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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>HIV-TRACE</title>
<!-- Latest compiled and minified CSS -->
<link href="dist/hivtrace.css" rel="stylesheet" />
<!-- no favicon, prevent 404 errors -->
<link rel="shortcut icon" href="#" />
<style>
.navbar {
position: relative;
}
</style>
</head>
<body>
<nav class="navbar navbar-default navbar-fixed-top">
<div class="container">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header">
<button
type="button"
class="navbar-toggle"
data-toggle="collapse"
data-target="#navbar-collapse-1"
>
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="#">HIV-TRACE</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="navbar-collapse-1">
<ul class="nav navbar-nav">
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown"
>File<b class="caret"></b
></a>
<ul class="dropdown-menu">
<li>
<label>Load network JSON</label>
<input type="file" id="json_file" />
</li>
<li>
<a
href="#"
data-toggle="modal"
data-target="#csv_loader_modal"
><span class="fa fa-database"></span>
Load .CSV data
</a>
</li>
</ul>
</li>
</ul>
<form class="navbar-form navbar-right">
<div class="form-group" id="network_status_string"></div>
</form>
</div>
<!-- /.navbar-collapse -->
</div>
<!-- /.container-fluid -->
</nav>
<div class="modal fade" id="csv_loader_modal" tabindex="-1" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button
type="button"
class="close"
data-dismiss="modal"
aria-label="Close"
>
<span aria-hidden="true">×</span>
</button>
<h4 class="modal-title">Load external network information</h4>
</div>
<div class="modal-body">
<form id="csv_enclosing_form">
<div class="form-group">
<label for="csv_import_text">Data type label</label>
<input type="text" id="csv_import_text" value="Social" />
<p class="help-block">
Descriptive name for the type of data being loaded.
</p>
</div>
<div class="form-group">
<label for="csv_node_progress">Node attribute file</label>
<button
id="csv_node_file_help"
type="button"
class="btn btn-xs btn-info"
>
<span class="fa fa-question"></span>
</button>
<input type="file" id="csv_node_file" />
<div id="csv_node_progress" style="display: none">
Loading...<span class="fa fa-spinner fa-spin"></span>
</div>
<p class="help-block">A CSV file with node attributes.</p>
</div>
<div class="input-group">
<label for="csv_edge_progress">Link attribute file</label>
<button
id="csv_edge_file_help"
type="button"
class="btn btn-xs btn-info"
>
<span class="fa fa-question"></span>
</button>
<input type="file" id="csv_edge_file" />
<div id="csv_edge_progress" style="display: none">
Loading...<span class="fa fa-spinner fa-spin"></span>
</div>
<p class="help-block">
A CSV file with links and their attribute.
</p>
</div>
<div
class="alert"
role="alert"
style="display: none"
id="csv_import_status"
></div>
</form>
</div>
<div class="modal-footer">
<!--<button type="button" class="btn btn-primary" id = "network_ui_bar_cluster_zoom_svg_export">Export <i class = "fa fa-image"></i></button>-->
<button
type="button"
class="btn btn-primary"
disabled
id="csv_proceed_button"
>
Proceed
</button>
<button type="button" class="btn btn-default" data-dismiss="modal">
Dismiss
</button>
</div>
</div>
</div>
</div>
<div class="container">
<div class="row" style="margin-top: 10px; margin-bottom: 10 px">
<div class="col-lg-12">
<div
class="alert alert-danger alert-lg"
id="app-error"
style="display: none"
></div>
</div>
</div>
<div
class="modal fade"
data-hivtrace-ui-role="cluster_list"
tabindex="-1"
role="dialog"
>
<div class="modal-dialog" role="document">
<div class="modal-content" data-hivtrace-ui-role="cluster_list_body">
<div class="modal-header">
<button
type="button"
class="close"
data-dismiss="modal"
aria-label="Close"
>
<span aria-hidden="true">×</span>
</button>
<h4 class="modal-title">Listing nodes in cluster X</h4>
<button
type="button"
data-hivtrace-ui-role="cluster_list_view_toggle"
class="btn btn-primary pull-right"
data-view="attribute"
>
Group by ID
</button>
<button type="button" class="btn btn-default btn-small">
<i
class="fa fa-download"
data-hivtrace-ui-role="cluster_list_data_export"
></i>
</button>
</div>
<ul
data-hivtrace-ui-role="cluster_list_payload"
class="list-unstyled"
></ul>
<div class="modal-footer">
<!--<button type="button" class="btn btn-primary" id = "network_ui_bar_cluster_zoom_svg_export">Export <i class = "fa fa-image"></i></button>-->
<button
type="button"
class="btn btn-default"
data-dismiss="modal"
>
Dismiss
</button>
</div>
</div>
</div>
</div>
<div class="tabbable">
<ul
class="nav nav-tabs main-hivtrace-tabs"
id="top_level_tab_container"
>
<li class="active" id="main-tab">
<a id="trace-default-tab" href="#trace-results" data-toggle="tab"
>Network</a
>
</li>
<li class="disabled" id="lanl-result-tab">
<a href="#lanl-trace-results" data-toggle="tab">Network + DB</a>
</li>
