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Commit 991519ba authored by Katja's avatar Katja
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save, self-cit, legend

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Output/bob/files.html deleted 100644 → 0
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<title>JsDoc Reference - File Index</title>
<meta name="generator" content="JsDoc Toolkit" />
<style type="text/css">
/* default.css */
body
{
font: 12px "Lucida Grande", Tahoma, Arial, Helvetica, sans-serif;
width: 800px;
}
.header
{
clear: both;
background-color: #ccc;
padding: 8px;
}
h1
{
font-size: 150%;
font-weight: bold;
padding: 0;
margin: 1em 0 0 .3em;
}
hr
{
border: none 0;
border-top: 1px solid #7F8FB1;
height: 1px;
}
pre.code
{
display: block;
padding: 8px;
border: 1px dashed #ccc;
}
#index
{
margin-top: 24px;
float: left;
width: 160px;
position: absolute;
left: 8px;
background-color: #F3F3F3;
padding: 8px;
}
#content
{
margin-left: 190px;
width: 600px;
}
.classList
{
list-style-type: none;
padding: 0;
margin: 0 0 0 8px;
font-family: arial, sans-serif;
font-size: 1em;
overflow: auto;
}
.classList li
{
padding: 0;
margin: 0 0 8px 0;
}
.summaryTable { width: 100%; }
h1.classTitle
{
font-size:170%;
line-height:130%;
}
h2 { font-size: 110%; }
caption, div.sectionTitle
{
background-color: #7F8FB1;
color: #fff;
font-size:130%;
text-align: left;
padding: 2px 6px 2px 6px;
border: 1px #7F8FB1 solid;
}
div.sectionTitle { margin-bottom: 8px; }
.summaryTable thead { display: none; }
.summaryTable td
{
vertical-align: top;
padding: 4px;
border-bottom: 1px #7F8FB1 solid;
border-right: 1px #7F8FB1 solid;
}
/*col#summaryAttributes {}*/
.summaryTable td.attributes
{
border-left: 1px #7F8FB1 solid;
width: 140px;
text-align: right;
}
td.attributes, .fixedFont
{
line-height: 15px;
color: #002EBE;
font-family: "Courier New",Courier,monospace;
font-size: 13px;
}
.summaryTable td.nameDescription
{
text-align: left;
font-size: 13px;
line-height: 15px;
}
.summaryTable td.nameDescription, .description
{
line-height: 15px;
padding: 4px;
padding-left: 4px;
}
.summaryTable { margin-bottom: 8px; }
ul.inheritsList
{
list-style: square;
margin-left: 20px;
padding-left: 0;
}
.detailList {
margin-left: 20px;
line-height: 15px;
}
.detailList dt { margin-left: 20px; }
.detailList .heading
{
font-weight: bold;
padding-bottom: 6px;
margin-left: 0;
}
.light, td.attributes, .light a:link, .light a:visited
{
color: #777;
font-style: italic;
}
.fineprint
{
text-align: right;
font-size: 10px;
}
</style>
</head>
<body>
<div id="header">
</div>
<div id="index">
<div align="center"><a href="index.html">Class Index</a>
| <a href="files.html">File Index</a></div>
<hr />
<h2>Classes</h2>
<ul class="classList">
<li><i><a href="symbols/_global_.html">_global_</a></i></li>
</ul>
<hr />
</div>
<div id="content">
<h1 class="classTitle">File Index</h1>
<div>
<h2><a href="symbols/src/cn.js.html">cn.js</a></h2>
<dl>
</dl>
</div>
<hr />
</div>
<div class="fineprint" style="clear:both">
Documentation generated by <a href="http://code.google.com/p/jsdoc-toolkit/" target="_blankt">JsDoc Toolkit</a> 2.4.0 on Tue Nov 23 2021 23:46:32 GMT+0100 (MEZ)
</div>
</body>
</html>
\ No newline at end of file
Output/bob/index.html deleted 100644 → 0
+ 0
− 210
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<title>JsDoc Reference - Index</title>
<meta name="generator" content="JsDoc Toolkit" />
<style type="text/css">
/* default.css */
body
{
font: 12px "Lucida Grande", Tahoma, Arial, Helvetica, sans-serif;
width: 800px;
}
.header
{
clear: both;
background-color: #ccc;
padding: 8px;
}
h1
{
font-size: 150%;
font-weight: bold;
padding: 0;
margin: 1em 0 0 .3em;
}
hr
{
border: none 0;
border-top: 1px solid #7F8FB1;
height: 1px;
}
pre.code
{
display: block;
padding: 8px;
border: 1px dashed #ccc;
}
#index
{
margin-top: 24px;
float: left;
width: 160px;
position: absolute;
