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<!DOCTYPE html>
<!--
SAMMI is a tool for visualization of metabolic networks
Copyright (C) 2019 The University of Texas MD Anderson Cancer Center.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
with this program. If not, see <https://www.gnu.org/licenses/>.
-->
<head>
<meta charset="utf-8" />
<link rel='stylesheet' href='sammi.css'>
<script type="text/javascript" src="https://d3js.org/d3.v4.js"></script>
<script type="text/javascript" src="helpfunctions.js"></script>
<script type="text/javascript" src="uploaddownload.js"></script>
<script type="text/javascript" src="simulationfunctions.js"></script>
<script type="text/javascript" src="https://bioinformatics.mdanderson.org/Software/SAMMI/liningfunctions.js"></script>
<script type="text/javascript" src="https://bioinformatics.mdanderson.org/Software/SAMMI/textandshapes.js"></script>
<script type="text/javascript" src="https://unpkg.com/tippy.js@2.5.2/dist/tippy.all.min.js"></script>
<script type="text/javascript" src="https://bioinformatics.mdanderson.org/Software/SAMMI/jscolor.js"></script>
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
<link rel="shortcut icon" href="https://bioinformatics.mdanderson.org/favicon.ico">
<script type="text/javascript" src="https://bioinformatics.mdanderson.org/Software/SAMMI/dialogwindow.js"></script>
<script type="text/javascript">
//http://api.jqueryui.com/dialog/
//https://www.w3schools.com/howto/howto_js_draggable.asp
$( function() {
$("#dialog").dialog({
dialogClass: "no-close",
minWidth: 400,
}).draggable()
.css("display","none");
});
$( function() {
$( "#dialog2" ).dialog({
dialogClass: "no-close",
minWidth: 600,
}).draggable()
.css("display","none");
});
</script>
</head>
<body>
<div id="topbar">
<div class="dropdown">
<button class="dropbtn" onclick="selectOpenMenu(this);">Upload/Download</button>
<div class="dropdown-content">
<h3>Secondaries</h3>
<button class="topmenubtn" onclick='shelveStandard()'>Shelve Standard Metabolites</button><br/>
<h3>Model Downloads</h3>
<button onclick="downloadSammi();" class="topmenubtn">Download SAMMI</button><br/>
<button onclick="downloadCurrent();" class="topmenubtn">Download Current</button><br/>
<button id="downloadescher" onclick="downloadEscher();" class="topmenubtn">Download ESCHER</button><br/>
<button id="downloadmez" onclick="downloadMEV();" class="topmenubtn">Download MetExploreViz</button>
<input type="checkbox" id='mezanimated'> Animated
<h3>Model Download Parameters</h3>
Scale: <input id="eschescale" type="number" min="0" step="1" value="3"><br/>
LB Field: <input id="lbfield" type="text" value="lower_bound"><br/>
Name Field: <input id="namefield" type="text" value="name"><br/>
Pathway Field: <input id="pathfield" type="text" value="subsystem"><br/>
Compartment Field: <input id="compfield" type="text" value="compartment">
</div>
</div>
<div class="dropdown">
<button class="dropbtn" onclick="selectOpenMenu(this);">Coloring</button>
<div class="dropdown-content">
<h3>Graph Coloring</h3>
<input type="color" class="jscolor" id="metcolor" value="#8080ff" onchange="reDefineColors()"> Metabolite<br/>
<input type="color" class="jscolor" id="rxncolor" value="#1919ff" onchange="reDefineColors()"> Reaction<br/>
<input type="color" class="jscolor" id="fixmetcolor" value="#ff8080" onchange="reDefineColors()"> Fixed Metabolite<br/>
<input type="color" class="jscolor" id="fixrxncolor" value="#ff0000" onchange="reDefineColors()"> Fixed Reaction<br/>
<input type="color" class="jscolor" id="edgecolor" value="#b3b6b7" onchange="reDefineColors()"> Edge<br/>
<input type="color" class="jscolor" id="metcolorsize" value="#8080ff" onchange="reDefineColors()"> Metabolites with size data<br/>
<input type="color" class="jscolor" id="rxncolorsize" value="#1919ff" onchange="reDefineColors()"> Reactions with size data<br/>
<input type="color" class="jscolor" id="widthcolorsize" value="#b3b6b7" onchange="reDefineColors()"> Links with link width data<br/>
