From 0fb873c3bb4585582627a19564cba3fb924a149d Mon Sep 17 00:00:00 2001
From: Merle Stahl <merle.stahl@studium.uni-hamburg.de>
Date: Tue, 14 Dec 2021 21:01:02 +0100
Subject: [PATCH] =?UTF-8?q?aufger=C3=A4umt?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
Output.zip | Bin 18182 -> 0 bytes
Output/Graph/json_text.json | 437 -------------
Output/Graph/json_text_version1.json | 437 -------------
Output/Graph/json_text_version2.json | 437 -------------
Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js | 582 ------------------
Output/Graph_mit_Zeitstrahl/index.html | 107 ----
Output/Graph_mit_Zeitstrahl/index_alt.html | 59 --
Output/Graph_mit_Zeitstrahl/json_text.json | 437 -------------
Output/README.md | 50 ++
Output/ToDo.txt | 23 -
Output/{Graph => graph}/cn.js | 118 ++--
Output/{Graph => graph}/index.html | 34 +-
.../json_text.json} | 0
13 files changed, 105 insertions(+), 2616 deletions(-)
delete mode 100644 Output.zip
delete mode 100644 Output/Graph/json_text.json
delete mode 100644 Output/Graph/json_text_version1.json
delete mode 100644 Output/Graph/json_text_version2.json
delete mode 100644 Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
delete mode 100644 Output/Graph_mit_Zeitstrahl/index.html
delete mode 100644 Output/Graph_mit_Zeitstrahl/index_alt.html
delete mode 100644 Output/Graph_mit_Zeitstrahl/json_text.json
create mode 100644 Output/README.md
delete mode 100644 Output/ToDo.txt
rename Output/{Graph => graph}/cn.js (86%)
rename Output/{Graph => graph}/index.html (79%)
rename Output/{Graph/json_with_citations.json => graph/json_text.json} (100%)
diff --git a/Output.zip b/Output.zip
deleted file mode 100644
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- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.8b00312",
- "target": "https://doi.org/10.1021/ci300604z"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/ci700036j"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.9b00557",
- "target": "https://doi.org/10.1021/ci700036j"
- },
- {
- "source": "https://doi.org/10.1021/ci500209e",
- "target": "https://doi.org/10.1021/ci700036j"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/ci500209e"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/jm2005145"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.8b00312",
- "target": "https://doi.org/10.1021/jm2005145"
- },
- {
- "source": "https://doi.org/10.1021/ci500209e",
- "target": "https://doi.org/10.1021/jm2005145"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.9b00778",
- "target": "https://doi.org/10.1021/acs.jcim.8b00312"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/acs.jcim.9b00778"
- }
- ]
-}
\ No newline at end of file
diff --git a/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js b/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
deleted file mode 100644
index 95d2792..0000000
--- a/Output/Graph_mit_Zeitstrahl/cn_Zeitstrahl.js
+++ /dev/null
@@ -1,582 +0,0 @@
-/**
-* 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");
-var textinfo='';
-var textabstract='';
-
-/**
-* 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, 250, 500]),
-linetype=d3.scaleOrdinal()
- .domain(["line","dotted"])
- .range([("8,0"),("8,8")]),
-toRemove;
-
-/**
-* creates link object
-*/
-var link;
-
-/**
-* 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 svg object (legend) and associated attributes
-*/
-var svglegend = d3.select("svg.legendsvg"),
-legendposition = [65,95,125],
-arrowlegendposition = [0,25],
-arrowgroupnames = ["citation","self-citation"],
-groupnames = ["citing","input","cited"];
-
-var legend = svglegend.selectAll(".legend")
- .data(legendposition)
- .enter()
- .append("g")
- .attr("class","legend")
- .attr("transform", function(d,i) {return "translate(0," + d + ")"; });
-
-legend.append("text")
- .attr("x", 80)
- .attr("y", 0)
- .attr("dy", ".35em")
- .style("text-anchor", "start")
- .text(function(d,i){return groupnames[i]});
-
-legend.append("circle")
- .attr("r", r)
- .attr("cx",30-r)
- .style("fill", color);
-
-var legendarrow = svglegend.selectAll(".legendarr")
- .data(arrowlegendposition)
- .enter()
- .append("g")
- .attr("class","legendarr")
- .attr("transform", function(d) { return "translate(0," + d + ")"; });
-
-legendarrow.append("line")
- .attr("x1", 10)
- .attr("x2", 50)
- .attr("y1", 10)