<li class="disabled" id="graph-tab">
<a href="#trace-graph" data-toggle="tab">Statistics</a>
</li>
<li class="disabled" id="clusters-tab">
<a href="#trace-clusters" data-toggle="tab">Clusters (1.5%)</a>
</li>
<li class="disabled" id="subclusters-tab">
<a href="#trace-subclusters" data-toggle="tab"
>Subclusters (0.5%)</a
>
</li>
<li class="disabled" id="nodes-tab">
<a href="#trace-nodes" data-toggle="tab">Nodes</a>
</li>
<li class="disabled" id="attributes-tab">
<a href="#trace-attributes" data-toggle="tab">Attributes</a>
</li>
<li class="disabled">
<a href="#trace-settings" data-toggle="tab">Settings</a>
</li>
</ul>
<div class="tab-content" id="top_level_tab_content">
<div id="trace-results" class="tab-pane active">
<!-- Warning bar -->
<div class="row" style="margin-top: 10px; margin-bottom: 10 px">
<div class="col-lg-12">
<div
class="alert alert-warning alert-dismissible"
id="main-warning"
style="display: none"
>
<button
type="button"
class="close"
data-dismiss="alert"
aria-label="Close"
>
<span aria-hidden="true">×</span>
</button>
</div>
</div>
</div>
<div class="row" data-hivtrace="cluster-clone">
<div class="col-lg-12">
<div class="nav-trace">
<div class="input-group input-group-sm">
<!-- UI Bar -->
<div class="nav-trace">
<div
class="input-group input-group-sm"
id="network_ui_bar"
data-hivtrace-button-bar="yes"
>
<div
class="input-group-btn"
data-hivtrace-ui-role="export_image"
></div>
<div
class="input-group-btn"
data-hivtrace-ui-role="button_group"
></div>
<span class="input-group-btn">
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
data-hivtrace-ui-role="cluster_operations_button"
>
Clusters <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
data-hivtrace-ui-role="cluster_operations_container"
></ul>
</span>
<!-- Dropdowns to Format Notes By Attributes (Color, Shape, Opacity and Label) -->
<div class="input-group-btn">
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
data-hivtrace-ui-role="attributes_label"
>
Color <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
data-hivtrace-ui-role="attributes"
></ul>
<button
type="button"
class="btn btn-default"
data-toggle="collapse"
href="#colorPickerRow"
title="Select Color Palette"
>
<i
class="fa fa-circle color-picker-toggle"
aria-hidden="true"
></i>
</button>
<button
type="button"
class="btn btn-default"
style="display: none"
data-hivtrace-ui-role="attributes_invert"
>
Invert
</button>
</div>
<div class="input-group-btn">
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
data-hivtrace-ui-role="shapes_label"
>
Shape <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
data-hivtrace-ui-role="shapes"
></ul>
</div>
<div class="input-group-btn">
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
data-hivtrace-ui-role="opacity_label"
>
Opacity <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
data-hivtrace-ui-role="opacity"
></ul>
<button
type="button"
class="btn btn-default"
style="display: none"
data-hivtrace-ui-role="opacity_invert"
>
Invert
</button>
</div>
<div class="input-group-btn">
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
data-hivtrace-ui-role="labels_label"
>
Label <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
data-hivtrace-ui-role="labels"
></ul>
</div>
<div
class="input-group-btn"
style="display: none"
data-hivtrace-ui-role="extra_operations_enclosure"
>
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
data-hivtrace-ui-role="extra_label"
>
Action <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
data-hivtrace-ui-role="extra_operations_container"
></ul>
</div>
<div class="input-group input-group-sm">
<span class="input-group-addon">
<i class="fa fa-search"></i>
</span>
<input
id="filter_input"
type="text"
class="form-control"
placeholder="Text in attributes"
data-hivtrace-ui-role="filter"
/>
<span class="input-group-addon">
Hide others
<input
type="checkbox"
data-hivtrace-ui-role="hide_filter"
/>
</span>
<span class="input-group-addon set-min-cluster-size">
Min cluster size
<input
id="min_cluster_size_input"
type="number"
data-hivtrace-ui-role="set_min_cluster_size"
placeholder="2"
min="0"
max="9999"
/>
</span>
<span
class="input-group-addon"
id="network_ui_bar_legend_icon_span"
>
<a
data-toggle="collapse"
href="#network_ui_bar_legend"
aria-expanded="false"
aria-controls="network_ui_bar_legend"
>
<i class="fa fa-question"></i>
</a>
</span>
</div>
</div>
</div>
</div>
</div>
<!-- Legend SVG -->
<div
class="row collapse"
id="network_ui_bar_legend"
style="margin-top: 0.1em"
data-hivtrace="cluster-clone"
>
<div class="well">
<span class="label label-primary">Clusters</span> are shown
as circles with thick rims
<svg
width="20"
height="20"
style="vertical-align: bottom; display: inline"
>
<circle cx="10" cy="10" r="7" class="cluster"></circle>
</svg>
with <em>area</em> proportional to the number of nodes in a
cluster. Click on clusters to show menu options, click and
drag to reposition.