<h3>Reaction Coloring</h3>
<button onclick="makeColorScaleGlobal('rxn')" class="topmenubtn">Make Color Scale Global</button><br/>
<input type="number" id="fluxmin" value="-1" max="0" onchange="fluxmin=this.valueAsNumber;defineFluxColorVectors()" onclick="typing=true;" onfocus="typing=true;">
<input type="color" class="jscolor" id="edgemin" value="#009933" onchange="defineFluxColorVectors();defineFluxColorBar();reDefineColors();">
- Minimum Flux<br/>
<input type="number" id="fluxmax" value="1" min="0" onchange="fluxmax=this.valueAsNumber;defineFluxColorVectors()" onclick="typing=true;" onfocus="typing=true;">
<input type="color" class="jscolor" id="edgemax" value="#cc3399" onchange="defineFluxColorVectors();defineFluxColorBar();reDefineColors();">
- Maximum Flux<br/>
<button onclick="addReactionColorBreak(this);defineFluxColorVectors();defineFluxColorBar();reDefineColors();" id="addrxnbreak" class="topmenubtn">Add Break</button><br/>
<canvas width="310" height="30" id="fluxcolorbar"></canvas>
<h3>Metabolite Coloring</h3>
<button onclick="makeColorScaleGlobal('met')" class="topmenubtn">Make Color Scale Global</button><br/>
<input type="number" id="metminvalue" value="-1" max="0" onchange="concentrationmin=this.valueAsNumber;defineMetColorVectors();defineMetColorBar();reDefineColors();" onclick="typing=true;" onfocus="typing=true;">
<input type="color" class="jscolor" id="metmin" value="#009933" onchange="defineMetColorVectors();defineMetColorBar();reDefineColors();">
- Minimum Concentration<br/>
<input type="number" id="metmaxvalue" value="1" min="0" onchange="concentrationmax=this.valueAsNumber;defineMetColorVectors();defineMetColorBar();reDefineColors();" onclick="typing=true;" onfocus="typing=true;">
<input type="color" class="jscolor" id="metmax" value="#cc3399" onchange="defineMetColorVectors();defineMetColorBar();reDefineColors();">
- Maximum concentration<br/>
<button onclick="addMetaboliteColorBreak(this);defineMetColorVectors();defineMetColorBar();reDefineColors();" id="addmetbreak" class="topmenubtn">Add Break</button><br/>
<canvas width="310" height="30" id="metcolorbar"></canvas>
<h3>Reference Node Color</h3>
<input type="color" class="jscolor" id="addednodecolor" value="#add8e6" onchange="reDefineColors()"> Reference Node
<h3>Link Strain Color</h3>
<input type="color" class="jscolor" id="linkstraincolor" value="#ff0000" onchange="reDefineColors()"> Link Strain Color
</div>
</div>
<div class="dropdown">
<button class="dropbtn" onclick="selectOpenMenu(this);">Sizing</button>
<div class="dropdown-content">
<h3>Graph Looks</h3>
<input id="labelsize" type="number" value="5" step="1" min="0" onchange="reDefineSimulation(),simulation.alpha(0);"> Label Size<br/>
<input id="addedtextsize" type="number" value="14" step="1" min="0" onchange="reDefineSimulation(),simulation.alpha(0);"> Added Text Size<br/>
<input id="strokewidth" type="number" value="1" step="1" min="0" onchange="manageArrows();reDefineSimulation();ticked();simulation.alpha(0)"> Link Width<br/>
<input id="nodescale" type="number" value="1" step="0.1" min="0" onchange="nodedegree();manageArrows();reDefineSimulation();simulation.alpha(0)"> Node size<br/>
<input id="refnodescale" type="number" value="2" step="0.1" min="0" onchange="nodedegree();manageArrows();reDefineSimulation();simulation.alpha(0)"> Reference Node size<br/>
<input id="arrowsize" type="number" value="4" step="1" min="1" onchange="manageArrows();reDefineSimulation();ticked();simulation.alpha(0)"> Arrow Size<br/>
<input id="sizeref" type="checkbox" onchange="reDefineSimulation(),simulation.alpha(0);"> View Size Reference<br/>
<h3>Reaction Size</h3>
<input type="number" id="maxrxnsize" value="2" min="0" onchange="maxrxnsize=this.valueAsNumber;checkSizeLimits(this.id)" onclick="typing=true;" onfocus="typing=true;">
- Maximum Size<br/>
<input type="number" id="minrxnsize" value="1" min="0" onchange="minrxnsize=this.valueAsNumber;checkSizeLimits(this.id)" onclick="typing=true;" onfocus="typing=true;">
