpp-plus-button\n{\n    display: inline-block;\n    margin: 1px;\n    border: solid 1px #545454;\n    font-size: .9em;\n    cursor: default;\n    padding: 2px 5px;\n}\n.sjpp-dshandleholder\n{\n    display: inline-block;\n    margin: 1px;\n    border: solid 1px #545454;\n    font-size: .9em;\n    cursor: default;\n}\n.sjpp-dslabel\n{\n    display: inline-block;\n    color: black;\n    padding: 2px 4px;\n\n}\n/* client/src/block.js end */\n/* client/src/app.js start */\n.sjpp-input-div-gene-pos\n{\n    display: inline-block;\n    padding-right: 5px;\n}\n.sjpp-input-gene-pos\n{\n    border: solid 1px #545454;\n    padding: 6px 10px;\n    border-radius: 5px;\n}\n.sjpp-genome-select-div\n{\n    display: inline-block;\n    padding-left: 5px;\n}\n.sjpp-genome-select\n{\n    border-radius: 5px;\n    margin: 1px 20px 1px 10px;\n}\n.sjpp-output-sandbox-title\n{\n    border-radius:4px; \n    color:white; \n    background-color: #969696; \n    padding: 1px 5px; \n    display:inline-block; \n    font-size:0.8em; \n    margin-left:4px;\n}\n/* client/src/app.js end */\n/* client/dom/sandbox.ts start */\n.sjpp-output-sandbox-header\n{\n    display: inline-block;\n    margin: 5px 10px;\n    padding-right: 8px;\n    margin-bottom: 0px;\n    /* box-shadow:2px 0px 2px #f2f2f2; */\n    border-radius: 5px 5px 0 0;\n    /* background-color: #f2f2f2; */\n    z-index: 99;\n}\n.sjpp-output-sandbox-content\n{\n    margin: 5px 10px;\n    margin-top: 0px;\n    padding-right: 8px;\n    display: inline-block;\n    /* box-shadow: 2px 2px 10px #f2f2f2; */\n    border: solid 1px #ccc;\n    border-top: solid 1px white;\n    border-radius: 0  0 5px 5px;\n}\n.sjpp-output-sandbox-collapse-btn,\n.sjpp-output-sandbox-expand-btn,\n.sjpp-output-sandbox-close-bt\n{\n    /* display: inline-block; */\n    /* margin: 0px; */\n    /* border-right: solid 2px white; */\n    font-size: 16px;\n    cursor: default;\n}\n.sjpp-output-sandbox-close-bt {\n    border-radius: 5px 0 0 0;\n}\n/* \nSeparated padding for sandbox buttons to fix close button's\nright, white border not extending to total height of\nsandbox header\n*/\n.sjpp-output-sandbox-collapse-btn,\n.sjpp-output-sandbox-expand-btn {\n    padding: 4px 10px;\n}\n.sjpp-output-sandbox-close-bt {\n    padding: 8px 10px;\n}\n/* client/dom/sandbox.ts end */\n.sjpp_row_wrapper:hover {\n    background: #fcfcca !important; \n}\n/*.sjpp_row_wrapper:nth-child(odd) {background: rgb(237, 237, 237)}*/\n.sjpp_table_header {\n    font-family: 'Arial';\n    font-size: 1em;\n    text-align: left;\n    position: sticky;\n    top: 0;\n    opacity: 0.7;\n    font-weight: normal;\n}\n.sjpp_table_item {\n    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n=1;if(t.indexOf("transcript_ablation")!=-1){return[Hr,Kr,n]}n++;if(t.indexOf("splice_acceptor_variant")!=-1)return[Pr,"L",n];n++;if(t.indexOf("splice_donor_variant")!=-1)return[Pr,"L",n];n++;if(t.indexOf("stop_gained")!=-1)return[Pr,"N",n];n++;if(t.indexOf("frameshift_variant")!=-1)return[Pr,"F",n];n++;if(t.indexOf("stop_lost")!=-1)return[Pr,"N",n];n++;if(t.indexOf("start_lost")!=-1)return[Pr,"N",n];n++;if(t.indexOf("transcript_amplification")!=-1){return[Pr,oa,n]}n++;if(t.indexOf("inframe_insertion")!=-1||t.indexOf("conservative_inframe_insertion")!=-1||t.indexOf("disruptive_inframe_insertion")!=-1)return[Pr,"I",n];n++;if(t.indexOf("inframe_deletion")!=-1||t.indexOf("conservative_inframe_deletion")!=-1||t.indexOf("disruptive_inframe_deletion")!=-1)return[Pr,"D",n];n++;if(t.indexOf("missense_variant")!=-1)return[Pr,"M",n];n++;if(t.indexOf("protein_altering_variant")!=-1)return[Pr,"ProteinAltering",n];n++;if(t.indexOf("splice_region_variant")!=-1)return[Pr,"P",n];n++;if(t.indexOf("incomplete_terminal_codon_variant")!=-1)return[Pr,"N",n];n++;if(t.indexOf("stop_retained_variant")!=-1)return[Pr,"S",n];n++;if(t.indexOf("synonymous_variant")!=-1)return[Pr,"S",n];n++;if(t.indexOf("coding_sequence_variant")!=-1)return[Pr,oa,n];n++;if(t.indexOf("mature_mirna_variant")!=-1)return[Pr,"E",n];n++;if(t.indexOf("5_prime_utr_variant")!=-1)return[Pr,na,n];n++;if(t.indexOf("3_prime_utr_variant")!=-1)return[Pr,ta,n];n++;if(t.indexOf("non_coding_transcript_exon_variant")!=-1)return[Pr,"E",n];n++;if(t.indexOf("intron_variant")!=-1)return[Pr,"Intron",n];n++;if(t.indexOf("nmd_transcript_variant")!=-1)return[Pr,"S",n];n++;if(t.indexOf("non_coding_transcript_variant")!=-1)return[Pr,"E",n];n++;if(t.indexOf("upstream_gene_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("downstream_gene_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("tfbs_ablation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("tfbs_amplification")!=-1)return[Pr,ia,n];n++;if(t.indexOf("tf_binding_site_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("regulatory_region_ablation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("regulatory_region_amplification")!=-1)return[Pr,ia,n];n++;if(t.indexOf("feature_elongation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("regulatory_region_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("feature_truncation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("intergenic_variant")!=-1)return[Pr,ia,n];n++;return[Pr,oa,n]};const ya='<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="#858585" stroke="none"></path>';const va={};const wa="S";va[wa]={label:"Somatic",desc:"A variant found only in a tumor sample. The proportion is indicated by lack of any arc.",legend:'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>'};const xa="G";va[xa]={label:"Germline",desc:"A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.",legend:ya};va.germline=va[xa];va.somatic=va[wa];const _a="R";va[_a]={label:"Relapse",desc:"A somatic variant found only in a relapse sample. The proportion is indicated by the span of the hollow arc within the whole circle.",legend:'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="none" stroke="#858585"></path>'};const ka="GP";va[ka]={label:"Germline pathogenic",desc:"A constitutional variant with pathogenic allele.",legend:ya};const ja="GNP";va[ja]={label:"Germline non-pathogenic",desc:"A constitutional variant with non-pathogenic allele.",legend:ya,hidden:true};const Na={usegm:"usegm",ds:"dataset",bigwig:"bigwig",bigwigstranded:"bigwigstranded",junction:"junction",mdsjunction:"mdsjunction",mdscnv:"mdscnv",mdssvcnv:"mdssvcnv",mdsexpressionrank:"mdsexpressionrank",mdsvcf:"mdsvcf",bedj:"bedj",pgv:"profilegenevalue",bampile:"bampile",hicstraw:"hicstraw",expressionrank:"expressionrank",aicheck:"aicheck",ase:"ase",mds2:"mds2",mds3:"mds3",bedgraphdot:"bedgraphdot",bam:"bam",ld:"ld"};function Sa(e){for(const t in Na){if(e==Na[t]){return true}}return false}const Aa={vcf:"vcf"};const Ca={vcf:"vcf",svcnvitd:"svcnvitd",geneexpression:"geneexpression"};const Ea={GCT:"A",GCC:"A",GCA:"A",GCG:"A",CGT:"R",CGC:"R",CGA:"R",CGG:"R",AGA:"R",AGG:"R",AAT:"N",AAC:"N",GAT:"D",GAC:"D",TGT:"C",TGC:"C",CAA:"Q",CAG:"Q",GAA:"E",GAG:"E",GGT:"G",GGC:"G",GGA:"G",GGG:"G",CAT:"H",CAC:"H",ATT:"I",ATC:"I",ATA:"I",TTA:"L",TTG:"L",CTT:"L",CTC:"L",CTA:"L",CTG:"L",AAA:"K",AAG:"K",ATG:"M",TTT:"F",TTC:"F",CCT:"P",CCC:"P",CCA:"P",CCG:"P",TCT:"S",TCC:"S",TCA:"S",TCG:"S",AGT:"S",AGC:"S",ACT:"T",ACC:"T",ACA:"T",ACG:"T",TGG:"W",TAT:"Y",TAC:"Y",GTT:"V",GTC:"V",GTA:"V",GTG:"V"};const Oa="*";function Ma(e){if(!e.genomicseq)return undefined;const t=[];if(e.coding){for(const[n,o]of e.coding.entries()){const n=e.genomicseq.substr(o[0]-e.start,o[1]-o[0]);if(e.strand=="-"){t.push(La(n))}else{t.push(n)}}}const n=t.join("");const o=[];const i=e.startCodonFrame?3-e.startCodonFrame:0;for(let e=i;e<n.length;e+=3){const t=Ea[n.substr(e,3)];o.push(t||Oa)}e.cdseq=n;return o.join("")}function Ia(e,t){if(e>=1e9)return(e/1e9).toFixed(1)+" Gb";if(e>=1e7)return Math.ceil(e/1e6)+" Mb";if(e>=1e6)return(e/1e6).toFixed(1)+" Mb";if(e>=1e4)return Math.ceil(e/1e3)+" Kb";if(e>=1e3)return(e/1e3).toFixed(1)+" Kb";return e+(t?"bytes":" bp")}const Ta={A:"#ca0020",T:"#f4a582",C:"#92c5de",G:"#0571b0"};function Ra(e){switch(e){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";case"a":return"t";case"t":return"a";case"c":return"g";case"g":return"c";default:return e}}function La(e){const t=[];for(let n=e.length-1;n>=0;n--){t.push(Ra(e[n]))}return t.join("")}function $a(e,t){const n={chr:e.chr,start:e.start,stop:e.stop,strand:e.strand,coding:[]};if(t.isskipexon||t.isaltexon){for(let o=0;o<e.exon.length;o++){const i=Math.max(e.codingstart,e.exon[o][0]);const s=Math.min(e.codingstop,e.exon[o][1]);if(i>s){continue}if(t.skippedexon.indexOf(o)==-1){n.coding.push([i,s])}}}else if(t.a5ss||t.a3ss){const o=e.exon.map((e=>[e[0],e[1]]));const i=e.strand=="+";if(t.a5ss){if(i){o[t.exon5idx][1]=t.junctionB.start}else{o[t.exon5idx+1][0]=t.junctionB.stop}}else{if(i){o[t.exon5idx+1][0]=t.junctionB.stop}else{o[t.exon5idx][1]=t.junctionB.start}}for(const t of o){const o=Math.max(e.codingstart,t[0]);const i=Math.min(e.codingstop,t[1]);if(o>i){continue}n.coding.push([o,i])}}return n}function za(e,t){const n=t.split("\n");n.shift();e.genomicseq=n.join("").toUpperCase();const o=Ma(e);let i=zr;const s=o.indexOf(Oa);if(s==o.length-1){i=$r}return i}function Pa(e){if(!e.lst)return".lst missing";if(!Array.isArray(e.lst))return"input is not an array";for(const t of e.lst){if(!t.name)return"name missing from a set of .vcfinfofilter.lst";if(t.autocategory||t.categories){if(!t.autocategory){for(const e in t.categories){const n=t.categories[e];if(!t.autocolor&&!n.color)return".color missing for class "+e+" from .categories of set "+t.name;if(!n.label){n.label=e}}}if(t.categoryhidden){for(const e in t.categoryhidden){if(!t.categories[e])return"unknown hidden-by-default category "+e+" from set "+t.name}}else{t.categoryhidden={}}}else if(t.numericfilter){const e=[];for(const n of t.numericfilter){if(typeof n=="number"){e.push({side:"<",value:n})}else{e.push({side:n.side||"<",value:n.value})}}t.numericfilter=e}if(t.altalleleinfo){if(!t.altalleleinfo.key){return".key missing from .altalleleinfo from set "+t.name}}else if(t.locusinfo){if(!t.locusinfo.key){return".key missing from .locusinfo from set "+t.name}}else{return"neither .altalleleinfo or .locusinfo is available from set "+t.name}}}function Da(e,t){for(const n in e.majorchr){if(t.indexOf(n.replace("chr",""))!=-1){return true}}if(e.minorchr){for(const n in e.minorchr){if(t.indexOf(n.replace("chr",""))!=-1){return true}}}return false}function Ua(e,t){let n=0,o=0;for(const i in e.majorchr){if(t.includes(i)){o++}else if(t.includes(i.replace("chr",""))){n++}}if(e.minorchr){for(const i in e.minorchr){if(t.includes(i)){o++}else 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e.ann){if(o._isoform!=t.usegm.isoform)continue;if(n){if(o._csqrank<n._csqrank){n=o}}else{n=o}}if(!n&&t.gmmode==qa.genomic){n=e.ann[0]}}else{n=e.ann[0];for(const t of e.ann){if(t._csqrank<n._csqrank){n=t}}}if(n){e.gene=n._gene;e.isoform=n._isoform;e.class=n._class;e.dt=n._dt;e.mname=n._mname;if(e.class==ia){delete e.class}}}if(e.class==undefined){if(Yr[e.type]){e.class=e.type;e.dt=Yr[e.type].dt;e.mname=e.id&&e.id!="."?e.id:e.ref+">"+e.alt;if(e.mname.length>15){e.mname=e.type}}else{e.class=oa;e.dt=Pr;e.mname=e.type}}delete e.type}const Ga="Unannotated";function Ja(e,t){return function(n){return t.map((t=>[t,n.map((n=>e(t-n))).reduce(((e,t)=>e+t),0)/n.length]))}}function Va(e){return function(t){return Math.abs(t/=e)<=1?.75*(1-t*t)/e:0}}const Wa=["#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b","#c49c94","#e377c2","#f7b6d2","#7f7f7f","#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"];const Xa=["#e75480","blue"];function 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td=ed;function nd(e){const t=e.div.append("input").attr("placeholder","Search gene").style("width",e.width||"100px");const n=e.resultdiv||(e.tip?e.tip.d:wc.d);function o(){if(e.resultdiv){e.resultdiv.selectAll("*").remove()}else if(e.tip){e.tip.hide()}else{wc.hide()}}t.on("keyup",(t=>{const i=t.target.value;if(i.length<=1){o();return}if(Jc(t)){const t=n.select(".sja_menuoption");if(t.size()>0){e.callback(t.text());o()}return}s()}));t.node().focus();function i(){Ll("genelookup",{genome:e.genome,input:t.property("value")}).then((i=>{if(i.error)throw i.error;if(!i.hits)throw".hits[] missing";if(e.resultdiv){e.resultdiv.selectAll("*").remove()}else if(e.tip){e.tip.clear().showunder(t.node())}else{wc.clear().showunder(t.node())}for(const t of i.hits){n.append("div").attr("class","sja_menuoption").text(t).on("click",(()=>{e.callback(t);o()}))}})).catch((e=>{n.append("div").text(e.message||e);if(e.stack)console.log(e.stack)}))}const s=td.debounce(i,300)}function od(e,t){return 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read count",o]);return}i.maf_normal={f:t/s,v1:t,v2:s}}delete i.maf_normal_v1;delete i.maf_normal_v2}n.good++;if(i.class=="M"){n.snv.missense++}else if(i.class=="S"){n.snv.silent++}const a=n.geneToUpper?i.gene.toUpperCase():i.gene;if(!n.data[a]){n.data[a]=[]}i.dt=Pr;n.data[a].push(i)}function ld(e,t,n){const o=e.toLowerCase().split("\t");if(o.length<=1)return"invalid file header for fusions";const i=(...e)=>{for(const t of e){const e=o.indexOf(t);if(e!=-1)return e}return-1};let s=i("gene_a","gene1","genea");if(s==-1)return"gene_a missing from header";o[s]="gene1";s=i("gene_b","gene2","geneb");if(s==-1)return"gene_b missing from header";o[s]="gene2";s=i("chr_a","chr1","chra");if(s==-1)return"chr_a missing from header";o[s]="chr1";s=i("chr_b","chr2","chrb");if(s==-1)return"chr_b missing from header";o[s]="chr2";s=i("pos_a","position_a","position1","posa");if(s==-1)return"pos_a missing from header";o[s]="position1";s=i("pos_b","position_b","position2","posb");if(s==-1)return"pos_b missing 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e=0;e<r.length;e++){s[r[e]]=i[e]}if(!s.chr1){a.push([e,"missing chr1",i]);return}if(s.chr1.toLowerCase().indexOf("chr")!=0){s.chr1="chr"+s.chr1}if(!s.chr2){a.push([e,"missing chr2",i]);return}if(s.chr2.toLowerCase().indexOf("chr")!=0){s.chr2="chr"+s.chr2}let l=s.position1;if(!l){a.push([e,"missing position1",i]);return}let c=Number.parseInt(l);if(Number.isNaN(c)||c<=0){a.push([e,"invalid value for position1",i]);return}s.position1=c;l=s.position2;if(!l){a.push([e,"missing position2",i]);return}c=Number.parseInt(l);if(Number.isNaN(c)||c<=0){a.push([e,"invalid value for position2",i]);return}s.position2=c;if(sd(s,n,e,i)){return}if(s.isoform1&&s.isoform1.indexOf(",")!=-1){const e=s.isoform1.split(",");s.isoform1=undefined;for(const t of e){if(t!="")s.isoform1=t}}if(s.isoform2&&s.isoform2.indexOf(",")!=-1){const e=s.isoform2.split(",");s.isoform2=undefined;for(const t of e){if(t!="")s.isoform2=t}}if(!s.gene1){s.isoform1=undefined}if(!s.gene2){s.isoform2=undefined}if(s.gene1){n.good++;const e={dt:o?Fr:Dr,class:o?aa:ra,isoform:s.isoform1,mname:s.gene2||s.chr2,sample:s.sample,patient:s.patient,sampletype:s.sampletype,origin:s.origin,disease:s.disease,pairlst:[{a:{name:s.gene1,isoform:s.isoform1,strand:s.strand1,chr:s.chr1,position:s.position1},b:{name:s.gene2,isoform:s.isoform2,strand:s.strand2,chr:s.chr2,position:s.position2}}]};const t=n.geneToUpper?s.gene1.toUpperCase():s.gene1;if(!n.data[t]){n.data[t]=[]}n.data[t].push(e)}if(s.gene2&&s.gene2!=s.gene1){n.good++;const e={dt:o?Fr:Dr,class:o?aa:ra,isoform:s.isoform2,mname:s.gene1||s.chr1,sample:s.sample,patient:s.patient,sampletype:s.sampletype,origin:s.origin,disease:s.disease,pairlst:[{a:{name:s.gene1,isoform:s.isoform1,strand:s.strand1,chr:s.chr1,position:s.position1},b:{name:s.gene2,isoform:s.isoform2,strand:s.strand2,chr:s.chr2,position:s.position2}}]};const t=n.geneToUpper?s.gene2.toUpperCase():s.gene2;if(!n.data[t]){n.data[t]=[]}n.data[t].push(e)}}function dd(e){const t={};for(const n in e){if(n=="pairlst")continue;const o=e[n];const i=typeof o;if(i=="object"){continue}t[n]=o}if(e.pairlst){t.pairlst=[];for(const n of e.pairlst){const e={};for(const t in n){if(t=="a"||t=="b"||t=="interstitial"){continue}e[t]=n[t]}if(n.a){e.a={};for(const t in n.a){const o=n.a[t];if(typeof o=="object"){continue}e.a[t]=o}}if(n.b){e.b={};for(const t in n.b){const o=n.b[t];if(typeof o=="object"){continue}e.b[t]=o}}if(n.interstitial){e.interstitial={};for(const t in n.interstitial){const o=n.interstitial[t];if(typeof o=="object"){continue}e.interstitial[t]=o}}t.pairlst.push(e)}}return t}function fd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid file header for svjson";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("sample");if(i!=-1)n[i]="sample";i=o("sampletype");if(i!=-1)n[i]="sampletype";i=o("patient");if(i!=-1)n[i]="patient";i=o("json","jsontext");if(i==-1)return["json missing from 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Gr:a.class=Qr;a.mname="N-loss";break;case Jr:a.class=ea;a.mname="C-loss";break;case Hr:a.class=Kr;a.mname="Del";break;case Fr:a.class=aa;a.mname="SV";break;default:r.push([e,"unknown datatype",i]);return}if(!a.gene){r.push([e,"json.gene missing",i]);return}n.good++;for(const e in s){if(e!="jsontext"){a[e]=s[e]}}const t=n.geneToUpper?a.gene.toUpperCase():a.gene.toUpperCase();if(!n.data[t]){n.data[t]=[]}n.data[t].push(a)}}function ud(e){const t=[];for(const n of e){const e={a:{},b:{}};for(const t in n){if(t!="a"&&t!="b")e[t]=n[t]}for(const t in n.a){e.a[t]=n.a[t]}for(const t in n.b){e.b[t]=n.b[t]}t.push(e)}return t}function hd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid file header for CNV";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("gene");if(i==-1)return"gene missing from header";n[i]="gene";i=o("cnv");if(i==-1)return"CNV missing from 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n.data)){n.data[r]=[]}n.data[r].push(i)}function gd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid header line for ITD";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("gene");if(i==-1)return"gene missing from header";n[i]="gene";i=o("annovar_isoform","mrna_accession","mrna accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq","isoform");if(i==-1)return"isoform missing from header";n[i]="isoform";i=o("rnaposition");if(i!=-1){n[i]="rnaposition";i=o("rnaduplength");if(i==-1)return"rnaduplength is required when rnaposition is present";n[i]="rnaduplength"}i=o("chromosome","chr");if(i!=-1){n[i]="chr";i=o("chr_start");if(i==-1)return"chr_start is required when chr is present";n[i]="chrpos1";i=o("chr_stop");if(i==-1)return"chr_stop is required when chr is 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t=Number.parseInt(i.chrpos1);if(Number.isNaN(t)||t<0){n.itd.badlines.push([e,"invalid chr_start value",o]);return}i.chrpos1=t;t=Number.parseInt(i.chrpos2);if(Number.isNaN(t)||t<0){n.itd.badlines.push([e,"invalid chr_stop value",o]);return}i.chrpos2=t}if(sd(i,n,e,o,n.itd.badlines)){return}i.dt=qr;i.class=Zr;i.mname="ITD";n.good++;var s=n.geneToUpper?i.gene.toUpperCase():i.gene;if(!(s in n.data)){n.data[s]=[]}n.data[s].push(i)}function yd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid header line for intragenic deletion";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("gene");if(i==-1)return"gene missing from header";n[i]="gene";i=o("annovar_isoform","mrna_accession","mrna accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq","isoform");if(i==-1)return"isoform missing from header";n[i]="isoform";i=o("rnaposition");if(i!=-1){n[i]="rnaposition";i=o("rnadellength");if(i==-1)return"rnadellength is required when rnaPosition is used";n[i]="rnadellength"}i=o("chromosome","chr");if(i!=-1){n[i]="chr";i=o("chr_start");if(i==-1)return"chr_start is required when chr is used";n[i]="chrpos1";i=o("chr_stop");if(i==-1)return"chr_stop is required when chr is used";n[i]="chrpos2"}i=o("sample","sample_name","tumor_sample_barcode");if(i!=-1)n[i]="sample";i=o("patient","donor","target_case_id");if(i!=-1)n[i]="patient";i=o("disease");if(i!=-1)n[i]="disease";i=o("origin");if(i!=-1)n[i]="origin";i=o("sampletype","sample type","sample_type");if(i!=-1)n[i]="sampletype";t.del.header=n;t.del.loaded=true;return false}function vd(e,t,n){if(t==""||t[0]=="#")return;const o=t.split("\t");const i={};for(let e=0;e<n.del.header.length;e++){if(o[e]==undefined)break;i[n.del.header[e]]=o[e]}if(!i.gene){n.del.badlines.push([e,"missing gene",o]);return}if(i.rnaposition){let t=Number.parseInt(i.rnaposition);if(Number.isNaN(t)||t<0){n.del.badlines.push([e,"invalid rnaPosition value",o]);return}i.rnaposition=t;if(!i.rnadellength){n.del.badlines.push([e,"missing rnaDellength value",o]);return}t=Number.parseInt(i.rnadellength);if(Number.isNaN(t)||t<0){n.del.badlines.push([e,"invalid rnaDellength value",o]);return}i.rnadellength=t}if(i.chr){let t=Number.parseInt(i.chrpos1);if(Number.isNaN(t)||t<0){n.del.badlines.push([e,"invalid chr_start value",o]);return}i.chrpos1=t;t=Number.parseInt(i.chrpos2);if(Number.isNaN(t)||t<0){n.del.badlines.push([e,"invalid chr_stop value",o]);return}i.chrpos2=t}if(sd(i,n,e,o,n.del.badlines)){return}i.dt=Hr;i.class=Kr;i.mname="DEL";n.good++;var s=n.geneToUpper?i.gene.toUpperCase():i.gene;if(!(s in n.data)){n.data[s]=[]}n.data[s].push(i)}function wd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid header line for truncation";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("gene");if(i==-1)return"gene missing from 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xd(e,t,n){if(t==""||t[0]=="#")return;const o=t.split("\t");const i={};for(let e=0;e<n.truncation.header.length;e++){i[n.truncation.header[e]]=o[e]}if(!i.gene){n.truncation.badlines.push([e,"missing gene",o]);return}if(i.rnaposition){const t=Number.parseInt(i.rnaposition);if(Number.isNaN(t)||t<0){n.truncation.badlines.push([e,"invalid rnaPosition value",o]);return}i.rnaposition=t}if(i.pos){const t=Number.parseInt(i.pos);if(Number.isNaN(t)||t<0){n.truncation.badlines.push([e,"invalid genomic position",o]);return}i.pos=t}if(!i.losstype){n.truncation.badlines.push([e,"missing lossType value",o]);return}if(i.losstype!="n"&&i.losstype!="c"){n.truncation.badlines.push([e,'lossType value not "n" or "c"',o]);return}if(sd(i,n,e,o,n.truncation.badlines)){return}if(i.losstype=="n"){i.dt=Gr;i.class=Qr;i.mname="N-loss"}else{i.dt=Jr;i.class=ea;i.mname="C-loss"}n.good++;const s=n.geneToUpper?i.gene.toUpperCase():i.gene;if(!(s in n.data)){n.data[s]=[]}n.data[s].push(i)}const _d=["heatmapJSON","piebarJSON","survivalJSON","discoJSON","riverJSON"];const kd={snvindel:0,si:0,sv:1,fusion:2,itd:3,deletion:4,truncation:5,cnv:6};let jd=false;class Nd{constructor(e){this.bt=e;this.err=this.errHandler();if(!jd){const e=Sd();if(e.project){this.getData(e.project);jd=true}}if(e.filediv){this.projectByInput(e.filediv)}}processData(e){const t=e.files.pop();const n=e.expectedFileNames.indexOf(t.name);if(n==-1){if(e.files.length)setTimeout((()=>{this.processData(e)}),1);return}e.expectedFileNames.splice(n,1);this.cohort={name:"project",genome:this.bt.genomes[this.bt.gselect.options[this.bt.gselect.selectedIndex].innerHTML]};if(!this.flag){this.flag=this.bt.init_bulk_flag(this.cohort.genome)}const o=this.bt.content2flag(t.content,t.type,this.flag);if(o){this.err(o);this.processData(e)}else if(!e.files.length){if(e.expectedFileNames.length){this.err('These referenced files were not found: "'+e.expectedFileNames.join('", 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r=this.getTracker(s,(()=>this.processData(i)));Object.keys(o).forEach((e=>{this.getjson("/data/projects/"+t+"/"+e,(t=>{i.schema[o[e]]=t;r()}))}));Object.keys(n).forEach((e=>{this.gettext("/data/projects/"+t+"/"+e,(t=>{i.files.push({name:e,type:n[e],content:t});r()}))}))}))}gettext(e,t){fetch(e).then((t=>{if(t.ok)return t.text();else this.err("File request error: "+e)})).then(t).catch((t=>this.err("File request error: "+e+" "+t)))}getjson(e,t){fetch(e).then((t=>{if(t.ok)return t.json();else this.err("Network error for "+e)})).then(t).catch((t=>this.err("file request error: "+e+" "+t)))}getTracker(e,t){let n=0;return function o(){n+=1;if(n==e){t()}}}projectByInput(e){this.tp=null;const t=e.append("div");t.append("span").html("Project: reference 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o=Array.from(e.target.files);const i=o.filter((e=>e.name==n))[0];if(!i){t.err("Missing reference file='"+n+"'.");return}const s={};const r={};const a={schema:{},files:[],expectedFileNames:[]};const l=new FileReader;let c="";let d=0;l.onload=e=>{e.target.result.trim().split("\n").forEach((e=>{const[n,o]=e.trim().split("\t");if(_d.includes(n)){r[o]=n}else if(!kd[n]&&kd[n]!==0){t.err("Unrecognized type "+n+" for file "+o+" in reference.txt.")}else{s[o]=kd[n]}}));a.expectedFileNames=Object.keys(s);const n=o.filter((e=>e.name in r));let i=0;if(!n.length){o.forEach(l)}else{n.forEach((e=>{const s=new FileReader;s.onload=s=>{const c=JSON.parse(s.target.result);i+=1;if(!c){t.err('Unable to parse schema file="'+e.name+'".')}else{a.schema[r[e.name]]=c}if(i==n.length){o.forEach(l)}};s.onerror=()=>{t.err("Error reading schema.txt.")};s.readAsText(e,"utf8")}))}function l(e){if(!a.expectedFileNames.includes(e.name)){d+=1;return}if(!e){t.err("Error reading 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l=Od(s,e-1,t);if(!s[r.k]){if(e>0){i[l]+=1}break}n[a]=l;if(!(a in i)){i[a]=0}if(!(a in o)){const n={lst:[]};if(r.full){n.full=s[r.full]}n.id0=t[0].k;n.v0=s[t[0].k];if(e==1){n.id1=t[1].k;n.v1=s[t[1].k]}if(e==2){n.id2=t[2].k;n.v1=s[t[2].k]}o[a]=n}o[a].lst.push(s);if(e==t.length-1){i[a]+=1}}}const s=[{id:Ad,name:Ad}];for(const e in n){const t=n[e];const r=o[e];const a=e.split(Cd);s.push({id:e,parentId:t,lst:r.lst,value:i[e],name:a[a.length-1],full:r.full,id0:r.id0,v0:r.v0,id1:r.id1,v1:r.v1,id2:r.id2,v2:r.v2})}return s}function Od(e,t,n){const o=[Ad];for(let i=0;i<t;i++){o.push(e[n[i].k])}if(t>=0){o.push(e[n[t].k])}return o.join(Cd)}function Md(e){const t={id2vcf:{},label:e.name||"Unnamed VCF file"};let n;if(e.file){const o=Math.random().toString();n={file:e.file,indexURL:e.indexURL,vcfid:o};t.id2vcf[o]=n}else if(e.url){const o=Math.random().toString();n={url:e.url,indexURL:e.indexURL,vcfid:o};t.id2vcf[o]=n}else{return["no .file or 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t.annotation[n]){o[e]=t.annotation[n][e]}e.push(o)}const n=Ed(e,t.levels);t.root=wr()(n);t.root.sum((e=>e.value))}if(t.variantsunburst){if(!t.levels)return[".levels missing when .variantsunburst is on from .sampleannotation"]}o.ds.cohort=t}if(e.vcfcohorttrack){if(!e.vcfcohorttrack.file&&!e.vcfcohorttrack.url)return["no .file or .url provided from .vcfcohorttrack"];o.ds.vcfcohorttrack=e.vcfcohorttrack}if(e.germline2dvafplot){if(!e.germline2dvafplot.individualkey)return[".individualkey missing from germline2dvafplot"];if(!e.germline2dvafplot.sampletypekey)return[".sampletypekey missing from germline2dvafplot"];if(!e.germline2dvafplot.xsampletype)return[".xsampletype missing from germline2dvafplot"];if(!e.germline2dvafplot.yleftsampletype)return[".yleftsampletype missing from germline2dvafplot"];if(e.germline2dvafplot.yrightsampletype){if(e.germline2dvafplot.yrightsampletype==e.germline2dvafplot.yleftsampletype)return[".yrightsampletype should not be same as 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e=d.select("path");e.attr("stroke",l)})).on("mouseleave",(()=>{const e=d.select("path");e.attr("stroke",c)})).html(`<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="#000" class="bi bi-x-lg" viewBox="0 0 16 16">\n\t\t  <path stroke='#000' d="M2.146 2.854a.5.5 0 1 1 .708-.708L8 7.293l5.146-5.147a.5.5 0 0 1 .708.708L8.707 8l5.147 5.146a.5.5 0 0 1-.708.708L8 8.707l-5.146 5.147a.5.5 0 0 1-.708-.708L7.293 8 2.146 2.854Z"/>\n\t\t</svg>`).on("mousedown",(e=>{document.body.dispatchEvent(new Event("mousedown"));e.stopPropagation()})).on("click",(()=>{a.on("click",null).on("mousedown",null);s.selectAll("*").remove();if(typeof t.close==="function")t.close()}));const f=a.append("div").classed("sjpp-output-sandbox-collapse-btn",true);const p=a.append("div").classed("sjpp-output-sandbox-expand-btn",true).style("display","none");const u=a.append("div").style("display","inline-flex").style("align-items","center").style("justify-content","left").style("padding","5px 10px");const h=s.append("div").attr("class","sjpp-output-sandbox-content").style("width",((o=t.style)===null||o===void 0?void 0:o.width)||"95vw");let m=true;Wd["collapse"](f,{fontSize:"1.5em",padding:"4px 10px",color:"black",handler:g});Wd["expand"](p,{fontSize:"1.5em",padding:"4px 10px",color:"black",display:"none",handler:g});f.on("mouseenter",(()=>{const e=f.select("path");e.attr("stroke",l)})).on("mouseleave",(()=>{const e=f.select("path");e.attr("stroke",c)}));p.on("mouseenter",(()=>{const e=p.select("path");e.attr("stroke",l)})).on("mouseleave",(()=>{const e=p.select("path");e.attr("stroke",c)}));function g(){m=!m;f.style("display",m==true?"inline-block":"none");p.style("display",m==true?"none":"inline-block");h.style("display",m==true?"block":"none")}return{header_row:a,header:u,body:h,app_div:s,id:r}}function ef(e,t,n,o,i,s){let r,a,l,c,d,f;if(i!