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tcarvertcarver
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Merge pull request #164 from tcarver/master
updates
2 parents fa0d5d9 + c54ceca commit 07ff772

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‎build/pedigreejs.v3.0.0-rc3.css

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‎build/pedigreejs.v3.0.0-rc3.min.css

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‎build/pedigreejs.v3.0.0-rc3.min.js

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‎build/pedigreejs.v3.0.0-rc3.min.js.map

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‎build/pedigreejs.v3.0.0-rc5.css

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‎build/pedigreejs.v3.0.0-rc3.js ‎build/pedigreejs.v3.0.0-rc5.js

+73-34
Original file line numberDiff line numberDiff line change
@@ -327,7 +327,7 @@ var pedigreejs = (function (exports) {
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});
328328
}
329329
} catch (err) {
330-
showDialog(title, msg, onConfirm, opts);
330+
showDialog(title, msg, onConfirm, opts, dataset);
331331
}
332332
}
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@@ -1069,37 +1069,40 @@ var pedigreejs = (function (exports) {
10691069
btn_target: 'pedigree_history'
10701070
}, options);
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let btns = [{
1072-
"fa": "fa-undo pull-left",
1072+
"fa": "fa-file-image",
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"title": "download PNG image"
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}, {
1075+
"fa": "fa-undo",
10731076
"title": "undo"
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}, {
1075-
"fa": "fa-redo pull-left",
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"fa": "fa-redo",
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"title": "redo"
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}, {
1078-
"fa": "fa-refresh pull-left",
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"fa": "fa-refresh",
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"title": "reset"
10801083
}];
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btns.push({
1082-
"fa": "fa-crosshairs pull-right",
1085+
"fa": "fa-crosshairs",
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"title": "scale-to-fit"
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});
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if (opts.zoomSrc && opts.zoomSrc.indexOf('button') > -1) {
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if (opts.zoomOut !== 1) btns.push({
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"fa": "fa-minus-circle pull-right",
1090+
"fa": "fa-minus-circle",
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"title": "zoom-out"
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});
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if (opts.zoomIn !== 1) btns.push({
1091-
"fa": "fa-plus-circle pull-right",
1094+
"fa": "fa-plus-circle",
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"title": "zoom-in"
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});
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}
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btns.push({
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"fa": "fa-arrows-alt pull-right",
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"fa": "fa-arrows-alt",
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"title": "fullscreen"
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});
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let lis = "";
11001103
for (let i = 0; i < btns.length; i++) {
11011104
lis += '<span>';
1102-
lis += '&nbsp;<i class="fa fa-lg ' + btns[i].fa + '" ' + (btns[i].fa === "fa-arrows-alt pull-right" ? 'id="fullscreen" ' : '') + ' aria-hidden="true" title="' + btns[i].title + '"></i>';
1105+
lis += '<i class="fa fa-lg ' + btns[i].fa + ' pe-2" aria-hidden="true" title="' + btns[i].title + '"' + (btns[i].fa === "fa-arrows-alt" ? 'id="fullscreen" ' : '') + '></i>';
11031106
lis += '</span>';
11041107
}
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$("#" + opts.btn_target).append(lis);
@@ -1173,7 +1176,10 @@ var pedigreejs = (function (exports) {
11731176
messages("Pedigree Reset", "This may result in loss of some data. Reset now?", reset, opts);
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} else if ($(e.target).hasClass('fa-crosshairs')) {
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scale_to_fit(opts);
1179+
} else if ($(e.target).hasClass('fa-file-image')) {
1180+
return;
11761181
}
1182+
11771183
// trigger fhChange event
11781184
$(document).trigger('fhChange', [opts]);
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});
@@ -1406,6 +1412,7 @@ var pedigreejs = (function (exports) {
14061412
};
14071413
let genetic_test1 = ['brca1', 'brca2', 'palb2', 'atm', 'chek2', 'rad51d', 'rad51c', 'brip1'];
14081414
let genetic_test2 = ['brca1', 'brca2', 'palb2', 'atm', 'chek2', 'bard1', 'rad51d', 'rad51c', 'brip1'];
1415+
let genetic_test4 = ['brca1', 'brca2', 'palb2', 'atm', 'chek2', 'bard1', 'rad51d', 'rad51c', 'brip1', 'hoxb13'];
14091416
let pathology_tests = ['er', 'pr', 'her2', 'ck14', 'ck56'];
14101417