- Minimum Size<br/>
<input type="number" id="rxnsizescale" value="5" min="0" step="0.1" onchange="reDefineSimulation();simulation.alpha(0)" onclick="typing=true;" onfocus="typing=true;">
- Size Scale<br/>
<h3>Metabolite Size</h3>
<input type="number" id="maxmetsize" value="2" min="0" onchange="maxmetsize=this.valueAsNumber;checkSizeLimits(this.id)" onclick="typing=true;" onfocus="typing=true;">
- Maximum Size<br/>
<input type="number" id="minmetsize" value="1" min="0" onchange="minmetsize=this.valueAsNumber;checkSizeLimits(this.id)" onclick="typing=true;" onfocus="typing=true;">
- Minimum Size<br/>
<input type="number" id="metsizescale" value="5" min="0" step="0.1" onchange="reDefineSimulation();simulation.alpha(0)" onclick="typing=true;" onfocus="typing=true;">
- Size Scale
<h3>Link Width</h3>
<input type="number" id="maxwidth" value="1" min="0" onchange="maxwidth=this.valueAsNumber;checkSizeLimits(this.id)" onclick="typing=true;" onfocus="typing=true;">
- Maximum Size<br/>
<input type="number" id="minwidth" value="0" min="0" onchange="minwidth=this.valueAsNumber;checkSizeLimits(this.id)" onclick="typing=true;" onfocus="typing=true;">
- Minimum Size<br/>
<input type="number" id="widthscale" value="5" min="0" step="0.1" onchange="reDefineSimulation();simulation.alpha(0)" onclick="typing=true;" onfocus="typing=true;">
- Size Scale
</div>
</div>
<div class="dropdown">
<button class="dropbtn" onclick="selectOpenMenu(this);">Settings</button>
<div class="dropdown-content">
<h3>Simulation Parameters</h3>
<input id="linkstrength" type="number" value="30" step="5" min="0" onchange="reDefineSimulationParameters()"> Link Repulsion Strength<br/>
<input id="nodestrength" type="number" value="0" step="1" min="0" onchange="reDefineSimulationParameters()"> Node Collision Buffer<br/>
<input id="maparea" type="number" value="30" step="5" min="0" onchange="reDefineSimulationParameters()"> Node Repulsion Strength<br/>
<input id="velocityDecay" type="number" value="0.4" step="0.1" min="0" max="1" onchange="reDefineSimulationParameters()"> Inertia<br/>
<input id="centerstrength" type="number" value="0.02" step="0.01" min="0" onchange="reDefineSimulationParameters()"> Center Strength<br/>
<input id="secondarystrength" type="number" value="0.1" step="0.01" min="0" onchange="reDefineSimulationParameters()"> Secondary Strength<br/>
<input id="shortpathtime" type="number" value="3" step="1" min="0"> Path Execution Timeout (s)<br/>
<input id="centersize" type="number" value="0" step="5" min="0" onchange="centerref._groups[0][0].attributes['r'].value = document.getElementById('centersize').value"> Center Size<br/>
<input id="pretify" type="number" value="40" step="5" min="0" onchange="pretify()"> Pretify Size
<h3>Naming</h3>
<!-- <button onclick="defineNameOptions()">Define Options</button><br/> -->
Primary Metabolites: <select id="metNameOpts" onchange="renameNodes();behave()"></select><br/>
Secondary Metabolites: <select id="secMetNameOpts" onchange="renameNodes();behave()"></select><br/>
Reactions: <select id="rxnNameOpts" onchange="renameNodes();behave()"></select>
<h3>Reversibility</h3>
<select id="reversibility" onchange="reDefineSimulation()">
<option>None</option>
<option>Both Ways</option>
<option>Diamond Arrowheads</option>
</select>
<h3>Node Shape</h3>
<select id="rxnshape" onchange="reDefineSimulation()">
<option value="rect" selected="selected">Square</option>
<option value="circle">Circle</option>
</select>
- Reaction Nodes<br/>
<select id="metshape" onchange="reDefineSimulation()">
<option value="rect">Square</option>
<option value="circle" selected="selected">Circle</option>
</select>
- Metabolite Nodes
</div>
</div>
<!-- <div class="dropdown">
<button class="dropbtn" onclick="openDocs('shortcuts')">Keyboard Shortcuts</button>
</div> -->
<div class="dropdown">
<button class="dropbtn" onclick="openDocs('documentation')">Documentation</button>
</div>
<div class="dropdown" style="float: right;">