- .attr("y2", 10)
- .style("stroke-dasharray",linetype)
- .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(function(d,i){return arrowgroupnames[i]});
-
-/**
-* creates a new simulation
-* arranges the nodes according to their group on the y-axis
-*/
-var simulation = d3.forceSimulation()
- .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(60))
- .force("collide", d3.forceCollide(50))
- //.force("manyBody", d3.forceManyBody())
- .force("charge", d3.forceManyBody())
- .force("center", d3.forceCenter(width/2, height/2))
- //.force("xscale", d3.forceX().strength(1).x(function(d) {return xscale(parseInt(d.year))}))
- .alpha(0.1)
- //.alphaDecay(0)
- //.force("yscale", d3.forceY().strength(0.5).y(function(d) {return yscale(d.group)}));
-
-/**
-* creates group element
-*/
-var g = svg.append("g")
- .attr("class", "everything")
-
-/**
-* creates xAxis element
-*/
-var xAxis = d3.axisBottom()
- .tickFormat(function(d) {return d;})
- .ticks(10);;
-
-/**
-* draw xAxis
-*/
-var gX = svg.append("g")
- .attr("class", "axis axis--x")
- .attr("transform", "translate(0,25)")
- gX.append("text")
- .attr("y", 0)
- .attr("x", 80)
- .attr("text-anchor", "end")
- .attr("stroke", "black")
- .text("year");
-
-/**
-* 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 xAxis, links and nodes
-* adds the nodes and links to the simulation
-* updates the positions of the links and nodes when the
- state of the layout has changed (simulation has advanced by a tick)
-* @param {object} nodes - nodes
-* @param {object} links - links
-*/
-function update(links, nodes) { //THISS
- updateXAxis(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")});
-}
-
-/**
-* initializes and shows xAxis THISS
-* @param {object} nodes - nodes
-*/
-function updateXAxis(nodes) {
- years = [];
- for (i = 0; i < nodes.length; i++) {
- years.push(parseInt((nodes[i]["year"]).split(" ")[2]));
- }
-
- console.log(years)
- xscale = d3.scaleLinear()
- .domain([d3.min(years)-10, d3.max(years)+10])
- .range([50, width-50])
-
- xAxis.scale(xscale);
- gX.call(xAxis);
-}
-
-/**
-* 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('dx', function(d) {return xscale(parseInt((d.year).split(" ")[2]))})
- .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)
- .on("end", dragended)
- );
-
- node.append("circle")
- .attr("class", "circle")
- .attr("r", function(d) {return 1.5*r+d.citations*0.05})
- .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) {
- const firstauthor = d.author[0].split(" ")
- return firstauthor[firstauthor.length-1];
- })
- .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=1.5*r+target.citations*0.05
- svg.append('defs').append('marker')//arrowhead
- .attr('id',color.replace("#", "")+radius)
- .attr('viewBox','-0 -5 10 10')
- .attr('refX',radius+9.5)
- .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)
- resetbuttonhighlight()
- highlightbutton("overview")
- fix_nodes(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";
- fix_nodes(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 source.author.some(item=>target.author.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){
- textinfo="Title:" + '</br>' + node.name +
- '</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Year:"+'</br>'
- +node.year+'</br>'+'</br>'+"doi:"+'</br>'+'<a href="'+node.doi+ '">'+node.doi
- +'</a>'+'</br>'+'</br>'+"Citations:"+'</br>'+node.citations;
- textabstract=node.abstract;
- document.getElementById('textbox').innerHTML = textinfo;
-}
-
-
-function highlightbutton(btn){
- resetbuttonhighlight();
- document.getElementById(btn).style.background="#DCDCDC";
-}
-function resetbuttonhighlight(){
- document.getElementById("overview").style.background='';
- document.getElementById("abstract").style.background='';
-}
-
-function displayabstract(a){
- if(textabstract=='' && textinfo==''){
- document.getElementById('textbox').innerHTML="Click node";
- }
- else{
- if (a==true){
- document.getElementById('textbox').innerHTML =textabstract;
- }
- else{
- document.getElementById('textbox').innerHTML =textinfo;
- }
- }
-}
-
-
-/**
-* updates the positions of the links and nodes
-*/
-function tickHandler() {
- link.attr("x1", function (d) {return xscale(parseInt((d.source.year).split(" ")[2]));})
- .attr("y1", function (d) {return d.source.y;})