14111418
// risk factor to storage
@@ -1423,6 +1430,9 @@ var pedigreejs = (function (exports) {
14231430
if (prs.ovarian_cancer_prs && prs.ovarian_cancer_prs.alpha !== 0 && prs.ovarian_cancer_prs.zscore !== 0) {
14241431
meta += "\n##PRS_OC=alpha=" + prs.ovarian_cancer_prs.alpha + ",zscore=" + prs.ovarian_cancer_prs.zscore;
14251432
}
1433+
if (prs.prostate_cancer_prs && prs.prostate_cancer_prs.alpha !== 0 && prs.prostate_cancer_prs.zscore !== 0) {
1434+
meta += "\n##PRS_PC=alpha=" + prs.prostate_cancer_prs.alpha + ",zscore=" + prs.prostate_cancer_prs.zscore;
1435+
}
14261436
} catch (err) {
14271437
console.warn("PRS", prs);
14281438
}
@@ -1468,6 +1478,13 @@ var pedigreejs = (function (exports) {
14681478
'percent': parseFloat($('#ovarian_prs_percent').val())
14691479
};
14701480
}
1481+
if (hasInput("prostate_prs_a") && hasInput("prostate_prs_z")) {
1482+
prs['prostate_cancer_prs'] = {
1483+
'alpha': parseFloat($('#prostate_prs_a').val()),
1484+
'zscore': parseFloat($('#prostate_prs_z').val()),
1485+
'percent': parseFloat($('#prostate_prs_percent').val())
1486+
};
1487+
}
14711488
console.log(prs);
14721489
return isEmpty(prs) ? 0 : prs;
14731490
}
@@ -1481,22 +1498,31 @@ var pedigreejs = (function (exports) {
14811498
}
14821499
return meta;
14831500
}
1501+
1502+
/**
1503+
* Get genetic test genes based on CanRisk version
1504+
*/
1505+
function getGeneticTest(version) {
1506+
version = parseInt(version);
1507+
if (version === 1) return genetic_test1;else if (version === 2) return genetic_test2;else if (version === 3) return genetic_test2;
1508+
return genetic_test4;
1509+
}
14841510
function readCanRisk(boadicea_lines) {
14851511
let lines = boadicea_lines.trim().split('\n');
14861512
let ped = [];
14871513
let hdr = []; // collect risk factor header lines
14881514
const regexp = /([0-9])/;
1489-
let version = 2;
1490-
let gt = version === 1 ? genetic_test1 : genetic_test2;
1491-
let ncol = [26, 27, 27]; // number of columns - v1, v2, v3
1515+
let version = 3;
1516+
let gt = getGeneticTest(version);
1517+
let ncol = [26, 27, 27, 28]; // number of columns - v1, v2, v3, v4
14921518
// assumes two line header
14931519
for (let i = 0; i < lines.length; i++) {
14941520
let ln = lines[i].trim();
14951521
if (ln.indexOf("##") === 0) {
14961522
if (ln.indexOf("##CanRisk") === 0) {
14971523
const match = ln.match(regexp);
14981524
version = parseInt(match[1]);
1499-
gt = version === 1 ? genetic_test1 : genetic_test2;
1525+
gt = getGeneticTest(version);
15001526
console.log("CanRisk File Format version " + version);
15011527
if (ln.indexOf(";") > -1) {
15021528
// contains surgical op data
@@ -1601,7 +1627,7 @@ var pedigreejs = (function (exports) {
16011627
* Get CanRisk formated pedigree.
16021628
*/
16031629
function get_pedigree(dataset, famid, meta, isanon) {
1604-
let version = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : 2;
1630+
let version = arguments.length > 4 && arguments[4] !== undefined ? arguments[4] : 3;
16051631
let ethnicity = arguments.length > 5 && arguments[5] !== undefined ? arguments[5] : undefined;
16061632
let v = Number.isInteger(version) ? version + ".0" : version.toString();
16071633
let msg = "##CanRisk " + v;
@@ -1655,7 +1681,7 @@ var pedigreejs = (function (exports) {
16551681
msg += "\n##ethnicity=" + ethnicity;
16561682
}
16571683
msg += "\n##FamID\tName\tTarget\tIndivID\tFathID\tMothID\tSex\tMZtwin\tDead\tAge\tYob\tBC1\tBC2\tOC\tPRO\tPAN\tAshkn";
1658-
let gt = version === 1 ? genetic_test1 : genetic_test2;
1684+
let gt = getGeneticTest(version);
16591685
for (let i = 0; i < gt.length; i++) {
16601686
msg += "\t" + gt[i].toUpperCase();
16611687
}
@@ -1745,6 +1771,7 @@ var pedigreejs = (function (exports) {
17451771
cancers: cancers,
17461772
genetic_test1: genetic_test1,
17471773
genetic_test2: genetic_test2,
1774+
genetic_test4: genetic_test4,
17481775
get_mdensity: get_mdensity,
17491776
get_meta: get_meta,
17501777
get_non_anon_pedigree: get_non_anon_pedigree,
@@ -1779,24 +1806,9 @@ var pedigreejs = (function (exports) {
17791806
$('#svg_download').click(function (_e) {
17801807
svg_download(get_printable_svg(opts));
17811808
});
1782-
$('#png_download').click(function (_e) {
1783-
let deferred = svg2img($('svg'), "pedigree");
1784-
$.when.apply($, [deferred]).done(function () {
1785-
let obj = getByName(arguments, "pedigree");
1786-
if (isEdge() || isIE()) {
1787-
let html = "<img src='" + obj.img + "' alt='canvas image'/>";
1788-
let newTab = window.open(); // pop-ups need to be enabled
1789-
newTab.document.write(html);
1790-
} else {
1791-
let a = document.createElement('a');
1792-
a.href = obj.img;
1793-
a.download = 'plot.png';
1794-
a.target = '_blank';
1795-
document.body.appendChild(a);
1796-
a.click();
1797-
document.body.removeChild(a);
1798-
}
1799-
});
1809+
$('#png_download, .fa-file-image').click(function (_e) {
1810+
let resolution = 1;
1811+
img_download(opts, resolution, "image/png");
18001812
});
18011813
}
18021814