left: 8px;
background-color: #F3F3F3;
padding: 8px;
}
#content
{
margin-left: 190px;
width: 600px;
}
.classList
{
list-style-type: none;
padding: 0;
margin: 0 0 0 8px;
font-family: arial, sans-serif;
font-size: 1em;
overflow: auto;
}
.classList li
{
padding: 0;
margin: 0 0 8px 0;
}
.summaryTable { width: 100%; }
h1.classTitle
{
font-size:170%;
line-height:130%;
}
h2 { font-size: 110%; }
caption, div.sectionTitle
{
background-color: #7F8FB1;
color: #fff;
font-size:130%;
text-align: left;
padding: 2px 6px 2px 6px;
border: 1px #7F8FB1 solid;
}
div.sectionTitle { margin-bottom: 8px; }
.summaryTable thead { display: none; }
.summaryTable td
{
vertical-align: top;
padding: 4px;
border-bottom: 1px #7F8FB1 solid;
border-right: 1px #7F8FB1 solid;
}
/*col#summaryAttributes {}*/
.summaryTable td.attributes
{
border-left: 1px #7F8FB1 solid;
width: 140px;
text-align: right;
}
td.attributes, .fixedFont
{
line-height: 15px;
color: #002EBE;
font-family: "Courier New",Courier,monospace;
font-size: 13px;
}
.summaryTable td.nameDescription
{
text-align: left;
font-size: 13px;
line-height: 15px;
}
.summaryTable td.nameDescription, .description
{
line-height: 15px;
padding: 4px;
padding-left: 4px;
}
.summaryTable { margin-bottom: 8px; }
ul.inheritsList
{
list-style: square;
margin-left: 20px;
padding-left: 0;
}
.detailList {
margin-left: 20px;
line-height: 15px;
}
.detailList dt { margin-left: 20px; }
.detailList .heading
{
font-weight: bold;
padding-bottom: 6px;
margin-left: 0;
}
.light, td.attributes, .light a:link, .light a:visited
{
color: #777;
font-style: italic;
}
.fineprint
{
text-align: right;
font-size: 10px;
}
</style>
</head>
<body>
<div id="header">
</div>
<div id="index">
<div align="center"><a href="index.html">Class Index</a>
| <a href="files.html">File Index</a></div>
<hr />
<h2>Classes</h2>
<ul class="classList">
<li><i><a href="symbols/_global_.html">_global_</a></i></li>
</ul>
<hr />
</div>
<div id="content">
<h1 class="classTitle">Class Index</h1>
<div>
<h2><a href="symbols/_global_.html">_global_</a></h2>
</div>
<hr />
</div>
<div class="fineprint" style="clear:both">
Documentation generated by <a href="http://code.google.com/p/jsdoc-toolkit/" target="_blankt">JsDoc Toolkit</a> 2.4.0 on Tue Nov 23 2021 23:46:32 GMT+0100 (MEZ)
</div>
</body>
</html>
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− 0
View file @ 991519ba
/**
* creates a new zoom behavior
*/
var zoom = d3.zoom().on("zoom", zoomHandler);
/**
* creates svg object and associated attributes
* applies the zoom behavior to svg
*/
var svg = d3.select("svg")
.call(zoom),
width = svg.attr("width"),
height = svg.attr("height");
/**
* creates node object and associated attributes
*/
var node,
r=10,
color = d3.scaleOrdinal()
.domain(["citing", "input", "cited"])
.range([' #01d7c0', ' #8b90fe ', ' #a15eb2 ']),
yscale = d3.scaleOrdinal()
.domain(["citing", "input", "cited"])
.range([0, 200, 400]),
toRemove;
/**
* creates link object
*/
/**
* creates a background
* creates a click functionality of the background
*/
var rect = svg.append("rect")
.attr("x", 0)
.attr("y", 0)
.attr("height", height)
.attr("width", width)
.style("fill", 'white')
.on('click', clickRect);
/**
* creates a new simulation
* updates the positions of the links and nodes when the
state of the layout has changed (simulation has advanced by a tick)
*/
var simulation = d3.forceSimulation()
.force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(100).strength(1))
.force("collide", d3.forceCollide(50))
.force("charge", d3.forceManyBody().strength(-30))
.force("center", d3.forceCenter(width/2, height/2))
.force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)}));
/**
* creates group element
*/
var g = svg.append("g")
.attr("class", "everything")
/**
* loads JSON data and calls the update function
*/
d3.json("json_text.json").then(function(graph) {
update(graph.links, graph.nodes);
})
/**