- .attr("x2", function (d) {return xscale(parseInt((d.target.year).split(" ")[2]));})
- .attr("y2", function (d) {return d.target.y;});
- node.attr("transform", function (d) {return "translate(" + xscale(parseInt((d.year).split(" ")[2])) + ", " + 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;
- fix_nodes(node);
-}
-
-/**
-* 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;
- fix_nodes(node);
-}
-function fix_nodes(this_node) {
- node.each(function(d) {
- if (this_node != d) {
- d.fx = d.x;
- d.fy = d.y;
- }
- });
- }
-
-/**
-* ends the dragging and resets the position of the node
-* @param {object} node - data of current node
-*/
-function dragended(node) {
- if (!d3.event.active) simulation.alphaTarget(.03);
- node.fx = null;
- //node.fy = null;
-}
-
-/**
-* 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);
- var new_xScale = d3.event.transform.rescaleX(xscale)
- gX.call(xAxis.scale(new_xScale));
-}
-
-/**
-* 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(d3.select("svg.legendsvg").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;
-}
\ No newline at end of file
diff --git a/Output/Graph_mit_Zeitstrahl/index.html b/Output/Graph_mit_Zeitstrahl/index.html
deleted file mode 100644
index ac85e8f..0000000
--- a/Output/Graph_mit_Zeitstrahl/index.html
+++ /dev/null
@@ -1,107 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
- <meta charset="utf-8">
-
- <style type="text/css">
- button {
- width: 100px;
- height:20px;
- display: flex;
- justify-content: center;
- position: absolute;
- left: 430px;
- top: 575px;
- }
-
- button.resetGraph {}
-
- button.resetZoom {
- margin-left: 110px;
- }
-
- button.center {
- margin-left: 220px;
- }
-
- button.save{
- margin-left: 330px;
- }
- button.abstract{
- width:146px;
- position:absolute;
- top: 181px;
- left: 1114px;
- border-radius:0;
- border:1px solid #909090;
- }
- button.overview{
- width:147px;
- position:absolute;
- display:inline-block;
- top: 181px;
- left: 968px;
- border-radius:0;
- border:1px solid #909090;
- }
-
- div.legendbox {
- width:270px;
- height:170px;
- padding: 10px;
- /*border: 1px solid #999;*/
- position: absolute;
- top: 10px;
- left: 968px;
- display: inline-block;
- margin: 0;
- }
-
- div.textbox{
- width:270px;
- min-height:200px;
- max-height:370px;
- padding: 10px;
- border: 1px solid #999;
- position: absolute;
- top: 200px;
- left: 968px;
- display: inline-block;
- overflow-y: scroll;
- margin: 0;
- }
- </style>
-</head>
-
-<body>
- <!-- for testing -->
- <p id="id"></p> <!--for commenting with document.getElementById("id").innerHTML = "text"; -->
-
- <!-- graph -->
- <svg class="graph" width="960" height="560"></svg>
-
- <!-- legend -->
- <div class="legendbox"> <svg class="legendsvg"></svg></div>
-
- <!-- textbox -->
- <div class="textbox" id = "textbox">Click node</div>
-
- <!-- reset buttons -->
- <!-- <button onclick="javascript:location.reload();">Reload</button>-->
- <button class="resetGraph" onclick="resetGraph()">Reset graph</button>
- <button class="resetZoom" onclick="resetZoom()">Reset zoom</button>
- <button class="center" onclick="center()">Center</button>
- <button class="save" onclick="savesvg()">Save</button>
- <button id="overview" class="overview" onclick='displayabstract(false),highlightbutton("overview")'>Overview</button>
- <button id="abstract" class="abstract" onclick='displayabstract(true),highlightbutton("abstract")'>Abstract</button>
-
-
- <!-- link D3 (version 5) -->
- <script src="https://d3js.org/d3.v5.min.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_Zeitstrahl.js"></script>
-
-</body>
-</html>
\ No newline at end of file
diff --git a/Output/Graph_mit_Zeitstrahl/index_alt.html b/Output/Graph_mit_Zeitstrahl/index_alt.html
deleted file mode 100644
index 9cdd0bd..0000000
--- a/Output/Graph_mit_Zeitstrahl/index_alt.html
+++ /dev/null
@@ -1,59 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
- <meta charset="utf-8">
-
- <style type="text/css">
- /*
- button {
- width: 150px;
- font-size: 15px;
- padding: 7px;
- border-radius: 3px;
- border: 3px solid #999;
- color: black;
- cursor: pointer;
- position : absolute;
- top: 500px;
- right: 550px;
- } */
-
- /* textbox */
- div {
- width:270px;
- min-height:200px;
- max-height:370px;
- padding: 10px;
- border: 1px solid #999;
- position: absolute;