==undefined)[a,l,c,d,f]=Xd(i,n);else{[r,a,l,c,d,f]=Mc(e,t,n);r.header.text("Load mutation from text files")}a.append("div").style("margin","20px 0px").style("color","#858585").html(`\n\t<p>Choose one file and upload to initiate the display panel.<br>From there you can add additional files.</p>\n\t<div>Supported data types:</div>\n\t<ul>\n\t  <li>SNV and indel</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1OJ9aXq2_-a3BfIQdKLYCYzrJRTpu4_9i3gephTY-Z38 target=_blank>Format</a>,\n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.snvindel.txt target=_blank>example file</a></li>\n\t  </ul>\n\t  <li>SV or fusion transcript</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1klDZ0MHVkQTW2-lCu_AvpRE4_FcbhdB-yI17wNdPaOM target=_blank>Tabular format</a>,\n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.svfusion.txt target=_blank>example file</a>\n\t\t</li>\n\t\t<li>JSON-format, to come</li>\n\t  </ul>\n\t  <li>CNV, gene-level</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1WHptqOWNf96V0bYEDpj-EsKZGYnbBNc9aQIrhzdEJaU target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.cnv.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>ITD</li>\n\t  <ul>\n\t  \t<li>Internal tandem duplication, in-frame</li>\n\t    <li><a href=https://drive.google.com/open?id=1Bh9awBsraoHbV8iWXv_3oDeXMsjIAHaOKHr973IJyZc target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.itd.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>Intragenic deletion, in-frame</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1tWbf3rg3BmVIZPGGPk023P0aBkDw_ry5XuZLGyGodyg target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.deletion.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>Truncation</li>\n\t  <ul>\n\t  \t<li>Either N-terminus loss or C-terminus loss</li>\n\t    <li><a href=https://drive.google.com/open?id=1P1g-Y8r30pSKfan1BhYZcsUtSk7wRb4plaO1S-JCJr4 target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.truncation.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t</ul>`);const p=()=>{c.selectAll("*").remove();new Nd({bulkin:nf,genomes:n,gselect:l,content2flag:tf,flag2tp:h,filediv:c,init_bulk_flag:id});c.append("span").html("Select data type&nbsp;");const e=Tc(c).style("margin-right","20px");const t=c.append("input").attr("type","file").on("change",(t=>{const o=id(n[l.options[l.selectedIndex].innerHTML]);o.geneToUpper=u.property("checked");d.text("");const i=t.target.files[0];if(!i){p();return}if(i.size==0){d.text("Wrong file: "+i.name);p();return}const s=new FileReader;s.onload=t=>{const n=tf(t.target.result,e.node().selectedIndex,o);if(n){d.text("Error: 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e.t})).then((e=>{e.default(l,u,o)}));return l}return function e(t,n){const o=tf(t.content,n,flag);if(o){d.text("Error: "+o);p();return}h(flag,t)}}function tf(e,t,n){if(!n)return"should not happen!";let o;switch(t){case 0:o=sf(e,n);if(o)return o;break;case 1:o=ff(e,n,true);if(o)return o;break;case 2:o=ff(e,n,false);if(o)return o;break;case 3:o=lf(e,n);if(o)return o;break;case 4:o=cf(e,n);if(o)return o;break;case 5:o=df(e,n);if(o)return o;break;case 6:o=af(e,n);if(o)return o;break;default:return"unknown option array index from file type <select>: "+t}}function nf(e,t=null){const n=e.flag;const o=e.cohort;if(!o.p2st){o.p2st={}}if(!o.dsset){o.dsset={}}if(!o.assaylst){o.assaylst=[]}if(n.variantgene){if(o.variantgene){return"variantgene already set for this cohort"}o.variantgene=n.variantgene}if(n.snv.badlines.length>0){Pc(n.snv.header,n.snv.badlines)}if(n.fusion.badlines.length>0){Pc(n.fusion.header,n.fusion.badlines)}if(n.sv.badlines.length>0){Pc(n.sv.header,n.sv.badlines)}if(n.cnv.badlines.length>0){Pc(n.cnv.header,n.cnv.badlines)}if(n.itd.badlines.length>0){Pc(n.itd.header,n.itd.badlines)}if(n.del.badlines.length>0){Pc(n.del.header,n.del.badlines)}if(n.truncation.badlines.length>0){Pc(n.truncation.header,n.truncation.badlines)}if(n.good==0){return false}const i={};let s=false;if(n.snv.loaded){for(const e of n.snv.header){i[e]=1}if("maf_tumor_v1"in i&&"maf_tumor_v2"in i){s=true}}if(n.cnv.loaded){for(const e of n.cnv.header){i[e]=1}}if(n.fusion.loaded){for(const e of n.fusion.header){i[e]=1}}if(n.sv.loaded){for(const e of n.sv.header){i[e]=1}}if(n.itd.loaded){for(const e of n.itd.header){i[e]=1}}if(n.del.loaded){for(const e of n.del.header){i[e]=1}}if(n.truncation.loaded){for(const e of n.truncation.header){i[e]=1}}const r="sample"in i||"patient"in i;const a="disease"in i;const l="sampletype"in i;let c;if(e.flag2thisds){c=e.flag2thisds;if(r&&!c.hassample){return'"sample" column found in new data but not in existing data'}if(!r&&c.hassample){return'"sample" column found in existing data but not in new data'}if(a&&!c.hasdisease){return'"disease" column found in new data but not in existing data'}if(!a&&c.hasdisease){return'"disease" column found in existing data but not in new data'}if(l&&!c.hasst){return'"sampletype" column found in new data but not in existing data'}if(!l&&c.hasst){return'"sampletype" column found in existing data but not in new data'}for(const e in n.data){const t=c.bulkdata[e];if(t){c.bulkdata[e]=t.concat(n.data[e])}else{c.bulkdata[e]=n.data[e]}}}else{let t=e.filename+(n.tpsetname?"_"+n.tpsetname:"");if(t in n.genome.datasets){let e=1;let o=t+" "+e;while(o in n.genome.datasets){e++;o=t+" "+e}t=o}c={label:t,bulkdata:n.data,hassample:r,hasdisease:a,hastumormaf:s,hasst:l,genome:o.genome,import:{},imported:{},importsilent:n.snv.silent==0?false:n.snv.missense/n.snv.silent>=5?false:true};n.genome.datasets[t]=c;o.dsset[t]=c;if(o.dbexpression){if(o.dbexpression.tidy){try{o.dbexpression.tidy=new Function(o.dbexpression.tidy)}catch(e){err("invalid JavaScript for dbexpression.tidy");delete o.dbexpression}}c.dbexpression=o.dbexpression}if(a){c.stratify=[{label:"disease",attr1:{k:"disease",label:"disease"}}]}}if(r){for(const e in n.data){for(const t of n.data[e]){let e=t.patient;if(!e){e=t.sample;if(!e){continue}}if(!o.p2st[e]){o.p2st[e]={}}let n=t.sampletype;if(!n){n=e}if(!o.p2st[e][n]){o.p2st[e][n]={dsset:{},tktemplate:[]}}if(!o.p2st[e][n].dsset[c.label]){o.p2st[e][n].dsset[c.label]=[]}o.p2st[e][n].dsset[c.label].push(t)}}}if(t)t();return false}function of(e){if(!e.name)e.name="Unnamed dataset";let t=e.holder;if(!t){const e=kc({x:100,y:100});t=e.body}const n=t.append("div");new Promise(((t,n)=>{const o={dsset:{}};for(const t in e){if(t=="snvindel"||t=="svjson"||t=="cnv"||t=="sv"||t=="mutationset"){continue}o[t]=e[t]}t(o)})).then((t=>{if(!e.snvindel&&!e.svjson&&!e.cnv&&!e.sv)return t;const n=id(t.genome);if(e.snvindel){const t=sf(e.snvindel,n);if(t)throw{message:"error in snvindel data: "+t};delete e.snvindel}if(e.svjson){const t=rf(e.svjson,n);if(t)throw{message:"error in svjson data: "+t};delete e.svjson}if(e.sv){const t=ff(e.sv,n);if(t)throw{message:"error in svjson data: "+t};delete e.sv}if(e.cnv){const t=af(e.cnv,n);if(t)throw{message:"error in cnv data: "+t};delete e.cnv}const o=nf({flag:n,filename:e.name,cohort:t});if(o)throw{message:"Error parsing data: "+o};return t})).then((t=>{if(!e.mutationset)return t;if(!Array.isArray(e.mutationset))throw{message:"mutationset is not an array"};const n=[];for(const o of e.mutationset){const i=id(t.genome);const s=[];if(o.snvindel){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.snvindel+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with snvindel file: "+e.error};const t=sf(e.text,i);if(t)throw{message:"error with snvindel file: "+t}}));s.push(n)}if(o.snvindel_url){s.push(Ll("urltextfile",{url:o.snvindel_url}).then((e=>{if(e.error)throw{message:"cannot get snvindel file from url"};const t=sf(e.text,i);if(t)throw{message:"error with snvindel file: "+t}})))}if(o.cnv){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.cnv+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with cnv file: "+e.error};const t=af(e.text,i);if(t)throw{message:"error with cnv file: "+t}}));s.push(n)}if(o.cnv_url){s.push(Ll("urltextfile",{url:o.cnv_url}).then((e=>{if(e.error)throw{message:"cannot get cnv file from url"};const t=af(e.text,i);if(t)throw{message:"error with cnv file: "+t}})))}if(o.sv){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.sv+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with sv file: "+e.error};const t=ff(e.text,i,true);if(t)throw{message:"error with sv file: "+t}}));s.push(n)}if(o.sv_url){s.push(Ll("urltextfile",{url:o.sv_url}).then((e=>{if(e.error)throw{message:"cannot get sv file from url"};const t=ff(e.text,i);if(t)throw{message:"error with sv file: "+t}})))}if(o.fusion){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.fusion+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with fusion file: "+e.error};const t=ff(e.text,i,false);if(t)throw{message:"error with fusion file: "+t}}));s.push(n)}if(o.svjson){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.svjson+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with svjson file: "+e.error};const 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e=s+1;e<o.length;e++){if(o[e]=="")continue;if(o[e][0]=="#")continue;cd(e,o[e],t,n)}}function pf(e,t){e.style("opacity",0).style("display",t||"block").transition().style("opacity",1)}function uf(e,t){e.style("opacity",1).transition().style("opacity",0).call((()=>{if(t){e.remove()}else{e.style("display","none").style("opacity",1)}}))}function hf(e,t){let n;if(typeof t=="string"){n=t}else{n=t.message||t.error;if(t.stack)console.log(t.stack)}const o=e.append("div").attr("class","sja_errorbar");o.append("div").text(n);o.append("div").html("&#10005;").on("click",(()=>{uf(o,true)}))}function mf(e){try{throw new Error}catch(t){const n=t.stack.split("\n");const o=n[2].trim();const i=/\s*at\s+(.*)\s+\((.*).proteinpaint.js:(\d+):(\d+)\)/;const s=o.match(i);if(s){const t=s[1];const n=s[2].replace(/^.*\/bin\//,"").replace(/_([^_]+)$/,".$1").replaceAll(/_/g,"/");const o=`${e} [${n} ${t}()]`;throw new Error(o)}else{throw new Error(e)}}}function gf(e,t){if(typeof e=="string")return hf(t,e);if(e.length===0)return;if(e.length===1)return hf(t,e[0]);let n=false;const o=t.append("div").attr("class","sja_errorbar").on("click",(()=>{n=!n;s.style("display",n?"block":"none")}));const i=o.append("div").style("display","inline-block");i.append("div").style("display","inline-block").style("color","white").style("background-color","red").style("border-radius","100px").style("padding","1px 4px").text(e.length);i.append("div").text("errors found.").style("padding","3px").style("display","inline-block");o.append("div").style("display","inline-block").style("float","right").html("&#10005;").on("click",(()=>{uf(o,true)}));const s=o.append("div").style("display","none").style("margin-left","10px");for(const t of e){s.append("div").text(t)}}async function bf(e,t){const n=await Bl("snp",{method:"POST",body:JSON.stringify({byName:true,genome:e.name,lst:[t]})});if(n.error)throw n.error;if(!n.results||n.results.length==0)throw t+": not a SNP";for(const t of n.results){const n=e.chrlookup[t.chrom.toUpperCase()];if(n&&n.major){return{chr:t.chrom,start:t.chromStart,stop:t.chromEnd}}}const o=n.results[0];return{chr:o.chrom,start:o.chromStart,stop:o.chromEnd}}async function yf(e){if(!e.holder)throw"No holder for block.init";if(!e.genome)throw"no genome";if(e.holder instanceof Element)e.holder=ot(e.holder);if(!e.tklst)e.tklst=[];if(e.query){await vf(e);return}if(e.model&&e.allmodels){await wf(e);return}}async function vf(e){const t=e.holder.append("p").style("font-size","2em").style("color","#858585").text("Searching for "+e.query+" ...");const n=await Bl("genelookup",{body:{deep:1,input:e.query,genome:e.genome.name}});if(!n)throw"querying genes: server error";if(n.error)throw"error querying genes: "+n.error;if(!n.gmlst||n.gmlst.length==0){if(e.genome.hasSNP){try{const n=await bf(e.genome,e.query);t.remove();const o={genome:e.genome,holder:e.holder,chr:n.chr,start:Math.max(0,n.start-300),stop:n.start+300,nobox:true,tklst:e.tklst,debugmode:e.debugmode};tc(e.genome,o.tklst);const i=await import("./block-ec76524e.js").then((function(e){return e.c}));const s=new i.Block(o);s.addhlregion(n.chr,n.start,n.stop-1)}catch(n){t.text("Not a gene or SNP: "+e.query)}}else{t.text("No match to gene: "+e.query)}return}t.remove();e.allmodels=n.gmlst;for(const t of e.allmodels){if(t.isoform.toUpperCase()==(n.found_isoform?n.found_isoform.toUpperCase():e.query.toUpperCase())){e.model=t;await wf(e);return}}const o=[];for(const t of e.allmodels){if(!t.isoform)throw"isoform missing from one gene model: "+JSON.stringify(t);const n=t.isoform.toUpperCase();if(e.genome.isoformcache.has(n)){let o=true;for(const i of e.genome.isoformcache.get(n)){if(i.chr==t.chr&&i.start==t.start&&i.stop==t.stop&&i.strand==t.strand){o=false;break}}if(o){e.genome.isoformcache.get(n).push(t)}}else{e.genome.isoformcache.set(n,[t])}if(t.isoform.toUpperCase()==e.query.toUpperCase()){o.push(t);break}if(t.isdefault){o.push(t)}}if(o.length==1){e.model=o[0]}else if(o.length>1){for(const t of o){if(t.chr=="chrY"){continue}const n=e.genome.chrlookup[t.chr.toUpperCase()];if(!n){continue}if(!n.major){continue}e.model=t;break}if(!e.model){e.model=o[0]}}if(!e.model){e.model=e.allmodels[0]}await wf(e)}async function wf(e){if(e.model.genomicseq){o();xf(e);return}const t={genome:e.genome.name,coord:e.model.chr+":"+(e.model.start+1)+"-"+e.model.stop};const n=await Bl("ntseq",{method:"POST",body:JSON.stringify(t)});if(!n)throw"getting sequence: server error";if(n.error)throw"getting sequence: "+n.error;if(!n.seq)throw"no nt seq???";e.model.genomicseq=n.seq.toUpperCase();e.model.aaseq=Ma(e.model);o();await xf(e);function o(){if(e.model.aaseq){const t=e.model.aaseq.indexOf(Oa);const n=e.model.cdslen-(e.model.startCodonFrame?3-e.model.startCodonFrame:0);if(t!=-1&&t<n/3-1){hf(e.holder,"Translating "+e.model.isoform+" ends at "+t+" AA, expecting "+n/3)}}}}async function xf(e){const t=new Map;for(const n of e.allmodels){if(!n.pdomains){n.pdomains=[];n.domain_hidden={};if(!t.has(n.isoform))t.set(n.isoform,[]);t.get(n.isoform).push(n)}}if(t.size==0){await _f(e);return}const n=await Bl("pdomain",{method:"POST",body:JSON.stringify({genome:e.genome.name,isoforms:[...t.keys()]})});if(n.error)throw"error getting protein domain: "+n.error;if(n.lst){const e=At().range(bc);for(const o of n.lst){for(const e of t.get(o.name)){e.pdomains=o.pdomains}for(const t of o.pdomains){if(!t.color){t.color=e(t.name+t.description)}}}}await _f(e)}async function _f(e){let t=e.gmmode;if(!t){if(e.model.cdslen){t=gc.protein}else{t=gc.exononly}}if(e.dataset){if(!Array.isArray(e.dataset))throw"dataset is not array";for(const t of 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n.Block({genome:e.genome,holder:e.holder,nobox:true,usegm:e.model,gmstackheight:37,allgm:e.allmodels,datasetlst:e.dataset,legacyDsFilter:e.legacyDsFilter,mset:e.mset,hlaachange:e.hlaachange,hlvariants:e.hlvariants,hlregions:e.hlregions,gmmode:t,hidedatasetexpression:e.hidedatasetexpression,hidegenecontrol:e.hidegenecontrol,hidegenelegend:e.hidegenelegend,variantPageCall_snv:e.variantPageCall_snv,datasetqueries:e.datasetqueries,samplecart:e.samplecart,debugmode:e.debugmode,tklst:e.tklst,mclassOverride:e.mclassOverride,hide_dsHandles:e.hide_dsHandles,onloadalltk_always:e.onloadalltk_always})}var kf=Object.freeze({__proto__:null,default:yf});async function jf(e,t){let n=[],o=[];if(e&&e.includes(","))n=e.split(",");else if(e)n.push(e);else if(t&&t.includes(","))o=t.split(",");else if(t)o.push(t);const i=[];if(n.length){const e=undefined;for(const t of n){i.push(await Nf(t,e))}}else if(o.length){const e=undefined;for(const t of o){i.push(await Nf(e,t))}}return i}async function Nf(e,t){const n=await Sf(e,t);Af(n);const o=Cf(n);return o}async function Sf(e,t){if(e!==undefined&&e=="")throw".jsonfile missing";if(t!==undefined&&t=="")throw".jsonurl missing";let n;if(e!==undefined)n=await Ll("textfile",{file:e});else if(t!==undefined)n=await Ll("urltextfile",{url:t});if(n.error){throw n.error}return JSON.parse(n.text)}function Af(e){if(!e)throw"file is missing";if(!e.type)throw"dataset type is missing";const t=e.svcnvfile||e.svcnvurl;const n=e.vcffile||e.vcfurl;if(!t&&!n)throw"vcf or cnv file/url is required";if(Object.keys(e).filter((e=>e.includes("expression"))).length){if(!e.expressionfile&&!e.expressionurl)throw"expression file/url is missing"}if(Object.keys(e).filter((e=>e.includes("rnabam"))).length){if(!e.rnabamfile&&!e.rnabamurl)throw"rnabam file/url is missing"}if(e.sampleset){for(const t of e.sampleset){if(e.sampleset.length!=1&&!t.name)throw"sampleset name is missing";if(!t.samples)throw"sampleset samples[] is missing"}}if(e.sample2assaytrack){for(const[t,n]of 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if(e.svcnvurl)t.url=e.svcnvurl;if(Object.keys(e).filter((e=>e.includes("expression"))).length){t.checkexpressionrank={file:e.expressionfile,url:e.expressionurl}}if(Object.keys(e).filter((e=>e.includes("vcf"))).length){t.checkvcf={file:e.vcffile,url:e.vcfurl}}if(e.vcf){if(e.vcf.hiddenclass){t.vcf=[];t.vcf.hiddenclass=e.vcf.hiddenclass}}if(Object.keys(e).filter((e=>e.includes("rnabam"))).length){t.checkrnabam={file:e.rnabamfile,url:e.rnabamurl}}if(e.sampleset){t.sampleset=e.sampleset}if(e.sample2assaytrack){t.sample2assaytrack=e.sample2assaytrack}if(e.groupsamplebyattr){t.groupsamplebyattr=e.groupsamplebyattr}t.fixedgeneexpression=e.fixedgeneexpression;t.getallsamples=e.getallsamples;t.valueCutoff=e.cnvValueCutoff!==undefined?e.cnvValueCutoff:undefined;t.bplengthUpperLimit=e.cnvLengthUpperLimit!==undefined?e.cnvLengthUpperLimit:undefined;t.segmeanValueCutoff=e.segmeanValueCutoff!==undefined?e.segmeanValueCutoff:undefined;t.lohLengthUpperLimit=e.lohLengthUpperLimit!==undefined?e.lohLengthUpperLimit:undefined;t.multihidelabel_vcf=e.multihidelabel_vcf!==undefined?e.multihidelabel_vcf:undefined;t.multihidelabel_fusion=e.multihidelabel_fusion!==undefined?e.multihidelabel_fusion:undefined;t.multihidelabel_sv=e.multihidelabel_sv!==undefined?e.multihidelabel_sv:undefined;t.legend_vorigin=e.legend_vorigin;return t}async function Ef(e,t){let n={};const o=await Sf(e,t);n.mdssamplescatterplot=o;return n}function Of(e){return!isNaN(parseFloat(e))&&isFinite(e)}function Mf(e,t,n,o,i){if(o>=1){const t=Math.floor(e*o);if(i)return`${t}${n.charAt(0)}`;return`${t} ${t>1?n+"s":""}`}const s=Math.floor(e*o);const r=Math.ceil(e%(1/o));if(r==0){if(i)return`${s}${n.charAt(0)}`;return`${s} ${s>1?n+"s":""}`}if(i)return`${s}${n.charAt(0)}${r}${t.charAt(0)}`;return`${s} ${s>1?n+"s":""} ${r} ${r>1?t+"s":""}`}function If(e="",t=console.warn){const n=e?{search:e}:window.location;const o=new Map;for(const e of n.search.substr(1).split("&")){if(!e)continue;const n=e.split("=");if(n.length==2&&n[0]!=""&&n[1]!=""){let e=decodeURIComponent(n[1]);if(e.startsWith('"')&&e.endsWith('"')||e.startsWith("{")&&e.endsWith("}")||e.startsWith("[")&&e.endsWith("]")){try{e=JSON.parse(e)}catch(e){t(e)}}else if(Of(e)){e=Number(e)}o.set(n[0].toLowerCase(),e)}else if(n.length>2){t(`unexpected '=' character in the URL parameter value for 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When the next window opens,`+`\n- You may need to allow popups.`+`\n- You may have to refresh it.`+`\n- After the session is recovered, this browser window should automatically close.`);document.body.innerHTML=`\n\t\t\t<div style='margin: 20px; padding: 20px; font-size: 24px'>\n\t\t\t\tPlease close this browser tab. The recovered session should visible in another browser tab.\n\t\t\t</div>\n\t\t`}const i=window.open(n.href,"_blank")}async function Rf(e){const t=If();if(t.has("appcard")){const n=await Promise.resolve().then((function(){return ih}));const o=t.get("appcard");const i=await Pl("/cards/index.json");e.app.drawer.opts.genomes=e.genomes;e.app.drawer.opts.fromApp=true;e.app.drawer.opts.app={cardsPath:"cards"};const s=i.elements.findIndex((e=>e.sandboxJson==o||e.sandboxHtml==o));if(s<=0){const t=[...i.elements.filter((e=>e.type=="nestedCard"))];let s,r;t.findIndex((e=>{for(const[t,n]of e.children.entries()){if(n.sandboxJson==o||n.sandboxHtml==o){s=e;r=t}}}));n.openSandbox(s.children[r],e.app.drawer.opts)}else{n.openSandbox(i.elements[s],e.app.drawer.opts)}return}if(t.has("gdcbamslice")){const n=await import("./bam-95f36008.js");n.bamsliceui({genomes:e.genomes,holder:e.holder,debugmode:e.debugmode,stream2download:t.has("stream2download")});return}if(t.has("gdcmaf")){const t=await import("./maf-72e5b7da.js");t.gdcMAFui({holder:e.holder,debugmode:e.debugmode});return}if(t.has("gdcsinglecell")){const t=await import("./singlecell-7c851ef8.js");t.gdcSinglecellUi({holder:e.holder,debugmode:e.debugmode});return}if(t.has("mdsjsonform")){const t=await import("./mdsjsonform-7f0b6cc7.js");await t.init_mdsjsonform(e);return}if(t.has("termdb")){const n=t.get("termdb");const o=typeof n==="string"?JSON.parse(n):n;const i={holder:e.holder,state:o};const s=await import("./app-bfce9bf5.js");s.appInit(i);return}if(t.has("massnative")){const n=t.get("massnative");const[o,i]=n.split(",");if(!o||!i)throw'value is not "genome,dslabel"';const s={holder:e.holder,genome:e.genomes[o],state:{genome:o,dslabel:i}};if(!s.genome)throw"invalid genome";const r=await import("./app-de19f41c.js");r.appInit(s);return}if(t.has("mass")){const n=t.get("mass");const o=typeof n==="string"?JSON.parse(n):n;const i={holder:e.holder,state:o};if(o.genome){i.genome=e.genomes[o.genome]}else if(o?.vocab?.genome){i.genome=e.genomes[o.vocab.genome]}const s=await import("./app-de19f41c.js");s.appInit(i);return}if(t.has("mass-session-file")||t.has("mass-session-url")){let n;if(t.has("mass-session-file")){const o=t.get("mass-session-file");const i=await Bl(`/textfile`,{method:"POST",body:JSON.stringify({file:o})});const s=JSON.parse(i.text);n={holder:e.holder,state:s,genome:e.genomes[s.vocab.genome]}}if(t.has("mass-session-url")){const o=t.get("mass-session-url");const i=await Bl("/urltextfile",{method:"POST",body:JSON.stringify({url:o})});const s=JSON.parse(i.text);n={holder:e.holder,state:s,genome:e.genomes[s.vocab.genome]}}const o=await import("./app-de19f41c.js");o.appInit(n);return}if(t.has("mass-session-id")){const n=t.get("mass-session-id");const o=t.get("src");let i;if(o=="browser"){const e=localStorage.getItem("savedMassSessions");const t=JSON.parse(e);i={state:t[n]}}else{const e={headers:{},body:{id:n}};if(o=="cred"){const n=t.get("dslabel");const o=t.get("route");e.body.dslabel=n;e.body.route=o;e.body.route=o;const i=localStorage.getItem("jwtByDsRoute")||`{}`;this.jwtByDsRoute=JSON.parse(i);const s=this.jwtByDsRoute[n][o];e.headers.authorization=`Bearer ${btoa(s)}`}i=await Bl(`/massSession`,e);if(i.error)throw i.error}const s=i.state?.embedder;if(s&&s.origin!=window.location.origin){Tf(i);return}const r={holder:e.holder,state:i.state,genome:e.genomes[i.state.vocab.genome],sessionDaysLeft:i.sessionDaysLeft,sessionId:n};const a=await import("./app-de19f41c.js");a.appInit(r);return}if(t.has("genome")&&e.selectgenome){const n=t.get("genome");const o=[...e.selectgenome.node().childNodes];const i=o.findIndex((e=>e.value==n));if(i==-1){hf(e.holder,`Invalid genome: ${n}. Please provide an available genome from this list: ${o.map((e=>e.value)).join(", ").replace(/,(?=[^,]*$)/,", or")}`);return}e.selectgenome.node().selectedIndex=i;e.selectgenome.node().dispatchEvent(new Event("change"))}if(t.has("hicfile")||t.has("hicurl")){let n,o,i;if(t.has("hicfile")){n=t.get("hicfile");i=n.split("/").pop()}else{o=t.get("hicurl");i=o.split("/").pop()}const s=t.get("genome");if(!s)throw"genome is required for hic";const r=e.genomes[s];if(!r)throw"invalid genome";const a={genome:r,file:n,url:o,name:i,hostURL:e.hostURL,enzyme:t.get("enzyme"),holder:e.holder};const l=await import("./HicApp-bcf8330c.js");await l.hicInit(a);return}if(t.has("singlecell")){if(!t.has("genome"))throw'"genome" is required for "singlecell"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i=await import("./singlecell-a668bb17.js");i.init({genome:o,jsonfile:t.get("singlecell")},e.holder);return}if(t.has("mavbfile")){if(!t.has("genome"))throw'"genome" is required for "mavb"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i=await import("./mavb-37fffd68.js");i.mavbparseinput({genome:o,hostURL:e.hostURL,file:t.get("mavbfile")},(()=>{}),e.holder,e.jwt);return}if(t.has("mavburl")){if(!t.has("genome"))throw'"genome" is required for "mavb"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i=await import("./mavb-37fffd68.js");i.mavbparseinput({genome:o,hostURL:e.hostURL,url:t.get("mavburl")},(()=>{}),e.holder,e.jwt);return}if(t.has("scatterplot")){if(!t.has("genome"))throw'"genome" is required for "scatterplot"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;let i;if(t.has("mdsjson")||t.has("mdsjsonurl")){const e=t.get("mdsjsonurl");const n=t.get("mdsjson");i=await Ef(n,e)}if(t.has("tsnejson")){const e=t.get("tsnejson");const n=await Ll("textfile",{file:e});if(n.error)throw n.error;else if(n.text){i={mdssamplescatterplot:{analysisdata:JSON.parse(n.text)}}}}i.mdssamplescatterplot.genome=o;const s=await import("./mds.samplescatterplot-362f3591.js");s.init(i.mdssamplescatterplot,e.holder,false);return}if(t.has("block")){if(!t.has("genome"))throw"missing genome for block";const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i={nobox:1,hostURL:e.hostURL,jwt:e.jwt,holder:e.holder,genome:o,dogtag:n,debugmode:e.debugmode};let s=null;let r=null;if(t.has("position")){const e=t.get("position").split(";");if(e[0]){const t=e[0].split(/[:-]/);const n=t[0];const o=Number.parseInt(t[1]);const i=Number.parseInt(t[2]);if(!n)throw"chr missing";if(Number.isNaN(o)||Number.isNaN(i))throw"Invalid start/stop value in position";s={chr:n,start:o,stop:i}}const n=[];for(let t=1;t<e.length;t++){if(!e[t])continue;const o=e[t].split(/[:-]/);const i=o[0];const s=Number.parseInt(o[1]);const r=Number.parseInt(o[2]);if(!i)throw"subpanel chr missing";if(Number.isNaN(s)||Number.isNaN(r))throw"Invalid start/stop value in subpanel position";n.push({chr:i,start:s,stop:r,width:600,leftborder:"rgba(200,0,0,.1)",leftpad:5})}if(n.length){i.subpanels=n}}if(t.has("regions")){r=[];for(const e of t.get("regions").split(",")){const t=e.split(/[:-]/);t[0];const n=Number.parseInt(t[1]);const o=Number.parseInt(t[2]);if(Number.isNaN(n)||Number.isNaN(o))throw"Invalid start/stop value in regions";r.push({chr:t[0],start:n,stop:o})}}if(!s&&!r){if(o.defaultcoord){s={chr:o.defaultcoord.chr,start:o.defaultcoord.start,stop:o.defaultcoord.stop}}}if(s){i.chr=s.chr;i.start=s.start;i.stop=s.stop}else if(r){i.rglst=r}if(t.has("hlregion")){const e=[];for(const n of t.get("hlregion").split(",")){const t=Ld(n,o,true);if(t)e.push(t)}if(e.length)i.hlregions=e}i.datasetqueries=Lf(t);i.tklst=await $f(t,o);tc(e.genomes[n],i.tklst);zf(t,i.tklst);const a=await import("./block-ec76524e.js").then((function(e){return e.c}));new a.Block(i);return}if(t.has("gene")){const n=t.get("gene");if(n.length==0)throw"zero length query string";const o={hostURL:e.hostURL,query:n,holder:e.holder,variantPageCall_snv:e.variantPageCall_snv,samplecart:e.samplecart,debugmode:e.debugmode};{let n;for(let t in e.genomes){if(e.genomes[t].isdefault){n=t;break}}if(t.has("genome")){n=t.get("genome")}if(!n)throw"No genome, and none set as default";o.genome=e.genomes[n];if(!o.genome)throw"invalid genome: "+n}if(t.has("dataset")){o.dataset=t.get("dataset").split(",")}if(t.has("hlaachange")){o.hlaachange=new Map;for(const e of t.get("hlaachange").split(",")){o.hlaachange.set(e,false)}}if(t.has("hlregion")){const e=[];for(const n of t.get("hlregion").split(",")){const t=Ld(n,o.genome,true);if(t)e.push(t)}if(e.length)o.hlregions=e}o.tklst=await $f(t,o.genome);zf(t,o.tklst);o.datasetqueries=Lf(t);await yf(o);return}if(t.has("disco")){const n=t.get("genome");const o=e.genomes[n];if(!o)throw"genome missing";const i=t.get("dslabel");if(!i)throw"dslabel missing";const s=t.get("sample");if(!s)throw"sample_id missing";const r=(await import("./FilterRxComp-0e75dd8d.js").then((function(e){return e.z}))).vocabInit({state:{genome:n,dslabel:i}});const a=await r.getTermdbConfig();await(await import("./plot.disco-70d493f4.js")).default(a,i,{sample_id:s},e.holder,o);return}if(t.has("study")){const n=t.get("study");if(n!