* calls update functions for links and nodes
* adds the nodes and links to the simulation
* @param {object} nodes - nodes
* @param {object} links - links
*/
function update(links, nodes) {
updateLinks(links);
updateNodes(nodes);
simulation
.nodes(nodes)
.on("tick", tickHandler);
simulation.force("link")
.links(links);
link.attr('marker-end', function(d) {return updateMarker("#999", d.target);})
.style("stroke-dasharray",function(d){return self_cit(d.source,d.target)? ("8,8"): ("1,0")});
}
var rect2 = svg.append("rect")
.attr("x", 0)
.attr("y", 0)
.attr("height", 180)
.attr("width", 210)
.style("fill", 'white');
legendposition=[70,110,150]
groupnames=["citing","input","cited"]
var legend = svg.selectAll(".legend")
.data(legendposition)
.enter()
.append("g")
.attr("class","legend")
.attr("transform", function(d) { return "translate(0," + d + ")"; });
legend.append("text")
.attr("x", 100)
.attr("y", 0)
.attr("dy", ".35em")
.style("text-anchor", "start")
.text(function(d){return groupnames[legendposition.indexOf(d)]});
legend.append("circle")
.attr("r", r)
.attr("cx",50-r)
.style("fill", color);
var legendarrow = svg.append("g")
.attr("class","legend")
.attr("transform","translate(20,20)");
legendarrow.append("line")
.attr("x1", 10)
.attr("x2", 50)
.attr("y1", 10)
.attr("y2", 10)
.style("stroke-dasharray","8,8")
.style("stroke", '#999')
.style("stroke-width", "1px")
.style('pointer-events', 'none')
.attr('marker-end',updateMarker('#999',this));
legendarrow.append("text")
.attr("x", 80)
.attr("y", 10)
.attr("dy", ".35em")
.style("text-anchor", "start")
.text("self-citation");
/**
* initializes and shows links
* @param {object} links - links
*/
function updateLinks(links) {
link = g.append("g")
.selectAll(".link")
.data(links)
.enter()
.append("line")
.style("stroke-width", "1px")
.style("stroke", "#999")
.attr("class", "link");
}
/**
* initializes and shows nodes with circles and texts
* creates a new drag behavior and applies it to the circles
* creates a click functionality of the circles and texts
* @param {object} nodes - nodes
*/
function updateNodes(nodes) {
node = g.selectAll(".node")
.data(nodes)
.enter()
.append("g")
.attr("class", "node")
.attr("initial_x", function(d) {return d.dx;})
.attr("initial_y", function(d) {return d.dy;})
.call(d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
);
node.append("circle")
.attr("class", "circle")
.attr("r", function(d) {return r+d.citations*0.1})
.style("fill", function(d){ return color(d.group)})
.on('click', clickNode);
node.append("text")
.attr("class", "text")
.style("font-size", "15px")
.style('pointer-events', 'auto')
.text(function (d) {return firstauthor(d.author);})
.on('click', clickNode);
}
/**
* creates arrowhead and returns its url
* @param {string} color - color of arrowhead
* @param {string} target - target-node
*/
function updateMarker(color, target) {
var radius = r+target.citations*0.1;
svg.append('defs').append('marker')//arrowhead
.attr('id',color.replace("#", "")+radius)
.attr('viewBox','-0 -5 10 10')
.attr('refX',radius+10)
.attr('refY',0)
.attr('orient','auto')
.attr('markerWidth',10)
.attr('markerHeight',15)
.attr('xoverflow','visible')
.append('svg:path')
.attr('d', 'M 0,-5 L 10 ,0 L 0,5')
.attr('fill', color)//arrowhead color
.style('stroke','none');
return "url(" + color + radius + ")";
};
/**
* colors the circle and its links black and removes the previous markings
* @param {object} node - node
*/
function clickNode(node) {
if(toRemove){
d3.select(toRemove).selectAll(".circle").style("stroke","none")
}
toRemove = this.parentNode;
d3.select(this.parentNode).selectAll(".circle").style("stroke","black")
marklink(node)
textfunc(node)
}
/**
* removes the markings of the circles and their links
*/
function clickRect() {
d3.selectAll(".circle").style("stroke", "none")
d3.selectAll(".link")
.style("stroke", "#999")
.attr('marker-end', function(d) {return updateMarker('#999', d.target);})