- top: 20px;
- left: 980px;
- display: inline-block;
- overflow-y: scroll;
- margin: 0;
- }
- </style>
-</head>
-
-<body>
- <!-- for testing -->
- <p id="id"></p> <!--for commenting with document.getElementById("id").innerHTML = "text"; -->
-
- <!-- graph -->
- <svg width="960" height="600"></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>
-
- <!-- link D3 (version 5) -->
- <script src="https://d3js.org/d3.v5.min.js"></script>
- <script type="text/javascript" src="cn_Zeitstrahl.js"></script>
-
-</body>
-</html>
\ No newline at end of file
diff --git a/Output/Graph_mit_Zeitstrahl/json_text.json b/Output/Graph_mit_Zeitstrahl/json_text.json
deleted file mode 100644
index 35b5f89..0000000
--- a/Output/Graph_mit_Zeitstrahl/json_text.json
+++ /dev/null
@@ -1,437 +0,0 @@
-{
- "nodes": [
- {
- "name": "AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings",
- "author": [
- "Jerome Eberhardt",
- "Diogo Santos-Martins",
- "Andreas F. Tillack",
- "Stefano Forli"
- ],
- "year": "July 19, 2021",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/acs.jcim.1c00203",
- "group": "input",
- "citations":20
- },
- {
- "name": "Accelerating AutoDock4 with GPUs and Gradient-Based Local Search",
- "author": [
- "Diogo Santos-Martins",
- "Leonardo Solis-Vasquez",
- "Andreas F Tillack",
- "Michel F Sanner",
- "Andreas Koch",
- "Stefano Forli"
- ],
- "year": "January 6, 2021",
- "journal": "Journal of Chemical Theory and Computation",
- "doi": "https://doi.org/10.1021/acs.jctc.0c01006",
- "group": "depth",
- "citations":21
- },
- {
- "name": "Docking Flexible Cyclic Peptides with AutoDock CrankPep",
- "author": [
- "Yuqi Zhang",
- "Michel F. Sanner"
- ],
- "year": "September 11, 2019",
- "journal": "Journal of Chemical Theory and Computation",
- "doi": "https://doi.org/10.1021/acs.jctc.9b00557",
- "group": "depth",
- "citations":40
- },
- {
- "name": "Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise",
- "author": [
- "David Ryan Koes",
- "Matthew P. Baumgartner",
- "Carlos J. Camacho"
- ],
- "year": "February 4, 2013",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/ci300604z",
- "group": "depth",
- "citations":80
- },
- {
- "name": "Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking",
- "author": [
- "Anita K. Nivedha",
- "David F. Thieker",
- "Spandana Makeneni",
- "Huimin Hu",
- "Andreas F Tillack",
- "Robert J. Woods"
- ],
- "year": "January 8, 2016",
- "journal": "Journal of Chemical Theory and Computation",
- "doi": "https://doi.org/10.1021/acs.jctc.5b00834",
- "group": "depth",
- "citations":100
- },
- {
- "name": "Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems",
- "author": [
- "Stefano Forli",
- "Maurizio Botta"
- ],
- "year": "June 22, 2007",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/ci700036j",
- "group": "depth",
- "citations":150
- },
- {
- "name": "AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins",
- "author": [
- "Diogo Santos-Martins",
- "Stefano Forli",
- "Maria Jo\u00e3o Ramos",
- "Arthur J. Olson"
- ],
- "year": "June 15, 2014",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/ci500209e",
- "group": "depth",
- "citations":100
- },
- {
- "name": "A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking",
- "author": [
- "Stefano Forli",
- "Arthur J. Olson"
- ],
- "year": "December 9, 2011",
- "journal": "Journal of Medicinal Chemistry",
- "doi": "https://doi.org/10.1021/jm2005145",
- "group": "depth",
- "citations":500
- },
- {
- "name": "Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context",
- "author": [
- "Douglas R. Houston",
- "Malcolm D. Walkinshaw"
- ],
- "year": "January 27, 2013",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/ci300399w",
- "group": "depth",
- "citations":200
- },
- {
- "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory",
- "author": [
- "Themis Lazaridis"
- ],
- "year": "April 14, 1998",
- "journal": "Journal of Physical Chemistry B",
- "doi": "https://doi.org/10.1021/jp9723574",
- "group": "depth",
- "citations":80
- },
- {
- "name": "Inhomogeneous Fluid Approach to Solvation Thermodynamics. 2. Applications to Simple Fluids",
- "author": [
- "Themis Lazaridis",
- "Andreas F Tillack"
- ],
- "year": "April 14, 1998",
- "journal": "Journal of Physical Chemistry B",
- "doi": "https://doi.org/10.1021/jp972358w",