=""){Fd(e.genomes,n,e.holder,e.hostURL,undefined,false,e.app||{debugmode:e.debugmode,instanceTracker:e.instanceTracker||{},callbacks:e.callbacks||{}})}}}function Lf(e){if(!e.has("mds"))return;const t=e.get("mds").split(",");if(t[0]&&t[1]){const n={dataset:t[0],querykey:t[1]};if(e.has("sample")){n.singlesample={name:e.get("sample")};n.getsampletrackquickfix=true}return[n]}return}async function $f(e,t){const n=[];if(e.has("mds3")){const t=e.get("mds3").split(",");for(const o of t){const t={type:mc.mds3,dslabel:o};if(e.has("token"))t.token=e.get("token");if(e.has("filterobj"))t.filterObj=e.get("filterobj");n.push(t)}}if(e.has("mds3bcffile")){const[t,o]=e.get("mds3bcffile").split(",");if(t&&o){n.push({type:mc.mds3,name:t,bcf:{file:o}})}}if(e.has("mds3bcfurl")){const[t,o,i]=e.get("mds3bcfurl").split(",");if(t&&o){n.push({type:mc.mds3,name:t,bcf:{url:o,indexURL:i}})}}if(e.has("arcfile")){const t=e.get("arcfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.hicstraw,name:t[e],bedfile:t[e+1],mode_hm:false,mode_arc:true})}}}if(e.has("mdsjsoncache")){const t=await Pl("mdsjsonform",{method:"POST",body:JSON.stringify({draw:e.get("mdsjsoncache")})});if(t.error)throw t.error;Af(t.json);const o=Cf(t.json);n.push(o)}if(e.has("mdsjson")||e.has("mdsjsonurl")){const t=e.get("mdsjsonurl");const o=e.get("mdsjson");const i=await jf(o,t);n.push(...i)}if(e.has("tkjsonfile")){const o=await Ll("textfile",{file:e.get("tkjsonfile")});if(o.error)throw o.error;if(!o.text)throw".text missing";const i=JSON.parse(o.text);for(const e of i){if(e.isfacet){if(!t.tkset)t.tkset=[];if(!e.tracks)throw".tracks[] missing from a facet table";if(!Array.isArray(e.tracks))throw".tracks[] not an array from a facet table";e.tklst=e.tracks;delete e.tracks;for(const t of e.tklst){if(!t.assay)throw".assay missing from a facet track";if(!t.sample)throw".sample missing from a facet track";t.tkid=Math.random().toString()}t.tkset.push(e)}else{n.push(e)}}}if(e.has("bamfile")){const t=e.get("bamfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bam,name:t[e],file:t[e+1]})}}}if(e.has("bamurl")){const t=e.get("bamurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bam,name:t[e],url:t[e+1]})}}}if(e.has("bedjfile")){const t=e.get("bedjfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bedj,name:t[e],file:t[e+1]})}}}if(e.has("bedjurl")){const t=e.get("bedjurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bedj,name:t[e],url:t[e+1]})}}}if(e.has("hictkfile")||e.has("hictkurl")){const t=e.has("hictkfile");const o=e.get(t?"hictkfile":"hictkurl").split(",");const i=e.has("hictknorm")?e.get("hictknorm").split(","):null;for(let e=0;e<o.length;e+=3){if(o[e]&&o[e+1]&&o[e+2]){const s={type:mc.hicstraw,name:o[e],enzyme:o[e+1],normalizationmethod:i?i[e/3]:null};if(t){s.file=o[e+2]}else{s.url=o[e+2]}n.push(s)}}}if(e.has("ldfile")){const t=e.get("ldfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.ld,name:t[e],file:t[e+1]})}}}if(e.has("bigwigfile")){const t=e.get("bigwigfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bigwig,name:t[e],file:t[e+1],scale:{auto:1}})}}}if(e.has("bigwigurl")){const t=e.get("bigwigurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bigwig,name:t[e],url:t[e+1],scale:{auto:1}})}}}if(e.has("junctionfile")){const t=e.get("junctionfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.junction,name:t[e],tracks:[{file:t[e+1]}]})}}}if(e.has("junctionurl")){const t=e.get("junctionurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.junction,name:t[e],tracks:[{url:t[e+1]}]})}}}if(e.has("vcffile")){const t=e.get("vcffile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"vcf",name:t[e],file:t[e+1]})}}}if(e.has("vcfurl")){const t=e.get("vcfurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"vcf",name:t[e],url:t[e+1]})}}}if(e.has("aicheckfile")){const t=e.get("aicheckfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"aicheck",name:t[e],file:t[e+1]})}}}if(e.has("bampilefile")){const t=e.get("bampilefile").split(",");let o=null;if(e.has("bampilelink")){o=e.get("bampilelink").split(",").map(decodeURIComponent)}for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){const i={type:mc.bampile,name:t[e],file:t[e+1]};if(o&&o[e/2]){i.link=o[e/2]}n.push(i)}}}if(e.has("svcnvfpkmurl")){const t=e.get("svcnvfpkmurl").split(",");const o=t[0];const i={};for(let e=1;e<t.length;e+=2){i[t[e]]=t[e+1]}if(i.svcnv||i.vcf){const e={type:mc.mdssvcnv,name:o};if(i.svcnv){e.url=i.svcnv}if(i.vcf){e.checkvcf={url:i.vcf,indexURL:i.vcfindex}}if(i.fpkm){e.checkexpressionrank={datatype:"FPKM",url:i.fpkm,indexURL:i.fpkmindex}}n.push(e)}}if(e.has("svcnvfpkmfile")){const t=e.get("svcnvfpkmfile").split(",");const o=t[0];const i={};for(let e=1;e<t.length;e+=2){i[t[e]]=t[e+1]}if(i.svcnv||i.vcf){const e={type:mc.mdssvcnv,name:o};if(i.svcnv){e.file=i.svcnv}if(i.vcf){e.checkvcf={file:i.vcf}}if(i.fpkm){e.checkexpressionrank={datatype:"FPKM",file:i.fpkm}}n.push(e)}}if(e.has("mdsjunctionfile")){const t=e.get("mdsjunctionfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"mdsjunction",name:t[e],file:t[e+1]})}}}if(e.has("junctionmatrix")){const t=e.get("junctionmatrix").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"mdsjunction",name:t[e],file2:t[e+1]})}}}if(e.has("junctionrnapeg")){const t=e.get("junctionrnapeg").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.junction,name:t[e],tracks:[{rnapegfile:t[e+1]}]})}}}for(const e of n){if(e.type=="mds3"&&e.dslabel)continue;e.iscustom=true}if(e.has("isdense")){n.filter((e=>e.type==mc.mdssvcnv)).forEach((e=>{e.isdense=true;e.isfull=false}))}if(e.has("sample")){n.filter((e=>e.type==mc.mdssvcnv)).forEach((t=>{t.singlesample={name:e.get("sample")};t.getsampletrackquickfix=true}))}return n}function zf(e,t){if(e.has("bedjfilterbyname")){for(const n of t){if(n.type=="bedj")n.filterByName=e.get("bedjfilterbyname")}}}function Pf(e){const t=e.div.append("button").attr("type","submit").style("background-color",e.backgroundColor?e.backgroundColor:"#cfe2f3").style("margin",e.margin?e.margin:"20px 20px 0px 20px").style("padding","8px").style("border","none").style("border-radius","3px").style("display","inline-block").text(e.text);return t}function Df(e){const t=e.tip,n=e.row;let o,i=150;if("placeholder"in e){o=e.placeholder}else if(e.geneOnly){o="Gene";i=100}else{o="Gene, position";if(e.genome.hasSNP){o+=", dbSNP";i+=40}if(e.allowVariant){o+=", variant";i+=40}}const s=n.append("input").attr("type","text").attr("placeholder",o).attr("aria-label","Gene symbol, position, or alias").attr("class","sja_genesearchinput").style("width",i+"px").on("focus",(e=>{e.target.select()})).on("keyup",(async n=>{const o=n.target;const i=o.value.trim();if(i.length<=1)return t.hide();r.mark.html("");r.word.style("font-size","0.7em");if(e.hideHelp){r.word.text("")}else{r.word.text("Press ENTER to search, ESC to cancel")}if(Jc(n)){o.blur();t.hide();if(e.geneOnly){const e=t.d.select(".sja_menuoption");if(e.size()>0&&e.attr("isgene")){const t=e.text();p({geneSymbol:t},i)}else{p(null,"not a 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r={mark:n.append("span").style("margin-left","5px"),word:n.append("span").style("margin-left","5px").style("font-size",".8em").style("opacity",.6)};async function a(){const n=s.property("value").trim();if(!n)return;if(e.allowVariant){const t=await Uf(n,e.genome);if(t){return}}const o=Ld(n,e.genome,true);if(o){return}t.showunder(s.node()).clear();try{const o=await Bl("genelookup",{body:{genome:e.genome.name,input:n}});if(o.error)throw o.error;if(!o.hits||o.hits.length==0)return t.hide();for(const n of o.hits){t.d.append("div").text(n).attr("class","sja_menuoption").style("border-radius","0px").attr("isgene",1).on("click",(()=>{if(e.geneOnly){p({geneSymbol:n},n);t.hide()}else{c(n)}}))}}catch(e){t.d.append("div").text(e.message||e)}}const l=td.debounce(a,500);async function c(n){t.hide();try{const o=await Bl("genelookup",{body:{genome:e.genome.name,input:n,deep:1}});if(o.error)throw o.error;if(!o.gmlst||o.gmlst.length==0){if(e.genome.hasSNP){if(n.toLowerCase().startsWith("rs")){await 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center; font-style:oblique; color: #403f3f;">${e.opts.element.description}</p>`)}e.makeRibbon=function(e){const n=t.append("div").classed("sjpp-app-drawer-card-ribbon",true).style("align-items","center").style("justify-content","center");const o=e.text.toUpperCase();const i=o=="BETA"?"#418cb5":o=="NEW"?"#1ba176":o=="UPDATED"?"orange":e.color?e.color:"red";n.append("span").text(o).style("color","white").style("background-color",Kt(i).darker()).style("height","auto").style("width","100%").style("top","15%").style("left","-30%").style("font-size","11.5px").style("text-transform","uppercase").style("text-align","center")};if(e.opts.element.ribbon){const t=new Date;const n=new Date(e.opts.element.ribbon.expireDate);if(n>t||n=="Invalid Date")e.makeRibbon(e.opts.element.ribbon)}t.on("click",(async t=>{t.stopPropagation();await e.app.dispatch({type:"is_apps_btn_active",value:false});vh(e);await zu(e.opts.element,e.opts)}))}class lh{constructor(e){this.type="button";this.opts=this.validateOpts(e);this.holder=e.holder;this.dom=e.dom;this.sandboxDiv=e.sandboxDiv;dh(this)}validateOpts(e){if(!e.element.name)throw`Button name is missing`;if(!e.element.sandboxJson&&!e.element.sandboxHtml)throw`Either .sandboxJson or .sandboxHtml is missing for button=${e.element.name}`;return e}main(){}}const ch=al(lh);function dh(e){const t=Pf({div:e.holder,text:e.opts.element.name,margin:"20px 20px 0px"});t.attr("class","sjpp-appdrawer-dataset-btn").on("click",(async t=>{t.stopPropagation();await e.app.dispatch({type:"is_apps_btn_active",value:false});vh(e);await zu(e.opts.element,e.opts)}))}class fh{constructor(e){this.type="layout";this.dom={holder:e.dom.drawerDiv,wrapper:e.dom.wrapper,sandboxDiv:e.dom.sandboxDiv};this.state=e.state;this.hasStatePreMain=true}async validateIndexJson(){const e=await this.getIndexJson();if(!e.elements)throw`Missing elements array`;if(!e.elements.length)throw`No element objects provided`;if(e.columnsLayout){if(e.columnsLayout.length==0)throw`Missing column objects`;const t=e.columnsLayout.map((e=>e.gridarea));if(t.length!=new Set(t).size)throw`Duplicate values for .gridarea found`;const n=[];for(const t of e.columnsLayout){if(!t.gridarea)throw`Missing column .gridarea for column = ${t.name}`;if(!t.sections||t.sections.length==0)throw`Missing section objects for column = ${t.name}`;for(const e of t.sections){if(!e.id)throw`Missing section .id in ${e.name?`section = ${e.name}`:`column = ${t.name} array`}`;n.push(e.id)}if(t.sections.length!=new Set(t.sections).size){throw`Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`}}if(n.length!=new Set(n).size)throw`Duplicate values for section.id found`;for(const t of e.elements){if(!t.section)throw`.section is missing for ${t.type} = ${t.name}`;if(!n.some((e=>e==t.section)))throw`section = ${t.section} for ${t.type} = ${t.name} is not a column section`}}return e}async getIndexJson(){const e=await Bl(this.app.cardsPath+"/index.json");if(e.error){xc(this.dom.holder.append("div"),e.error);return}return e}async init(){this.index=await this.validateIndexJson();this.elementsRendered=false;uh(this);this.elements=this.index.elements.filter((e=>!e.hidden));this.layout=this.index.columnsLayout?this.index.columnsLayout:null;this.components={elements:[]}}async main(){if(this.elementsRendered==true)return;this.elementsRendered=true;for(const e of this.elements){const t=ot(this.layout?`#${e.section} > .sjpp-element-list`:`.sjpp-element-list`);if(e.type=="card"||e.type=="nestedCard"){this.components.elements.push(await rh({app:this.app,holder:t.style("display","grid").style("grid-template-columns","repeat(auto-fit, minmax(320px, 1fr))").style("gap","10px").style("list-style","none").style("margin","15px 0px"),element:e,dom:this.opts.dom,state:this.state,sandboxDiv:this.dom.sandboxDiv}))}else if(e.type=="dsButton"){this.components.elements.push(await ch({app:this.app,holder:t,element:e,dom:this.opts.dom,state:this.state,sandboxDiv:this.dom.sandboxDiv}))}}}}const ph=dl(fh);function uh(e){if(!e.index.columnsLayout)hh(e);if(e.index.columnsLayout)mh(e)}function hh(e){const t=e.dom.wrapper.append("div").style("display","flex").style("padding","10px").classed("sjpp-element-list",true);return t}function mh(e){const t=e.dom.wrapper.append("div").style("display","grid").style("grid-template-columns","repeat(auto-fit, minmax(425px, 1fr))").style("gap","10px").style("padding","10px").style("text-align","left");const n=[];for(const t of e.index.columnsLayout)n.push(t.gridarea);t.style("grid-template-areas",`"${n.toString().replace(","," ")}"`);for(const n of e.index.columnsLayout){const e=t.append("div").style("grid-area",n.gridarea).classed(".sjpp-track-cols",true);for(const t of n.sections)o(t,e)}function o(e,t){const n=t.append("div").attr("id",e.id);if(e.name)n.append("h5").classed("sjpp-appdrawer-cols",true).style("color",Kt(Ir).darker()).text(e.name);n.append("div").classed("sjpp-element-list",true).style("padding","10px");return n}}class gh{constructor(e){this.type="mainBtn";this.opts=this.validateOpts(e);this.dom=e.dom;this.state=e.state;this.hasStatePreMain=true;yh(this)}validateOpts(e){return e.app.opts}getState(e){return{appBtnActive:e.appBtnActive}}async init(){this.btnRendered=false;this.drawerFullHeight="";try{if(window.location.pathname=="/"&&!window.location.search.length)await this.app.dispatch({type:"is_apps_btn_active",value:true});this.components={layout:[]}}catch(e){throw e}}async main(e){if(this.app.getState(e).appBtnActive==true&&this.btnRendered==false){this.dom.drawerDiv.style("background-color","#f5f5f5");this.components.layout.push(await ph({app:this.app,dom:this.dom,state:this.state}));setTimeout((()=>{this.drawerFullHeight=this.dom.drawerDiv.node().getBoundingClientRect().height+5}),this.state.duration+5);vh(this);this.btnRendered=true}if(this.state.appBtnActive==false&&this.btnRendered==true)vh(this)}}const bh=dl(gh);function yh(e){e.dom.btnWrapper.style("background-color",e.state.appBtnActive?"#b2b2b2":"#f2f2f2").style("color",e.state.appBtnActive?"#fff":"#000").on("click",(async t=>{t.stopPropagation();await e.app.dispatch({type:"is_apps_btn_active"});vh(e);if(e.state.appBtnActive){setTimeout((()=>{e.drawerFullHeight=e.dom.drawerDiv.node().getBoundingClientRect().height+5}),e.state.duration+5)}}));e.dom.btn.attr("class","sja_menuoption").style("display","inline-block").style("background-color","transparent").style("color",e.state.appBtnActive?"#fff":"#000").style("padding",e.opts.padw_sm).style("margin","0px 5px").style("cursor","pointer").text("Apps");e.dom.drawerHint.style("position","relative").style("display","inline-block").style("height",e.state.arrowSize.closed+"px").style("width",e.state.appBtnActive?e.state.hintWidth.open:e.state.hintWidth.closed).style("background-color","transparent").style("text-align","center").style("cursor","pointer");e.dom.drawerArrow.style("position","absolute").style("font-size",e.state.arrowSize.closed+"px").style("right",e.state.hintPos.closed.rt+"px").style("bottom",e.state.hintPos.closed.btm+"px").style("background-color","transparent").style("color",e.state.arrowColor.closed).style("opacity",e.state.appBtnActive?0:1).style("cursor","pointer").html("&#9660;");e.dom.drawerArrowOpen.style("position","absolute").style("font-size",e.state.arrowSize.open+"px").style("left",e.state.hintPos.open.left+"px").style("bottom",e.state.hintPos.open.btm+"px").style("transform","rotate(180deg)").style("background-color","transparent").style("color",e.state.arrowColor.open).style("opacity",e.state.appBtnActive?1:0).style("cursor","pointer").style("pointer-events",e.state.appBtnActive?"auto":"none").html("&#9660;");e.drawerFullHeight=e.dom.drawerRow.node().getBoundingClientRect().height+5}async function vh(e){e.dom.btnWrapper.transition().duration(e.opts.state.duration).style("background-color",e.state.appBtnActive?"#b2b2b2":"#f2f2f2").style("color",e.state.appBtnActive?"#fff":"#000");e.dom.btn.transition().duration(e.opts.state.duration).style("color",e.state.appBtnActive?"#fff":"#000");e.dom.drawerDiv.style("display","inline-block").transition().duration(e.opts.state.duration).style("top",e.state.appBtnActive?"0px":"-"+e.drawerFullHeight+"px");e.dom.drawerRow.transition().duration(e.opts.state.duration).style("height",e.state.appBtnActive?e.drawerFullHeight+"px":"0px");e.dom.drawerHint.transition().duration(e.opts.state.duration).style("width",e.state.appBtnActive?e.opts.state.hintWidth.open:e.opts.state.hintWidth.closed);e.dom.drawerArrow.transition().duration(e.opts.state.duration).style("opacity",e.state.appBtnActive?0:1);e.dom.drawerArrowOpen.style("pointer-events",e.state.appBtnActive?"auto":"none").transition().duration(e.opts.state.duration).style("opacity",e.state.appBtnActive?1:0)}class wh{constructor(e){this.type="store";this.defaultState={duration:500,hintPos:{open:{btm:-42,left:13},closed:{btm:3,rt:5}},hintWidth:{open:"0px",closed:"18px"},arrowSize:{open:42,closed:20},arrowColor:{open:"rgb(242,242,242)",closed:"rgb(85,85,85)"},appBtnActive:false}}async init(){}}const xh=cl(wh);wh.prototype.actions={is_apps_btn_active(e){this.state.appBtnActive="value"in e?e.value:!this.state.appBtnActive}};class _h{constructor(e){this.type="app";const t=e.drawerRow.append("div").style("position","relative").style("margin","0 20px").style("padding",`0 ${e.padw_sm}`).style("display","inline-block").style("overflow","hidden").style("border-radius","0px 0px 5px 5px").style("width","93vw").classed("sjpp-drawer-div",true);const n=e.headbox.append("div").style("position","relative").style("display","inline-block").style("margin-left","5px").style("margin-right","5px").style("border-radius","5px").classed("sjpp-apps-btn-wrapper",true);this.dom={drawerRow:e.drawerRow,drawerDiv:t,sandboxDiv:e.sandboxDiv,btnWrapper:n,btn:n.append("div"),drawerHint:n.append("div"),drawerArrow:n.append("div"),drawerArrowOpen:n.append("div"),wrapper:t.append("div")}}preApiFreeze(e){e.cardsPath=this.opts.cardsPath}async init(){try{this.store=await xh({app:this.api,state:this.opts.state});this.state=await this.store.copyState();this.components={mainBtn:await bh({app:this.api,dom:this.dom,state:this.state,indexJson:this.indexJson})};await this.api.dispatch()}catch(e){throw e}}main(){}}const kh=ll(_h);class jh{constructor(e){this.holder=e.holder;this.input=e.holder.append("input");this.tip=e.tip||new ec({border:"",padding:"0px"});this.style=e.style||{};this.size=e.size||20;this.placeholder=e.placeholder||"";this.title=e.title||"";this.searchItems=e.searchItems;this.app=e.app}initUI(){this.holder.style("padding","padding"in this.style?this.style.padding:"5px").style("display","inline-block");this.input.attr("class","sjpp-input-search").style("border","border"in this.style?this.style.border:"5px").attr("size",this.size).attr("placeholder",this.placeholder).attr("title",this.title).on("keyup",(e=>Wf(this,void 0,void 0,(function*(){if(Jc(e))yield this.enterSearch();td.debounce(this.addSearchItems(),400)}))))}addSearchItems(){return Wf(this,void 0,void 0,(function*(){if(!this.input.property("value").trim()){this.tip.hide();return}try{this.tip.clear().showunder(this.input.node());const e=this.tip.d.append("div");const t=yield this.searchItems();yield e.append("div").style("display","flex").selectAll().data(t.filter((e=>e.items.length>=1))).enter().append("div").style("display","block").style("border-left","0.5px solid lightgrey").each(this.showResultsList)}catch(e){if(e.stack)console.log(e.stack);else mf(e)}}))}showResultsList(e){return Wf(this,void 0,void 0,(function*(){e.wrapper=ot(this);e.wrapper.style("padding","5px");e.titleDiv=e.wrapper.append("span").style("padding","3px 0px 5px").style("opacity",.65).style("font-size","0.8em").text(e.title);yield e.wrapper.append("div").classed("sjpp-result-wrapper",true).selectAll("div").data(e.items).enter().append("div").classed("sja_menuoption",true).classed("sjpp-search-result",true).style("display","block").style("padding-left","10px").style("background-color",e.color||"").text((e=>e.name||e.label||e)).on("click",((t,n)=>{t.stopPropagation();e.callback(n)}))}))}enterSearch(){return Wf(this,void 0,void 0,(function*(){if(!this.input.property("value").trim())return;const e=this.tip.d.select(".sjpp-result-wrapper").node();const t=this.tip.d.select(".sjpp-search-result").node();if(t!=null&&t.__data__)e.__data__.callback(t.__data__);else{const e=yield this.searchItems();const t=e.filter((e=>e.default));t[0].callback(this.input.property("value"))}this.input.property("value","");this.tip.hide()}))}updatePlaceholder(e){this.input.attr("placeholder",e)}}async function Nh(e,t,n,o){const i=await Bl(e.cardsPath+"/index.json");if(i.error)mf(`Problem retrieving cards/index.json`);const s=t.toLowerCase().trim();const r=[...i.elements];let a;if(s.length>2){await Sh(r,e);a=Ah(r,s)}else{a=Ah(r,s)}const l={app:e.drawer.opts,sandboxDiv:e.drawer.opts.sandboxDiv,genomes:e.genomes,fromApp:true};n.push({title:"Tracks and Apps",items:a.filter((e=>e.type=="card")),color:"#e1edf7",callback:t=>{e.drawer.dispatch({type:"is_apps_btn_active",value:false});o.hide();zu(t,l)}},{title:"Datasets",items:a.filter((e=>e.type=="dsButton")),color:"#e5f5e4",callback:t=>{e.drawer.dispatch({type:"is_apps_btn_active",value:false});o.hide();zu(t,l)}});return n}async function Sh(e,t){const n=e.map((async e=>{if(e.hidden||e.type!="card"||!e.sandboxJson)return e;const n=await Bl(t.cardsPath+`/${e.sandboxJson}.json`);if(n?.ppcalls.length>0){for(const t of n.ppcalls){if(t.isUI)return;if(t?.label)e.searchterms.push(t.label)}}}));await Promise.all(n)}function Ah(e,t){return e.filter((e=>{if(e.hidden)return false;let n=(e.searchterms||[]).reduce(((e,n)=>{if(e)return true;return n.toLowerCase().includes(t)}),false);return n||e.name.toLowerCase().includes(t)})).sort(((e,t)=>e.name.localeCompare(t.name)))}async function Ch(e,t,n){if(e.length==0)return;try{const o=await Bl("/genelookup",{body:{input:e,genome:t,jwt:n}});if(o.error)throw o.error;if(!o.hits)throw".hits[] missing";return o.hits}catch(e){}}async function Eh(e,t,n,o){const i=t.genomes[n];if(!i){console.error("unknown genome "+n);return}const s=Qd(t.drawer.opts.sandboxDiv);s.header.html('<div style="display:inline-block;">'+e+'</div><div class="sjpp-output-sandbox-title">'+n+"</div>");const r=If();const a=await $f(r,i);const l=Ld(e,i);if(l){const e={hostURL:t.hostURL,jwt:o,holder:s.body,genome:i,nobox:true,chr:l.chr,start:l.start,stop:l.stop,dogtag:n,tklst:a,debugmode:t.debugmode};tc(i,e.tklst);import("./block-ec76524e.js").then((function(e){return e.c})).then((t=>new t.Block(e))).catch((e=>{t.error0(e)}));return}const c={hostURL:t.hostURL,jwt:o,query:e,genome:i,holder:s.body,variantPageCall_snv:t.variantPageCall_snv,samplecart:t.samplecart,tklst:a,debugmode:t.debugmode};const d=sessionStorage.getItem("urlp_mds");if(d){const e=d.split(",");if(e.length==2){c.datasetqueries=[{dataset:e[0],querykey:e[1]}]}}await yf(c)}const Oh=new ec({padding:"0px",offsetX:0,offsetY:0});Oh.d.style("z-index",5555);function Mh(e){if(!window.structuredClone)window.structuredClone=e=>JSON.parse(JSON.stringify(e));const t={error0(e){xc(t.holder0,e)},debugmode:false,callbacks:e.callbacks||{sjcharts:{}},instanceTracker:e.instanceTracker||{sjcharts:{}}};Ih(e,t);if(!t.instanceTracker.sjcharts){t.instanceTracker.sjcharts={}}if(!t.callbacks.sjcharts){t.callbacks.sjcharts={}}if(e.clear){it(".sja_pane").remove();return}t.holder=ot(e.holder?e.holder:document.body).append("div").attr("class","sja_root_holder").attr("data-ppclientversion",`2.63.0`).style("font","1em Arial, sans-serif").style("color","black");t.sandbox_header=e.sandbox_header||undefined;if(e.jwt){sessionStorage.setItem("jwt",e.jwt)}sessionStorage.setItem("suppressErrors",JSON.stringify(e.suppressErrors));if(e.variantPageCall_snv){t.variantPageCall_snv=e.variantPageCall_snv}if(e.samplecart){t.samplecart=e.samplecart}if(e.base_zindex){kc({setzindex:e.base_zindex})}const n=e.serverData||e.termdb&&e.termdb.serverData;const o=Bl("genomes",{},{serverData:n});return o.then((async n=>{if(n.error)throw{message:"Cannot get genomes: "+n.error};if(!n.genomes)throw{message:"no genome data!?"};if(n.base_zindex){kc({setzindex:n.base_zindex})}if(n.features){sessionStorage.setItem("optionalFeatures",JSON.stringify(n.features))}t.genomes=n.genomes;t.cardsPath=n.cardsPath;if(n.debugmode){t.debugmode=true}Xl({dsAuth:n.dsAuth,holder:t.holder});if(n.commonOverrides||e.commonOverrides){ga(Object.assign(n.commonOverrides||{},e.commonOverrides||{}))}if(n.targetPortal&&n.targetPortal=="gdc")await import("./style.gdc-40ec2784.js");for(const e in t.genomes){const n=cm(t.genomes[e]);if(n){throw{message:"Error with "+e+" genome: "+n}}}if(!e.noheader&&!window.location.search.includes("noheader")&&!window.location.search.includes("mass-session-id")&&!window.location.search.includes("mass-session-file")&&!window.location.search.includes("mass-session-url")){Th(t,n,e.jwt)}t.holder0=t.holder.append("div").style("margin","20px");const o=await $h(e,t);return o||t})).catch((e=>{t.holder.text(e.message||e);if(e.stack)console.log(e.stack)}))}Mh.getStatus=async function e(t=""){return await fetch("/healthcheck").then((e=>e.json())).then((e=>{const n={clientVersion:document.querySelector(".sja_root_holder")?.dataset.ppclientversion,versionInfo:e.versionInfo};if(t=="log")console.info(n);else if(t=="json")return JSON.stringify(n);else return n})).catch(console.error)};function Ih(e,t){if(e.host){t.hostURL=e.host}else if(window.location.hostname=="localhost"){const e=If();if(e.has("hosturl"))t.hostURL=e.get("hosturl");else if(window.testHost){t.hostURL=window.testHost}else{const n=e.get("hostname");const o=e.get("hostport");const i=window.location.protocol+"//";if(n&&o)t.hostURL=i+n+":"+o;else if(n)t.hostURL=i+n;else if(o)t.hostURL=i+window.location.hostname+":"+o}}if(!t.hostURL){t.hostURL=import.meta.url.split("/bin/dist")[0]}if(t.hostURL.endsWith("/"))t.hostURL=t.hostURL.slice(0,-1);sessionStorage.setItem("hostURL",t.hostURL)}async function Th(e,t,n){const o=Kt(Ir);const i="13px";const s="5px 10px";const r="7px 10px";document.documentElement.clientWidth;const a=e.holder.append("div").style("white-space","nowrap").style("border-bottom","solid 1px rgba("+o.r+","+o.g+","+o.b+",.3)");const l=a.append("div").style("margin","10px").style("padding","8px").style("padding-bottom","12px").style("display","inline-block").style("border-bottom","");const c=a.append("div").style("display","inline-block").style("padding",r).style("padding-left","25px").style("font-size",".8em").style("color",Kt(Ir).darker());{const e=c.append("div").style("padding-left","15px");e.append("span").text("Code updated: "+(t.codedate||"??")+", server launched: "+(t.launchdate||"??")+".");if(t.hasblat){e.append("a").style("margin-left","10px").text("Running BLAT").on("click",(async e=>{Oh.clear().showunder(e.target);const t=Oh.d.append("div").style("margin","10px");const n=t.append("div").text("Loading...");try{const e=await Pl("blat?serverstat=1");if(e.error)throw e.error;if(!e.lst)throw"invalid response";n.remove();for(const n of e.lst){t.append("div").text(n)}}catch(e){n.text(e.message||e);if(e.stack)console.log(e.stack)}}))}}if(t.headermessage){c.append("div").html(t.headermessage)}l.append("div").text("ProteinPaint").style("display","inline-block").style("padding",i).style("color",Ir).style("font-size","1.3em").style("font-weight","bold");const d=new ec({border:"",padding:"0px"});const f=async()=>{const t=ot("input").property("value").trim();const o=[{title:"Genes",default:true,items:await Ch(t,e.selectgenome.property("value"),n),callback:t=>{e.drawer.dispatch({type:"is_apps_btn_active",value:false});d.hide();Eh(t,e,e.selectgenome.property("value"),n)}}];await Nh(e,t,o,d);o.push({title:"Help",items:m.filter((e=>e.label.toLowerCase().includes(t.toLowerCase()))),color:"#faebd9",callback:e=>{window.open(e.link,e.label)}});return o};const p=new jh({holder:l,tip:d,style:{padding:r,border:`'solid 1px ${Ir}`},size:32,placeholder:"Gene, position, SNP, app, or dataset",title:"Search by gene, SNP, position, app, or dataset",searchItems:f});p.initUI();const u=l.append("div").attr("class","sjpp-genome-select-div").style("padding",r);const h=()=>{const t=e.genomes[e.selectgenome.property("value")];const n=["Gene","position","app"];if(t.hasSNP)n.splice(2,0,"SNP");if(Object.keys(t.datasets).length)n.push("dataset");const o=n.join(", ").replace(/,(?