@@ -1832,6 +1844,32 @@ var pedigreejs = (function (exports) {
18321844
}
18331845
}
18341846

1847+
/**
1848+
* Export pedigree as image, e.g. PNG
1849+
*/
1850+
function img_download(opts, resolution, img_type) {
1851+
let deferred = svg2img($('#' + opts.targetDiv).find('svg'), "pedigree", {
1852+
resolution: resolution,
1853+
img_type: img_type
1854+
});
1855+
$.when.apply($, [deferred]).done(function () {
1856+
let obj = getByName(arguments, "pedigree");
1857+
if (isEdge() || isIE()) {
1858+
let html = "<img src='" + obj.img + "' alt='canvas image'/>";
1859+
let newTab = window.open(); // pop-ups need to be enabled
1860+
newTab.document.write(html);
1861+
} else {
1862+
let a = document.createElement('a');
1863+
a.href = obj.img;
1864+
a.download = 'plot.png';
1865+
a.target = '_blank';
1866+
document.body.appendChild(a);
1867+
a.click();
1868+
document.body.removeChild(a);
1869+
}
1870+
});
1871+
}
1872+
18351873
/**
18361874
* Given a SVG document element convert to image (e.g. jpeg, png - default png).
18371875
*/
@@ -2431,6 +2469,7 @@ var pedigreejs = (function (exports) {
24312469
__proto__: null,
24322470
addIO: addIO,
24332471
copy_svg: copy_svg,
2472+
img_download: img_download,
24342473
load_data: load_data,
24352474
print: print,
24362475
readBoadiceaV4: readBoadiceaV4,
@@ -3586,7 +3625,7 @@ var pedigreejs = (function (exports) {
35863625
'type': 'prostate_cancer',
35873626
'colour': '#D5494A'
35883627
}],
3589-
labels: ['stillbirth', ['age', 'yob'], 'alleles', ['brca1_gene_test', 'brca2_gene_test', 'palb2_gene_test', 'chek2_gene_test', 'atm_gene_test'], ['rad51d_gene_test', 'rad51c_gene_test', 'brip1_gene_test'], ['er_bc_pathology', 'pr_bc_pathology', 'her2_bc_pathology', 'ck14_bc_pathology', 'ck56_bc_pathology']],
3628+
labels: ['stillbirth', ['age', 'yob'], 'alleles', ['brca1_gene_test', 'brca2_gene_test', 'palb2_gene_test', 'chek2_gene_test', 'atm_gene_test'], ['rad51d_gene_test', 'rad51c_gene_test', 'brip1_gene_test', 'hoxb13_gene_test'], ['er_bc_pathology', 'pr_bc_pathology', 'her2_bc_pathology', 'ck14_bc_pathology', 'ck56_bc_pathology']],
35903629
keep_proband_on_reset: false,
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font_size: '.75em',
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font_family: 'Helvetica',