document.getElementById('textbox').innerHTML = "Click node";
}
function create_author_array(authors){
authorarray=authors.split(",")
authorarray=authorarray.map(elem =>{return elem.trim();})
return authorarray
}
function self_cit(source,target){
sourceauthors=create_author_array(source.author)
targetauthors=create_author_array(target.author)
return sourceauthors.some(item=>targetauthors.includes(item))
}
/**
* sets color of link (line and arrowhead) to black if it is directly connected to node
* and to grey otherwise
* @param {object} node - node
*/
function marklink(node){
d3.selectAll(".link")
.style("stroke", function(o) {
return isLinkForNode(node, o) ? "black" : "#999";})
.attr('marker-end', function(o) {
return isLinkForNode(node, o) ? updateMarker('#000000', o.target) : updateMarker('#999', o.target);})
}
/**
* returns true if link is directly connected to node and false if it is not
* @param {object} node - node
* @param {object} link - link
*/
function isLinkForNode(node, link){
return link.source.index == node.index || link.target.index == node.index;
}
/**
* returns last name of first author
* @param {string} authors - the comma-separated string of authors
*/
function firstauthor(authors){
if (/,/.test(authors)==false){
var firstauthor=/^.*\s+([\w\-]+)[\.\s]*$/.exec(authors)
}
else {
var firstauthor=/^[\s\w\.\-]*\s([\w\-]+)[\.\s]*,.*$/.exec(authors)
}
return firstauthor[1]
}
/**
* outputs node info to textbox
* @param {object} node - data of current node
*/
function textfunc(node){
document.getElementById('textbox').innerHTML = "Title:" + '</br>' + node.name +
'</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Year:"+'</br>'
+node.year+'</br>'+'</br>'+"doi:"+'</br>'+node.doi;
}
/**
* updates the positions of the links and nodes
*/
function tickHandler() {
link.attr("x1", function (d) {return d.source.x;})
.attr("y1", function (d) {return d.source.y;})
.attr("x2", function (d) {return d.target.x;})
.attr("y2", function (d) {return d.target.y;});
node.attr("transform", function (d) {return "translate(" + d.x + ", " + d.y + ")";});
}
/**
* initializes the dragging of the node
* @param {object} node - data of current node
*/
function dragstarted(node) {
if (!d3.event.active)
simulation.alphaTarget(0.3).restart()
node.fx = node.x;
node.fy = node.y;
}
/**
* applies the dragging to the node
* @param {object} node - data of current node
*/
function dragged(node) {
node.fx = d3.event.x;
node.fy = d3.event.y;
}
/**
* resets the positions of the nodes
*/
function resetGraph() {
d3.selectAll(".node").each(function(d) {
d.fx = d.initial_x;
d.fy = d.initial_y;
})
}
/**
* applies the transformation (zooming or dragging) to the g element
*/
function zoomHandler() {
d3.select('g').attr("transform", d3.event.transform);
}
/**
* transforms svg so that that the zoom is reset
*/
function resetZoom() {
d3.select('svg')
.call(zoom.scaleTo, 1);
}
/**
* transforms svg so that it is centered
*/
function center() {
d3.select('svg')
.call(zoom.translateTo, 0.5 * width, 0.5 * height);
}
function savesvg(){
var svgString = getSVGString(svg.node());
svgString2Image( svgString, 2*width, 2*height, 'png', save ); // passes Blob and filesize String to the callback
function save( dataBlob, filesize ){
saveAs( dataBlob, 'D3 vis exported to PNG.png' ); // FileSaver.js function
}
};
// Below are the functions that handle actual exporting:
// getSVGString ( svgNode ) and svgString2Image( svgString, width, height, format, callback )
function getSVGString( svgNode ) {
svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink');
var cssStyleText = getCSSStyles( svgNode );
appendCSS( cssStyleText, svgNode );
var serializer = new XMLSerializer();
var svgString = serializer.serializeToString(svgNode);
svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace
svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix
return svgString;