=[^,]*$)/,", or");return o};e.selectgenome=u.append("select").attr("title","Select a genome").attr("class","sjpp-genome-select").style("padding",s).style("border","solid 1px "+Ir).on("change",(()=>{Lh(e);p.updatePlaceholder(h())}));for(const t in e.genomes){e.selectgenome.append("option").attr("n",t).text(e.genomes[t].species+" "+t).property("value",t)}e.genome_browser_btn=Rh(e,l,n);e.drawer=await kh({holder:e.holder,genomes:e.genomes,drawerRow:e.holder.append("div").style("position","relative").style("overflow-x","visible").style("overflow-y","hidden").classed("sjpp-drawer-row",true),sandboxDiv:e.holder.append("div").style("margin-top","15px").classed("sjpp-drawer-sandbox",true),genome_browser_btn:e.genome_browser_btn,debugmode:e.debugmode,headbox:l,padw_sm:r,cardsPath:e.cardsPath});const m=[{label:"Embed in your website",link:"https://docs.google.com/document/d/1KNx4pVCKd4wgoHI4pjknBRTLrzYp6AL_D-j6MjcQSvQ/edit?usp=sharing"},{label:"URL parameters",link:"https://github.com/stjude/proteinpaint/wiki/URL-parameters"},{label:"All tutorials",link:"https://github.com/stjude/proteinpaint/wiki/"},{label:"User community",link:"https://groups.google.com/g/proteinpaint"},{label:"License ProteinPaint",link:"https://www.stjude.org/research/why-st-jude/shared-resources/technology-licensing/technologies/proteinpaint-web-application-for-visualizing-genomic-data-sj-15-0021.html",onlySearch:true},{label:"Our Team",link:"https://proteinpaint.stjude.org/team/",onlySearch:true}];l.append("span").classed("sja_menuoption",true).style("padding",r).text("Help").on("click",(async e=>{const t=e.target.getBoundingClientRect();const n=Oh.clear().show(t.left-0,t.top+t.height+5);await n.d.append("div").style("padding","5px 20px").selectAll("p").data(m.filter((e=>!e.onlySearch))).enter().append("p").html((e=>`<a href=${e.link} target=_blank>${e.label}</a>`))}))}function Rh(e,t,n){const o="8px";const i=t.append("span");const s=e.selectgenome.node().options[e.selectgenome.property("selectedIndex")].value;const r=i.attr("class","sja_menuoption").attr("id","genome_btn").style("padding",o).datum(s).text(s+" genome browser").on("click",((t,o)=>{const i=e.genomes[o];if(!i){alert("Invalid genome name: "+o);return}const s=Qd(e.drawer.opts.sandboxDiv);s.header.text(o+" genome browser");const r={hostURL:e.hostURL,jwt:n,holder:s.body,genome:i,chr:i.defaultcoord.chr,start:i.defaultcoord.start,stop:i.defaultcoord.stop,nobox:true,tklst:[],debugmode:e.debugmode};tc(i,r.tklst);import("./block-ec76524e.js").then((function(e){return e.c})).then((e=>new e.Block(r)));e.drawer.dispatch({type:"is_apps_btn_active",value:false})}));return r}function Lh(e){e.genome_browser_btn.text(e.selectgenome.node().value+" genome browser");e.genome_browser_btn.datum(e.selectgenome.node().value)}async function $h(e,t){if(e.genome&&t.selectgenome){for(let n=0;n<t.selectgenome.node().childNodes.length;n++){if(t.selectgenome.node().childNodes[n].value==e.genome){t.selectgenome.property("selectedIndex",n);break}}}if(e.mclassOverride){if(!e.mclassOverride.mclassName)e.mclassOverride.mclassName="Class";for(const t in e.mclassOverride.classes){const n=Yr[t];if(n){Object.assign(n,e.mclassOverride.classes[t])}}}if(e.singlecell){om(e.singlecell,t);return t}if(e.fimo){Uh(e.fimo,t);return t}if(e.mdssurvivalplot){if(e.genome)e.mdssurvivalplot.genome=e.genome;Dh(e.mdssurvivalplot,t);return t}if(e.mdssamplescatterplot){if(e.genome)e.mdssamplescatterplot.genome=e.genome;Ph(e.mdssamplescatterplot,t);return t}if(e.samplematrix){e.samplematrix.jwt=e.jwt;Fh(e.samplematrix,t);return t}if(e.hic){e.hic.jwt=e.jwt;Bh(e.hic,t);return t}if(e.block){return Hh(e,t)}if(e.study){Fd(t.genomes,e.study,t.holder0,t.hostURL,e.jwt,false,t);return t}if(e.studyview){const n=e.studyview;n.hostURL=e.host;const o=n.genome||e.genome;n.genome=t.genomes[o];n.hostURL=t.hostURL;n.jwt=e.jwt;n.holder=t.holder0;of(n);return t}if(await zh(e,t)){return t}if(e.fusioneditor){Gh(e,t);return t}if(e.genefusion){rm(e,t);return t}if(e.mavolcanoplot){Qh(e,t);return t}if(e.twodmaf){em(e,t);return t}if(e.junctionbymatrix){nm(e,t);return}if(e.mdsjsonform){await Jh(e,t);return}if(e.selectGenomeWithTklst){await Vh(e,t);return}if(e.disco){return await dm(e,t)}if(e.geneSearch4GDCmds3){return await Wh(e,t)}if(e.launchGdcMatrix){return await Xh(e,t)}if(e.launchGdcHierCluster){return await Yh(e,t)}if(e.launchGdcMaf){return await Zh(e,t)}if(e.parseurl&&location.search.length){try{await Rf({app:t,genomes:t.genomes,hostURL:t.hostURL,variantPageCall_snv:t.variantPageCall_snv,samplecart:t.samplecart,holder:t.holder,selectgenome:t.selectgenome,genome_browser_btn:t.genome_browser_btn,debugmode:t.debugmode})}catch(e){t.error0(e);console.error(e.stack||e)}}if(e.project){let n=undefined;if(e.project.uionly)n=t.holder0;ef(0,0,t.genomes,t.hostURL,n,t.sandbox_header)}if(e.termdb){await sm(e.termdb,t)}if(e.maftimeline){tm(e,t)}if(e.gdcbamslice){return await Kh(e,t)}if(e.mass){return await lm(e,t)}if(e.tkui){im(e,t)}if(e.massSessionId){const n=await Bl(`/massSession?id=${e.massSessionId}`);if(n.error)throw n.error;const o={holder:t.holder0,state:n.state,genome:t.genomes[n.state.vocab.genome],massSessionDuration:n.massSessionDuration,getDatasetAccessToken:e.getDatasetAccessToken,addLoginCallback:e.addLoginCallback};const i=await import("./app-de19f41c.js");i.appInit(o);return}if(e.massSessionFile||e.massSessionURL){let n;if(e.massSessionFile){const t=e.massSessionFile;const o=await Bl(`/textfile`,{method:"POST",body:JSON.stringify({file:t})});if(o.error)throw o.error;n=JSON.parse(o.text)}else{const t=e.massSessionURL;const o=await Bl(`/urltextfile`,{method:"POST",body:JSON.stringify({url:t})});if(o.error)throw o.error;n=JSON.parse(o.text)}const o={holder:t.holder0,state:n,genome:t.genomes[n.vocab.genome]};const i=await import("./app-de19f41c.js");i.appInit(o);return}if(e.profileHome){const t=await import("./profileHome-a555583d.js");t.init(e);return}}async function zh(e,t){if(e.p){e.gene=e.p;delete e.p}if(e.gene2canonicalisoform){if(!e.genome)throw".genome missing for gene2canonicalisoform";const t=await Pl("gene2canonicalisoform?genome="+e.genome+"&gene="+e.gene2canonicalisoform);if(t.error)throw t.error;if(!t.isoform)throw"no canonical isoform for given gene accession";e.gene=t.isoform}if(e.mds3_ssm2canonicalisoform){if(!e.genome)throw".genome missing";if(!e.mds3_ssm2canonicalisoform.ssm_id)throw".ssm_id missing from mds3_ssm2canonicalisoform";if(!e.mds3_ssm2canonicalisoform.dslabel)throw".dslabel missing from mds3_ssm2canonicalisoform";const t=await Pl("mds3?"+"genome="+e.genome+"&dslabel="+e.mds3_ssm2canonicalisoform.dslabel+"&ssm2canonicalisoform=1"+"&ssm_id="+e.mds3_ssm2canonicalisoform.ssm_id);if(t.error)throw t.error;if(!t.isoform)throw"no isoform found for given ssm_id";e.gene=t.isoform;if(e.tracks){const t=e.tracks.find((t=>t.dslabel==e.mds3_ssm2canonicalisoform.dslabel));if(t){t.hlssmid=e.mds3_ssm2canonicalisoform.ssm_id}}}if(e.gene){qh(e,t);return true}return false}async function Ph(e,t){if(!e.genome){t.error0("missing genome for mdssamplescatterplot");return}const n=t.genomes[e.genome];if(!n){t.error0("invalid genome for mdssamplescatterplot");return}e.genome=n;if(e.dataset){e.mds=n.datasets[e.dataset];if(!e.mds){t.error0("invalid dataset for mdssamplescatterplot");return}e.dslabel=e.dataset;delete e.dataset;if(e.mds.mdsIsUninitiated){const t=await Bl(`getDataset?genome=${e.genome.name}&dsname=${e.dslabel}`);if(t.error)throw t.error;if(!t.ds)throw"ds missing";Object.assign(e.mds,t.ds);delete e.mds.mdsIsUninitiated}}else if(e.analysisdata);else if(e.analysisdata_file){try{const t=await Ll("textfile",{file:e.analysisdata_file});if(t.error)throw tmp.error;else if(t.text)e.analysisdata=JSON.parse(t.text)}catch(e){t.error0(e);return}}else{t.error0("neither .dataset or .analysisdata is given");return}import("./mds.samplescatterplot-362f3591.js").then((n=>{n.init(e,t.holder0,t.debugmode)}))}function Dh(e,t){if(!e.genome){t.error0("missing genome for mdssurvivalplot");return}const n=t.genomes[e.genome];if(!n){t.error0("invalid genome for mdssurvivalplot");return}e.genome=n;if(!e.dataset){t.error0("missing dataset for mdssurvivalplot");return}e.mds=n.datasets[e.dataset];if(!e.mds){t.error0("invalid dataset for mdssurvivalplot");return}delete e.dataset;if(e.plotlist){for(const t of e.plotlist){t.renderplot=1}}import("./mds.survivalplot-f5bda05a.js").then((n=>{n.init(e,t.holder0,t.debugmode)}))}function Uh(e,t){if(!e.genome){t.error0("missing genome for fimo");return}const n=t.genomes[e.genome];if(!n){t.error0("invalid genome for fimo");return}e.genome=n;e.div=t.holder0;import("./mds.fimo-68f0eaf5.js").then((t=>{t.init(e)}))}function Bh(e,t){if(!e.genome){t.error0("missing genome for hic");return}e.genome=t.genomes[e.genome];if(!e.genome){t.error0("invalid genome for hic");return}if(!e.file){t.error0("missing file for hic");return}e.hostURL=t.hostURL;e.holder=t.holder0;import("./HicApp-bcf8330c.js").then((async n=>{await n.hicInit(e,t.debugmode)}))}function Fh(e,t){if(!e.genome){t.error0("missing genome for launching samplematrix");return}e.genome=t.genomes[e.genome];if(!e.genome){t.error0("invalid genome for samplematrix");return}e.hostURL=t.hostURL;e.holder=t.holder0;e.debugmode=t.debugmode;import("./samplematrix-7aa0a780.js").then((t=>{new t.Samplematrix(e)}))}async function qh(e,t){if(!e.genome){t.error0("Cannot embed: must specify reference genome");return}if(e.tracks){for(const t of e.tracks){if(t.type=="mds3"&&t.dslabel)continue;t.iscustom=true}}if(e.tkjsonfile){if(!e.tracks)e.tracks=[];const t=new Map([["tkjsonfile",e.tkjsonfile]]);const n=await $f(t,genomeobj);for(const t of n){e.tracks.push(t)}}const n={jwt:e.jwt,hostURL:t.hostURL,query:e.gene,genome:t.genomes[e.genome],holder:t.holder0,variantPageCall_snv:t.variantPageCall_snv,samplecart:t.samplecart,debugmode:t.debugmode,datasetqueries:e.datasetqueries,mset:e.mset,tklst:e.tracks,gmmode:e.gmmode,mclassOverride:e.mclassOverride,hide_dsHandles:e.hide_dsHandles,onloadalltk_always:e.onloadalltk_always};if(e.dataset){n.dataset=e.dataset.split(",");n.legacyDsFilter=e.legacyDsFilter;if(e.hidedatasetexpression){n.hidedatasetexpression=true}}if(e.hidegenecontrol){n.hidegenecontrol=true}if(e.hidegenelegend){n.hidegenelegend=true}let o=null;if(e.hlaachange){o=new Map;if(Array.isArray(e.hlaachange)){for(const t of e.hlaachange){if(t.name){o.set(t.name,t)}}}else{for(const t of e.hlaachange.split(",")){o.set(t,false)}}if(o.size){n.hlaachange=o}}if(e.hlvariants){n.hlvariants=e.hlvariants}await yf(n)}async function Hh(e,t){if(!e.genome){t.error0("Cannot embed: must specify reference genome");return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}if(e.study){Fd(t.genomes,e.study,t.holder0,t.hostURL,e.jwt,true,t)}if(e.studyview);if(e.tracks){for(const n of e.tracks){if(n.type==mc.mds3&&n.dslabel)continue;if(n.mdsjsonfile||n.mdsjsonurl){try{const t=await jf(n.mdsjsonfile,n.mdsjsonurl);e.tracks=e.tracks.filter((e=>e!=n));e.tracks.push(...t)}catch(e){hf(t.holder0,e)}}n.iscustom=true}}if(e.tkjsonfile){if(!e.tracks)e.tracks=[];const t=new Map([["tkjsonfile",e.tkjsonfile]]);const o=await $f(t,n);for(const t of o){e.tracks.push(t)}}const o={genome:n,hostURL:t.hostURL,jwt:e.jwt,holder:t.holder0,nativetracks:e.nativetracks,tklst:e.tracks,debugmode:t.debugmode,legendimg:e.legendimg};if(e.width){const n=Number.parseInt(e.width);if(Number.isNaN(n))return t.error0("browser width must be integer");o.width=n}if(e.subpanels){if(!Array.isArray(e.subpanels))return t.error0("subpanels is not array");const n=[];for(const o of e.subpanels){if(!o.chr){t.error0("missing chr in one subpanel");continue}if(!o.start||!o.stop){t.error0("missing start or stop in one subpanel");continue}if(!o.width){o.width=400}if(!o.leftpad){o.leftpad=5}n.push(o)}if(n.length){o.subpanels=n}}if(e.nobox){o.nobox=true}else{o.dogtag=e.dogtag||e.genome}if(e.chr&&Number.isInteger(e.start)){o.chr=e.chr;o.start=e.start;o.stop=Number.isInteger(e.stop)?e.stop:e.start+1}else if(e.position){const t=Ld(e.position,n);if(t){o.chr=t.chr;o.start=t.start;o.stop=t.stop}}else if(e.positionbygene){try{const t=await od(e.genome,e.positionbygene);if(t&&t[0]){const e=t[0];o.chr=e.chr;o.start=e.start;o.stop=e.stop}}catch(e){t.error0(e)}}if(!o.chr){o.chr=n.defaultcoord.chr;o.start=n.defaultcoord.start;o.stop=n.defaultcoord.stop}if(e.datasetqueries){o.datasetqueries=e.datasetqueries}if(e.hlregions){const t=[];for(const o of e.hlregions){const e=Ld(o,n,true);if(e)t.push(e)}if(t.length)o.hlregions=t}const i=If();if(i){if(i.has("position")){const e=Ld(i.get("position"),n);if(e){o.chr=e.chr;o.start=e.start;o.stop=e.stop}}if(i.has("hlregion")){const e=[];for(const t of i.get("hlregion").split(",")){const o=Ld(t,n,true);if(o){e.push(o)}}if(e.length){o.hlregions=e}}if(i.has("bedgraphdotfile")){if(!o.tklst)o.tklst=[];const e=i.get("bedgraphdotfile").split(",");for(let t=0;t<e.length;t+=2){if(e[t]&&e[t+1]){o.tklst.push({type:mc.bedgraphdot,name:e[t],file:e[t+1]})}}}}return import("./block-ec76524e.js").then((function(e){return e.c})).then((e=>{t.block=new e.Block(o);return t}))}function Gh(e,t){if(e.fusioneditor.uionly){const[n,o,i,s,r]=Xd(t.holder0,t.genomes);import("./svmr-3dd531ef.js").then((a=>{a.svmrui([null,n,o,i,s,r],t.genomes,t.hostURL,e.jwt)}));return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}import("./svmr-3dd531ef.js").then((o=>{o.svmrparseinput(e.fusioneditor,t.error0,n,t.holder0,t.hostURL,e.jwt)}))}async function Jh(e,t){if(e.mdsjsonform.uionly){const e=await import("./mdsjsonform-7f0b6cc7.js");await e.init_mdsjsonform({holder:t.holder0,genomes:t.genomes})}}async function Vh(e,t){const n=await import("./selectGenomeWithTklst-51cd21a4.js");await n.init(e,t.holder0,t.genomes)}async function Wh(e,t){const n=await import("./lollipop-59f65024.js");return await n.init(e,t.holder0,t.genomes)}async function Xh(e,t){const n=await import("./oncomatrix-cd9fa01b.js");return await n.init(e,t.holder0,t.genomes)}async function Yh(e,t){const n=await import("./geneExpClustering-96d09008.js");return await n.init(e,t.holder0,t.genomes)}async function Zh(e,t){const n=await import("./maf-72e5b7da.js");return await n.gdcMAFui({holder:t.holder0,filter0:e.filter0,callbacks:e.callbacks||{},debugmode:e.debugmode})}function Kh(e,t){return import("./bam-95f36008.js").then((n=>n.bamsliceui({genomes:t.genomes,holder:t.holder0,hideTokenInput:e.gdcbamslice.hideTokenInput,callbacks:e.gdcbamslice.callbacks||{},filter0:e.filter0,stream2download:e.gdcbamslice.stream2download,inputValue:e.gdcbamslice.inputValue})))}function Qh(e,t){if(e.mavolcanoplot.uionly){import("./mavb-37fffd68.js").then((n=>{n.mavbui(t.genomes,t.hostURL,e.jwt,t.holder0,t.sandbox_header)}));return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}e.mavolcanoplot.hostURL=t.hostURL;e.mavolcanoplot.genome=n;import("./mavb-37fffd68.js").then((n=>{n.mavbparseinput(e.mavolcanoplot,t.error0,t.holder0,e.jwt)}))}function em(e,t){if(e.twodmaf.uionly){import("./2dmaf-70c0b6bb.js").then((e=>{e.d2mafui(t.genomes,t.holder0)}));return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}e.twodmaf.hostURL=t.hostURL;e.twodmaf.genome=n;import("./2dmaf-70c0b6bb.js").then((n=>{n.d2mafparseinput(e.twodmaf,t.holder0)}))}function tm(e,t){if(e.maftimeline.uionly){import("./maftimeline-ed8aaae8.js").then((e=>{e.default(t.genomes,t.holder0,t.sandbox_header)}))}}function nm(e,t){if(e.junctionbymatrix.uionly){import("./block.tk.junction.textmatrixui-6ec019e1.js").then((n=>{n.default(t.genomes,t.hostURL,e.jwt,t.holder0)}))}}async function om(e,t){try{const n=t.genomes[e.genome];if(!n)throw"Invalid genome: "+e.genome;e.genome=n;const o=await import("./singlecell-a668bb17.js");await o.init(e,t.holder0)}catch(e){t.error0("Error launching single cell viewer: "+e);if(e.stack)console.log(e.stack)}}async function im(e,t){if(e.tkui=="bigwig"){const e=await import("./block.tk.bigwig.ui-0c96dce5.js");e.bigwigUI(t.genomes,t.holder)}if(e.tkui=="databrowser"){const e=await import("./databrowser.ui-c50862e4.js");e.init_databrowserUI(t.holder,t.debugmode)}if(e.tkui=="genefusion"){const e=await import("./genefusion.ui-3e2a3a73.js");e.init_geneFusionUI(t.holder,t.genomes,t.debugmode)}if(e.tkui=="disco"){const e=await import("./Disco.UI-a38a12e6.js");e.init_discoplotUI(t.holder,t.genomes,t.debugmode)}}async function sm(e,t){if(!e.holder)e.holder=t.holder0;import("./app-bfce9bf5.js").then((t=>{t.appInit(e)}))}async function rm(e,t){try{const n=t.genomes[e.genome];if(!n)throw"Invalid genome: "+e.genome;const o=await import("./fusion.parse-ae1253f4.js");const i=await o.parseFusion({line:e.genefusion.text,genome:n,positionType:e.genefusion.positionType});await am(i.pairlst[0].a,n);await am(i.pairlst[0].b,n);const s=await import("./svgraph-3c5cd8d2.js");s.default({pairlst:i.pairlst,genome:n,holder:t.holder})}catch(e){t.error0(e)}}async function am(e,t){const n=await Bl("genelookup",{body:{genome:t.name,input:e.isoform,deep:1}});if(n.error)throw n.error;if(!Array.isArray(n.gmlst))throw"gmlst not array";const o=n.gmlst.find((t=>t.isoform==e.isoform));if(!o)throw"no match to isoform";e.chr=o.chr;e.name=o.name;e.gm={isoform:o.isoform}}async function lm(e,t){const n=e.mass;if(!n.holder)n.holder=t.holder0;if(n.state){if(n.state.genome){n.genome=t.genomes[n.state.genome]}else if(n.state?.vocab?.genome){n.genome=t.genomes[n.state.vocab.genome]}}n.getDatasetAccessToken=e.getDatasetAccessToken;n.addLoginCallback=e.addLoginCallback;const o=sessionStorage.getItem("hostURL");if(window.opener&&o!=window.location.origin){n.embeddedSessionState=JSON.parse(sessionStorage.getItem("embeddedSessionState")||`{}`);const e=t=>{if(t.origin!=window.location.origin&&t.origin!==o)return;if(t.data.state){window.removeEventListener("message",e);Object.assign(n.embeddedSessionState,t.data.state);sessionStorage.setItem("embeddedSessionState",JSON.stringify(n.embeddedSessionState))}};window.addEventListener("message",e,false);setTimeout((()=>window.removeEventListener("message",e)),1e3);let t;try{if(window.opener.origin){t=window.opener.origin}else{t=o}}catch(e){t=o}try{window.opener.postMessage("getActiveMassSession",t)}catch(e){console.log(e)}}const i=await import("./app-de19f41c.js");return await i.appInit(n)}function cm(e){e.tkset=[];e.isoformcache=new Map;e.junctionframecache=new Map;e.isoformmatch=(t,n,o)=>{if(!t)return null;const i=t.toUpperCase();if(!e.isoformcache.has(i))return null;const s=e.isoformcache.get(i);if(s.length==1)return s[0];if(!n){console.log("no chr provided for matching with "+i);return s[0]}let r=null;for(const e of 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+function e(e,t){if(t===void 0)t={};var n=t.insertAt;if(!e||typeof document==="undefined"){return}var o=document.head||document.getElementsByTagName("head")[0];var i=document.createElement("style");i.type="text/css";if(n==="top"){if(o.firstChild){o.insertBefore(i,o.firstChild)}else{o.appendChild(i)}}else{o.appendChild(i)}if(i.styleSheet){i.styleSheet.cssText=e}else{i.appendChild(document.createTextNode(e))}}var t='\n/**\n * Render the `main` element consistently in IE.\n */\n\n.sja_root_holder main, .sja_menu_div main, .sja_pane main {\n  display: block;\n}\n\n/**\n * Correct the font size and margin on `h1` elements within `section` and\n * `article` contexts in Chrome, Firefox, and Safari.\n */\n\n.sja_root_holder h1, .sja_menu_div h1, .sja_pane h1 {\n  font-size: 2em;\n  margin: 0.67em 0;\n}\n\n/* Grouping content\n   ========================================================================== */\n\n/**\n * 1. Add the correct box sizing in Firefox.\n * 2. 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Add the correct text decoration in Chrome, Edge, IE, Opera, and Safari.\n */\n\n.sja_root_holder abbr[title], .sja_menu_div abbr[title], .sja_pane abbr[title] {\n  border-bottom: none; /* 1 */\n  text-decoration: underline; /* 2 */\n  text-decoration: underline dotted; /* 2 */\n}\n\n/**\n * Add the correct font weight in Chrome, Edge, and Safari.\n */\n\n.sja_root_holder b, .sja_menu_div b, .sja_pane b,\n.sja_root_holder strong, .sja_menu_div strong, .sja_pane strong {\n  font-weight: bolder;\n}\n\n/**\n * 1. Correct the inheritance and scaling of font size in all browsers.\n * 2. Correct the odd `em` font sizing in all browsers.\n */\n\n.sja_root_holder code, .sja_menu_div code, .sja_pane code,\n.sja_root_holder kbd, .sja_menu_div kbd, .sja_pane kbd,\n.sja_root_holder samp, .sja_menu_div samp, .sja_pane samp {\n  font-family: monospace, monospace; /* 1 */\n  font-size: 1em; /* 2 */\n}\n\n/**\n * Add the correct font size in all browsers.\n */\n\n.sja_root_holder small, .sja_menu_div small, .sja_pane small {\n  font-size: 80%;\n}\n\n/**\n * Prevent `sub` and `sup` elements from affecting the line height in\n * all browsers.\n */\n\n.sja_root_holder sub, .sja_menu_div sub, .sja_pane sub,\n.sja_root_holder sup, .sja_menu_div sup, .sja_pane sup {\n  font-size: 75%;\n  line-height: 0;\n  position: relative;\n  vertical-align: baseline;\n}\n\n.sja_root_holder sub, .sja_menu_div sub, .sja_pane sub {\n  bottom: -0.25em;\n}\n\n.sja_root_holder sup, .sja_menu_div sup, .sja_pane sup {\n  top: -0.5em;\n}\n\n/* Embedded content\n   ========================================================================== */\n\n/**\n * Remove the border on images inside links in IE 10.\n */\n\n.sja_root_holder img, .sja_menu_div img, .sja_pane img {\n  border-style: none;\n}\n\n/* Forms\n   ========================================================================== */\n\n/**\n * 1. Change the font styles in all browsers.\n * 2. Remove the margin in Firefox and Safari.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder input, .sja_menu_div input, .sja_pane input,\n.sja_root_holder optgroup, .sja_menu_div optgroup, .sja_pane optgroup,\n.sja_root_holder select, .sja_menu_div select, .sja_pane select,\n.sja_root_holder textarea, .sja_menu_div textarea, .sja_pane textarea {\n  font-family: inherit; /* 1 */\n  font-size: 100%; /* 1 */\n  line-height: 1.15; /* 1 */\n  margin: 0; /* 2 */\n}\n\n/**\n * Show the overflow in IE.\n * 1. Show the overflow in Edge.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder input  /* 1 */, .sja_menu_div input  /* 1 */, .sja_pane input  /* 1 */ {\n  overflow: visible;\n}\n\n/**\n * Remove the inheritance of text transform in Edge, Firefox, and IE.\n * 1. Remove the inheritance of text transform in Firefox.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder select  /* 1 */, .sja_menu_div select  /* 1 */, .sja_pane select  /* 1 */ {\n  text-transform: none;\n}\n\n/**\n * Correct the inability to style clickable types in iOS and Safari.\n */\n\n.sja_root_holder button, .sja_menu_div button, .sja_pane button,\n.sja_root_holder [type="button"], .sja_menu_div [type="button"], .sja_pane [type="button"],\n.sja_root_holder [type="reset"], .sja_menu_div [type="reset"], .sja_pane [type="reset"],\n.sja_root_holder [type="submit"], .sja_menu_div [type="submit"], .sja_pane [type="submit"] {\n  -webkit-appearance: button;\n}\n\n/**\n * Remove the inner border and padding in Firefox.\n */\n\n.sja_root_holder button::-moz-focus-inner, .sja_menu_div button::-moz-focus-inner, .sja_pane button::-moz-focus-inner,\n.sja_root_holder [type="button"]::-moz-focus-inner, .sja_menu_div [type="button"]::-moz-focus-inner, .sja_pane [type="button"]::-moz-focus-inner,\n.sja_root_holder [type="reset"]::-moz-focus-inner, .sja_menu_div [type="reset"]::-moz-focus-inner, .sja_pane [type="reset"]::-moz-focus-inner,\n.sja_root_holder [type="submit"]::-moz-focus-inner, .sja_menu_div [type="submit"]::-moz-focus-inner, .sja_pane [type="submit"]::-moz-focus-inner {\n  border-style: none;\n  padding: 0;\n}\n\n/**\n * Restore the focus styles unset by the previous rule.\n */\n\n.sja_root_holder button:-moz-focusring, .sja_menu_div button:-moz-focusring, .sja_pane button:-moz-focusring,\n.sja_root_holder [type="button"]:-moz-focusring, .sja_menu_div [type="button"]:-moz-focusring, .sja_pane [type="button"]:-moz-focusring,\n.sja_root_holder [type="reset"]:-moz-focusring, .sja_menu_div [type="reset"]:-moz-focusring, .sja_pane [type="reset"]:-moz-focusring,\n.sja_root_holder [type="submit"]:-moz-focusring, .sja_menu_div [type="submit"]:-moz-focusring, .sja_pane [type="submit"]:-moz-focusring {\n  outline: 1px dotted ButtonText;\n}\n\n/**\n * Correct the padding in Firefox.\n */\n\n.sja_root_holder fieldset, .sja_menu_div fieldset, .sja_pane fieldset {\n  padding: 0.35em 0.75em 0.625em;\n}\n\n/**\n * 1. Correct the text wrapping in Edge and IE.\n * 2. Correct the color inheritance from `fieldset` elements in IE.\n * 3. Remove the padding so developers are not caught out when they zero out\n *    `fieldset` elements in all browsers.\n */\n\n.sja_root_holder legend, .sja_menu_div legend, .sja_pane legend {\n  box-sizing: border-box; /* 1 */\n  color: inherit; /* 2 */\n  display: table; /* 1 */\n  max-width: 100%; /* 1 */\n  padding: 0; /* 3 */\n  white-space: normal; /* 1 */\n}\n\n/**\n * Add the correct vertical alignment in Chrome, Firefox, and Opera.\n */\n\n.sja_root_holder progress, .sja_menu_div progress, .sja_pane progress {\n  vertical-align: baseline;\n}\n\n/**\n * Remove the default vertical scrollbar in IE 10+.\n */\n\n.sja_root_holder textarea, .sja_menu_div textarea, .sja_pane textarea {\n  overflow: auto;\n}\n\n/**\n * 1. Add the correct box sizing in IE 10.\n * 2. Remove the padding in IE 10.\n */\n\n.sja_root_holder [type="checkbox"], .sja_menu_div [type="checkbox"], .sja_pane [type="checkbox"],\n.sja_root_holder [type="radio"], .sja_menu_div [type="radio"], .sja_pane [type="radio"] {\n  box-sizing: border-box; /* 1 */\n  padding: 0; /* 2 */\n}\n\n/**\n * Correct the cursor style of increment and decrement buttons in Chrome.\n */\n\n.sja_root_holder [type="number"]::-webkit-inner-spin-button, .sja_menu_div [type="number"]::-webkit-inner-spin-button, .sja_pane [type="number"]::-webkit-inner-spin-button,\n.sja_root_holder [type="number"]::-webkit-outer-spin-button, .sja_menu_div [type="number"]::-webkit-outer-spin-button, .sja_pane [type="number"]::-webkit-outer-spin-button {\n  height: auto;\n}\n\n/**\n * 1. Correct the odd appearance in Chrome and Safari.\n * 2. Correct the outline style in Safari.\n */\n\n.sja_root_holder [type="search"], .sja_menu_div [type="search"], .sja_pane [type="search"] {\n  -webkit-appearance: textfield; /* 1 */\n  outline-offset: -2px; /* 2 */\n}\n\n/**\n * Remove the inner padding in Chrome and Safari on macOS.\n */\n\n.sja_root_holder [type="search"]::-webkit-search-decoration, .sja_menu_div [type="search"]::-webkit-search-decoration, .sja_pane [type="search"]::-webkit-search-decoration {\n  -webkit-appearance: none;\n}\n\n/**\n * 1. Correct the inability to style clickable types in iOS and Safari.\n * 2. Change font properties to `inherit` in Safari.\n */\n\n.sja_root_holder ::-webkit-file-upload-button, .sja_menu_div ::-webkit-file-upload-button, .sja_pane ::-webkit-file-upload-button {\n  -webkit-appearance: button; /* 1 */\n  font: inherit; /* 2 */\n}\n\n/* Interactive\n   ========================================================================== */\n\n/*\n * Add the correct display in Edge, IE 10+, and Firefox.\n */\n\n.sja_root_holder details, .sja_menu_div details, .sja_pane details {\n  display: block;\n}\n\n/*\n * Add the correct display in all browsers.\n */\n\n.sja_root_holder summary, .sja_menu_div summary, .sja_pane summary {\n  display: list-item;\n}\n\n/* Misc\n   ========================================================================== */\n\n/**\n * Add the correct display in IE 10+.\n */\n\n.sja_root_holder template, .sja_menu_div template, .sja_pane template {\n  display: none;\n}\n\n/**\n * Add the correct display in IE 10.\n */\n\n.sja_root_holder [hidden], .sja_menu_div [hidden], .sja_pane [hidden] {\n  display: none;\n}';e(t);var n="pre code.hljs{display:block;overflow-x:auto;padding:1em}code.hljs{padding:3px 5px}/*!