- "group": "depth",
- "citations":110
- },
- {
- "name": "ZINC20\u2014A Free Ultralarge-Scale Chemical Database for Ligand Discovery",
- "author": [
- "John J. Irwin",
- "Khanh G. Tang",
- "Jennifer Young",
- "Chinzorig Dandarchuluun",
- "Benjamin R. Wong",
- "Munkhzul Khurelbaatar",
- "Yurii S. Moroz",
- "John Mayfield",
- "Roger A. Sayle"
- ],
- "year": "October 29, 2020",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/acs.jcim.0c00675",
- "group": "depth",
- "citations":270
- },
- {
- "name": "Structural Biology-Inspired Discovery of Novel KRAS\u2013PDE\u03b4 Inhibitors",
- "author": [
- "Yan Jiang",
- "Chunlin Zhuang",
- "Long Chen",
- "Junjie Lu",
- "Guoqiang Dong",
- "Zhenyuan Miao",
- "Wannian Zhang",
- "Jian Li",
- "Chunquan Sheng"
- ],
- "year": "September 20, 2017",
- "journal": "Journal of Medicinal Chemistry",
- "doi": "https://doi.org/10.1021/acs.jmedchem.7b01243",
- "group": "depth",
- "citations":70
- },
- {
- "name": "Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking",
- "author": [
- "Michael M. Mysinger",
- "Michael Carchia",
- "John. J. Irwin",
- "Brian K. Shoichet"
- ],
- "year": "June 20, 2012",
- "journal": "Journal of Medicinal Chemistry",
- "doi": "https://doi.org/10.1021/jm300687e",
- "group": "depth",
- "citations":400
- },
- {
- "name": "Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark",
- "author": [
- "Thomas Gaillard"
- ],
- "year": "July 10, 2018",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/acs.jcim.8b00312",
- "group": "depth",
- "citations":310
- },
- {
- "name": "Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity",
- "author": [
- "Nguyen Thanh Nguyen",
- "Trung Hai Nguyen",
- "T. Ngoc Han Pham",
- "Nguyen Truong Huy",
- "Mai Van Bay",
- "Minh Quan Pham",
- "Pham Cam Nam",
- "Van V. Vu",
- "Son Tung Ngo"
- ],
- "year": "December 30, 2019",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/acs.jcim.9b00778",
- "group": "depth",
- "citations":170
- },
- {
- "name": "Glide:\u2009 A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy",
- "author": [
- "Richard A. Friesner",
- "Jay L. Banks",
- "Robert B. Murphy",
- "Thomas A. Halgren",
- "Jasna J. Klicic",
- "Daniel T. Mainz",
- "Matthew P. Repasky",
- "Eric H. Knoll",
- "Mee Shelley",
- "Jason K. Perry",
- "David E. Shaw",
- "Perry Francis",
- "Peter S. Shenkin"
- ],
- "year": "February 27, 2004",
- "journal": "Journal of Medicinal Chemistry",
- "doi": "https://doi.org/10.1021/jm0306430",
- "group": "depth",
- "citations":130
- },
- {
- "name": "Surflex:\u2009 Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine",
- "author": [
- "Ajay N. Jain"
- ],
- "year": "January 21, 2003",
- "journal": "Journal of Medicinal Chemistry",
- "doi": "https://doi.org/10.1021/jm020406h",
- "group": "depth",
- "citations":86
- },
- {
- "name": "ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein\u2013Ligand Interactions",
- "author": [
- "Guo-Bo Li",
- "Ling-Ling Yang",
- "Wen-Jing Wang",
- "Lin-Li Li",
- "Sheng-Yong Yang"
- ],
- "year": "February 9, 2013",
- "journal": "Journal of Chemical Information and Modeling",
- "doi": "https://doi.org/10.1021/ci300493w",
- "group": "depth",
- "citations":20
- },
- {
- "name": "A Knowledge-Based Energy Function for Protein\u2212Ligand, Protein\u2212Protein, and Protein\u2212DNA Complexes",
- "author": [
- "Chi Zhang",
- "Song Liu",
- "Qianqian Zhu",
- "Yaoqi Zhou"
- ],
- "year": "February 16, 2005",
- "journal": "Journal of Medicinal Chemistry",
- "doi": "https://doi.org/10.1021/jm049314d",
- "group": "depth",
- "citations":39
- },
- {
- "name": "Novel Anti-Hepatitis B Virus Activity of Euphorbia schimperi and Its Quercetin and Kaempferol Derivatives",
- "author": [
- "Mohammad K. Parvez",
- "Sarfaraz Ahmed",
- "Mohammed S. Al-Dosari",
- "Mazin A. S. Abdelwahid",
- "Ahmed H. Arbab",
- "Stefano Forli",
- "Adnan J. Al-Rehaily",
- "Mai M. Al-Oqail"
- ],
- "year": "October 21, 2021",
- "journal": "ACS Omega",
- "doi": "https://doi.org/10.1021/acsomega.1c04320",
- "group": "height",
- "citations":180
- }
- ],
- "links": [