‎build/pedigreejs.v3.0.0-rc5.min.css

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‎build/pedigreejs.v3.0.0-rc5.min.js

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‎build/pedigreejs.v3.0.0-rc5.min.js.map

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‎css/pedigreejs.css

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.addsibling, .addchild {
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cursor: default;
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.pull-right { float: right; margin-left:.3em; line-height: 1; }
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.pull-left { float: left; margin-right:.3em; line-height: 1; }
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.pe-2 { padding-right: 0.75em; }
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‎docs/demo.html

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<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" type="text/css" media="all" />
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<link href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" rel="stylesheet" type="text/css" media="all" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc3.css" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.css" />
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‎docs/example1.html

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<link href="https://code.jquery.com/ui/1.12.1/themes/cupertino/jquery-ui.min.css" rel="stylesheet" type="text/css" media="all" />
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<link href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" rel="stylesheet" type="text/css" media="all" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/d3.min.js" integrity="sha256-yUdn/lyl/rHBn4bD4HkKmnR7S6Fj+tXIO0ozSay1Bik=" crossorigin="anonymous"></script>
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<script src="../build/pedigreejs.v3.0.0-rc5.min.js"></script>
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body {

‎docs/example2.html

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<link href="https://code.jquery.com/ui/1.12.1/themes/cupertino/jquery-ui.min.css" rel="stylesheet" type="text/css" media="all" />
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<link href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" rel="stylesheet" type="text/css" media="all" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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‎docs/example3.html

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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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‎docs/example4.html

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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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‎docs/example5.html

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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/d3.min.js" integrity="sha256-yUdn/lyl/rHBn4bD4HkKmnR7S6Fj+tXIO0ozSay1Bik=" crossorigin="anonymous"></script>
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<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc3.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc5.min.js"></script>
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body {

‎docs/example6.html

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<link href="https://code.jquery.com/ui/1.12.1/themes/cupertino/jquery-ui.min.css" rel="stylesheet" type="text/css" media="all" />
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<link href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" rel="stylesheet" type="text/css" media="all" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc3.min.css" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/jquery.min.js"></script>
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/d3.min.js" integrity="sha256-yUdn/lyl/rHBn4bD4HkKmnR7S6Fj+tXIO0ozSay1Bik=" crossorigin="anonymous"></script>
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<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc3.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc5.min.js"></script>
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‎docs/example7.html

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<link href="https://code.jquery.com/ui/1.12.1/themes/cupertino/jquery-ui.min.css" rel="stylesheet" type="text/css" media="all" />
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<link href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" rel="stylesheet" type="text/css" media="all" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc3.min.css" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/jquery.min.js"></script>
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/d3.min.js" integrity="sha256-yUdn/lyl/rHBn4bD4HkKmnR7S6Fj+tXIO0ozSay1Bik=" crossorigin="anonymous"></script>
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<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc3.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc5.min.js"></script>
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‎docs/example8.html

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<link href="https://code.jquery.com/ui/1.12.1/themes/cupertino/jquery-ui.min.css" rel="stylesheet" type="text/css" media="all" />
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<link href="https://cdn.jsdelivr.net/npm/@fortawesome/[email protected]/css/all.min.css" rel="stylesheet" type="text/css" media="all" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc3.min.css" />
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<link rel="stylesheet" href="../build/pedigreejs.v3.0.0-rc5.min.css" />
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/jquery.min.js"></script>
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<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/d3.min.js" integrity="sha256-yUdn/lyl/rHBn4bD4HkKmnR7S6Fj+tXIO0ozSay1Bik=" crossorigin="anonymous"></script>
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<script src="https://code.jquery.com/ui/1.12.1/jquery-ui.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc3.min.js"></script>
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<script src="../build/pedigreejs.v3.0.0-rc5.min.js"></script>
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