\n  Theme: GitHub\n  Description: Light theme as seen on github.com\n  Author: github.com\n  Maintainer: @Hirse\n  Updated: 2021-05-15\n\n  Outdated base version: https://github.com/primer/github-syntax-light\n  Current colors taken from GitHub's CSS\n*/.hljs{color:#24292e;background:#fff}.hljs-doctag,.hljs-keyword,.hljs-meta .hljs-keyword,.hljs-template-tag,.hljs-template-variable,.hljs-type,.hljs-variable.language_{color:#d73a49}.hljs-title,.hljs-title.class_,.hljs-title.class_.inherited__,.hljs-title.function_{color:#6f42c1}.hljs-attr,.hljs-attribute,.hljs-literal,.hljs-meta,.hljs-number,.hljs-operator,.hljs-selector-attr,.hljs-selector-class,.hljs-selector-id,.hljs-variable{color:#005cc5}.hljs-meta .hljs-string,.hljs-regexp,.hljs-string{color:#032f62}.hljs-built_in,.hljs-symbol{color:#e36209}.hljs-code,.hljs-comment,.hljs-formula{color:#6a737d}.hljs-name,.hljs-quote,.hljs-selector-pseudo,.hljs-selector-tag{color:#22863a}.hljs-subst{color:#24292e}.hljs-section{color:#005cc5;font-weight:700}.hljs-bullet{color:#735c0f}.hljs-emphasis{color:#24292e;font-style:italic}.hljs-strong{color:#24292e;font-weight:700}.hljs-addition{color:#22863a;background-color:#f0fff4}.hljs-deletion{color:#b31d28;background-color:#ffeef0}";e(n);var o="/*\n    see client/generateScopedCss.js on how to generate style-normalize-*.css\n\n    also see a TODO comment in client/src/app.js, of dynamically importing\n    style-normalize-unscoped.css only if it's known to not conflict in\n    the embedder portal\n*/\n/* directly import these in src/app.js so that they will be processed as CSSStyleSheet\n@import './style-normalize-scoped.css';\n@import 'highlight.js/styles/github.css';\n*/\n/*\nhtml {\n    height:100%;\n}\nbody {\n    min-height:100%;\n}\ntable {\n    font-size:1em;\n    border-spacing:1px;\n    border-collapse:separate;\n}\n*/\n/*\n    !!! NOTE !!!\n    FireFox does not support the @scope (selector) syntax\n    that can enclose all affected rules inside a nested block,\n    so for now, will need to prepend the .sja_root_holder scope for each selector\n*/\n/***************************************\nCSS properties that are not covered \nby normalize.css are covered here\n\n!!! make sure to scope to sja_root_holder\n****************************************/\n.sja_root_holder h2 {\n    margin-block-start: 0.83em;\n    margin-block-end: 0.83em;\n}\n/***************************************\n    tag-based styles\n\n  prevent embedder styles from overriding\n  the styles within pp-controlled divs\n****************************************/\n/* use default browser styles within pp-controlled divs */\n/* using the !important flag:\n- this flag is used to override conflicting styles\n- this flag will override both embedder styling and inline styling\n- it is not necessary to use this flag to prevent embedder styles from overriding pp styles, because specifying styles within pp-specific classes will usually prevent this issue\n- the only time when it is necessary to use this flag is when (1) the conflicting styling also has an !important flag or (2) the conflicting styling is also specified in this same file\n*/\n.sja_root_holder {\n    /*background-color: #fff;*/\n}\n.sja_root_holder,\n.sja_menu_div,\n.sja_pane {\n    all: initial;\n    /* block inheritance for all properties */\n}\n.sja_root_holder table,\n.sja_menu_div table,\n.sja_pane table {\n    border-collapse: separate;\n    border-spacing: 2px;\n}\n.sja_root_holder svg {\n    display: inline-block;\n}\n/*\n    override the thicker button border\n    that results when a button's \n    border-radius: 0 which seems to override\n    all associated styles of \n    -webkit-appearance: button;\n*/\n.sja_root_holder button,\n.sja_menu_div button,\n.sja_pane button {\n    padding: 2px 3px;\n    border-width: 1px;\n    border-style: solid;\n    border-radius: 3px;\n    box-shadow: inset 0 0 0 99999px rgba(255, 255, 255, 0.3);\n    font-family: Arial;\n    color: black;\n    background-color: buttonface;\n    border-color: buttonborder;\n}\n.sja_root_holder button:disabled,\n.sja_menu_div button:disabled,\n.sja_pane button:disabled {\n    background-color: rgba(239, 239, 239, 0.3);\n    color: rgba(16, 16, 16, 0.3);\n    border-color: rgba(118, 118, 118, 0.3);\n}\n.sja_root_holder button:hover,\n.sja_menu_div button:hover,\n.sja_pane button:hover {\n    box-shadow: none;\n}\n.sja_root_holder label,\n.sja_menu_div label,\n.sja_pane label {\n    margin-bottom: 0;\n}\n.sja_root_holder a,\n.sja_menu_div a,\n.sja_pane a,\n.linkText {\n    color: rgb(0, 0, 238);\n    cursor: pointer;\n    text-decoration: underline;\n}\n.sja_root_holder input,\n.sja_menu_div input,\n.sja_pane input {\n    padding: 1px 3px;\n    margin:  2px 5px;\n    border:  1px solid #ccc;\n}\n.sja_root_holder select,\n.sja_menu_div select,\n.sja_pane select {\n    padding: 1px 3px;\n    padding-right: 30px; /* padding between text and arrow */\n    background-size: auto;\n    background-position: right;\n    border: 1px solid #ccc;\n}\n.sja_root_holder textarea,\n.sja_menu_div textarea,\n.sja_pane textarea {\n    padding: 2px;\n}\n.sja_root_holder input[type=\"search\"].tree_search {\n    -webkit-appearance: searchfield;\n}\n.sja_root_holder ul {\n    display: block;\n    list-style-type: disc;\n    margin-block-start: 1em;\n    margin-block-end: 1em;\n    margin-inline-start: 0px;\n    margin-inline-end: 0px;\n    padding-inline-start: 40px;\n}\n.sja_root_holder ul ul {\n    list-style-type: circle;\n}\n.sja_root_holder li {\n    display: list-item;\n    text-align: -webkit-match-parent;\n}\n/*************************\n    class-specific styles\n*************************/\n.sja_errorbar {\n    position: relative;\n    padding: 5px 50px 5px 10px;\n    background-color: rgba(200, 0, 0, .1);\n    color: rgba(190, 0, 0, .5);\n    border: solid 1px rgba(200, 0, 0, .2);\n    /*border-width: 1px 0px;*/\n}\n.sja_errorbar>:nth-child(2) {\n    position: absolute;\n    padding: 5px 10px;\n    cursor: default;\n    top: 0px;\n    right: 10px;\n}\n.sja_inset_a {\n    background-color: #ebedeb;\n    box-shadow: inset 0px 0px 14px 0px #858585;\n    padding: 5px 10px;\n}\n.sja_menu,\n.sja_menu_persist,\n.sja_tooltip {\n    position: absolute;\n    background-color: white;\n    font-family: Arial;\n    z-index: 1000;\n}\n/* /client/src/app.js start */\n.sja_menuoption {\n    color: black;\n    padding: 5px 10px;\n    cursor: default;\n    background-color: #f2f2f2;\n    margin: 1px;\n    border-radius: 5px;\n}\n.sja_menuoption_not_interactive {\n    padding: 5px 10px;\n    cursor: default;\n    margin: 1px;\n}\n.sja_sharp_border {\n    border-radius: 0px;\n}\n.sja_menuoption:hover {\n    background-color: #e6e6e6\n}\n.sja_menuoption:active {\n    color: #cc0000;\n    background-color: #FCE2E1;\n}\n/* /client/src/app.js end */\n.sja_filter_tag_btn {\n    display: inline-block;\n    color: black;\n    padding: 5px 8px;\n    background-color: #cfe2f3;\n    cursor: default;\n}\n/* .sja_filter_tag_btn:hover { opacity: 0.8; cursor:default} */\n.sja_filter_tag_btn:active {\n    color: #cc0000;\n    opacity: 0.6;\n}\n.ts_pill:hover,\n.tvs_pill:hover {\n    opacity: 0.8;\n    cursor: default\n}\n.sjpp_apply_btn {\n    background-color: #d0e0e3;\n    border-radius: 13px !important; \n    padding: 7px 15px !important;\n    border: 0px !important;\n}\n.sjpp_delete_btn,\n.remove_btn {\n    background-color: #f4cccc;\n}\n.ts_summary_btn {\n    background-color: #d9d2e9;\n}\n/* mostly for table tr */\n.sja_clb {\n    padding: 5px 10px;\n    cursor: default;\n}\n.sja_clb:hover {\n    background: #ffff99;\n}\n.sja_clb:active {\n    background: #ffcc99;\n}\n.sja_clb_selected {\n    padding: 5px 10px;\n    cursor: default;\n    background: #FAF0C8;\n    border-bottom: solid 2px #E3CA64;\n}\n.sja_clb_selected:hover {\n    background: #FCE68B\n}\n.sja_clb_selected:active {\n    background: #ffcc99\n}\n/* table tr, gray highlight */\n.sja_clb_gray {\n    padding: 5px 10px;\n    cursor: default;\n}\n.sja_clb_gray:hover {\n    background-color: #f1f1f1;\n}\n.sja_clb_gray:active {\n    background-color: #ffffcc;\n}\n.sja_hideable_legend {\n    cursor: default;\n}\n.sja_hideable_legend:hover {\n    background: #ffff99;\n}\n.sja_legend_more_btn {\n    padding: 3px;\n    text-align: center;\n    font-size: 0.7em;\n    opacity: 0.5;\n    cursor: default;\n}\n.sja_legend_more_btn:hover {\n    text-decoration: underline;\n}\n/* text only */\n.sja_clbtext2 {\n    cursor: default;\n    text-decoration: none;\n}\n.sja_clbtext2:hover {\n    text-decoration: underline;\n}\n.sja_clbtext2:active {\n    fill: #CC0000;\n    color: #CC0000;\n}\n.sja_clbtext {\n    cursor: default;\n    color: black;\n    fill: black;\n    border-bottom: solid 1px transparent;\n}\n.sja_clbtext:hover {\n    color: #631318;\n    fill: #631318;\n    border-color: black;\n}\n.sja_clbtext:active {\n    color: #CC0000;\n    border-color: #cc0000;\n    fill: #cc0000;\n}\n.sja_clbtextbold {\n    cursor: default;\n    color: black;\n    fill: black;\n    font-weight: normal;\n}\n.sja_clbtextbold:hover {\n    color: #631318;\n    fill: #631318;\n    font-weight: bold;\n}\n.sja_clbtextbold:active {\n    color: #CC0000;\n    fill: #cc0000;\n    font-weight: bold;\n}\n.sja_opaque6 {\n    opacity: .6;\n    cursor: default;\n}\n.sja_opaque6:hover {\n    opacity: .9;\n}\n.sja_opaque8 {\n    opacity: .8;\n    cursor: default;\n}\n.sja_opaque8:hover {\n    opacity: 1;\n}\n.sja_simpletable tr td {\n    border-bottom: solid 1px #ededed;\n}\n.sja_mcdot {\n    cursor: default;\n    border-radius: 8px;\n    padding: 1px 2px;\n    margin-right: 1px;\n    color: white;\n    font-size: .8em;\n}\n.sja_variantpagesnv {\n    cursor: default;\n    display: inline-block;\n    border-radius: 3px;\n    padding: 3px 10px;\n    margin-right: 2px;\n    color: white;\n    background-color: #0099FF;\n    opacity: .6;\n}\n.sja_variantpagesnv:hover {\n    opacity: 1;\n}\n.sja_variantpagesnv:active {\n    background-color: #3366FF;\n}\n.sja_selectsample {\n    cursor: default;\n    display: inline-block;\n    border-radius: 2px;\n    border: solid 1px #545454;\n    padding: 3px 10px;\n    margin-right: 2px;\n    color: #545454;\n    background-color: white;\n    font-size: .8em;\n}\n.sja_selectsample:hover {\n    background-color: #f1f1f1;\n}\n.sja_selectsample:active {\n    background-color: #F2E1E3;\n}\n.sja_pane {\n    position: absolute;\n    /*border:solid 1px #ccc;\n    */\n    box-shadow: 0px 2px 4px 1px #999;\n    background-color: white;\n}\n.sja_pane>:first-child {\n    padding-right: 10px;\n    cursor: move;\n    background-color: #f0f0f0;\n}\n.sja_pane>:nth-child(2) {\n    padding: 0px 10px 10px 10px;\n    font-family: Arial;\n}\n.sja_cursor_hmove {\n    cursor: ew-resize;\n}\n.sja_svgtext {\n    cursor: default;\n    fill-opacity: .8\n}\n.sja_svgtext2 {\n    cursor: default;\n    fill: black;\n}\n.sja_svgtext2:hover {\n    fill: #B30000\n}\n.sja_clb5 {\n    /* tree button */\n    cursor: default;\n    display: inline-block;\n    border: solid 1px #006600;\n    color: #006600;\n    background-color: white;\n    margin-left: 6px;\n    padding: 0px 4px;\n    font-size: 80%;\n}\n.sja_clb5:hover {\n    background-color: #006600;\n    color: white;\n}\n.sja_clb5:active {\n    background-color: #009900;\n}\n.sja_clb2 {\n    color: black;\n    font-family: Courier;\n    display: inline-block;\n    padding: 1px 5px;\n    cursor: default;\n}\n.sja_clb2:hover {\n    background-color: #ffff99;\n}\n.sja_clb2:active {\n    background-color: #ccff99;\n}\n.sja_clbb {\n    /* highlight border */\n    border: solid 1px transparent;\n    cursor: default;\n}\n.sja_clbb:hover {\n    border-color: #ccc;\n}\n.sja_clbbox {\n    cursor: default;\n    padding: 2px 5px;\n    color: white;\n    font-size: .7em;\n    font-weight: normal;\n}\n.sja_clbbox:hover {\n    font-weight: bold;\n}\n.sja_tr {\n    cursor: default;\n    background-color: #f1f1f1;\n}\n.sja_tr:hover {\n    background-color: white;\n}\n.sja_tr:active {\n    background-color: #ffffcc;\n}\n.sja_tr2 {\n    cursor: default;\n}\n.sja_tr2:hover {\n    background-color: #ffffcc;\n}\n.sja_tr2:active {\n    background-color: #ffff00;\n}\n.sja_aa_disclabel {\n    cursor: default;\n}\n.sja_aa_discnum {\n    cursor: default;\n    text-rendering: geometricPrecision;\n}\n.sja_aa_skkick:hover {\n    stroke: #858585;\n}\n.sja_aa_disckick:hover {\n    stroke-opacity: 1;\n}\n.sja_menuoption_y {\n    display: inline-block;\n    color: black;\n    padding: 2px 4px;\n    cursor: default;\n    background-color: #E6E5C5;\n    margin: 2px;\n}\n.sja_menuoption_y:hover {\n    background-color: #DEDCA9\n}\n.sja_menuoption_y:active {\n    background-color: #FFFF99\n}\n.sja_menuoption_r {\n    display: inline-block;\n    color: black;\n    padding: 2px 4px;\n    cursor: default;\n    background-color: #EDDDDE;\n    margin: 2px;\n}\n.sja_menuoption_r:hover {\n    background-color: #E8CFD1\n}\n.sja_menuoption_r:active {\n    background-color: #FCD9DD\n}\n.sja_error2 {\n    display: inline-block;\n    padding: 5px 50px 5px 10px;\n    margin: 10px 20px;\n    background-color: rgba(200, 0, 0, .5);\n    color: white;\n    border-radius: 6px;\n}\n.sja_paint {\n    position: relative;\n}\n.sja_paint>:first-child {}\n.sja_paint>:nth-child(2) {\n    position: absolute;\n    padding: 3px 6px;\n    cursor: default;\n    top: 10px;\n    right: 30px;\n    font-size: 80%;\n}\n.sja_tree_ul {\n    list-style-type: none;\n    padding-left: 25px;\n    line-height: 1.4;\n}\n.sja_input {\n    display: inline-block;\n    padding: 2px 6px;\n}\n.sja_bulkcell {\n    display: inline-block;\n    width: 3px;\n    height: 9px;\n    margin: 1px 1px 0px 0px;\n}\n.sja_tag {\n    display: inline-block;\n    margin-left: 10px;\n    padding: 1px 3px;\n    background-color: #858585;\n    color: white;\n    font-size: 80%;\n}\n.sja_bgbox {\n    cursor: default;\n    fill: yellow;\n    fill-opacity: 0;\n}\n.sja_bgbox:hover {\n    fill-opacity: .2;\n}\n.sja_diseasehm_search_item {\n    display: inline-block;\n    margin: 3px;\n    padding: 2px;\n}\n.sja_pulse {\n    animation: pulse .5s alternate infinite;\n}\n@keyframes pulse {\n    from {\n        opacity: .2;\n    }\n    to {\n        opacity: 1;\n    }\n}\n.sja_hm-edittool-table td {\n    padding: 0 2px;\n    cursor: pointer;\n    text-align: center;\n    font-size: 14px;\n}\n.sja_hm-edittool-table td:hover {\n    opacity: 1;\n    font-weight: 600;\n}\n.sja_tinylogo_head {\n    display: inline-block;\n    background-color: #858585;\n    color: white;\n    font-size: .6em;\n    padding: 1px 3px;\n}\n.sja_tinylogo_body {\n    display: inline-block;\n    margin-left: 10px;\n    background-color: #ededed;\n    font-size: .9em;\n    color: black;\n    padding: 1px 5px;\n}\n.sja_handle_green {\n    display: inline-block;\n    font-size: .9em;\n    padding: 3px 6px;\n    background-color: #f0f7f1;\n    color: #146E17;\n    cursor: default;\n}\n.sja_handle_green:hover {\n    background-color: #D5F0D8;\n}\n.sja_handle_green:active {\n    background-color: #BAD1BC;\n    color: black;\n}\n.sja_handle_red {\n    display: inline-block;\n    font-size: .9em;\n    padding: 3px 6px;\n    background-color: #F5EBEC;\n    color: #991F1F;\n    cursor: default;\n}\n.sja_handle_red:hover {\n    background-color: #F2D8DB;\n}\n.sja_handle_red:active {\n    background-color: #E3B1B7;\n    color: black;\n}\n.sja_btn {\n    -webkit-appearance: button;\n    -moz-appearance: button;\n    appearance: button;\n    text-decoration: none;\n    color: initial;\n}\n.sja_button {\n    display: inline-block;\n    background: white;\n    padding: 3px 5px;\n    border: solid 1px black;\n    opacity: .8;\n    cursor: default;\n}\n.sja_button:hover {\n    opacity: 1;\n}\n.sja_button_open {\n    display: inline-block;\n    background: #ddd;\n    padding: 3px 5px;\n    border: solid 1px black;\n    opacity: .8;\n    cursor: default;\n}\n.sja_button_open:hover {\n    opacity: 1;\n}\n.sja_button_fold {\n    display: inline-block;\n    background: #aaa;\n    color: white;\n    padding: 3px 5px;\n    border: solid 1px black;\n    opacity: .8;\n    cursor: default;\n}\n.sja_button_fold:hover {\n    opacity: 1;\n}\n.sja-termdb-config-row-label {\n    padding: 5px;\n    text-align: left;\n    vertical-align: middle;\n}\n.sjpp-controls-table {\n  margin-bottom: 10px;\n}\n.sjpp-controls-table > tr:hover {\n  /*font-weight: 600;*/\n  text-shadow:0px 0px 0.5px black;\n  background-color: rgba(239, 236, 149, 0.389);\n}\n.sja_edit_btn {\n    display: inline-block;\n    color: black;\n    background-color: #f2f2f2;\n    border-radius: 5px;\n    border: solid 1px #aaa;\n    padding: 5px 10px;\n    cursor: default;\n    margin: 1px;\n    font-size: 0.8em;\n    margin-left: 20px;\n}\n.sja_edit_btn:hover {\n    background-color: #e6e6e6\n}\n.sja_edit_btn:active {\n    color: #cc0000;\n    background-color: #FCE2E1;\n}\n/* App Drawer style */\n.sjpp-appdrawer-cols {\n    font-family: Verdana, Geneva, Tahoma, sans-serif;\n    font-weight: 500;\n    font-size: 17px;\n    text-align: left;\n    color: #324870;\n    margin: 10px 10px 0px 10px;\n}\n.sjpp-track, .sjpp-track li {\n    display: grid !important;\n    grid-template-columns: 2fr 4fr 40px;\n    grid-template-areas: 'image header' 'image blurb';\n    gap: 5px;\n}\n.sjpp-app-drawer-card,\n.sjpp-track {\n    background-color: white;\n    max-width: 400px;\n    /* min-width: 320px; */\n    border-radius: 5px;\n    padding: 0px;\n    align-items: center;\n    justify-items: left;\n    box-shadow: 0 1px 2px rgba(0, 0, 0, 0.1);\n    -webkit-transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n    transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n}\n.sjpp-app-drawer-card::after,\n.sjpp-track::after {\n    content: \"\";\n    border-radius: 8px;\n    position: absolute;\n    z-index: -1;\n    top: 0;\n    left: 0;\n    width: 100%;\n    height: 100%;\n    box-shadow: 0 5px 15px rgba(0, 0, 0, 0.3);\n    opacity: 0;\n    -webkit-transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n    transition: all 0.6s cubic-bezier(0.165, 0.84, 0.44, 1);\n}\n.sjpp-app-drawer-card:hover,\n.sjpp-track:hover {\n    -webkit-transform: scale(1, 1);\n    transform: scale(1, 1);\n}\n.sjpp-app-drawer-card:hover::after,\n.sjpp-track:hover::after {\n    opacity: 1;\n}\n.sjpp-track-image {\n    grid-area: image;\n    width: 75px;\n    height: 75px;\n    align-self: start;\n    justify-self: start;\n}\n.sjpp-track-image img {\n    width: 100%;\n    height: 100%;\n    object-fit: cover;\n    border-radius: 5px 0px 0px 5px;\n}\n.sjpp-app-drawer-card-ribbon{\n    grid-area: image;\n    overflow: hidden;\n    width: 100%;\n    height: 100%;\n}\n.sjpp-app-drawer-card-ribbon::before,\n.sjpp-app-drawer-card-ribbon::after {\n  position: relative;\n  z-index: -1;\n  content: '';\n  display: block;\n  border-top-color: transparent;\n  border-left-color: transparent;\n}\n.sjpp-app-drawer-card-ribbon span {\n  position: relative;\n  display: block;\n  width: 100%;\n  padding: 1px 0;\n  border-color: transparent transparent transparent darkgray;\n  box-shadow: 0 2px 7.5px rgba(0, 0, 0, 0.3);\n  opacity: 1;\n  font-family: 'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif;\n  transform: rotate(-45deg);\n}\n.sjpp-app-drawer-card-ribbon::before {\n    top: 0;\n    right: 0;\n}\n.sjpp-app-drawer-card-ribbon::after {\n    bottom: 0;\n    left: 0;\n}\n.sjpp-track-h {\n    grid-area: header;\n    font-family: 'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif;\n    margin-left: 5px;\n    padding: 0px;\n}\n.sjpp-track-blurb {\n    grid-area: blurb;\n    font-size: 13px;\n    font-weight: 300;\n    margin-left: 5px;\n    justify-content: center;\n    font-style: oblique;\n    color: #403f3f;\n}\n/* client/src/block.js start */\n.sjpp-active-tiny-button {\n\tdisplay: inline-block;\n\tbackground-color: #1C5E86;\n\tfont-size: .8em;\n\tcolor: white;\n\tpadding: 1px 5px;\n\tmargin-right: 5px;\n\tborder-radius: 4px;\n}\n.sjpp-plus-button\n{\n    display: inline-block;\n    margin: 1px;\n    border: solid 1px #545454;\n    font-size: .9em;\n    cursor: default;\n    padding: 2px 5px;\n}\n.sjpp-dshandleholder\n{\n    display: inline-block;\n    margin: 1px;\n    border: solid 1px #545454;\n    font-size: .9em;\n    cursor: default;\n}\n.sjpp-dslabel\n{\n    display: inline-block;\n    color: black;\n    padding: 2px 4px;\n\n}\n/* client/src/block.js end */\n/* client/src/app.js start */\n.sjpp-input-div-gene-pos\n{\n    display: inline-block;\n    padding-right: 5px;\n}\n.sjpp-input-gene-pos\n{\n    border: solid 1px #545454;\n    padding: 6px 10px;\n    border-radius: 5px;\n}\n.sjpp-genome-select-div\n{\n    display: inline-block;\n    padding-left: 5px;\n}\n.sjpp-genome-select\n{\n    border-radius: 5px;\n    margin: 1px 20px 1px 10px;\n}\n.sjpp-output-sandbox-title\n{\n    border-radius:4px; \n    color:white; \n    background-color: #969696; \n    padding: 1px 5px; \n    display:inline-block; \n    font-size:0.8em; \n    margin-left:4px;\n}\n/* client/src/app.js end */\n/* client/dom/sandbox.ts start */\n.sjpp-output-sandbox-header\n{\n    display: inline-block;\n    margin: 5px 10px;\n    padding-right: 8px;\n    margin-bottom: 0px;\n    /* box-shadow:2px 0px 2px #f2f2f2; */\n    border-radius: 5px 5px 0 0;\n    /* background-color: #f2f2f2; */\n    z-index: 99;\n}\n.sjpp-output-sandbox-content\n{\n    margin: 5px 10px;\n    margin-top: 0px;\n    padding-right: 8px;\n    display: inline-block;\n    /* box-shadow: 2px 2px 10px #f2f2f2; */\n    border: solid 1px #ccc;\n    border-top: solid 1px white;\n    border-radius: 0  0 5px 5px;\n}\n.sjpp-output-sandbox-collapse-btn,\n.sjpp-output-sandbox-expand-btn,\n.sjpp-output-sandbox-close-bt\n{\n    /* display: inline-block; */\n    /* margin: 0px; */\n    /* border-right: solid 2px white; */\n    font-size: 16px;\n    cursor: default;\n}\n.sjpp-output-sandbox-close-bt {\n    border-radius: 5px 0 0 0;\n}\n/* \nSeparated padding for sandbox buttons to fix close button's\nright, white border not extending to total height of\nsandbox header\n*/\n.sjpp-output-sandbox-collapse-btn,\n.sjpp-output-sandbox-expand-btn {\n    padding: 4px 10px;\n}\n.sjpp-output-sandbox-close-bt {\n    padding: 8px 10px;\n}\n/* client/dom/sandbox.ts end */\n.sjpp_row_wrapper:hover {\n    background: #fcfcca !important; \n}\n/*.sjpp_row_wrapper:nth-child(odd) {background: rgb(237, 237, 237)}*/\n.sjpp_table_header {\n    font-family: 'Arial';\n    font-size: 1em;\n    text-align: left;\n    position: sticky;\n    top: 0;\n    opacity: 0.7;\n    font-weight: normal;\n}\n.sjpp_table_item {\n    padding: 3px 5px;\n    font-size: 1em;\n    text-align: left;\n}\n.sjpp_show_scrollbar{\n\t/* set to \"auto\" to avoid showing a gray track as non-functional scrollbar when contents don't scroll at all, since scrollbar track is now gray and no longer white */\n    overflow-y: auto;\n    overflow-x: auto;\n}\n.sjpp_show_scrollbar::-webkit-scrollbar{\n    background-color: #f1f1f1; /* use non-white track color so the presence of scrollbar is apparent (gdc requirement) */\n    border-radius: 7px;\n    width: 14px;\n}\n/* This will handle the thumb (scrolling part) */\n.sjpp_show_scrollbar::-webkit-scrollbar-thumb{\n    background-color: #858585;\n    border-radius: 7px;\n    border: 1px solid white;\n}\n.sjpp_show_scrollbar::-webkit-scrollbar-thumb:vertical{\n    height: 14px!important;\n    width: 14px;\n}\n.sjpp-matrix-series-group-label-g text,\n.sjpp-matrix-series-label-g text,\n.sjpp-matrix-term-group-label-g text,\n.sjpp-matrix-term-label-g text,\n.sjpp-matrix-label text {\n    -webkit-user-select:  none;\n    -moz-user-select: none;\n    -ms-user-select: none;\n    -user-select: none;\n}\n.sjpp-nav\n{\n    position: sticky;\n    background-color: white;\n    width: 100%;\n    z-index: 10;\n    top: 0px;\n    left: 0px;\n    padding: 0px 0px 15px 0px;\n}\n.add_term_btn {\n    border-radius: 6px;\n}\n#sjpp-loading-overlay {\n    position: absolute;\n    top: 0;\n    left: 0;\n    width: 100%;\n    height: 100%;\n    background-color:rgba(255, 255, 255, 0.8);\n}\n.sjpp-spinner {\n    position: absolute;\n    left: 50%;\n    top: 30%;\n    height: 60px;\n    width: 60px;\n    margin: 0px auto;\n    -webkit-animation: rotation .6s infinite linear;\n    -moz-animation: rotation .6s infinite linear;\n    -o-animation: rotation .6s infinite linear;\n    animation: rotation .6s infinite linear;\n    border-left: 6px solid rgba(0, 174, 239, .15);\n    border-right: 6px solid rgba(0, 174, 239, .15);\n    border-bottom: 6px solid rgba(0, 174, 239, .15);\n    border-top: 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ga(e={}){if(e.mclass){for(const t in e.mclass){if(!Yr[t])Yr[t]={};for(const n in e.mclass[t]){Yr[t][n]=e.mclass[t][n]}}}}const ba=function(e){const t=e.toLowerCase().split(",");let n=1;if(t.indexOf("transcript_ablation")!=-1){return[Hr,Kr,n]}n++;if(t.indexOf("splice_acceptor_variant")!=-1)return[Pr,"L",n];n++;if(t.indexOf("splice_donor_variant")!=-1)return[Pr,"L",n];n++;if(t.indexOf("stop_gained")!=-1)return[Pr,"N",n];n++;if(t.indexOf("frameshift_variant")!=-1)return[Pr,"F",n];n++;if(t.indexOf("stop_lost")!=-1)return[Pr,"N",n];n++;if(t.indexOf("start_lost")!=-1)return[Pr,"N",n];n++;if(t.indexOf("transcript_amplification")!=-1){return[Pr,oa,n]}n++;if(t.indexOf("inframe_insertion")!=-1||t.indexOf("conservative_inframe_insertion")!=-1||t.indexOf("disruptive_inframe_insertion")!=-1)return[Pr,"I",n];n++;if(t.indexOf("inframe_deletion")!=-1||t.indexOf("conservative_inframe_deletion")!=-1||t.indexOf("disruptive_inframe_deletion")!=-1)return[Pr,"D",n];n++;if(t.indexOf("missense_variant")!=-1)return[Pr,"M",n];n++;if(t.indexOf("protein_altering_variant")!=-1)return[Pr,"ProteinAltering",n];n++;if(t.indexOf("splice_region_variant")!=-1)return[Pr,"P",n];n++;if(t.indexOf("incomplete_terminal_codon_variant")!=-1)return[Pr,"N",n];n++;if(t.indexOf("stop_retained_variant")!=-1)return[Pr,"S",n];n++;if(t.indexOf("synonymous_variant")!=-1)return[Pr,"S",n];n++;if(t.indexOf("coding_sequence_variant")!=-1)return[Pr,oa,n];n++;if(t.indexOf("mature_mirna_variant")!=-1)return[Pr,"E",n];n++;if(t.indexOf("5_prime_utr_variant")!=-1)return[Pr,na,n];n++;if(t.indexOf("3_prime_utr_variant")!=-1)return[Pr,ta,n];n++;if(t.indexOf("non_coding_transcript_exon_variant")!=-1)return[Pr,"E",n];n++;if(t.indexOf("intron_variant")!=-1)return[Pr,"Intron",n];n++;if(t.indexOf("nmd_transcript_variant")!=-1)return[Pr,"S",n];n++;if(t.indexOf("non_coding_transcript_variant")!=-1)return[Pr,"E",n];n++;if(t.indexOf("upstream_gene_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("downstream_gene_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("tfbs_ablation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("tfbs_amplification")!=-1)return[Pr,ia,n];n++;if(t.indexOf("tf_binding_site_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("regulatory_region_ablation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("regulatory_region_amplification")!=-1)return[Pr,ia,n];n++;if(t.indexOf("feature_elongation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("regulatory_region_variant")!=-1)return[Pr,ia,n];n++;if(t.indexOf("feature_truncation")!=-1)return[Pr,ia,n];n++;if(t.indexOf("intergenic_variant")!