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/acs.jctc.0c01006"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/acs.jctc.9b00557"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/ci300604z"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/acs.jctc.5b00834"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/ci700036j"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/ci500209e"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/jm2005145"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/ci300399w"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/ci300399w"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/jp9723574"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/jp972358w"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/acs.jcim.0c00675"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/acs.jmedchem.7b01243"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/jm300687e"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/acs.jcim.8b00312"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/acs.jcim.9b00778"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/jm0306430"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/jm020406h"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/ci300493w"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.1c00203",
- "target": "https://doi.org/10.1021/jm049314d"
- },
- {
- "source": "https://doi.org/10.1021/acsomega.1c04320",
- "target": "https://doi.org/10.1021/acs.jcim.1c00203"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.8b00312",
- "target": "https://doi.org/10.1021/ci300604z"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/ci700036j"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.9b00557",
- "target": "https://doi.org/10.1021/ci700036j"
- },
- {
- "source": "https://doi.org/10.1021/ci500209e",
- "target": "https://doi.org/10.1021/ci700036j"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/ci500209e"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/jm2005145"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.8b00312",
- "target": "https://doi.org/10.1021/jm2005145"
- },
- {
- "source": "https://doi.org/10.1021/ci500209e",
- "target": "https://doi.org/10.1021/jm2005145"
- },
- {
- "source": "https://doi.org/10.1021/acs.jcim.9b00778",
- "target": "https://doi.org/10.1021/acs.jcim.8b00312"
- },
- {
- "source": "https://doi.org/10.1021/acs.jctc.0c01006",
- "target": "https://doi.org/10.1021/acs.jcim.9b00778"
- }
- ]
-}
\ No newline at end of file
diff --git a/Output/README.md b/Output/README.md
new file mode 100644
index 0000000..a1dcced
--- /dev/null
+++ b/Output/README.md
@@ -0,0 +1,50 @@
+# Projekt CiS-Projekt 2021/22
+
+Citation Network
+
+## Usage
+Input: Json-Datei json\_text.json in directory graph
+```json
+{
+ "nodes": [
+ {
+ "name": <title: string>,
+ "author": [<author1: string>, <author2: string>, ...],
+ "year": <date: tring>,
+ "journal": <journal: string>,
+ "doi": <doi: string>,
+ "group": <"input"/"height"/"depth">,
+ "citations": <citation: int>
+ }, ...
+ ],
+ "links": [
+ {
+ "source": <doi: string>,
+ "target": <doi: string>
+ }, ...
+ ]
+}
+```
+
+Starting a Python-HTTP Server:
+```sh
+ cd <path to file> &&python3 -m http.server <port>
+```
+
+Opening Server:
+[http://0.0.0.0/:\<port\>](http://0.0.0.0/:<port>)
+
+## Files in directory:
+
+### index.html
+webpage
+
+### cn.js
+javascript code for force-directed graph, text elements and legend
+
+### json_with_citations.json
+example data
+
+## Authors
+- Katja Ehlers
+- Merle Stahl
\ No newline at end of file
diff --git a/Output/ToDo.txt b/Output/ToDo.txt
deleted file mode 100644
index e4905e4..0000000
--- a/Output/ToDo.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-Erledigt:
-- Graphstruktur mit Knoten und Kanten (+ Schnittstelle mit Verarbeitung (Json))
-- 3 senkrechte Schichten für Input, Citing und Cited (+ Farben)
-- Legende
-- Knotengröße nach Zitierungsanzahl
-- Markierung der Selbstzitierung
-- Zoom- und Schiebefunktionen des gesamten Graphen
-- Schiebefunktionen der einzelnen Knoten
-- Hervorhebung von Knoten und deren verbundenen Kanten auf Klick (Knoten oder Beschriftung)
-- Informationsfenster für Knoten auf Klick (Knoten oder Beschriftung)
--> Zurücksetzen auf Klick (Hintergrund)
-- Knopf zum Zurücksetzen der verschobenen Knoten
-- Knopf zum Zurücksetzen des verschobenen Graphen (Zentrieren)
-- Knopf zum Zurücksetzen der Zoom-Funktion
-- Zeitstrahl auf x-Achse
-
-Noch offen:
-- Skalierung an unterschiedliche Geräte anpassen
-- Schnittstelle zu Benutzeroberfläche (!)