<p></p>
<span class="label label-primary">Nodes</span> are shown as
different symbols (depending on rendering options), with
thin rims
<svg
width="20"
height="20"
style="vertical-align: bottom; display: inline"
>
<circle cx="10" cy="10" r="7" class="node"></circle></svg
>, and <em>area</em> scaling with the number of links.
<p></p>
Type in text to search for clusters and nodes whose
<em>attributes contain the term</em>. <br />
For example, typing in <code>MSM</code> will highlight nodes
and/or clusters that have 'MSM' in any of the data fields.
<br />
Type in space separated terms (<code>MSM IDU</code>) to
search for <b>either</b> term. <br />
Type in terms in quotes (<code>\"male\"</code>) will search
for this <b>exact</b> term. <br />
Type in <code><0.01</code> to search for nodes that have
edges which are 0.01 (1%) or shorter. Any positive threshold
works <br />
<p></p>
Matching node
<svg
width="20"
height="20"
style="vertical-align: bottom; display: inline"
>
<circle
cx="10"
cy="10"
r="7"
class="node selected_object"
></circle></svg
><br />
Cluster where 25% of nodes match the term
<svg
width="28"
height="28"
style="vertical-align: bottom; display: inline"
>
<circle cx="14" cy="14" r="8" class="cluster"></circle>
<path
d="M 2 14 A 12 12 0 0 1 14 2"
style="fill: none; stroke: #337ab7; stroke-width: 3px"
/></svg
><br />
Cluster where 75% of nodes match the term
<svg
width="28"
height="28"
style="vertical-align: bottom; display: inline"
>
<circle cx="14" cy="14" r="8" class="cluster"></circle>
<path
d="M 2 14 A 12 12 0 1 1 14 26"
style="fill: none; stroke: #337ab7; stroke-width: 3px"
/>
</svg>
<p></p>
Use the <code>Hide others</code> checkbox to automatically
hide all clusters/nodes that do not match the search terms
<br />
Use the <code>Show small clusters</code> checkbox to display
small clusters that may have been hidden for clarity
</div>
</div>
<div id="colorPickerOption">
<div id="colorPickerRow" class="row collapse"></div>
</div>
<!-- Main SVG -->
<div id="network_tag">
<div class="my_progress">
<div
class="progress-bar progress-bar-striped disabled"
role="progressbar"
aria-valuenow="100"
aria-valuemin="0"
aria-valuemax="100"
style="width: 100%; height: 50px"
>
Loading the network
</div>
</div>
</div>
</div>
</div>
</div>
<div id="trace-graph" class="tab-pane">
<div class="row">
<div class="col-lg-6">
<p class="lead">Network Statistics</p>
<table
class="table table-striped table-condensed table-responsive"
id="graph_summary_table"
></table>
</div>
<div class="col-lg-6">
<p id="histogram_label" class="lead"></p>
<div
class="row"
id="histogram_tag"
style="margin-left: 5px"
></div>
</div>
</div>
</div>
<div id="lanl-trace-results" class="tab-pane">
<div class="row" style="margin-top: 10px; margin-bottom: 10 px">
<div class="col-lg-12">
<div
class="alert alert-info"
id="lanl-main-warning"
style="display: none"
></div>
</div>
</div>
<div class="row">
<div class="col-lg-12">
<div class="row">
<div
class="input-group input-group-sm"
id="lanl_network_ui_bar"
>
<span class="input-group-btn">
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
id="lanl_network_ui_bar_cluster_operations_button"
>
Clusters <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
id="lanl_network_ui_bar_cluster_operations_container"
></ul>
</span>
<div class="input-group-btn">
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
id="lanl_network_ui_bar_attribute_label"
>
Attribute <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
id="lanl_network_ui_bar_attributes"
></ul>
</div>
<input
type="text"
class="form-control"
placeholder="search"
id="lanl_network_ui_bar_search"
/>
</div>
</div>
<div class="row" id="lanl-network_tag">
<div class="my_progress">
<div
class="progress-bar progress-bar-striped active"
role="progressbar"
aria-valuenow="100"
aria-valuemin="0"
aria-valuemax="100"
style="width: 100%"
>
Loading the network...