=-1)return[Pr,ia,n];n++;return[Pr,oa,n]};const ya='<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="#858585" stroke="none"></path>';const va={};const wa="S";va[wa]={label:"Somatic",desc:"A variant found only in a tumor sample. The proportion is indicated by lack of any arc.",legend:'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>'};const xa="G";va[xa]={label:"Germline",desc:"A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.",legend:ya};va.germline=va[xa];va.somatic=va[wa];const _a="R";va[_a]={label:"Relapse",desc:"A somatic variant found only in a relapse sample. The proportion is indicated by the span of the hollow arc within the whole circle.",legend:'<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="none" stroke="#858585"></path>'};const ka="GP";va[ka]={label:"Germline pathogenic",desc:"A constitutional variant with pathogenic allele.",legend:ya};const ja="GNP";va[ja]={label:"Germline non-pathogenic",desc:"A constitutional variant with non-pathogenic allele.",legend:ya,hidden:true};const Na={usegm:"usegm",ds:"dataset",bigwig:"bigwig",bigwigstranded:"bigwigstranded",junction:"junction",mdsjunction:"mdsjunction",mdscnv:"mdscnv",mdssvcnv:"mdssvcnv",mdsexpressionrank:"mdsexpressionrank",mdsvcf:"mdsvcf",bedj:"bedj",pgv:"profilegenevalue",bampile:"bampile",hicstraw:"hicstraw",expressionrank:"expressionrank",aicheck:"aicheck",ase:"ase",mds2:"mds2",mds3:"mds3",bedgraphdot:"bedgraphdot",bam:"bam",ld:"ld"};function Sa(e){for(const t in Na){if(e==Na[t]){return true}}return false}const Aa={vcf:"vcf"};const Ca={vcf:"vcf",svcnvitd:"svcnvitd",geneexpression:"geneexpression"};const Ea={GCT:"A",GCC:"A",GCA:"A",GCG:"A",CGT:"R",CGC:"R",CGA:"R",CGG:"R",AGA:"R",AGG:"R",AAT:"N",AAC:"N",GAT:"D",GAC:"D",TGT:"C",TGC:"C",CAA:"Q",CAG:"Q",GAA:"E",GAG:"E",GGT:"G",GGC:"G",GGA:"G",GGG:"G",CAT:"H",CAC:"H",ATT:"I",ATC:"I",ATA:"I",TTA:"L",TTG:"L",CTT:"L",CTC:"L",CTA:"L",CTG:"L",AAA:"K",AAG:"K",ATG:"M",TTT:"F",TTC:"F",CCT:"P",CCC:"P",CCA:"P",CCG:"P",TCT:"S",TCC:"S",TCA:"S",TCG:"S",AGT:"S",AGC:"S",ACT:"T",ACC:"T",ACA:"T",ACG:"T",TGG:"W",TAT:"Y",TAC:"Y",GTT:"V",GTC:"V",GTA:"V",GTG:"V"};const Oa="*";function Ma(e){if(!e.genomicseq)return undefined;const t=[];if(e.coding){for(const[n,o]of e.coding.entries()){const n=e.genomicseq.substr(o[0]-e.start,o[1]-o[0]);if(e.strand=="-"){t.push(La(n))}else{t.push(n)}}}const n=t.join("");const o=[];const i=e.startCodonFrame?3-e.startCodonFrame:0;for(let e=i;e<n.length;e+=3){const t=Ea[n.substr(e,3)];o.push(t||Oa)}e.cdseq=n;return o.join("")}function Ia(e,t){if(e>=1e9)return(e/1e9).toFixed(1)+" Gb";if(e>=1e7)return Math.ceil(e/1e6)+" Mb";if(e>=1e6)return(e/1e6).toFixed(1)+" Mb";if(e>=1e4)return Math.ceil(e/1e3)+" Kb";if(e>=1e3)return(e/1e3).toFixed(1)+" Kb";return e+(t?"bytes":" bp")}const Ta={A:"#ca0020",T:"#f4a582",C:"#92c5de",G:"#0571b0"};function Ra(e){switch(e){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";case"a":return"t";case"t":return"a";case"c":return"g";case"g":return"c";default:return e}}function La(e){const t=[];for(let n=e.length-1;n>=0;n--){t.push(Ra(e[n]))}return t.join("")}function $a(e,t){const n={chr:e.chr,start:e.start,stop:e.stop,strand:e.strand,coding:[]};if(t.isskipexon||t.isaltexon){for(let o=0;o<e.exon.length;o++){const i=Math.max(e.codingstart,e.exon[o][0]);const s=Math.min(e.codingstop,e.exon[o][1]);if(i>s){continue}if(t.skippedexon.indexOf(o)==-1){n.coding.push([i,s])}}}else if(t.a5ss||t.a3ss){const 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t.categoryhidden){if(!t.categories[e])return"unknown hidden-by-default category "+e+" from set "+t.name}}else{t.categoryhidden={}}}else if(t.numericfilter){const e=[];for(const n of t.numericfilter){if(typeof n=="number"){e.push({side:"<",value:n})}else{e.push({side:n.side||"<",value:n.value})}}t.numericfilter=e}if(t.altalleleinfo){if(!t.altalleleinfo.key){return".key missing from .altalleleinfo from set "+t.name}}else if(t.locusinfo){if(!t.locusinfo.key){return".key missing from .locusinfo from set "+t.name}}else{return"neither .altalleleinfo or .locusinfo is available from set "+t.name}}}function Da(e,t){for(const n in e.majorchr){if(t.indexOf(n.replace("chr",""))!=-1){return true}}if(e.minorchr){for(const n in e.minorchr){if(t.indexOf(n.replace("chr",""))!=-1){return true}}}return false}function Ua(e,t){let n=0,o=0;for(const i in e.majorchr){if(t.includes(i)){o++}else if(t.includes(i.replace("chr",""))){n++}}if(e.minorchr){for(const i in e.minorchr){if(t.includes(i)){o++}else 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e=0;e<r.length;e++){s[r[e]]=i[e]}if(!s.chr1){a.push([e,"missing chr1",i]);return}if(s.chr1.toLowerCase().indexOf("chr")!=0){s.chr1="chr"+s.chr1}if(!s.chr2){a.push([e,"missing chr2",i]);return}if(s.chr2.toLowerCase().indexOf("chr")!=0){s.chr2="chr"+s.chr2}let l=s.position1;if(!l){a.push([e,"missing position1",i]);return}let c=Number.parseInt(l);if(Number.isNaN(c)||c<=0){a.push([e,"invalid value for position1",i]);return}s.position1=c;l=s.position2;if(!l){a.push([e,"missing position2",i]);return}c=Number.parseInt(l);if(Number.isNaN(c)||c<=0){a.push([e,"invalid value for position2",i]);return}s.position2=c;if(sd(s,n,e,i)){return}if(s.isoform1&&s.isoform1.indexOf(",")!=-1){const e=s.isoform1.split(",");s.isoform1=undefined;for(const t of e){if(t!="")s.isoform1=t}}if(s.isoform2&&s.isoform2.indexOf(",")!=-1){const e=s.isoform2.split(",");s.isoform2=undefined;for(const t of e){if(t!="")s.isoform2=t}}if(!s.gene1){s.isoform1=undefined}if(!s.gene2){s.isoform2=undefined}if(s.gene1){n.good++;const e={dt:o?Fr:Dr,class:o?aa:ra,isoform:s.isoform1,mname:s.gene2||s.chr2,sample:s.sample,patient:s.patient,sampletype:s.sampletype,origin:s.origin,disease:s.disease,pairlst:[{a:{name:s.gene1,isoform:s.isoform1,strand:s.strand1,chr:s.chr1,position:s.position1},b:{name:s.gene2,isoform:s.isoform2,strand:s.strand2,chr:s.chr2,position:s.position2}}]};const t=n.geneToUpper?s.gene1.toUpperCase():s.gene1;if(!n.data[t]){n.data[t]=[]}n.data[t].push(e)}if(s.gene2&&s.gene2!=s.gene1){n.good++;const e={dt:o?Fr:Dr,class:o?aa:ra,isoform:s.isoform2,mname:s.gene1||s.chr1,sample:s.sample,patient:s.patient,sampletype:s.sampletype,origin:s.origin,disease:s.disease,pairlst:[{a:{name:s.gene1,isoform:s.isoform1,strand:s.strand1,chr:s.chr1,position:s.position1},b:{name:s.gene2,isoform:s.isoform2,strand:s.strand2,chr:s.chr2,position:s.position2}}]};const t=n.geneToUpper?s.gene2.toUpperCase():s.gene2;if(!n.data[t]){n.data[t]=[]}n.data[t].push(e)}}function dd(e){const t={};for(const n in e){if(n=="pairlst")continue;const o=e[n];const i=typeof o;if(i=="object"){continue}t[n]=o}if(e.pairlst){t.pairlst=[];for(const n of e.pairlst){const e={};for(const t in n){if(t=="a"||t=="b"||t=="interstitial"){continue}e[t]=n[t]}if(n.a){e.a={};for(const t in n.a){const o=n.a[t];if(typeof o=="object"){continue}e.a[t]=o}}if(n.b){e.b={};for(const t in n.b){const o=n.b[t];if(typeof o=="object"){continue}e.b[t]=o}}if(n.interstitial){e.interstitial={};for(const t in n.interstitial){const o=n.interstitial[t];if(typeof o=="object"){continue}e.interstitial[t]=o}}t.pairlst.push(e)}}return t}function fd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid file header for svjson";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("sample");if(i!=-1)n[i]="sample";i=o("sampletype");if(i!=-1)n[i]="sampletype";i=o("patient");if(i!=-1)n[i]="patient";i=o("json","jsontext");if(i==-1)return["json missing from 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Gr:a.class=Qr;a.mname="N-loss";break;case Jr:a.class=ea;a.mname="C-loss";break;case Hr:a.class=Kr;a.mname="Del";break;case Fr:a.class=aa;a.mname="SV";break;default:r.push([e,"unknown datatype",i]);return}if(!a.gene){r.push([e,"json.gene missing",i]);return}n.good++;for(const e in s){if(e!="jsontext"){a[e]=s[e]}}const t=n.geneToUpper?a.gene.toUpperCase():a.gene.toUpperCase();if(!n.data[t]){n.data[t]=[]}n.data[t].push(a)}}function ud(e){const t=[];for(const n of e){const e={a:{},b:{}};for(const t in n){if(t!="a"&&t!="b")e[t]=n[t]}for(const t in n.a){e.a[t]=n.a[t]}for(const t in n.b){e.b[t]=n.b[t]}t.push(e)}return t}function hd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid file header for CNV";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("gene");if(i==-1)return"gene missing from header";n[i]="gene";i=o("cnv");if(i==-1)return"CNV missing from 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n.data)){n.data[r]=[]}n.data[r].push(i)}function gd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid header line for ITD";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("gene");if(i==-1)return"gene missing from header";n[i]="gene";i=o("annovar_isoform","mrna_accession","mrna accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq","isoform");if(i==-1)return"isoform missing from header";n[i]="isoform";i=o("rnaposition");if(i!=-1){n[i]="rnaposition";i=o("rnaduplength");if(i==-1)return"rnaduplength is required when rnaposition is present";n[i]="rnaduplength"}i=o("chromosome","chr");if(i!=-1){n[i]="chr";i=o("chr_start");if(i==-1)return"chr_start is required when chr is present";n[i]="chrpos1";i=o("chr_stop");if(i==-1)return"chr_stop is required when chr is 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t=Number.parseInt(i.chrpos1);if(Number.isNaN(t)||t<0){n.itd.badlines.push([e,"invalid chr_start value",o]);return}i.chrpos1=t;t=Number.parseInt(i.chrpos2);if(Number.isNaN(t)||t<0){n.itd.badlines.push([e,"invalid chr_stop value",o]);return}i.chrpos2=t}if(sd(i,n,e,o,n.itd.badlines)){return}i.dt=qr;i.class=Zr;i.mname="ITD";n.good++;var s=n.geneToUpper?i.gene.toUpperCase():i.gene;if(!(s in n.data)){n.data[s]=[]}n.data[s].push(i)}function yd(e,t){const n=e.toLowerCase().split("\t");if(n.length<=1)return"invalid header line for intragenic deletion";const o=(...e)=>{for(const t of e){const e=n.indexOf(t);if(e!=-1)return e}return-1};let i=o("gene");if(i==-1)return"gene missing from header";n[i]="gene";i=o("annovar_isoform","mrna_accession","mrna accession","refseq_mrna_id","annovar_sj_filter_isoform","refseq","isoform");if(i==-1)return"isoform missing from header";n[i]="isoform";i=o("rnaposition");if(i!=-1){n[i]="rnaposition";i=o("rnadellength");if(i==-1)return"rnadellength is required when 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xd(e,t,n){if(t==""||t[0]=="#")return;const o=t.split("\t");const i={};for(let e=0;e<n.truncation.header.length;e++){i[n.truncation.header[e]]=o[e]}if(!i.gene){n.truncation.badlines.push([e,"missing gene",o]);return}if(i.rnaposition){const t=Number.parseInt(i.rnaposition);if(Number.isNaN(t)||t<0){n.truncation.badlines.push([e,"invalid rnaPosition value",o]);return}i.rnaposition=t}if(i.pos){const t=Number.parseInt(i.pos);if(Number.isNaN(t)||t<0){n.truncation.badlines.push([e,"invalid genomic position",o]);return}i.pos=t}if(!i.losstype){n.truncation.badlines.push([e,"missing lossType value",o]);return}if(i.losstype!="n"&&i.losstype!="c"){n.truncation.badlines.push([e,'lossType value not "n" or "c"',o]);return}if(sd(i,n,e,o,n.truncation.badlines)){return}if(i.losstype=="n"){i.dt=Gr;i.class=Qr;i.mname="N-loss"}else{i.dt=Jr;i.class=ea;i.mname="C-loss"}n.good++;const s=n.geneToUpper?i.gene.toUpperCase():i.gene;if(!(s in n.data)){n.data[s]=[]}n.data[s].push(i)}const _d=["heatmapJSON","piebarJSON","survivalJSON","discoJSON","riverJSON"];const kd={snvindel:0,si:0,sv:1,fusion:2,itd:3,deletion:4,truncation:5,cnv:6};let jd=false;class Nd{constructor(e){this.bt=e;this.err=this.errHandler();if(!jd){const e=Sd();if(e.project){this.getData(e.project);jd=true}}if(e.filediv){this.projectByInput(e.filediv)}}processData(e){const t=e.files.pop();const n=e.expectedFileNames.indexOf(t.name);if(n==-1){if(e.files.length)setTimeout((()=>{this.processData(e)}),1);return}e.expectedFileNames.splice(n,1);this.cohort={name:"project",genome:this.bt.genomes[this.bt.gselect.options[this.bt.gselect.selectedIndex].innerHTML]};if(!this.flag){this.flag=this.bt.init_bulk_flag(this.cohort.genome)}const o=this.bt.content2flag(t.content,t.type,this.flag);if(o){this.err(o);this.processData(e)}else if(!e.files.length){if(e.expectedFileNames.length){this.err('These referenced files were not found: "'+e.expectedFileNames.join('", 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r=this.getTracker(s,(()=>this.processData(i)));Object.keys(o).forEach((e=>{this.getjson("/data/projects/"+t+"/"+e,(t=>{i.schema[o[e]]=t;r()}))}));Object.keys(n).forEach((e=>{this.gettext("/data/projects/"+t+"/"+e,(t=>{i.files.push({name:e,type:n[e],content:t});r()}))}))}))}gettext(e,t){fetch(e).then((t=>{if(t.ok)return t.text();else this.err("File request error: "+e)})).then(t).catch((t=>this.err("File request error: "+e+" "+t)))}getjson(e,t){fetch(e).then((t=>{if(t.ok)return t.json();else this.err("Network error for "+e)})).then(t).catch((t=>this.err("file request error: "+e+" "+t)))}getTracker(e,t){let n=0;return function o(){n+=1;if(n==e){t()}}}projectByInput(e){this.tp=null;const t=e.append("div");t.append("span").html("Project: reference 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o=Array.from(e.target.files);const i=o.filter((e=>e.name==n))[0];if(!i){t.err("Missing reference file='"+n+"'.");return}const s={};const r={};const a={schema:{},files:[],expectedFileNames:[]};const l=new FileReader;let c="";let d=0;l.onload=e=>{e.target.result.trim().split("\n").forEach((e=>{const[n,o]=e.trim().split("\t");if(_d.includes(n)){r[o]=n}else if(!kd[n]&&kd[n]!==0){t.err("Unrecognized type "+n+" for file "+o+" in reference.txt.")}else{s[o]=kd[n]}}));a.expectedFileNames=Object.keys(s);const n=o.filter((e=>e.name in r));let i=0;if(!n.length){o.forEach(l)}else{n.forEach((e=>{const s=new FileReader;s.onload=s=>{const c=JSON.parse(s.target.result);i+=1;if(!c){t.err('Unable to parse schema file="'+e.name+'".')}else{a.schema[r[e.name]]=c}if(i==n.length){o.forEach(l)}};s.onerror=()=>{t.err("Error reading schema.txt.")};s.readAsText(e,"utf8")}))}function l(e){if(!a.expectedFileNames.includes(e.name)){d+=1;return}if(!e){t.err("Error reading 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l=Od(s,e-1,t);if(!s[r.k]){if(e>0){i[l]+=1}break}n[a]=l;if(!(a in i)){i[a]=0}if(!(a in o)){const n={lst:[]};if(r.full){n.full=s[r.full]}n.id0=t[0].k;n.v0=s[t[0].k];if(e==1){n.id1=t[1].k;n.v1=s[t[1].k]}if(e==2){n.id2=t[2].k;n.v1=s[t[2].k]}o[a]=n}o[a].lst.push(s);if(e==t.length-1){i[a]+=1}}}const s=[{id:Ad,name:Ad}];for(const e in n){const t=n[e];const r=o[e];const a=e.split(Cd);s.push({id:e,parentId:t,lst:r.lst,value:i[e],name:a[a.length-1],full:r.full,id0:r.id0,v0:r.v0,id1:r.id1,v1:r.v1,id2:r.id2,v2:r.v2})}return s}function Od(e,t,n){const o=[Ad];for(let i=0;i<t;i++){o.push(e[n[i].k])}if(t>=0){o.push(e[n[t].k])}return o.join(Cd)}function Md(e){const t={id2vcf:{},label:e.name||"Unnamed VCF file"};let n;if(e.file){const o=Math.random().toString();n={file:e.file,indexURL:e.indexURL,vcfid:o};t.id2vcf[o]=n}else if(e.url){const o=Math.random().toString();n={url:e.url,indexURL:e.indexURL,vcfid:o};t.id2vcf[o]=n}else{return["no .file or .url"]}n.headernotloaded=true;if(e.samplenamemap){n.samplenamemap=e.samplenamemap}if(e.variant2img){if(!e.variant2img.path)return[".path missing from .variant2img{}"]}const o={type:mc.ds,isvcf:true,name:t.label,ds:t,populationfrequencyfilter:e.populationfrequencyfilter,vcfinfofilter:e.vcfinfofilter,itemlabelname:e.itemlabelname,viewrangeupperlimit:e.viewrangeupperlimit,variant2img:e.variant2img,axisheight:e.axisheight};if(e.url4variant){const t=Id(e.url4variant);if(t)return[".url4variant error: "+t];o.url4variant=e.url4variant}if(e.button4variant){const t=Td(e.button4variant);if(t)return[".button4variant error: "+t];o.button4variant=e.button4variant}if(e.sampleannotation){const t=e.sampleannotation;if(!t.annotation)return[".annotation{} missing from .sampleannotation"];if(t.levels){if(!Array.isArray(t.levels))return[".sampleannotation.levels should be array"];const e=[];for(const n in t.annotation){const o={sample_name:n};for(const e in t.annotation[n]){o[e]=t.annotation[n][e]}e.push(o)}const n=Ed(e,t.levels);t.root=wr()(n);t.root.sum((e=>e.value))}if(t.variantsunburst){if(!t.levels)return[".levels missing when .variantsunburst is on from .sampleannotation"]}o.ds.cohort=t}if(e.vcfcohorttrack){if(!e.vcfcohorttrack.file&&!e.vcfcohorttrack.url)return["no .file or .url provided from .vcfcohorttrack"];o.ds.vcfcohorttrack=e.vcfcohorttrack}if(e.germline2dvafplot){if(!e.germline2dvafplot.individualkey)return[".individualkey missing from germline2dvafplot"];if(!e.germline2dvafplot.sampletypekey)return[".sampletypekey missing from germline2dvafplot"];if(!e.germline2dvafplot.xsampletype)return[".xsampletype missing from germline2dvafplot"];if(!e.germline2dvafplot.yleftsampletype)return[".yleftsampletype missing from germline2dvafplot"];if(e.germline2dvafplot.yrightsampletype){if(e.germline2dvafplot.yrightsampletype==e.germline2dvafplot.yleftsampletype)return[".yrightsampletype should not be same as yleftsampletype"]}o.ds.germline2dvafplot=e.germline2dvafplot}if(e.vaf2coverageplot){if(e.vaf2coverageplot.categorykey){if(!e.vaf2coverageplot.categories)return[".categories missing when .categorykey is in use for .vaf2coverageplot"]}o.ds.vaf2coverageplot=e.vaf2coverageplot}if(e.genotype2boxplot){if(e.genotype2boxplot.boxplotvaluekey);else if(e.genotype2boxplot.sampleannotationkey){if(!o.ds.cohort)return["sampleannotation missing when using genotype2boxplot.sampleannotationkey"];if(!o.ds.cohort.annotation)return["sampleannotation.annotation missing when using genotype2boxplot.sampleannotationkey"];let t=false;for(const n in o.ds.cohort.annotation){if(e.genotype2boxplot.sampleannotationkey in o.ds.cohort.annotation[n]){t=true;break}}if(!t)return[e.genotype2boxplot.sampleannotationkey+" not found in any sample annotation"]}else{return["incomplete instruction for 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h=s.append("div").attr("class","sjpp-output-sandbox-content").style("width",((o=t.style)===null||o===void 0?void 0:o.width)||"95vw");let m=true;Wd["collapse"](f,{fontSize:"1.5em",padding:"4px 10px",color:"black",handler:g});Wd["expand"](p,{fontSize:"1.5em",padding:"4px 10px",color:"black",display:"none",handler:g});f.on("mouseenter",(()=>{const e=f.select("path");e.attr("stroke",l)})).on("mouseleave",(()=>{const e=f.select("path");e.attr("stroke",c)}));p.on("mouseenter",(()=>{const e=p.select("path");e.attr("stroke",l)})).on("mouseleave",(()=>{const e=p.select("path");e.attr("stroke",c)}));function g(){m=!m;f.style("display",m==true?"inline-block":"none");p.style("display",m==true?"none":"inline-block");h.style("display",m==true?"block":"none")}return{header_row:a,header:u,body:h,app_div:s,id:r}}function ef(e,t,n,o,i,s){let r,a,l,c,d,f;if(i!==undefined)[a,l,c,d,f]=Xd(i,n);else{[r,a,l,c,d,f]=Mc(e,t,n);r.header.text("Load mutation from text files")}a.append("div").style("margin","20px 0px").style("color","#858585").html(`\n\t<p>Choose one file and upload to initiate the display panel.<br>From there you can add additional files.</p>\n\t<div>Supported data types:</div>\n\t<ul>\n\t  <li>SNV and indel</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1OJ9aXq2_-a3BfIQdKLYCYzrJRTpu4_9i3gephTY-Z38 target=_blank>Format</a>,\n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.snvindel.txt target=_blank>example file</a></li>\n\t  </ul>\n\t  <li>SV or fusion transcript</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1klDZ0MHVkQTW2-lCu_AvpRE4_FcbhdB-yI17wNdPaOM target=_blank>Tabular format</a>,\n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.svfusion.txt target=_blank>example file</a>\n\t\t</li>\n\t\t<li>JSON-format, to come</li>\n\t  </ul>\n\t  <li>CNV, gene-level</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1WHptqOWNf96V0bYEDpj-EsKZGYnbBNc9aQIrhzdEJaU target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.cnv.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>ITD</li>\n\t  <ul>\n\t  \t<li>Internal tandem duplication, in-frame</li>\n\t    <li><a href=https://drive.google.com/open?id=1Bh9awBsraoHbV8iWXv_3oDeXMsjIAHaOKHr973IJyZc target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.itd.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>Intragenic deletion, in-frame</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1tWbf3rg3BmVIZPGGPk023P0aBkDw_ry5XuZLGyGodyg target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.deletion.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>Truncation</li>\n\t  <ul>\n\t  \t<li>Either N-terminus loss or C-terminus loss</li>\n\t    <li><a href=https://drive.google.com/open?id=1P1g-Y8r30pSKfan1BhYZcsUtSk7wRb4plaO1S-JCJr4 target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.truncation.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t</ul>`);const p=()=>{c.selectAll("*").remove();new Nd({bulkin:nf,genomes:n,gselect:l,content2flag:tf,flag2tp:h,filediv:c,init_bulk_flag:id});c.append("span").html("Select data type&nbsp;");const e=Tc(c).style("margin-right","20px");const t=c.append("input").attr("type","file").on("change",(t=>{const o=id(n[l.options[l.selectedIndex].innerHTML]);o.geneToUpper=u.property("checked");d.text("");const i=t.target.files[0];if(!i){p();return}if(i.size==0){d.text("Wrong file: "+i.name);p();return}const s=new FileReader;s.onload=t=>{const n=tf(t.target.result,e.node().selectedIndex,o);if(n){d.text("Error: "+n);p();return}h(o,i)};s.onerror=function(){d.text("Error reading file "+i.name);p();return};d.text("Parsing file "+i.name+" ...");s.readAsText(i,"utf8")}));setTimeout((()=>t.node().focus()),1100)};p();c.append("span").html("<br/>Convert gene name to uppercase &nbsp;");const u=c.append("span").append("input").attr("type","checkbox").property("checked",true);function h(e,t,n=null,s=null){if(typeof e=="string"){d.text(e);p();return}d.text("");p();const l=n?n:Object.assign({genome:e.genome,name:t.name});const c=nf({flag:e,filename:t.name,cohort:l,flag2thisds:s});if(c){d.text("Error with "+t.name+": "+c);return}if(e.good==0){d.text("No mutations can be loaded");return}let u;if(r){vc(r.pane);const e=kc({x:100,y:100,toshrink:true});e.header.html('<span style="opacity:.5">FILE</span> '+t.name);u=e.body}if(i!==undefined){u=f.append("div").html('<span style="opacity:.5">FILE</span> '+t.name)}a.selectAll("*").remove();import("./tp.ui-23151bb1.js").then((function(e){return e.t})).then((e=>{e.default(l,u,o)}));return l}return function e(t,n){const o=tf(t.content,n,flag);if(o){d.text("Error: "+o);p();return}h(flag,t)}}function tf(e,t,n){if(!n)return"should not happen!";let o;switch(t){case 0:o=sf(e,n);if(o)return o;break;case 1:o=ff(e,n,true);if(o)return o;break;case 2:o=ff(e,n,false);if(o)return o;break;case 3:o=lf(e,n);if(o)return o;break;case 4:o=cf(e,n);if(o)return o;break;case 5:o=df(e,n);if(o)return o;break;case 6:o=af(e,n);if(o)return o;break;default:return"unknown option array index from file type <select>: "+t}}function nf(e,t=null){const n=e.flag;const o=e.cohort;if(!o.p2st){o.p2st={}}if(!o.dsset){o.dsset={}}if(!o.assaylst){o.assaylst=[]}if(n.variantgene){if(o.variantgene){return"variantgene already set for this cohort"}o.variantgene=n.variantgene}if(n.snv.badlines.length>0){Pc(n.snv.header,n.snv.badlines)}if(n.fusion.badlines.length>0){Pc(n.fusion.header,n.fusion.badlines)}if(n.sv.badlines.length>0){Pc(n.sv.header,n.sv.badlines)}if(n.cnv.badlines.length>0){Pc(n.cnv.header,n.cnv.badlines)}if(n.itd.badlines.length>0){Pc(n.itd.header,n.itd.badlines)}if(n.del.badlines.length>0){Pc(n.del.header,n.del.badlines)}if(n.truncation.badlines.length>0){Pc(n.truncation.header,n.truncation.badlines)}if(n.good==0){return false}const i={};let s=false;if(n.snv.loaded){for(const e of n.snv.header){i[e]=1}if("maf_tumor_v1"in i&&"maf_tumor_v2"in i){s=true}}if(n.cnv.loaded){for(const e of n.cnv.header){i[e]=1}}if(n.fusion.loaded){for(const e of n.fusion.header){i[e]=1}}if(n.sv.loaded){for(const e of n.sv.header){i[e]=1}}if(n.itd.loaded){for(const e of n.itd.header){i[e]=1}}if(n.del.loaded){for(const e of n.del.header){i[e]=1}}if(n.truncation.loaded){for(const e of n.truncation.header){i[e]=1}}const r="sample"in i||"patient"in i;const a="disease"in i;const l="sampletype"in i;let c;if(e.flag2thisds){c=e.flag2thisds;if(r&&!c.hassample){return'"sample" column found in new data but not in existing data'}if(!r&&c.hassample){return'"sample" column found in existing data but not in new data'}if(a&&!c.hasdisease){return'"disease" column found in new data but not in existing data'}if(!a&&c.hasdisease){return'"disease" column found in existing data but not in new data'}if(l&&!c.hasst){return'"sampletype" column found in new data but not in existing data'}if(!l&&c.hasst){return'"sampletype" column found in existing data but not in new data'}for(const e in n.data){const t=c.bulkdata[e];if(t){c.bulkdata[e]=t.concat(n.data[e])}else{c.bulkdata[e]=n.data[e]}}}else{let t=e.filename+(n.tpsetname?"_"+n.tpsetname:"");if(t in n.genome.datasets){let e=1;let o=t+" "+e;while(o in n.genome.datasets){e++;o=t+" "+e}t=o}c={label:t,bulkdata:n.data,hassample:r,hasdisease:a,hastumormaf:s,hasst:l,genome:o.genome,import:{},imported:{},importsilent:n.snv.silent==0?false:n.snv.missense/n.snv.silent>=5?false:true};n.genome.datasets[t]=c;o.dsset[t]=c;if(o.dbexpression){if(o.dbexpression.tidy){try{o.dbexpression.tidy=new Function(o.dbexpression.tidy)}catch(e){err("invalid JavaScript for dbexpression.tidy");delete o.dbexpression}}c.dbexpression=o.dbexpression}if(a){c.stratify=[{label:"disease",attr1:{k:"disease",label:"disease"}}]}}if(r){for(const e in n.data){for(const t of n.data[e]){let e=t.patient;if(!e){e=t.sample;if(!e){continue}}if(!o.p2st[e]){o.p2st[e]={}}let n=t.sampletype;if(!n){n=e}if(!o.p2st[e][n]){o.p2st[e][n]={dsset:{},tktemplate:[]}}if(!o.p2st[e][n].dsset[c.label]){o.p2st[e][n].dsset[c.label]=[]}o.p2st[e][n].dsset[c.label].push(t)}}}if(t)t();return false}function of(e){if(!e.name)e.name="Unnamed dataset";let t=e.holder;if(!t){const e=kc({x:100,y:100});t=e.body}const n=t.append("div");new Promise(((t,n)=>{const o={dsset:{}};for(const t in e){if(t=="snvindel"||t=="svjson"||t=="cnv"||t=="sv"||t=="mutationset"){continue}o[t]=e[t]}t(o)})).then((t=>{if(!e.snvindel&&!e.svjson&&!e.cnv&&!e.sv)return t;const n=id(t.genome);if(e.snvindel){const t=sf(e.snvindel,n);if(t)throw{message:"error in snvindel data: "+t};delete e.snvindel}if(e.svjson){const t=rf(e.svjson,n);if(t)throw{message:"error in svjson data: "+t};delete e.svjson}if(e.sv){const t=ff(e.sv,n);if(t)throw{message:"error in svjson data: "+t};delete e.sv}if(e.cnv){const t=af(e.cnv,n);if(t)throw{message:"error in cnv data: "+t};delete e.cnv}const o=nf({flag:n,filename:e.name,cohort:t});if(o)throw{message:"Error parsing data: "+o};return t})).then((t=>{if(!e.mutationset)return t;if(!Array.isArray(e.mutationset))throw{message:"mutationset is not an array"};const n=[];for(const o of e.mutationset){const i=id(t.genome);const s=[];if(o.snvindel){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.snvindel+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with snvindel file: "+e.error};const t=sf(e.text,i);if(t)throw{message:"error with snvindel file: "+t}}));s.push(n)}if(o.snvindel_url){s.push(Ll("urltextfile",{url:o.snvindel_url}).then((e=>{if(e.error)throw{message:"cannot get snvindel file from url"};const t=sf(e.text,i);if(t)throw{message:"error with snvindel file: "+t}})))}if(o.cnv){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.cnv+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with cnv file: "+e.error};const t=af(e.text,i);if(t)throw{message:"error with cnv file: "+t}}));s.push(n)}if(o.cnv_url){s.push(Ll("urltextfile",{url:o.cnv_url}).then((e=>{if(e.error)throw{message:"cannot get cnv file from url"};const t=af(e.text,i);if(t)throw{message:"error with cnv file: "+t}})))}if(o.sv){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.sv+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with sv file: "+e.error};const t=ff(e.text,i,true);if(t)throw{message:"error with sv file: "+t}}));s.push(n)}if(o.sv_url){s.push(Ll("urltextfile",{url:o.sv_url}).then((e=>{if(e.error)throw{message:"cannot get sv file from url"};const t=ff(e.text,i);if(t)throw{message:"error with sv file: "+t}})))}if(o.fusion){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.fusion+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with fusion file: "+e.error};const t=ff(e.text,i,false);if(t)throw{message:"error with fusion file: "+t}}));s.push(n)}if(o.svjson){const t=new Request(e.hostURL+"/textfile",{method:"POST",body:'{"file":"'+o.svjson+'"}'});const n=fetch(t).then((e=>e.json())).then((e=>{if(e.error)throw{message:"error with svjson file: "+e.error};const 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hf(t,e);if(e.length===0)return;if(e.length===1)return hf(t,e[0]);let n=false;const o=t.append("div").attr("class","sja_errorbar").on("click",(()=>{n=!n;s.style("display",n?"block":"none")}));const i=o.append("div").style("display","inline-block");i.append("div").style("display","inline-block").style("color","white").style("background-color","red").style("border-radius","100px").style("padding","1px 4px").text(e.length);i.append("div").text("errors found.").style("padding","3px").style("display","inline-block");o.append("div").style("display","inline-block").style("float","right").html("&#10005;").on("click",(()=>{uf(o,true)}));const s=o.append("div").style("display","none").style("margin-left","10px");for(const t of e){s.append("div").text(t)}}async function bf(e,t){const n=await Bl("snp",{method:"POST",body:JSON.stringify({byName:true,genome:e.name,lst:[t]})});if(n.error)throw n.error;if(!n.results||n.results.length==0)throw t+": not a SNP";for(const t of n.results){const 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o={genome:e.genome,holder:e.holder,chr:n.chr,start:Math.max(0,n.start-300),stop:n.start+300,nobox:true,tklst:e.tklst,debugmode:e.debugmode};tc(e.genome,o.tklst);const i=await import("./block-4f585abe.js").then((function(e){return e.c}));const s=new i.Block(o);s.addhlregion(n.chr,n.start,n.stop-1)}catch(n){t.text("Not a gene or SNP: "+e.query)}}else{t.text("No match to gene: "+e.query)}return}t.remove();e.allmodels=n.gmlst;for(const t of e.allmodels){if(t.isoform.toUpperCase()==(n.found_isoform?n.found_isoform.toUpperCase():e.query.toUpperCase())){e.model=t;await wf(e);return}}const o=[];for(const t of e.allmodels){if(!t.isoform)throw"isoform missing from one gene model: "+JSON.stringify(t);const n=t.isoform.toUpperCase();if(e.genome.isoformcache.has(n)){let o=true;for(const i of e.genome.isoformcache.get(n)){if(i.chr==t.chr&&i.start==t.start&&i.stop==t.stop&&i.strand==t.strand){o=false;break}}if(o){e.genome.isoformcache.get(n).push(t)}}else{e.genome.isoformcache.set(n,[t])}if(t.isoform.toUpperCase()==e.query.toUpperCase()){o.push(t);break}if(t.isdefault){o.push(t)}}if(o.length==1){e.model=o[0]}else if(o.length>1){for(const t of o){if(t.chr=="chrY"){continue}const n=e.genome.chrlookup[t.chr.toUpperCase()];if(!n){continue}if(!n.major){continue}e.model=t;break}if(!e.model){e.model=o[0]}}if(!e.model){e.model=e.allmodels[0]}await wf(e)}async function wf(e){if(e.model.genomicseq){o();xf(e);return}const t={genome:e.genome.name,coord:e.model.chr+":"+(e.model.start+1)+"-"+e.model.stop};const n=await Bl("ntseq",{method:"POST",body:JSON.stringify(t)});if(!n)throw"getting sequence: server error";if(n.error)throw"getting sequence: "+n.error;if(!n.seq)throw"no nt seq???";e.model.genomicseq=n.seq.toUpperCase();e.model.aaseq=Ma(e.model);o();await xf(e);function 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The recovered session should visible in another browser tab.