- - Suchfunktion
- - Informationen zu Funktionen anzeigen
- - Zeitstrahl auf x-Achse (optional)
-- Speicherfunktion
diff --git a/Output/Graph/cn.js b/Output/graph/cn.js
similarity index 86%
rename from Output/Graph/cn.js
rename to Output/graph/cn.js
index ae6d127..452a8a2 100644
--- a/Output/Graph/cn.js
+++ b/Output/graph/cn.js
@@ -14,6 +14,7 @@ height = svg.attr("height");
var textinfo='';
var textabstract='';
var perc;
+
/**
* creates node object and associated attributes
*/
@@ -106,32 +107,22 @@ legendarrow.append("text")
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(50).strength(function(d){
- if (d.group == "input") {return 0;}
- else {return 5;}
- }))
- .force("collide", d3.forceCollide(function(d){
- if (d.group == "input") {return 100;}
- else {return 65;}
- }).strength(0.5))
+ .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(50).strength(function(d) {
+ if (d.group == "input") {return 0;}
+ else {return 5;}
+ }))
+ .force("collide", d3.forceCollide(function(d) {
+ if (d.group == "input") {return 100;}
+ else {return 65;}
+ }).strength(0.5))
.force("charge", d3.forceManyBody().strength(0.001))
.force("center", d3.forceCenter(width/2, height/2+20))
- //.force("yscale", d3.forceY().strength(150).y(function(d) {return yscale(d.group)}))
- .force("yscale", d3.forceY().strength(function(d){
+ .force("yscale", d3.forceY().strength(function(d) {
if (d.group == "input") {return 1000;}
else {return 50;}
}).y(function(d) {return yscale(d.group)}))
.alpha(0.005)
.on("end", zoomTo);
-/*
-var simulation = d3.forceSimulation()
- .force("link", d3.forceLink().id(function(d) {return d.doi;}).distance(200))
- .force("collide", d3.forceCollide(50).strength(0.5))
- .force("charge", d3.forceManyBody())
- .force("center", d3.forceCenter(width/2, height/2+20))
- .force("yscale", d3.forceY().strength(1).y(function(d) {return yscale(d.group)}))
- .alpha(0.1)
- .on("end", zoomTo,ahaa);*/
/**
* creates group element
@@ -142,7 +133,7 @@ var g = svg.append("g")
/**
* loads JSON data and calls the update function
*/
-d3.json("json_with_citations.json").then(function(graph) {
+d3.json("json_text.json").then(function(graph) {
update(graph.links, graph.nodes);
})
@@ -164,33 +155,7 @@ function update(links, nodes) {
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")});
-
}
-function ahaa(){
- d3.selectAll(".node").attr("initial_x", function(d) {return d.dx;})
- .attr("initial_y", function(d) {return d.dy;})
-
-}
-
-
-function zoomTo() {
- node_bounds = d3.selectAll("svg.graph").node().getBBox();
- svg_bounds = d3.select("rect").node().getBBox();
- //console.log(node_bounds, svg_bounds)
-
- //var diff_x = Math.abs(node_bounds.x)+Math.abs(node_bounds.width);
- perc_x = width/(node_bounds.width+100);
-
- //var diff_y = Math.abs(node_bounds.y)+Math.abs(node_bounds.height);
- perc_y = height/(node_bounds.height+100);
-
- perc = d3.min([perc_x, perc_y])
- //console.log(perc_x, perc)
- d3.select('svg')
- .call(zoom.scaleBy, perc);
-}
-
-
/**
* initializes and shows links
@@ -219,8 +184,6 @@ function updateNodes(nodes) {
.enter()
.append("g")
.attr("class", "node")
- //.attr("abs_x", function(d) {return parseInt(d.attr("cx")) + d[0][0].getCTM().e})
- //.attr("abs_y", function(d) {return parseInt(d.attr("cy")) + d[0][0].getCTM().f})
.call(d3.drag()
.on("start", dragstarted)
.on("drag", dragged)
@@ -334,7 +297,7 @@ function isLinkForNode(node, link){
* outputs node info to textbox
* @param {object} node - data of current node
*/
-function textfunc(node){
+function textfunc(node) {
textinfo="Title:" + '</br>' + node.name +
'</br>' +'</br>'+"Author:"+ '</br>' +node.author+'</br>'+'</br>'+"Date:"+'</br>'
+node.year+'</br>'+'</br>'+"doi:"+'</br>'+'<a href="'+node.doi+ '">'+node.doi
@@ -343,26 +306,27 @@ function textfunc(node){
document.getElementById('textbox').innerHTML = textinfo;
}
-function highlightbutton(btn){
+function highlightbutton(btn) {
resetbuttonhighlight();
- document.getElementById(btn).style.background="#cacaca";
+ document.getElementById(btn).style.background="#CACACA";
}
-function resetbuttonhighlight(){
+
+function resetbuttonhighlight() {