</div>
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-lg-9">
<p id="lanl-network_status_string" class="text-info"></p>
</div>
</div>
</div>
<div id="trace-clusters" class="tab-pane">
<div class="row">
<div class="col-lg-12">
<span class="pull-right" id="cluster-table-export"> </span>
<p class="lead">Clusters</p>
<table
class="table table-striped table-condensed table-hover"
id="cluster_table"
></table>
</div>
</div>
</div>
<div id="trace-subclusters" class="tab-pane">
<div class="row">
<div class="col-lg-12">
<span class="pull-right" id="subcluster-table-export"> </span>
<p class="lead">Subclusters</p>
<table
class="table table-striped table-condensed table-hover"
id="subcluster_table"
></table>
</div>
</div>
</div>
<div id="trace-nodes" class="tab-pane">
<div class="row">
<div class="col-lg-12">
<span class="pull-right" id="node-table-export"> </span>
<p class="lead">Linked individuals</p>
<table
class="table table-striped table-condensed table-hover"
id="node_table"
></table>
</div>
</div>
</div>
<div id="trace-attributes" class="tab-pane">
<div class="row">
<div class="nav-trace">
<div
class="input-group input-group-sm"
data-hivtrace-ui-role="attributes_container"
>
<span class="input-group-btn">
Categorical
<button
type="button"
class="btn btn-default dropdown-toggle"
data-toggle="dropdown"
data-hivtrace-ui-role="attributes_cat_label"
>
Attributes <span class="caret"></span>
</button>
<ul
class="dropdown-menu"
role="menu"
data-hivtrace-ui-role="attributes_cat"
></ul>
</span>
</div>
</div>
<div
class="col-lg-6"
data-hivtrace-ui-role="aux_svg_holder_enclosed"
style="display: none"
>
<div class="row">
<button
type="button"
class="btn btn-info"
id="network_pairwise_chord_legend"
>
<i class="fa fa-question"></i>
</button>
</div>
<div
data-hivtrace-ui-role="aux_svg_holder"
class="row style = margin-left: 5px"
></div>
</div>
<div
class="col-lg-6"
data-hivtrace-ui-role="attribute_table_enclosed"
style="display: none"
>
<div class="row">
<div class="col-lg-2">
<div class="input-group input-group-sm">
<span
class="input-group-addon"
id="network_pairwise_table_legend"
>
<i class="fa fa-question"></i>
</span>
<span class="input-group-addon">
<span id="show_as">Show as %</span>
<input
type="checkbox"
data-hivtrace-ui-role="pairwise_table_pecentage"
/>
</span>
</div>
</div>
</div>
<div class="row">
<table
class="table table-striped table-condensed table-hover"
data-hivtrace-ui-role="attribute_table"
></table>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<img class="hidden" id="hyphy-chart-image" />
<canvas class="hidden" id="hyphy-chart-canvas"></canvas>
<script src="dist/hivtrace.js"></script>
<!-- <script src="dist/hivtrace.es.js"></script> -->
<script>
var network_container = "#network_tag",
network_status_string = "#network_status_string",
network_warning = "#main-warning",
histogram_tag = "#histogram_tag",
histogram_label = "#histogram_label",
button_bar_prefix = "network_ui_bar",
csvexport_label = "#csvexport",
fasta_export_label = "#fasta-export",
filter_edges_toggle = "#network_ui_bar_toggle_filter_edges",
graph_summary_tag = "#graph_summary_table",
cluster_table = "#cluster_table",
subcluster_table = "#subcluster_table",
parent_container = "#top_level_tab_container",
node_table = "#node_table",
user_graph,
countryCenersObject = null,
countryOutlines = null;
function HandleAppError(err_string) {
$("#main-tab").tab("show");
d3.select("#app-error").text(err_string).style("display", null);
d3.select(parent_container).selectAll("li").classed("disabled", true);
d3.select(parent_container)
.selectAll("li")
.selectAll("a")
.each(function (d) {
d3.select(d3.select(this).attr("href")).style("display", "none");
});
}
var init = function (data) {
try {