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/MDACC2.png" id="toplogo">
</div>
</div>
<div id="dialog" title="Menu">
<div id="onloadoptions">
</div>
<h3>Modes:</h3>
<h4>Arrows: </h4><input type='checkbox' id='arrows' onclick='checkchange=true;manageArrows();' checked>
<h4>Tooltips: </h4><input type='checkbox' id='tooltipbool' onclick='manageTooltips();'>
<h4>Hide Rxns: </h4><input type='checkbox' id='hiderxns' onclick='checkchange=true;reDefineSimulation();'><br/>
<h4>Move Labels (m): </h4><input type='checkbox' id='movelabels' onclick='dragLabels();'>
<h4>Link Strain: </h4><input type='checkbox' id='linkstrain' onclick='reDefineColors();'><br/>
<h3>Graph Manipulations:</h3>
<div class="wrapper">
<button onclick="behave()" class="menubutton">Reload Graph (r)</button>
<button onclick="simulation.stop()" class="menubutton">Pause Simulation (p)</button>
<button onclick="zoom.transform(gMain, d3.zoomIdentity.translate(0,0).scale(1));" class="menubutton">Recenter Graph</button>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); fixSelected()" class="menubutton">Fix Nodes (f)</button>
<button onclick="defineBackupGraph(); toggleSelected()" class="menubutton">Toggle Fix (t)</button>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); isolateRxn()" class="menubutton">Isolate Reaction (i)</button>
<button onclick="defineBackupGraph(); isolateMetabolite()" class="menubutton">Isolate Metabolite (i)</button>
<button onclick="defineBackupGraph(); selectConnected()" class="menubutton">Select Neighbors (n)</button>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); splitMet()" class="menubutton">Break Metabolite (b)</button>
<button onclick="defineBackupGraph(); joinMetabolite()" class="menubutton">Join Metabolite (j)</button>
<button onclick="defineBackupGraph(); suspendMetabolite()" class="menubutton">Shelve Metabolite (s)</button>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); deleteNodes()" class="menubutton">Delete Nodes (del)</button>
<button onclick="defineBackupGraph(); keepNodes()" class="menubutton">Keep Nodes</button>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); makeSecondary()" class="menubutton">Make Secondary (q)</button>
<button onclick="defineBackupGraph(); makePrimary()" class="menubutton">Make Primary (q)</button>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); editBezier()" class="menubutton">Curve Link (c)</button>
<button onclick="defineBackupGraph(); deleteBezi()" class="menubutton">Delete Curve</button>
<button onclick="defineBackupGraph(); autoBezi()" class="menubutton">Auto Curve (d)</button>
</div>
<div class="wrapper">
<button onclick="groupNodes()" class="menubutton">Group Nodes</button>
<button onclick="unGroupNodes()" class="menubutton">Ungroup Nodes</button>
<button onclick="defineBackupGraph(); collapse()" class="menubutton">Collapse</button>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); shortestPath('short')" class="menubutton">Shortest Path (p)</button>
<button onclick="defineBackupGraph(); shortestPath('long')" class="menubutton">Find Long Path</button>
<button onclick="defineBackupGraph(); shortestCircle()" class="menubutton">Smallest Circle</button>
<button onclick="defineBackupGraph(); getComponent()" class="menubutton">Find Component</button>
</div>
<div class="wrapper">
<button onclick="editNodeProperties(graph.nodes[selected[0]])" class="menubutton">Edit Attributes</button>
<button onclick="defineBackupGraph(); reverseReactions()" class="menubutton">Reverse Reaction</button>
<div style="width:32%;height:40px;font-size: 12px;float:right;line-height:normal"><input type="checkbox" id="reverseflux" checked><b>Reverse Flux</b></div>
</div>
<div class="wrapper">
<button onclick="defineBackupGraph(); pretify()" class="menubutton">Pretify Reactions</button>
<button onclick="defineBackupGraph(); untrap()" class="menubutton">Untrap Nodes (u)</button>
</div>
<h3>Subgraph Manipulations:</h3>