document.getElementById("overview").style.background='';
document.getElementById("abstract").style.background='';
}
function displayabstract(a){
- if(textabstract=='' && textinfo==''){
+ if (textabstract=='' && textinfo=='') {
document.getElementById('textbox').innerHTML="Click node";
}
- else{
- if (a==true){
- document.getElementById('textbox').innerHTML =textabstract;
- }
- else{
- document.getElementById('textbox').innerHTML =textinfo;
- }
+ else {
+ if (a==true) {
+ document.getElementById('textbox').innerHTML =textabstract;
+ }
+ else {
+ document.getElementById('textbox').innerHTML =textinfo;
+ }
}
}
@@ -409,22 +373,6 @@ function fix_nodes(this_node) {
});
}
-/**
-* resets the positions of the nodes
-*/
-function resetGraph() {
-
- node.each(function(d) {
- d.fx = d.initial_x;
- d.fy = d.initial_y;
- });
- simulation.tick();
- simulation.tick();
- simulation.stop();
-
-
-}
-
/**
* applies the transformation (zooming or dragging) to the g element
*/
@@ -439,7 +387,23 @@ d3.selection.prototype.moveToFront = function() {
};
/**
-* transforms svg so that that the zoom is reset
+* transforms svg so that the zoom is adapted to the size of the graph
+*/
+function zoomTo() {
+ node_bounds = d3.selectAll("svg.graph").node().getBBox();
+ svg_bounds = d3.select("rect").node().getBBox();
+
+ perc_x = width/(node_bounds.width+100);
+ perc_y = height/(node_bounds.height+100);
+ perc = d3.min([perc_x, perc_y])
+
+ d3.select('svg')
+ .call(zoom.scaleBy, perc);
+}
+
+
+/**
+* transforms svg so that the zoom is reset
*/
function resetView() {
d3.select('svg')
diff --git a/Output/Graph/index.html b/Output/graph/index.html
similarity index 79%
rename from Output/Graph/index.html
rename to Output/graph/index.html
index 8999fad..5785b09 100644
--- a/Output/Graph/index.html
+++ b/Output/graph/index.html
@@ -18,20 +18,18 @@
}
.button:hover {
- background-color: #cacaca;
+ background-color: #CACACA;
}
-
- button.resetGraph {}
-
button.resetZoom {
margin-left: 110px;
}
- button.save{
+ button.save {
margin-left: 220px;
}
- button.abstract{
+
+ button.abstract {
width:146px;
position:absolute;
top: 181px;
@@ -39,7 +37,8 @@
border-radius:0;
border:1px solid #909090;
}
- button.overview{
+
+ button.overview {
width:147px;
position:absolute;
display:inline-block;
@@ -61,7 +60,7 @@
margin: 0;
}
- div.textbox{
+ div.textbox {
width:270px;
min-height:200px;
max-height:370px;
@@ -78,9 +77,6 @@
</head>
<body>
- <!-- for testing -->
- <p id="id"></p> <!--for commenting with document.getElementById("id").innerHTML = "text"; -->
-
<!-- graph -->
<svg class="graph" width="960" height="560"></svg>
@@ -89,22 +85,20 @@
<!-- textbox -->
<div class="textbox" id = "textbox">Click node</div>
-
- <!-- reset buttons -->
- <button class="resetGraph" onclick="javascript:location.reload();">Reload Graph</button>
- <!-- <button class="resetGraph" onclick="resetGraph(),fix_all()">Reset graph</button>-->
+ <button id="overview" class="overview" onclick='displayabstract(false), highlightbutton("overview")'>Overview</button>
+ <button id="abstract" class="abstract" onclick='displayabstract(true), highlightbutton("abstract")'>Abstract</button>
+
+ <!-- buttons -->
+ <button class="reloadGraph" onclick="location.reload()">Reload Graph</button>
<button class="resetZoom" onclick="resetView()">Reset View</button>
<button class="save" onclick="savesvg()">Save</button>
- <button id="overview" class="overview" onclick='displayabstract(false),highlightbutton("overview")'>Overview</button>
- <button id="abstract" class="abstract" onclick='displayabstract(true),highlightbutton("abstract")'>Abstract</button>
-
-
+
<!-- link D3 (version 5) -->
<script src="https://d3js.org/d3.v5.min.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.js"></script>
+ <script type="text/javascript" id="cn" src="cn.js"></script>
</body>
</html>
\ No newline at end of file
diff --git a/Output/Graph/json_with_citations.json b/Output/graph/json_text.json
similarity index 100%
rename from Output/Graph/json_with_citations.json
rename to Output/graph/json_text.json
--
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