function getCSSStyles( parentElement ) {
var selectorTextArr = [];
// Add Parent element Id and Classes to the list
selectorTextArr.push( '#'+parentElement.id );
for (var c = 0; c < parentElement.classList.length; c++)
if ( !contains('.'+parentElement.classList[c], selectorTextArr) )
selectorTextArr.push( '.'+parentElement.classList[c] );
// Add Children element Ids and Classes to the list
var nodes = parentElement.getElementsByTagName("*");
for (var i = 0; i < nodes.length; i++) {
var id = nodes[i].id;
if ( !contains('#'+id, selectorTextArr) )
selectorTextArr.push( '#'+id );
var classes = nodes[i].classList;
for (var c = 0; c < classes.length; c++)
if ( !contains('.'+classes[c], selectorTextArr) )
selectorTextArr.push( '.'+classes[c] );
}
// Extract CSS Rules
var extractedCSSText = "";
for (var i = 0; i < document.styleSheets.length; i++) {
var s = document.styleSheets[i];
try {
if(!s.cssRules) continue;
} catch( e ) {
if(e.name !== 'SecurityError') throw e; // for Firefox
continue;
}
var cssRules = s.cssRules;
for (var r = 0; r < cssRules.length; r++) {
if ( contains( cssRules[r].selectorText, selectorTextArr ) )
extractedCSSText += cssRules[r].cssText;
}
}
return extractedCSSText;
function contains(str,arr) {
return arr.indexOf( str ) === -1 ? false : true;
}
}
function appendCSS( cssText, element ) {
var styleElement = document.createElement("style");
styleElement.setAttribute("type","text/css");
styleElement.innerHTML = cssText;
var refNode = element.hasChildNodes() ? element.children[0] : null;
element.insertBefore( styleElement, refNode );
}
}
function svgString2Image( svgString, width, height, format, callback ) {
var format = format ? format : 'png';
var imgsrc = 'data:image/svg+xml;base64,'+ btoa( unescape( encodeURIComponent( svgString ) ) ); // Convert SVG string to data URL
var canvas = document.createElement("canvas");
var context = canvas.getContext("2d");
canvas.width = width;
canvas.height = height;
var image = new Image();
image.onload = function() {
context.clearRect ( 0, 0, width, height );
context.drawImage(image, 0, 0, width, height);
canvas.toBlob( function(blob) {
var filesize = Math.round( blob.length/1024 ) + ' KB';
if ( callback ) callback( blob, filesize );
});
};
image.src = imgsrc;
}
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Output/index.html
+ 10
− 4
View file @ 991519ba
......@@ -18,6 +18,7 @@
right: 550px;
} */
/* textbox */
div {
width:270px;
......@@ -26,7 +27,7 @@
padding: 10px;
border: 1px solid #999;
position: absolute;
top: 20px;
top: 100px;
left: 980px;
display: inline-block;
overflow-y: scroll;
......@@ -40,20 +41,25 @@
<p id="id"></p> <!--for commenting with document.getElementById("id").innerHTML = "text"; -->
<!-- graph -->
<svg width="960" height="600"></svg>
<svg width="960" height="500" ></svg>
<!-- textbox -->
<div id = "textbox" style="border:1px solid" >Click node</div>
<!-- reset-buttons -->
<button onclick="javascript:location.reload();">Reload</button>
<button onclick="resetGraph()">Reset graph</button>
<button onclick="resetZoom()">Reset zoom</button>
<button onclick="center()">Center</button>
<button onclick="savesvg()">Save</button>
<!-- link D3 (version 5) -->
<script src="https://d3js.org/d3.v5.min.js"></script>
<script type="text/javascript" src="cn.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3-legend/2.13.0/d3-legend.js"></script>
<script src="https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js"></script>
<script src="https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js"></script>
<script type="text/javascript" src="cn_26_11_1.js"></script>
</body>
</html>
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Output/json_text.json
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View file @ 6f060a66
# Projekt CiS-Biochemie 2021-22
Automated citation loop finder for ACS articles.
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