var graph = "trace_results" in data ? data.trace_results : data;
var attributes = null;
user_graph = new hivtrace.clusterNetwork(
graph,
network_container,
network_status_string,
network_warning,
button_bar_prefix,
attributes,
filter_edges_toggle,
cluster_table,
node_table,
parent_container,
{
no_cdc: true,
"subcluster-table": subcluster_table,
//"country-centers": countryCentersObject,
//"country-outlines": countryOutlines,
seguro: true,
"subcluster-table": subcluster_table,
}
);
if (user_graph.is_empty()) {
HandleAppError(
"This network contains no clusters and cannot be displayed"
);
} else {
d3.select("#app-error").style("display", "none");
hivtrace.histogramDistances(graph, histogram_tag, histogram_label);
hivtrace.graphSummary(graph, graph_summary_tag);
[
"#main-tab",
"#graph-tab",
"#clusters-tab",
"#subclusters-tab",
"#nodes-tab",
"#attributes-tab",
].forEach(function (tab) {
d3.select(tab).classed("disabled", false);
});
d3.select(parent_container)
.selectAll("li")
.selectAll("a")
.each(function (d) {
d3.select(d3.select(this).attr("href")).style("display", null);
});
hivtrace.misc.export_table_to_text(
"#cluster-table-export",
cluster_table
);
hivtrace.misc.export_table_to_text(
"#subcluster-table-export",
subcluster_table
);
hivtrace.misc.export_table_to_text(
"#node-table-export",
node_table
);
$("#main-tab a[data-toggle='tab']").on(
"shown.bs.tab",
function (e) {
if (user_graph.needs_an_update) {
user_graph.update(false, 0.5);
}
}
);
$("#clusters-tab a[data-toggle='tab']").on(
"shown.bs.tab",
function (e) {
user_graph.update_volatile_elements(d3.select(cluster_table));
}
);
$("#nodes-tab a[data-toggle='tab']").on(
"shown.bs.tab",
function (e) {
user_graph.update_volatile_elements(d3.select(node_table));
}
);
if (data.lanl_trace_results > 0) {
// Only if the comparison was done
var lanl_network_container = "#lanl-network_tag",
lanl_network_status_string = "#lanl-network_status_string",
lanl_network_warning = "#lanl-main-warning",
lanl_histogram_tag = "#lanl-histogram_tag",
lanl_histogram_label = "#lanl-histogram_label",
lanl_csvexport_label = "#lanl-csvexport",
lanl_button_bar_prefix = "lanl_network_ui_bar";
d3.select("#lanl-trace-results").classed("disabled", false);
var lanl_graph = data.lanl_trace_results;
var lanl_graph_rendered = new hivtrace.clusterNetwork(
lanl_graph,
lanl_network_container,
lanl_network_status_string,
lanl_network_warning,
lanl_button_bar_prefix,
attributes,
filter_edges_toggle,
null,
null,
parent_container
);
}
}
document
.getElementById("min_cluster_size_input")
.setAttribute("placeholder", user_graph.minimum_cluster_size);
} catch (e) {
console.log(e);
HandleAppError(
"Network loading failed with the following error " + e
);
}
};
var initialize_cluster_network_graphs = function () {
//Initialize clusternetworkgraph with json url
url = "sample_data/example/example.json";
//url = "sample_data/example/vl_recent_value_adj.json";
//url = "sample_data/example/example_with_random_countries.json" // For testing the mapping feature.
//url = "sample_data/LA.json"
//url = "private/new.json";
d3.json(url, function (error, results) {
if (error) {
HandleAppError("Failed loading file " + error.responseURL);
} else {
init(results);
}
});
};
function in_progress() {
return $(".progress").length > 0;
}
$(document).ready(function () {
d3.json("./assets/mapping/outlines.json", function (error, outlines) {
countryOutlines = outlines;
d3.csv("./assets/mapping/country_centers.csv", function (data) {
countryCentersObject = {};
for (var i = 0; i < data.length; i++) {
let countryCode = data[i]["Alpha-2 code"];
let countryCodeNumeric = data[i]["Numeric code"];
countryCodeNumeric.length === 2
? (countryCodeNumeric = "0" + countryCodeNumeric)