<button onclick="joinSubGraphs()" class="menubutton">Join Subgraphs</button>
<button onclick="renameSubgraph()" class="menubutton">Rename Subgraph</button><br/>
<h3>Search:</h3> <input id="searchbox" type="text" onkeypress="getSearchNodes(event,this.value)" onclick="typing=true;" onfocus="typing=true;" style="width:120px;"><br/>
<input type="checkbox" id="searchhighlight" checked> Focus
<input type="checkbox" id="searchregexp" checked> RegExp<br/>
<button onclick="trackMet()" class="menubutton" id="trackmet">Highlight Metabolite (h)</button><br/>
<h3>Arranging:</h3>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/vertline.png" width="25" onclick="defineBackupGraph(); vertline()" title="Arrange nodes in a vertical line" class="imgbtn"/>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/horzline.png" width="25" onclick="defineBackupGraph(); horzline()" title="Arrange nodes in a horizontal line" class="imgbtn"/>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/diagline.png" width="25" onclick="defineBackupGraph(); diagline()" title="Arrange nodes in a line" class="imgbtn"/>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/circle.png" width="25" onclick="defineBackupGraph(); circle()" title="Arrange nodes in a circle" class="imgbtn"/>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/rectangle.png" width="25" onclick="defineBackupGraph(); rectangleInit()" title="Arrange nodes in a rectangle" class="imgbtn"/>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/rotate.png" width="25" onclick="defineBackupGraph(); rotateNodesInit()" title="Rotate nodes" class="imgbtn"/>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/scale.png" width="25" onclick="defineBackupGraph(); scaleAll();" title="Scale node position" class="imgbtn"/><br/>
<input type="checkbox" id="reverseline"> Reverse
<select id="orderby">
<option value="selection order">Selection Order</option>
<option value="position">Position</option>
</select><br/>
<h3>Text and Shapes:</h3>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/text.png" width="30" onclick="texting=true;this.style='opacity: 0.2'" id="textingImage" title="Add text (double click to edit)"/>
<img src="https://bioinformatics.mdanderson.org/Software/SAMMI/Thumbnails/shape.png" width="30" onclick="shaping=true;this.style='opacity: 0.2'" id="shapingImage" title="Add shape (Drop nodes inside to trap)"/><br/>
<h3>Shelved Metabolites:</h3>
<select id="suspended" onchange="putBack(this)">
<option id="suspendeddefault">Select Node</option>
</select><button onclick="putAllBack()" class="topmenubtn">Put All Back</button><br/>
<h3>Commits:</h3>
Description: <input id="commitname" type="text" onclick="typing=true;" onfocus="typing=true;"><br/>
<button id="commitgraph" onclick="commitGraph()" class="topmenubtn">Commit Current</button><br/>
<select id="commits" onchange="putBackCommit(this)">
<option id="commitdefault">Select Commit</option>
</select><br/>
<h3>Add Nodes and Edges:</h3>
<div class="autocomplete" style="width:230px;">
Reaction: <input id="existingReactions" type="text" placeholder="Reaction" onkeydown="addExistingReaction(event)" onclick="typing=true;" onfocus="typing=true;" style="width:120px">
</div>
<div class="autocomplete" style="width:230px;">
Metabolite: <input id="existingMetabolites" type="text" placeholder="Metabolite" onkeydown=addExistingMetabolite(event) onclick="typing=true;" onfocus="typing=true;" style="width:120px">
</div>
<button onclick="defineBackupGraph(); addAs('substrate')" class="topmenubtn">Connect as Substrate</button>
<button onclick="defineBackupGraph(); addAs('product')" class="topmenubtn">Connect as Product</button>
</div>
<div id="dialog2" title="Edit"></div>
<div id="d3_selectable_force_directed_graph" style="display:none;" class="svg-container">
<!-- <svg id="graphsvg"></svg> -->
</div>
<div id="blankdiv"></div>
<script type="text/javascript">
//document.getElementById("savePNG").addEventListener('click', savePNG);
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