\n\t\t\t</div>\n\t\t`}const i=window.open(n.href,"_blank")}async function Rf(e){const t=If();if(t.has("appcard")){const n=await Promise.resolve().then((function(){return ih}));const o=t.get("appcard");const i=await Pl("/cards/index.json");e.app.drawer.opts.genomes=e.genomes;e.app.drawer.opts.fromApp=true;e.app.drawer.opts.app={cardsPath:"cards"};const s=i.elements.findIndex((e=>e.sandboxJson==o||e.sandboxHtml==o));if(s<=0){const t=[...i.elements.filter((e=>e.type=="nestedCard"))];let s,r;t.findIndex((e=>{for(const[t,n]of e.children.entries()){if(n.sandboxJson==o||n.sandboxHtml==o){s=e;r=t}}}));n.openSandbox(s.children[r],e.app.drawer.opts)}else{n.openSandbox(i.elements[s],e.app.drawer.opts)}return}if(t.has("gdcbamslice")){const n=await import("./bam-e7f6baea.js");n.bamsliceui({genomes:e.genomes,holder:e.holder,debugmode:e.debugmode,stream2download:t.has("stream2download")});return}if(t.has("gdcmaf")){const t=await import("./maf-dfada1c8.js");t.gdcMAFui({holder:e.holder,debugmode:e.debugmode});return}if(t.has("gdcsinglecell")){const t=await import("./singlecell-75f8af89.js");t.gdcSinglecellUi({holder:e.holder,debugmode:e.debugmode});return}if(t.has("mdsjsonform")){const t=await import("./mdsjsonform-09b4e1cb.js");await t.init_mdsjsonform(e);return}if(t.has("termdb")){const n=t.get("termdb");const o=typeof n==="string"?JSON.parse(n):n;const i={holder:e.holder,state:o};const s=await import("./app-fb676934.js");s.appInit(i);return}if(t.has("massnative")){const n=t.get("massnative");const[o,i]=n.split(",");if(!o||!i)throw'value is not "genome,dslabel"';const s={holder:e.holder,genome:e.genomes[o],state:{genome:o,dslabel:i}};if(!s.genome)throw"invalid genome";const r=await import("./app-59194db0.js");r.appInit(s);return}if(t.has("mass")){const n=t.get("mass");const o=typeof n==="string"?JSON.parse(n):n;const i={holder:e.holder,state:o};if(o.genome){i.genome=e.genomes[o.genome]}else if(o?.vocab?.genome){i.genome=e.genomes[o.vocab.genome]}const s=await import("./app-59194db0.js");s.appInit(i);return}if(t.has("mass-session-file")||t.has("mass-session-url")){let n;if(t.has("mass-session-file")){const o=t.get("mass-session-file");const i=await Bl(`/textfile`,{method:"POST",body:JSON.stringify({file:o})});const s=JSON.parse(i.text);n={holder:e.holder,state:s,genome:e.genomes[s.vocab.genome]}}if(t.has("mass-session-url")){const o=t.get("mass-session-url");const i=await Bl("/urltextfile",{method:"POST",body:JSON.stringify({url:o})});const s=JSON.parse(i.text);n={holder:e.holder,state:s,genome:e.genomes[s.vocab.genome]}}const o=await import("./app-59194db0.js");o.appInit(n);return}if(t.has("mass-session-id")){const n=t.get("mass-session-id");const o=t.get("src");let i;if(o=="browser"){const e=localStorage.getItem("savedMassSessions");const t=JSON.parse(e);i={state:t[n]}}else{const e={headers:{},body:{id:n}};if(o=="cred"){const n=t.get("dslabel");const o=t.get("route");e.body.dslabel=n;e.body.route=o;e.body.route=o;const i=localStorage.getItem("jwtByDsRoute")||`{}`;this.jwtByDsRoute=JSON.parse(i);const s=this.jwtByDsRoute[n][o];e.headers.authorization=`Bearer ${btoa(s)}`}i=await Bl(`/massSession`,e);if(i.error)throw i.error}const s=i.state?.embedder;if(s&&s.origin!=window.location.origin){Tf(i);return}const r={holder:e.holder,state:i.state,genome:e.genomes[i.state.vocab.genome],sessionDaysLeft:i.sessionDaysLeft,sessionId:n};const a=await import("./app-59194db0.js");a.appInit(r);return}if(t.has("genome")&&e.selectgenome){const n=t.get("genome");const o=[...e.selectgenome.node().childNodes];const i=o.findIndex((e=>e.value==n));if(i==-1){hf(e.holder,`Invalid genome: ${n}. Please provide an available genome from this list: ${o.map((e=>e.value)).join(", ").replace(/,(?=[^,]*$)/,", or")}`);return}e.selectgenome.node().selectedIndex=i;e.selectgenome.node().dispatchEvent(new Event("change"))}if(t.has("hicfile")||t.has("hicurl")){let n,o,i;if(t.has("hicfile")){n=t.get("hicfile");i=n.split("/").pop()}else{o=t.get("hicurl");i=o.split("/").pop()}const s=t.get("genome");if(!s)throw"genome is required for hic";const r=e.genomes[s];if(!r)throw"invalid genome";const a={genome:r,file:n,url:o,name:i,hostURL:e.hostURL,enzyme:t.get("enzyme"),holder:e.holder};const l=await import("./HicApp-aac413df.js");await l.hicInit(a);return}if(t.has("singlecell")){if(!t.has("genome"))throw'"genome" is required for "singlecell"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i=await import("./singlecell-29c1cbb1.js");i.init({genome:o,jsonfile:t.get("singlecell")},e.holder);return}if(t.has("mavbfile")){if(!t.has("genome"))throw'"genome" is required for "mavb"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i=await import("./mavb-9a6fa2e9.js");i.mavbparseinput({genome:o,hostURL:e.hostURL,file:t.get("mavbfile")},(()=>{}),e.holder,e.jwt);return}if(t.has("mavburl")){if(!t.has("genome"))throw'"genome" is required for "mavb"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i=await import("./mavb-9a6fa2e9.js");i.mavbparseinput({genome:o,hostURL:e.hostURL,url:t.get("mavburl")},(()=>{}),e.holder,e.jwt);return}if(t.has("scatterplot")){if(!t.has("genome"))throw'"genome" is required for "scatterplot"';const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;let i;if(t.has("mdsjson")||t.has("mdsjsonurl")){const e=t.get("mdsjsonurl");const n=t.get("mdsjson");i=await Ef(n,e)}if(t.has("tsnejson")){const e=t.get("tsnejson");const n=await Ll("textfile",{file:e});if(n.error)throw n.error;else if(n.text){i={mdssamplescatterplot:{analysisdata:JSON.parse(n.text)}}}}i.mdssamplescatterplot.genome=o;const s=await import("./mds.samplescatterplot-a54b9e93.js");s.init(i.mdssamplescatterplot,e.holder,false);return}if(t.has("block")){if(!t.has("genome"))throw"missing genome for block";const n=t.get("genome");const o=e.genomes[n];if(!o)throw"invalid genome: "+n;const i={nobox:1,hostURL:e.hostURL,jwt:e.jwt,holder:e.holder,genome:o,dogtag:n,debugmode:e.debugmode};let s=null;let r=null;if(t.has("position")){const e=t.get("position").split(";");if(e[0]){const t=e[0].split(/[:-]/);const n=t[0];const o=Number.parseInt(t[1]);const i=Number.parseInt(t[2]);if(!n)throw"chr missing";if(Number.isNaN(o)||Number.isNaN(i))throw"Invalid start/stop value in position";s={chr:n,start:o,stop:i}}const n=[];for(let t=1;t<e.length;t++){if(!e[t])continue;const o=e[t].split(/[:-]/);const i=o[0];const s=Number.parseInt(o[1]);const r=Number.parseInt(o[2]);if(!i)throw"subpanel chr missing";if(Number.isNaN(s)||Number.isNaN(r))throw"Invalid start/stop value in subpanel position";n.push({chr:i,start:s,stop:r,width:600,leftborder:"rgba(200,0,0,.1)",leftpad:5})}if(n.length){i.subpanels=n}}if(t.has("regions")){r=[];for(const e of t.get("regions").split(",")){const t=e.split(/[:-]/);t[0];const n=Number.parseInt(t[1]);const o=Number.parseInt(t[2]);if(Number.isNaN(n)||Number.isNaN(o))throw"Invalid start/stop value in regions";r.push({chr:t[0],start:n,stop:o})}}if(!s&&!r){if(o.defaultcoord){s={chr:o.defaultcoord.chr,start:o.defaultcoord.start,stop:o.defaultcoord.stop}}}if(s){i.chr=s.chr;i.start=s.start;i.stop=s.stop}else if(r){i.rglst=r}if(t.has("hlregion")){const e=[];for(const n of t.get("hlregion").split(",")){const t=Ld(n,o,true);if(t)e.push(t)}if(e.length)i.hlregions=e}i.datasetqueries=Lf(t);i.tklst=await $f(t,o);tc(e.genomes[n],i.tklst);zf(t,i.tklst);const a=await import("./block-4f585abe.js").then((function(e){return e.c}));new a.Block(i);return}if(t.has("gene")){const n=t.get("gene");if(n.length==0)throw"zero length query string";const o={hostURL:e.hostURL,query:n,holder:e.holder,variantPageCall_snv:e.variantPageCall_snv,samplecart:e.samplecart,debugmode:e.debugmode};{let n;for(let t in e.genomes){if(e.genomes[t].isdefault){n=t;break}}if(t.has("genome")){n=t.get("genome")}if(!n)throw"No genome, and none set as default";o.genome=e.genomes[n];if(!o.genome)throw"invalid genome: "+n}if(t.has("dataset")){o.dataset=t.get("dataset").split(",")}if(t.has("hlaachange")){o.hlaachange=new Map;for(const e of t.get("hlaachange").split(",")){o.hlaachange.set(e,false)}}if(t.has("hlregion")){const e=[];for(const n of t.get("hlregion").split(",")){const t=Ld(n,o.genome,true);if(t)e.push(t)}if(e.length)o.hlregions=e}o.tklst=await $f(t,o.genome);zf(t,o.tklst);o.datasetqueries=Lf(t);await yf(o);return}if(t.has("disco")){const n=t.get("genome");const o=e.genomes[n];if(!o)throw"genome missing";const i=t.get("dslabel");if(!i)throw"dslabel missing";const s=t.get("sample");if(!s)throw"sample_id missing";const r=(await import("./FilterRxComp-fc769f34.js").then((function(e){return e.z}))).vocabInit({state:{genome:n,dslabel:i}});const a=await r.getTermdbConfig();await(await import("./plot.disco-621d1b8e.js")).default(a,i,{sample_id:s},e.holder,o);return}if(t.has("study")){const n=t.get("study");if(n!=""){Fd(e.genomes,n,e.holder,e.hostURL,undefined,false,e.app||{debugmode:e.debugmode,instanceTracker:e.instanceTracker||{},callbacks:e.callbacks||{}})}}}function Lf(e){if(!e.has("mds"))return;const t=e.get("mds").split(",");if(t[0]&&t[1]){const n={dataset:t[0],querykey:t[1]};if(e.has("sample")){n.singlesample={name:e.get("sample")};n.getsampletrackquickfix=true}return[n]}return}async function $f(e,t){const n=[];if(e.has("mds3")){const t=e.get("mds3").split(",");for(const o of t){const t={type:mc.mds3,dslabel:o};if(e.has("token"))t.token=e.get("token");if(e.has("filterobj"))t.filterObj=e.get("filterobj");n.push(t)}}if(e.has("mds3bcffile")){const[t,o]=e.get("mds3bcffile").split(",");if(t&&o){n.push({type:mc.mds3,name:t,bcf:{file:o}})}}if(e.has("mds3bcfurl")){const[t,o,i]=e.get("mds3bcfurl").split(",");if(t&&o){n.push({type:mc.mds3,name:t,bcf:{url:o,indexURL:i}})}}if(e.has("arcfile")){const t=e.get("arcfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.hicstraw,name:t[e],bedfile:t[e+1],mode_hm:false,mode_arc:true})}}}if(e.has("mdsjsoncache")){const t=await Pl("mdsjsonform",{method:"POST",body:JSON.stringify({draw:e.get("mdsjsoncache")})});if(t.error)throw t.error;Af(t.json);const o=Cf(t.json);n.push(o)}if(e.has("mdsjson")||e.has("mdsjsonurl")){const t=e.get("mdsjsonurl");const o=e.get("mdsjson");const i=await jf(o,t);n.push(...i)}if(e.has("tkjsonfile")){const o=await Ll("textfile",{file:e.get("tkjsonfile")});if(o.error)throw o.error;if(!o.text)throw".text missing";const i=JSON.parse(o.text);for(const e of i){if(e.isfacet){if(!t.tkset)t.tkset=[];if(!e.tracks)throw".tracks[] missing from a facet table";if(!Array.isArray(e.tracks))throw".tracks[] not an array from a facet table";e.tklst=e.tracks;delete e.tracks;for(const t of e.tklst){if(!t.assay)throw".assay missing from a facet track";if(!t.sample)throw".sample missing from a facet track";t.tkid=Math.random().toString()}t.tkset.push(e)}else{n.push(e)}}}if(e.has("bamfile")){const t=e.get("bamfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bam,name:t[e],file:t[e+1]})}}}if(e.has("bamurl")){const t=e.get("bamurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bam,name:t[e],url:t[e+1]})}}}if(e.has("bedjfile")){const t=e.get("bedjfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bedj,name:t[e],file:t[e+1]})}}}if(e.has("bedjurl")){const t=e.get("bedjurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bedj,name:t[e],url:t[e+1]})}}}if(e.has("hictkfile")||e.has("hictkurl")){const t=e.has("hictkfile");const o=e.get(t?"hictkfile":"hictkurl").split(",");const i=e.has("hictknorm")?e.get("hictknorm").split(","):null;for(let e=0;e<o.length;e+=3){if(o[e]&&o[e+1]&&o[e+2]){const s={type:mc.hicstraw,name:o[e],enzyme:o[e+1],normalizationmethod:i?i[e/3]:null};if(t){s.file=o[e+2]}else{s.url=o[e+2]}n.push(s)}}}if(e.has("ldfile")){const t=e.get("ldfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.ld,name:t[e],file:t[e+1]})}}}if(e.has("bigwigfile")){const t=e.get("bigwigfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bigwig,name:t[e],file:t[e+1],scale:{auto:1}})}}}if(e.has("bigwigurl")){const t=e.get("bigwigurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.bigwig,name:t[e],url:t[e+1],scale:{auto:1}})}}}if(e.has("junctionfile")){const t=e.get("junctionfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.junction,name:t[e],tracks:[{file:t[e+1]}]})}}}if(e.has("junctionurl")){const t=e.get("junctionurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.junction,name:t[e],tracks:[{url:t[e+1]}]})}}}if(e.has("vcffile")){const t=e.get("vcffile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"vcf",name:t[e],file:t[e+1]})}}}if(e.has("vcfurl")){const t=e.get("vcfurl").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"vcf",name:t[e],url:t[e+1]})}}}if(e.has("aicheckfile")){const t=e.get("aicheckfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"aicheck",name:t[e],file:t[e+1]})}}}if(e.has("bampilefile")){const t=e.get("bampilefile").split(",");let o=null;if(e.has("bampilelink")){o=e.get("bampilelink").split(",").map(decodeURIComponent)}for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){const i={type:mc.bampile,name:t[e],file:t[e+1]};if(o&&o[e/2]){i.link=o[e/2]}n.push(i)}}}if(e.has("svcnvfpkmurl")){const t=e.get("svcnvfpkmurl").split(",");const o=t[0];const i={};for(let e=1;e<t.length;e+=2){i[t[e]]=t[e+1]}if(i.svcnv||i.vcf){const e={type:mc.mdssvcnv,name:o};if(i.svcnv){e.url=i.svcnv}if(i.vcf){e.checkvcf={url:i.vcf,indexURL:i.vcfindex}}if(i.fpkm){e.checkexpressionrank={datatype:"FPKM",url:i.fpkm,indexURL:i.fpkmindex}}n.push(e)}}if(e.has("svcnvfpkmfile")){const t=e.get("svcnvfpkmfile").split(",");const o=t[0];const i={};for(let e=1;e<t.length;e+=2){i[t[e]]=t[e+1]}if(i.svcnv||i.vcf){const e={type:mc.mdssvcnv,name:o};if(i.svcnv){e.file=i.svcnv}if(i.vcf){e.checkvcf={file:i.vcf}}if(i.fpkm){e.checkexpressionrank={datatype:"FPKM",file:i.fpkm}}n.push(e)}}if(e.has("mdsjunctionfile")){const t=e.get("mdsjunctionfile").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"mdsjunction",name:t[e],file:t[e+1]})}}}if(e.has("junctionmatrix")){const t=e.get("junctionmatrix").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:"mdsjunction",name:t[e],file2:t[e+1]})}}}if(e.has("junctionrnapeg")){const t=e.get("junctionrnapeg").split(",");for(let e=0;e<t.length;e+=2){if(t[e]&&t[e+1]){n.push({type:mc.junction,name:t[e],tracks:[{rnapegfile:t[e+1]}]})}}}for(const e of n){if(e.type=="mds3"&&e.dslabel)continue;e.iscustom=true}if(e.has("isdense")){n.filter((e=>e.type==mc.mdssvcnv)).forEach((e=>{e.isdense=true;e.isfull=false}))}if(e.has("sample")){n.filter((e=>e.type==mc.mdssvcnv)).forEach((t=>{t.singlesample={name:e.get("sample")};t.getsampletrackquickfix=true}))}return n}function zf(e,t){if(e.has("bedjfilterbyname")){for(const n of t){if(n.type=="bedj")n.filterByName=e.get("bedjfilterbyname")}}}function Pf(e){const t=e.div.append("button").attr("type","submit").style("background-color",e.backgroundColor?e.backgroundColor:"#cfe2f3").style("margin",e.margin?e.margin:"20px 20px 0px 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Please provide`;if(e.element.ribbon.expireDate){if(e.element.ribbon.expireDate>=0){throw`Flag for ${e.element.type} = ${e.element.name} is not a valid date`}}}return e}main(){}}const rh=dl(sh);function ah(e){const t=e.holder.append("li");if(e.opts.element.type=="card"){t.classed("sjpp-track",true).html(`<div class="sjpp-track-h"><span style="font-size:14.5px;font-weight:500;">${e.opts.element.name}</span></div>\n\t\t\t\t${e.opts.element.description?`<span class="sjpp-track-blurb" style="cursor:default">${e.opts.element.description}</span></div>`:" "}\n\t\t\t\t<span class="sjpp-track-image"><img src="${e.opts.element.image}" alt="${e.opts.element.description}"></img></span>\n\t\t\t\t</div>`)}else if(e.opts.element.type=="nestedCard"){t.classed("sjpp-app-drawer-card",true).html(`<p style="margin-left: 12px; font-size:14.5px;font-weight:500; display: block;">${e.opts.element.name}</p>\n\t\t\t<p style="display: block; font-size: 13px; font-weight: 300; margin-left: 20px; justify-content: center; font-style:oblique; color: #403f3f;">${e.opts.element.description}</p>`)}e.makeRibbon=function(e){const n=t.append("div").classed("sjpp-app-drawer-card-ribbon",true).style("align-items","center").style("justify-content","center");const o=e.text.toUpperCase();const i=o=="BETA"?"#418cb5":o=="NEW"?"#1ba176":o=="UPDATED"?"orange":e.color?e.color:"red";n.append("span").text(o).style("color","white").style("background-color",Kt(i).darker()).style("height","auto").style("width","100%").style("top","15%").style("left","-30%").style("font-size","11.5px").style("text-transform","uppercase").style("text-align","center")};if(e.opts.element.ribbon){const t=new Date;const n=new Date(e.opts.element.ribbon.expireDate);if(n>t||n=="Invalid Date")e.makeRibbon(e.opts.element.ribbon)}t.on("click",(async t=>{t.stopPropagation();await e.app.dispatch({type:"is_apps_btn_active",value:false});vh(e);await zu(e.opts.element,e.opts)}))}class lh{constructor(e){this.type="button";this.opts=this.validateOpts(e);this.holder=e.holder;this.dom=e.dom;this.sandboxDiv=e.sandboxDiv;dh(this)}validateOpts(e){if(!e.element.name)throw`Button name is missing`;if(!e.element.sandboxJson&&!e.element.sandboxHtml)throw`Either .sandboxJson or .sandboxHtml is missing for button=${e.element.name}`;return e}main(){}}const ch=al(lh);function dh(e){const t=Pf({div:e.holder,text:e.opts.element.name,margin:"20px 20px 0px"});t.attr("class","sjpp-appdrawer-dataset-btn").on("click",(async t=>{t.stopPropagation();await e.app.dispatch({type:"is_apps_btn_active",value:false});vh(e);await zu(e.opts.element,e.opts)}))}class fh{constructor(e){this.type="layout";this.dom={holder:e.dom.drawerDiv,wrapper:e.dom.wrapper,sandboxDiv:e.dom.sandboxDiv};this.state=e.state;this.hasStatePreMain=true}async validateIndexJson(){const e=await this.getIndexJson();if(!e.elements)throw`Missing elements array`;if(!e.elements.length)throw`No element objects provided`;if(e.columnsLayout){if(e.columnsLayout.length==0)throw`Missing column objects`;const t=e.columnsLayout.map((e=>e.gridarea));if(t.length!=new Set(t).size)throw`Duplicate values for .gridarea found`;const n=[];for(const t of e.columnsLayout){if(!t.gridarea)throw`Missing column .gridarea for column = ${t.name}`;if(!t.sections||t.sections.length==0)throw`Missing section objects for column = ${t.name}`;for(const e of t.sections){if(!e.id)throw`Missing section .id in ${e.name?`section = ${e.name}`:`column = ${t.name} array`}`;n.push(e.id)}if(t.sections.length!=new Set(t.sections).size){throw`Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`}}if(n.length!=new Set(n).size)throw`Duplicate values for section.id found`;for(const t of e.elements){if(!t.section)throw`.section is missing for ${t.type} = ${t.name}`;if(!n.some((e=>e==t.section)))throw`section = ${t.section} for ${t.type} = ${t.name} is not a column section`}}return e}async getIndexJson(){const e=await Bl(this.app.cardsPath+"/index.json");if(e.error){xc(this.dom.holder.append("div"),e.error);return}return e}async init(){this.index=await this.validateIndexJson();this.elementsRendered=false;uh(this);this.elements=this.index.elements.filter((e=>!e.hidden));this.layout=this.index.columnsLayout?this.index.columnsLayout:null;this.components={elements:[]}}async main(){if(this.elementsRendered==true)return;this.elementsRendered=true;for(const e of this.elements){const t=ot(this.layout?`#${e.section} > .sjpp-element-list`:`.sjpp-element-list`);if(e.type=="card"||e.type=="nestedCard"){this.components.elements.push(await rh({app:this.app,holder:t.style("display","grid").style("grid-template-columns","repeat(auto-fit, minmax(320px, 1fr))").style("gap","10px").style("list-style","none").style("margin","15px 0px"),element:e,dom:this.opts.dom,state:this.state,sandboxDiv:this.dom.sandboxDiv}))}else if(e.type=="dsButton"){this.components.elements.push(await ch({app:this.app,holder:t,element:e,dom:this.opts.dom,state:this.state,sandboxDiv:this.dom.sandboxDiv}))}}}}const ph=dl(fh);function uh(e){if(!e.index.columnsLayout)hh(e);if(e.index.columnsLayout)mh(e)}function hh(e){const t=e.dom.wrapper.append("div").style("display","flex").style("padding","10px").classed("sjpp-element-list",true);return t}function mh(e){const t=e.dom.wrapper.append("div").style("display","grid").style("grid-template-columns","repeat(auto-fit, minmax(425px, 1fr))").style("gap","10px").style("padding","10px").style("text-align","left");const n=[];for(const t of e.index.columnsLayout)n.push(t.gridarea);t.style("grid-template-areas",`"${n.toString().replace(","," ")}"`);for(const n of e.index.columnsLayout){const e=t.append("div").style("grid-area",n.gridarea).classed(".sjpp-track-cols",true);for(const t of n.sections)o(t,e)}function o(e,t){const n=t.append("div").attr("id",e.id);if(e.name)n.append("h5").classed("sjpp-appdrawer-cols",true).style("color",Kt(Ir).darker()).text(e.name);n.append("div").classed("sjpp-element-list",true).style("padding","10px");return n}}class gh{constructor(e){this.type="mainBtn";this.opts=this.validateOpts(e);this.dom=e.dom;this.state=e.state;this.hasStatePreMain=true;yh(this)}validateOpts(e){return e.app.opts}getState(e){return{appBtnActive:e.appBtnActive}}async init(){this.btnRendered=false;this.drawerFullHeight="";try{if(window.location.pathname=="/"&&!window.location.search.length)await this.app.dispatch({type:"is_apps_btn_active",value:true});this.components={layout:[]}}catch(e){throw e}}async main(e){if(this.app.getState(e).appBtnActive==true&&this.btnRendered==false){this.dom.drawerDiv.style("background-color","#f5f5f5");this.components.layout.push(await ph({app:this.app,dom:this.dom,state:this.state}));setTimeout((()=>{this.drawerFullHeight=this.dom.drawerDiv.node().getBoundingClientRect().height+5}),this.state.duration+5);vh(this);this.btnRendered=true}if(this.state.appBtnActive==false&&this.btnRendered==true)vh(this)}}const bh=dl(gh);function yh(e){e.dom.btnWrapper.style("background-color",e.state.appBtnActive?"#b2b2b2":"#f2f2f2").style("color",e.state.appBtnActive?"#fff":"#000").on("click",(async t=>{t.stopPropagation();await e.app.dispatch({type:"is_apps_btn_active"});vh(e);if(e.state.appBtnActive){setTimeout((()=>{e.drawerFullHeight=e.dom.drawerDiv.node().getBoundingClientRect().height+5}),e.state.duration+5)}}));e.dom.btn.attr("class","sja_menuoption").style("display","inline-block").style("background-color","transparent").style("color",e.state.appBtnActive?"#fff":"#000").style("padding",e.opts.padw_sm).style("margin","0px 5px").style("cursor","pointer").text("Apps");e.dom.drawerHint.style("position","relative").style("display","inline-block").style("height",e.state.arrowSize.closed+"px").style("width",e.state.appBtnActive?e.state.hintWidth.open:e.state.hintWidth.closed).style("background-color","transparent").style("text-align","center").style("cursor","pointer");e.dom.drawerArrow.style("position","absolute").style("font-size",e.state.arrowSize.closed+"px").style("right",e.state.hintPos.closed.rt+"px").style("bottom",e.state.hintPos.closed.btm+"px").style("background-color","transparent").style("color",e.state.arrowColor.closed).style("opacity",e.state.appBtnActive?0:1).style("cursor","pointer").html("&#9660;");e.dom.drawerArrowOpen.style("position","absolute").style("font-size",e.state.arrowSize.open+"px").style("left",e.state.hintPos.open.left+"px").style("bottom",e.state.hintPos.open.btm+"px").style("transform","rotate(180deg)").style("background-color","transparent").style("color",e.state.arrowColor.open).style("opacity",e.state.appBtnActive?1:0).style("cursor","pointer").style("pointer-events",e.state.appBtnActive?"auto":"none").html("&#9660;");e.drawerFullHeight=e.dom.drawerRow.node().getBoundingClientRect().height+5}async function vh(e){e.dom.btnWrapper.transition().duration(e.opts.state.duration).style("background-color",e.state.appBtnActive?"#b2b2b2":"#f2f2f2").style("color",e.state.appBtnActive?"#fff":"#000");e.dom.btn.transition().duration(e.opts.state.duration).style("color",e.state.appBtnActive?"#fff":"#000");e.dom.drawerDiv.style("display","inline-block").transition().duration(e.opts.state.duration).style("top",e.state.appBtnActive?"0px":"-"+e.drawerFullHeight+"px");e.dom.drawerRow.transition().duration(e.opts.state.duration).style("height",e.state.appBtnActive?e.drawerFullHeight+"px":"0px");e.dom.drawerHint.transition().duration(e.opts.state.duration).style("width",e.state.appBtnActive?e.opts.state.hintWidth.open:e.opts.state.hintWidth.closed);e.dom.drawerArrow.transition().duration(e.opts.state.duration).style("opacity",e.state.appBtnActive?0:1);e.dom.drawerArrowOpen.style("pointer-events",e.state.appBtnActive?"auto":"none").transition().duration(e.opts.state.duration).style("opacity",e.state.appBtnActive?1:0)}class wh{constructor(e){this.type="store";this.defaultState={duration:500,hintPos:{open:{btm:-42,left:13},closed:{btm:3,rt:5}},hintWidth:{open:"0px",closed:"18px"},arrowSize:{open:42,closed:20},arrowColor:{open:"rgb(242,242,242)",closed:"rgb(85,85,85)"},appBtnActive:false}}async init(){}}const xh=cl(wh);wh.prototype.actions={is_apps_btn_active(e){this.state.appBtnActive="value"in e?e.value:!this.state.appBtnActive}};class _h{constructor(e){this.type="app";const t=e.drawerRow.append("div").style("position","relative").style("margin","0 20px").style("padding",`0 ${e.padw_sm}`).style("display","inline-block").style("overflow","hidden").style("border-radius","0px 0px 5px 5px").style("width","93vw").classed("sjpp-drawer-div",true);const n=e.headbox.append("div").style("position","relative").style("display","inline-block").style("margin-left","5px").style("margin-right","5px").style("border-radius","5px").classed("sjpp-apps-btn-wrapper",true);this.dom={drawerRow:e.drawerRow,drawerDiv:t,sandboxDiv:e.sandboxDiv,btnWrapper:n,btn:n.append("div"),drawerHint:n.append("div"),drawerArrow:n.append("div"),drawerArrowOpen:n.append("div"),wrapper:t.append("div")}}preApiFreeze(e){e.cardsPath=this.opts.cardsPath}async init(){try{this.store=await xh({app:this.api,state:this.opts.state});this.state=await this.store.copyState();this.components={mainBtn:await bh({app:this.api,dom:this.dom,state:this.state,indexJson:this.indexJson})};await this.api.dispatch()}catch(e){throw e}}main(){}}const kh=ll(_h);class jh{constructor(e){this.holder=e.holder;this.input=e.holder.append("input");this.tip=e.tip||new ec({border:"",padding:"0px"});this.style=e.style||{};this.size=e.size||20;this.placeholder=e.placeholder||"";this.title=e.title||"";this.searchItems=e.searchItems;this.app=e.app}initUI(){this.holder.style("padding","padding"in this.style?this.style.padding:"5px").style("display","inline-block");this.input.attr("class","sjpp-input-search").style("border","border"in this.style?this.style.border:"5px").attr("size",this.size).attr("placeholder",this.placeholder).attr("title",this.title).on("keyup",(e=>Wf(this,void 0,void 0,(function*(){if(Jc(e))yield this.enterSearch();td.debounce(this.addSearchItems(),400)}))))}addSearchItems(){return Wf(this,void 0,void 0,(function*(){if(!this.input.property("value").trim()){this.tip.hide();return}try{this.tip.clear().showunder(this.input.node());const e=this.tip.d.append("div");const t=yield this.searchItems();yield e.append("div").style("display","flex").selectAll().data(t.filter((e=>e.items.length>=1))).enter().append("div").style("display","block").style("border-left","0.5px solid lightgrey").each(this.showResultsList)}catch(e){if(e.stack)console.log(e.stack);else mf(e)}}))}showResultsList(e){return Wf(this,void 0,void 0,(function*(){e.wrapper=ot(this);e.wrapper.style("padding","5px");e.titleDiv=e.wrapper.append("span").style("padding","3px 0px 5px").style("opacity",.65).style("font-size","0.8em").text(e.title);yield e.wrapper.append("div").classed("sjpp-result-wrapper",true).selectAll("div").data(e.items).enter().append("div").classed("sja_menuoption",true).classed("sjpp-search-result",true).style("display","block").style("padding-left","10px").style("background-color",e.color||"").text((e=>e.name||e.label||e)).on("click",((t,n)=>{t.stopPropagation();e.callback(n)}))}))}enterSearch(){return Wf(this,void 0,void 0,(function*(){if(!this.input.property("value").trim())return;const e=this.tip.d.select(".sjpp-result-wrapper").node();const t=this.tip.d.select(".sjpp-search-result").node();if(t!=null&&t.__data__)e.__data__.callback(t.__data__);else{const e=yield this.searchItems();const t=e.filter((e=>e.default));t[0].callback(this.input.property("value"))}this.input.property("value","");this.tip.hide()}))}updatePlaceholder(e){this.input.attr("placeholder",e)}}async function Nh(e,t,n,o){const i=await Bl(e.cardsPath+"/index.json");if(i.error)mf(`Problem retrieving cards/index.json`);const s=t.toLowerCase().trim();const r=[...i.elements];let a;if(s.length>2){await Sh(r,e);a=Ah(r,s)}else{a=Ah(r,s)}const l={app:e.drawer.opts,sandboxDiv:e.drawer.opts.sandboxDiv,genomes:e.genomes,fromApp:true};n.push({title:"Tracks and Apps",items:a.filter((e=>e.type=="card")),color:"#e1edf7",callback:t=>{e.drawer.dispatch({type:"is_apps_btn_active",value:false});o.hide();zu(t,l)}},{title:"Datasets",items:a.filter((e=>e.type=="dsButton")),color:"#e5f5e4",callback:t=>{e.drawer.dispatch({type:"is_apps_btn_active",value:false});o.hide();zu(t,l)}});return n}async function Sh(e,t){const n=e.map((async e=>{if(e.hidden||e.type!="card"||!e.sandboxJson)return e;const n=await Bl(t.cardsPath+`/${e.sandboxJson}.json`);if(n?.ppcalls.length>0){for(const t of n.ppcalls){if(t.isUI)return;if(t?.label)e.searchterms.push(t.label)}}}));await Promise.all(n)}function Ah(e,t){return e.filter((e=>{if(e.hidden)return false;let n=(e.searchterms||[]).reduce(((e,n)=>{if(e)return true;return n.toLowerCase().includes(t)}),false);return n||e.name.toLowerCase().includes(t)})).sort(((e,t)=>e.name.localeCompare(t.name)))}async function Ch(e,t,n){if(e.length==0)return;try{const o=await Bl("/genelookup",{body:{input:e,genome:t,jwt:n}});if(o.error)throw o.error;if(!o.hits)throw".hits[] missing";return o.hits}catch(e){}}async function Eh(e,t,n,o){const i=t.genomes[n];if(!i){console.error("unknown genome "+n);return}const s=Qd(t.drawer.opts.sandboxDiv);s.header.html('<div style="display:inline-block;">'+e+'</div><div class="sjpp-output-sandbox-title">'+n+"</div>");const r=If();const a=await $f(r,i);const l=Ld(e,i);if(l){const e={hostURL:t.hostURL,jwt:o,holder:s.body,genome:i,nobox:true,chr:l.chr,start:l.start,stop:l.stop,dogtag:n,tklst:a,debugmode:t.debugmode};tc(i,e.tklst);import("./block-4f585abe.js").then((function(e){return e.c})).then((t=>new t.Block(e))).catch((e=>{t.error0(e)}));return}const c={hostURL:t.hostURL,jwt:o,query:e,genome:i,holder:s.body,variantPageCall_snv:t.variantPageCall_snv,samplecart:t.samplecart,tklst:a,debugmode:t.debugmode};const d=sessionStorage.getItem("urlp_mds");if(d){const e=d.split(",");if(e.length==2){c.datasetqueries=[{dataset:e[0],querykey:e[1]}]}}await yf(c)}const Oh=new ec({padding:"0px",offsetX:0,offsetY:0});Oh.d.style("z-index",5555);function Mh(e){if(!window.structuredClone)window.structuredClone=e=>JSON.parse(JSON.stringify(e));const t={error0(e){xc(t.holder0,e)},debugmode:false,callbacks:e.callbacks||{sjcharts:{}},instanceTracker:e.instanceTracker||{sjcharts:{}}};Th(e,t);if(!t.instanceTracker.sjcharts){t.instanceTracker.sjcharts={}}if(!t.callbacks.sjcharts){t.callbacks.sjcharts={}}if(e.clear){it(".sja_pane").remove();return}t.holder=ot(e.holder?e.holder:document.body).append("div").attr("class","sja_root_holder").attr("data-ppclientversion",`2.63.2`).style("font","1em Arial, sans-serif").style("color","black");t.sandbox_header=e.sandbox_header||undefined;if(e.jwt){sessionStorage.setItem("jwt",e.jwt)}sessionStorage.setItem("suppressErrors",JSON.stringify(e.suppressErrors));if(e.variantPageCall_snv){t.variantPageCall_snv=e.variantPageCall_snv}if(e.samplecart){t.samplecart=e.samplecart}if(e.base_zindex){kc({setzindex:e.base_zindex})}const n=e.serverData||e.termdb&&e.termdb.serverData;const o=Bl("genomes",{},{serverData:n});return o.then((async n=>{if(n.error)throw{message:"Cannot get genomes: "+n.error};if(!n.genomes)throw{message:"no genome data!?"};if(n.base_zindex){kc({setzindex:n.base_zindex})}if(n.features){sessionStorage.setItem("optionalFeatures",JSON.stringify(n.features))}t.genomes=n.genomes;t.cardsPath=n.cardsPath;if(n.debugmode){t.debugmode=true}Xl({dsAuth:n.dsAuth,holder:t.holder});if(n.commonOverrides||e.commonOverrides){ga(Object.assign(n.commonOverrides||{},e.commonOverrides||{}))}if(n.targetPortal&&n.targetPortal=="gdc")await import("./style.gdc-4ac9b96b.js");for(const e in t.genomes){const n=dm(t.genomes[e]);if(n){throw{message:"Error with "+e+" genome: 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if(window.testHost){t.hostURL=window.testHost}else{const n=e.get("hostname");const o=e.get("hostport");const i=window.location.protocol+"//";if(n&&o)t.hostURL=i+n+":"+o;else if(n)t.hostURL=i+n;else if(o)t.hostURL=i+window.location.hostname+":"+o}}if(!t.hostURL){if(Ih.includes("://")){t.hostURL=Ih.split("://")[0]+"://"+Ih.split("://")[1].split("/")[0]}else{t.hostURL=""}}if(t.hostURL.endsWith("/"))t.hostURL=t.hostURL.slice(0,-1);sessionStorage.setItem("hostURL",t.hostURL)}async function Rh(e,t,n){const o=Kt(Ir);const i="13px";const s="5px 10px";const r="7px 10px";document.documentElement.clientWidth;const a=e.holder.append("div").style("white-space","nowrap").style("border-bottom","solid 1px rgba("+o.r+","+o.g+","+o.b+",.3)");const l=a.append("div").style("margin","10px").style("padding","8px").style("padding-bottom","12px").style("display","inline-block").style("border-bottom","");const c=a.append("div").style("display","inline-block").style("padding",r).style("padding-left","25px").style("font-size",".8em").style("color",Kt(Ir).darker());{const e=c.append("div").style("padding-left","15px");e.append("span").text("Code updated: "+(t.codedate||"??")+", server launched: "+(t.launchdate||"??")+".");if(t.hasblat){e.append("a").style("margin-left","10px").text("Running BLAT").on("click",(async e=>{Oh.clear().showunder(e.target);const t=Oh.d.append("div").style("margin","10px");const n=t.append("div").text("Loading...");try{const e=await Pl("blat?serverstat=1");if(e.error)throw e.error;if(!e.lst)throw"invalid response";n.remove();for(const n of e.lst){t.append("div").text(n)}}catch(e){n.text(e.message||e);if(e.stack)console.log(e.stack)}}))}}if(t.headermessage){c.append("div").html(t.headermessage)}l.append("div").text("ProteinPaint").style("display","inline-block").style("padding",i).style("color",Ir).style("font-size","1.3em").style("font-weight","bold");const d=new ec({border:"",padding:"0px"});const f=async()=>{const t=ot("input").property("value").trim();const o=[{title:"Genes",default:true,items:await Ch(t,e.selectgenome.property("value"),n),callback:t=>{e.drawer.dispatch({type:"is_apps_btn_active",value:false});d.hide();Eh(t,e,e.selectgenome.property("value"),n)}}];await Nh(e,t,o,d);o.push({title:"Help",items:m.filter((e=>e.label.toLowerCase().includes(t.toLowerCase()))),color:"#faebd9",callback:e=>{window.open(e.link,e.label)}});return o};const p=new jh({holder:l,tip:d,style:{padding:r,border:`'solid 1px ${Ir}`},size:32,placeholder:"Gene, position, SNP, app, or dataset",title:"Search by gene, SNP, position, app, or dataset",searchItems:f});p.initUI();const u=l.append("div").attr("class","sjpp-genome-select-div").style("padding",r);const h=()=>{const t=e.genomes[e.selectgenome.property("value")];const n=["Gene","position","app"];if(t.hasSNP)n.splice(2,0,"SNP");if(Object.keys(t.datasets).length)n.push("dataset");const o=n.join(", ").replace(/,(?=[^,]*$)/,", or");return o};e.selectgenome=u.append("select").attr("title","Select a genome").attr("class","sjpp-genome-select").style("padding",s).style("border","solid 1px "+Ir).on("change",(()=>{$h(e);p.updatePlaceholder(h())}));for(const t in e.genomes){e.selectgenome.append("option").attr("n",t).text(e.genomes[t].species+" "+t).property("value",t)}e.genome_browser_btn=Lh(e,l,n);e.drawer=await kh({holder:e.holder,genomes:e.genomes,drawerRow:e.holder.append("div").style("position","relative").style("overflow-x","visible").style("overflow-y","hidden").classed("sjpp-drawer-row",true),sandboxDiv:e.holder.append("div").style("margin-top","15px").classed("sjpp-drawer-sandbox",true),genome_browser_btn:e.genome_browser_btn,debugmode:e.debugmode,headbox:l,padw_sm:r,cardsPath:e.cardsPath});const m=[{label:"Embed in your website",link:"https://docs.google.com/document/d/1KNx4pVCKd4wgoHI4pjknBRTLrzYp6AL_D-j6MjcQSvQ/edit?usp=sharing"},{label:"URL parameters",link:"https://github.com/stjude/proteinpaint/wiki/URL-parameters"},{label:"All tutorials",link:"https://github.com/stjude/proteinpaint/wiki/"},{label:"User community",link:"https://groups.google.com/g/proteinpaint"},{label:"License ProteinPaint",link:"https://www.stjude.org/research/why-st-jude/shared-resources/technology-licensing/technologies/proteinpaint-web-application-for-visualizing-genomic-data-sj-15-0021.html",onlySearch:true},{label:"Our Team",link:"https://proteinpaint.stjude.org/team/",onlySearch:true}];l.append("span").classed("sja_menuoption",true).style("padding",r).text("Help").on("click",(async e=>{const t=e.target.getBoundingClientRect();const n=Oh.clear().show(t.left-0,t.top+t.height+5);await n.d.append("div").style("padding","5px 20px").selectAll("p").data(m.filter((e=>!e.onlySearch))).enter().append("p").html((e=>`<a href=${e.link} target=_blank>${e.label}</a>`))}))}function Lh(e,t,n){const o="8px";const i=t.append("span");const s=e.selectgenome.node().options[e.selectgenome.property("selectedIndex")].value;const r=i.attr("class","sja_menuoption").attr("id","genome_btn").style("padding",o).datum(s).text(s+" genome browser").on("click",((t,o)=>{const i=e.genomes[o];if(!i){alert("Invalid genome name: "+o);return}const s=Qd(e.drawer.opts.sandboxDiv);s.header.text(o+" genome browser");const r={hostURL:e.hostURL,jwt:n,holder:s.body,genome:i,chr:i.defaultcoord.chr,start:i.defaultcoord.start,stop:i.defaultcoord.stop,nobox:true,tklst:[],debugmode:e.debugmode};tc(i,r.tklst);import("./block-4f585abe.js").then((function(e){return e.c})).then((e=>new e.Block(r)));e.drawer.dispatch({type:"is_apps_btn_active",value:false})}));return r}function $h(e){e.genome_browser_btn.text(e.selectgenome.node().value+" genome browser");e.genome_browser_btn.datum(e.selectgenome.node().value)}async function zh(e,t){if(e.genome&&t.selectgenome){for(let n=0;n<t.selectgenome.node().childNodes.length;n++){if(t.selectgenome.node().childNodes[n].value==e.genome){t.selectgenome.property("selectedIndex",n);break}}}if(e.mclassOverride){if(!e.mclassOverride.mclassName)e.mclassOverride.mclassName="Class";for(const t in e.mclassOverride.classes){const n=Yr[t];if(n){Object.assign(n,e.mclassOverride.classes[t])}}}if(e.singlecell){im(e.singlecell,t);return t}if(e.fimo){Bh(e.fimo,t);return t}if(e.mdssurvivalplot){if(e.genome)e.mdssurvivalplot.genome=e.genome;Uh(e.mdssurvivalplot,t);return t}if(e.mdssamplescatterplot){if(e.genome)e.mdssamplescatterplot.genome=e.genome;Dh(e.mdssamplescatterplot,t);return t}if(e.samplematrix){e.samplematrix.jwt=e.jwt;qh(e.samplematrix,t);return t}if(e.hic){e.hic.jwt=e.jwt;Fh(e.hic,t);return t}if(e.block){return Gh(e,t)}if(e.study){Fd(t.genomes,e.study,t.holder0,t.hostURL,e.jwt,false,t);return t}if(e.studyview){const n=e.studyview;n.hostURL=e.host;const o=n.genome||e.genome;n.genome=t.genomes[o];n.hostURL=t.hostURL;n.jwt=e.jwt;n.holder=t.holder0;of(n);return t}if(await Ph(e,t)){return t}if(e.fusioneditor){Jh(e,t);return t}if(e.genefusion){am(e,t);return t}if(e.mavolcanoplot){em(e,t);return t}if(e.twodmaf){tm(e,t);return t}if(e.junctionbymatrix){om(e,t);return}if(e.mdsjsonform){await Vh(e,t);return}if(e.selectGenomeWithTklst){await Wh(e,t);return}if(e.disco){return await fm(e,t)}if(e.geneSearch4GDCmds3){return await Xh(e,t)}if(e.launchGdcMatrix){return await Yh(e,t)}if(e.launchGdcHierCluster){return await Zh(e,t)}if(e.launchGdcMaf){return await Kh(e,t)}if(e.parseurl&&location.search.length){try{await Rf({app:t,genomes:t.genomes,hostURL:t.hostURL,variantPageCall_snv:t.variantPageCall_snv,samplecart:t.samplecart,holder:t.holder,selectgenome:t.selectgenome,genome_browser_btn:t.genome_browser_btn,debugmode:t.debugmode})}catch(e){t.error0(e);console.error(e.stack||e)}}if(e.project){let n=undefined;if(e.project.uionly)n=t.holder0;ef(0,0,t.genomes,t.hostURL,n,t.sandbox_header)}if(e.termdb){await rm(e.termdb,t)}if(e.maftimeline){nm(e,t)}if(e.gdcbamslice){return await Qh(e,t)}if(e.mass){return await cm(e,t)}if(e.tkui){sm(e,t)}if(e.massSessionId){const n=await Bl(`/massSession?id=${e.massSessionId}`);if(n.error)throw n.error;const o={holder:t.holder0,state:n.state,genome:t.genomes[n.state.vocab.genome],massSessionDuration:n.massSessionDuration,getDatasetAccessToken:e.getDatasetAccessToken,addLoginCallback:e.addLoginCallback};const i=await import("./app-59194db0.js");i.appInit(o);return}if(e.massSessionFile||e.massSessionURL){let n;if(e.massSessionFile){const t=e.massSessionFile;const o=await Bl(`/textfile`,{method:"POST",body:JSON.stringify({file:t})});if(o.error)throw o.error;n=JSON.parse(o.text)}else{const t=e.massSessionURL;const o=await Bl(`/urltextfile`,{method:"POST",body:JSON.stringify({url:t})});if(o.error)throw o.error;n=JSON.parse(o.text)}const o={holder:t.holder0,state:n,genome:t.genomes[n.vocab.genome]};const i=await import("./app-59194db0.js");i.appInit(o);return}if(e.profileHome){const t=await import("./profileHome-9c5e266b.js");t.init(e);return}}async function Ph(e,t){if(e.p){e.gene=e.p;delete e.p}if(e.gene2canonicalisoform){if(!e.genome)throw".genome missing for gene2canonicalisoform";const t=await Pl("gene2canonicalisoform?genome="+e.genome+"&gene="+e.gene2canonicalisoform);if(t.error)throw t.error;if(!t.isoform)throw"no canonical isoform for given gene accession";e.gene=t.isoform}if(e.mds3_ssm2canonicalisoform){if(!e.genome)throw".genome missing";if(!e.mds3_ssm2canonicalisoform.ssm_id)throw".ssm_id missing from mds3_ssm2canonicalisoform";if(!e.mds3_ssm2canonicalisoform.dslabel)throw".dslabel missing from mds3_ssm2canonicalisoform";const t=await Pl("mds3?"+"genome="+e.genome+"&dslabel="+e.mds3_ssm2canonicalisoform.dslabel+"&ssm2canonicalisoform=1"+"&ssm_id="+e.mds3_ssm2canonicalisoform.ssm_id);if(t.error)throw t.error;if(!t.isoform)throw"no isoform found for given ssm_id";e.gene=t.isoform;if(e.tracks){const t=e.tracks.find((t=>t.dslabel==e.mds3_ssm2canonicalisoform.dslabel));if(t){t.hlssmid=e.mds3_ssm2canonicalisoform.ssm_id}}}if(e.gene){Hh(e,t);return true}return false}async function Dh(e,t){if(!e.genome){t.error0("missing genome for mdssamplescatterplot");return}const n=t.genomes[e.genome];if(!n){t.error0("invalid genome for mdssamplescatterplot");return}e.genome=n;if(e.dataset){e.mds=n.datasets[e.dataset];if(!e.mds){t.error0("invalid dataset for mdssamplescatterplot");return}e.dslabel=e.dataset;delete e.dataset;if(e.mds.mdsIsUninitiated){const t=await Bl(`getDataset?genome=${e.genome.name}&dsname=${e.dslabel}`);if(t.error)throw t.error;if(!t.ds)throw"ds missing";Object.assign(e.mds,t.ds);delete e.mds.mdsIsUninitiated}}else if(e.analysisdata);else if(e.analysisdata_file){try{const t=await Ll("textfile",{file:e.analysisdata_file});if(t.error)throw tmp.error;else if(t.text)e.analysisdata=JSON.parse(t.text)}catch(e){t.error0(e);return}}else{t.error0("neither .dataset or .analysisdata is given");return}import("./mds.samplescatterplot-a54b9e93.js").then((n=>{n.init(e,t.holder0,t.debugmode)}))}function Uh(e,t){if(!e.genome){t.error0("missing genome for mdssurvivalplot");return}const n=t.genomes[e.genome];if(!n){t.error0("invalid genome for mdssurvivalplot");return}e.genome=n;if(!e.dataset){t.error0("missing dataset for mdssurvivalplot");return}e.mds=n.datasets[e.dataset];if(!e.mds){t.error0("invalid dataset for mdssurvivalplot");return}delete e.dataset;if(e.plotlist){for(const t of e.plotlist){t.renderplot=1}}import("./mds.survivalplot-c5093f73.js").then((n=>{n.init(e,t.holder0,t.debugmode)}))}function Bh(e,t){if(!e.genome){t.error0("missing genome for fimo");return}const n=t.genomes[e.genome];if(!n){t.error0("invalid genome for fimo");return}e.genome=n;e.div=t.holder0;import("./mds.fimo-ce97371c.js").then((t=>{t.init(e)}))}function Fh(e,t){if(!e.genome){t.error0("missing genome for hic");return}e.genome=t.genomes[e.genome];if(!e.genome){t.error0("invalid genome for hic");return}if(!e.file){t.error0("missing file for hic");return}e.hostURL=t.hostURL;e.holder=t.holder0;import("./HicApp-aac413df.js").then((async n=>{await n.hicInit(e,t.debugmode)}))}function qh(e,t){if(!e.genome){t.error0("missing genome for launching samplematrix");return}e.genome=t.genomes[e.genome];if(!e.genome){t.error0("invalid genome for samplematrix");return}e.hostURL=t.hostURL;e.holder=t.holder0;e.debugmode=t.debugmode;import("./samplematrix-4f0ec523.js").then((t=>{new t.Samplematrix(e)}))}async function Hh(e,t){if(!e.genome){t.error0("Cannot embed: must specify reference genome");return}if(e.tracks){for(const t of e.tracks){if(t.type=="mds3"&&t.dslabel)continue;t.iscustom=true}}if(e.tkjsonfile){if(!e.tracks)e.tracks=[];const t=new Map([["tkjsonfile",e.tkjsonfile]]);const n=await $f(t,genomeobj);for(const t of n){e.tracks.push(t)}}const n={jwt:e.jwt,hostURL:t.hostURL,query:e.gene,genome:t.genomes[e.genome],holder:t.holder0,variantPageCall_snv:t.variantPageCall_snv,samplecart:t.samplecart,debugmode:t.debugmode,datasetqueries:e.datasetqueries,mset:e.mset,tklst:e.tracks,gmmode:e.gmmode,mclassOverride:e.mclassOverride,hide_dsHandles:e.hide_dsHandles,onloadalltk_always:e.onloadalltk_always};if(e.dataset){n.dataset=e.dataset.split(",");n.legacyDsFilter=e.legacyDsFilter;if(e.hidedatasetexpression){n.hidedatasetexpression=true}}if(e.hidegenecontrol){n.hidegenecontrol=true}if(e.hidegenelegend){n.hidegenelegend=true}let o=null;if(e.hlaachange){o=new Map;if(Array.isArray(e.hlaachange)){for(const t of e.hlaachange){if(t.name){o.set(t.name,t)}}}else{for(const t of e.hlaachange.split(",")){o.set(t,false)}}if(o.size){n.hlaachange=o}}if(e.hlvariants){n.hlvariants=e.hlvariants}await yf(n)}async function Gh(e,t){if(!e.genome){t.error0("Cannot embed: must specify reference genome");return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}if(e.study){Fd(t.genomes,e.study,t.holder0,t.hostURL,e.jwt,true,t)}if(e.studyview);if(e.tracks){for(const n of e.tracks){if(n.type==mc.mds3&&n.dslabel)continue;if(n.mdsjsonfile||n.mdsjsonurl){try{const t=await jf(n.mdsjsonfile,n.mdsjsonurl);e.tracks=e.tracks.filter((e=>e!=n));e.tracks.push(...t)}catch(e){hf(t.holder0,e)}}n.iscustom=true}}if(e.tkjsonfile){if(!e.tracks)e.tracks=[];const t=new Map([["tkjsonfile",e.tkjsonfile]]);const o=await $f(t,n);for(const t of o){e.tracks.push(t)}}const o={genome:n,hostURL:t.hostURL,jwt:e.jwt,holder:t.holder0,nativetracks:e.nativetracks,tklst:e.tracks,debugmode:t.debugmode,legendimg:e.legendimg};if(e.width){const n=Number.parseInt(e.width);if(Number.isNaN(n))return t.error0("browser width must be integer");o.width=n}if(e.subpanels){if(!Array.isArray(e.subpanels))return t.error0("subpanels is not array");const n=[];for(const o of e.subpanels){if(!o.chr){t.error0("missing chr in one subpanel");continue}if(!o.start||!o.stop){t.error0("missing start or stop in one subpanel");continue}if(!o.width){o.width=400}if(!o.leftpad){o.leftpad=5}n.push(o)}if(n.length){o.subpanels=n}}if(e.nobox){o.nobox=true}else{o.dogtag=e.dogtag||e.genome}if(e.chr&&Number.isInteger(e.start)){o.chr=e.chr;o.start=e.start;o.stop=Number.isInteger(e.stop)?e.stop:e.start+1}else if(e.position){const t=Ld(e.position,n);if(t){o.chr=t.chr;o.start=t.start;o.stop=t.stop}}else if(e.positionbygene){try{const t=await od(e.genome,e.positionbygene);if(t&&t[0]){const e=t[0];o.chr=e.chr;o.start=e.start;o.stop=e.stop}}catch(e){t.error0(e)}}if(!o.chr){o.chr=n.defaultcoord.chr;o.start=n.defaultcoord.start;o.stop=n.defaultcoord.stop}if(e.datasetqueries){o.datasetqueries=e.datasetqueries}if(e.hlregions){const t=[];for(const o of e.hlregions){const e=Ld(o,n,true);if(e)t.push(e)}if(t.length)o.hlregions=t}const i=If();if(i){if(i.has("position")){const e=Ld(i.get("position"),n);if(e){o.chr=e.chr;o.start=e.start;o.stop=e.stop}}if(i.has("hlregion")){const e=[];for(const t of i.get("hlregion").split(",")){const o=Ld(t,n,true);if(o){e.push(o)}}if(e.length){o.hlregions=e}}if(i.has("bedgraphdotfile")){if(!o.tklst)o.tklst=[];const e=i.get("bedgraphdotfile").split(",");for(let t=0;t<e.length;t+=2){if(e[t]&&e[t+1]){o.tklst.push({type:mc.bedgraphdot,name:e[t],file:e[t+1]})}}}}return import("./block-4f585abe.js").then((function(e){return e.c})).then((e=>{t.block=new e.Block(o);return t}))}function Jh(e,t){if(e.fusioneditor.uionly){const[n,o,i,s,r]=Xd(t.holder0,t.genomes);import("./svmr-248055c8.js").then((a=>{a.svmrui([null,n,o,i,s,r],t.genomes,t.hostURL,e.jwt)}));return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}import("./svmr-248055c8.js").then((o=>{o.svmrparseinput(e.fusioneditor,t.error0,n,t.holder0,t.hostURL,e.jwt)}))}async function Vh(e,t){if(e.mdsjsonform.uionly){const e=await import("./mdsjsonform-09b4e1cb.js");await e.init_mdsjsonform({holder:t.holder0,genomes:t.genomes})}}async function Wh(e,t){const n=await import("./selectGenomeWithTklst-895106fb.js");await n.init(e,t.holder0,t.genomes)}async function Xh(e,t){const n=await import("./lollipop-6ad9ec3c.js");return await n.init(e,t.holder0,t.genomes)}async function Yh(e,t){const n=await import("./oncomatrix-6950c48c.js");return await n.init(e,t.holder0,t.genomes)}async function Zh(e,t){const n=await import("./geneExpClustering-a916ebda.js");return await n.init(e,t.holder0,t.genomes)}async function Kh(e,t){const n=await import("./maf-dfada1c8.js");return await n.gdcMAFui({holder:t.holder0,filter0:e.filter0,callbacks:e.callbacks||{},debugmode:e.debugmode})}function Qh(e,t){return import("./bam-e7f6baea.js").then((n=>n.bamsliceui({genomes:t.genomes,holder:t.holder0,hideTokenInput:e.gdcbamslice.hideTokenInput,callbacks:e.gdcbamslice.callbacks||{},filter0:e.filter0,stream2download:e.gdcbamslice.stream2download,inputValue:e.gdcbamslice.inputValue})))}function em(e,t){if(e.mavolcanoplot.uionly){import("./mavb-9a6fa2e9.js").then((n=>{n.mavbui(t.genomes,t.hostURL,e.jwt,t.holder0,t.sandbox_header)}));return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}e.mavolcanoplot.hostURL=t.hostURL;e.mavolcanoplot.genome=n;import("./mavb-9a6fa2e9.js").then((n=>{n.mavbparseinput(e.mavolcanoplot,t.error0,t.holder0,e.jwt)}))}function tm(e,t){if(e.twodmaf.uionly){import("./2dmaf-0cabb4a4.js").then((e=>{e.d2mafui(t.genomes,t.holder0)}));return}const n=t.genomes[e.genome];if(!n){t.error0("Invalid genome: "+e.genome);return}e.twodmaf.hostURL=t.hostURL;e.twodmaf.genome=n;import("./2dmaf-0cabb4a4.js").then((n=>{n.d2mafparseinput(e.twodmaf,t.holder0)}))}function nm(e,t){if(e.maftimeline.uionly){import("./maftimeline-1b715a01.js").then((e=>{e.default(t.genomes,t.holder0,t.sandbox_header)}))}}function om(e,t){if(e.junctionbymatrix.uionly){import("./block.tk.junction.textmatrixui-09e5e02f.js").then((n=>{n.default(t.genomes,t.hostURL,e.jwt,t.holder0)}))}}async function im(e,t){try{const n=t.genomes[e.genome];if(!n)throw"Invalid genome: "+e.genome;e.genome=n;const o=await import("./singlecell-29c1cbb1.js");await o.init(e,t.holder0)}catch(e){t.error0("Error launching single cell viewer: "+e);if(e.stack)console.log(e.stack)}}async function sm(e,t){if(e.tkui=="bigwig"){const e=await import("./block.tk.bigwig.ui-a92f286b.js");e.bigwigUI(t.genomes,t.holder)}if(e.tkui=="databrowser"){const e=await import("./databrowser.ui-4799f04d.js");e.init_databrowserUI(t.holder,t.debugmode)}if(e.tkui=="genefusion"){const e=await import("./genefusion.ui-3ce190c7.js");e.init_geneFusionUI(t.holder,t.genomes,t.debugmode)}if(e.tkui=="disco"){const e=await import("./Disco.UI-54228bb6.js");e.init_discoplotUI(t.holder,t.genomes,t.debugmode)}}async function rm(e,t){if(!e.holder)e.holder=t.holder0;import("./app-fb676934.js").then((t=>{t.appInit(e)}))}async function am(e,t){try{const n=t.genomes[e.genome];if(!n)throw"Invalid genome: "+e.genome;const o=await import("./fusion.parse-fc25e5bd.js");const i=await o.parseFusion({line:e.genefusion.text,genome:n,positionType:e.genefusion.positionType});await lm(i.pairlst[0].a,n);await lm(i.pairlst[0].b,n);const s=await import("./svgraph-a12d89da.js");s.default({pairlst:i.pairlst,genome:n,holder:t.holder})}catch(e){t.error0(e)}}async function lm(e,t){const n=await Bl("genelookup",{body:{genome:t.name,input:e.isoform,deep:1}});if(n.error)throw n.error;if(!Array.isArray(n.gmlst))throw"gmlst not array";const o=n.gmlst.find((t=>t.isoform==e.isoform));if(!o)throw"no match to isoform";e.chr=o.chr;e.name=o.name;e.gm={isoform:o.isoform}}async function cm(e,t){const n=e.mass;if(!n.holder)n.holder=t.holder0;if(n.state){if(n.state.genome){n.genome=t.genomes[n.state.genome]}else if(n.state?.vocab?.genome){n.genome=t.genomes[n.state.vocab.genome]}}n.getDatasetAccessToken=e.getDatasetAccessToken;n.addLoginCallback=e.addLoginCallback;const o=sessionStorage.getItem("hostURL");if(window.opener&&o!=window.location.origin){n.embeddedSessionState=JSON.parse(sessionStorage.getItem("embeddedSessionState")||`{}`);const e=t=>{if(t.origin!=window.location.origin&&t.origin!==o)return;if(t.data.state){window.removeEventListener("message",e);Object.assign(n.embeddedSessionState,t.data.state);sessionStorage.setItem("embeddedSessionState",JSON.stringify(n.embeddedSessionState))}};window.addEventListener("message",e,false);setTimeout((()=>window.removeEventListener("message",e)),1e3);let t;try{if(window.opener.origin){t=window.opener.origin}else{t=o}}catch(e){t=o}try{window.opener.postMessage("getActiveMassSession",t)}catch(e){console.log(e)}}const i=await import("./app-59194db0.js");return await i.appInit(n)}function dm(e){e.tkset=[];e.isoformcache=new Map;e.junctionframecache=new Map;e.isoformmatch=(t,n,o)=>{if(!t)return null;const i=t.toUpperCase();if(!e.isoformcache.has(i))return null;const s=e.isoformcache.get(i);if(s.length==1)return s[0];if(!n){console.log("no chr provided for matching with "+i);return s[0]}let r=null;for(const e of s){if(e.chr.toUpperCase()==n.toUpperCase()&&e.start<=o&&e.stop>=o){r=e}}if(r)return r;for(const e of s){if(e.chr.toUpperCase()==n.toUpperCase())return e}return null};e.chrlookup={};for(const t in e.majorchr){e.chrlookup[t.toUpperCase()]={name:t,len:e.majorchr[t],major:true}}if(e.minorchr){for(const t in e.minorchr){e.chrlookup[t.toUpperCase()]={name:t,len:e.minorchr[t]}}}if(!e.tracks){e.tracks=[]}for(const t of e.tracks){t.tkid=Math.random().toString()}for(const t in e.datasets){const n=e.datasets[t];if(n.isMds);else if(n.isMds3){if(!n.label)return"ds.label missing"}}return null}async function fm(e,t){if(!e.genome)throw'"genome" parameter missing';const n=t.genomes[e.genome];if(!n)throw"unknown genome";const o=await import("./launch.adhoc-1b356f97.js");return await o.launch(e.disco,n,t.holder0)}export{it as $,Ed as A,ic as B,mc as C,Pa as D,Yr as E,Hr as F,Jr as G,Gr as H,qr as I,Dr as J,Fr as K,Pr as L,ec as M,Rc as N,Xr as O,Rd as P,uf as Q,pf as R,Bl as S,Ir as T,Md as U,qc as V,uc 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as bd,Vr as be,Qr as bf,ea as bg,ra as bh,cc as bi,dc as bj,pc as bk,Pc as bl,Zc as bm,If as bn,nc as bo,Uf as bp,Xd as bq,Mc as br,at as bs,kt as bt,vo as bu,Go as bv,po as bw,Nt as bx,Yn as by,nd as bz,Ll as c,nl as c0,zn as c1,Mh as c2,kf as c3,Pl as d,Fc as e,Po as f,yc as g,vc as h,$c as i,zc as j,Jc as k,Jo as l,Ia as m,gc as n,xc as o,sc as p,ot as q,Gc as r,e as s,$d as t,jc as u,Tr as v,Pd as w,Kt as x,Ra as y,wr as z};