sybila · daemontus · Nov 4, 2023 · Oct 23, 2023 · Oct 24, 2023 · Oct 24, 2023
diff --git a/fe/computation-window.html b/fe/computation-window.html
@@ -2,7 +2,7 @@
 
 <html lang="en">
 <head>
-    <title>Biodivine/Aeon</title>
+    <title>Biodivine/Aeon - Computation</title>
     <meta charset="utf-8">
 
     <!-- Favicon -->
@@ -33,28 +33,37 @@
 
     <script src="script/common/const.js"></script>
     <script src="script/common/Strings.js"></script>
+    <script src="script/common/Model.js"></script>
     <script src="script/Results.js"></script>
     <script src="script/Computation.js"></script>
-    <script src="script/endpoints/ModelEndpoints.js"></script>
+    <script src="script/tauriCommands/ModelCommands.js"></script>
+    <script src="script/tauriCommands/WindowsCommands.js"></script>
     <script src="script/common/Examples.js"></script>
     <script src="script/LiveModel.js"></script>
     <script src="script/UI.js"></script>
     <script src="script/CytoscapeEditor.js"></script>
     <script src="script/ModelEditor.js"></script>
     <script src="script/common/Dialog.js"></script>
     <script src="script/events/ComputationWindowEvent.js"></script>
-    <script src="script/Session.js"></script>
-    <script src="script/endpoints/ComputationResultsEndpoints.js"></script>
-    <script src="script/endpoints/ComputationEndpoints.js"></script>
+    <script src="script/tauriCommands/SessionCommands.js"></script>
+    <script src="script/tauriCommands/ComputationResultsCommands.js"></script>
+    <script src="script/tauriCommands/ComputationCommands.js"></script>
     <script src="script/Windows.js"></script>
     <script src="script/computationMain.js"></script>
+    <script src="script/Menu.js"></script>
 </head>
 
 <body onload="init()" style="background-color: #f5f5f5;">
 
+<div id="loading-indicator" class="invisible">
+    <img src="img/progress.gif"/><br><br>Loading...
+</div>
+
+<div id="content">
+
 <div style="position: absolute;">
 
-    <div id="tab-engine" class="new-window-panel">
+    <div id="content-engine" class="new-window-panel">
         <h3 id="compute-engine-status" style="margin: 0 auto; font-size: 20px; text-align: center;  font-family: 'FiraMono'; text-transform: uppercase;"> ● Computation</h3>
         <div style="height: 20px;"></div>
 
@@ -65,15 +74,15 @@ <h3 id="compute-engine-status" style="margin: 0 auto; font-size: 20px; text-alig
             Discovered classes: <span id="computation-classes">-</span></span>
 
             <div style="margin-top: 25px; text-align: center;">
-                <button id="computation-cancel" class="image-button" onclick="ComputationEndpoints.cancelComputation();" style="margin-right: 4px;">Cancel job <img src="img/cancel-24px.svg" alt="cancel"></button>
+                <button id="computation-cancel" class="image-button" onclick="ComputationCommands.cancelComputation();" style="margin-right: 4px;">Cancel job <img src="img/cancel-24px.svg" alt="cancel"></button>
                 <button id="computation-download" class="image-button" onclick="Results.show();" style="margin-left: 4px;">Show partial result <img src="img/cloud_download-24px.svg" alt="download"></button>
             </div>
         </div>
 
         <div style="clear: both;"></div>
     </div>
 
-    <div id="tab-results" class="new-window-panel gone">
+    <div id="content-results" class="new-window-panel gone">
         <h2 style="margin: 0 auto; font-size: 20px; text-align: center;">Bifurcation Function</h2>
 
         <div style="text-align: center; padding: 12px;">
@@ -93,6 +102,11 @@ <h2 style="margin: 0 auto; font-size: 20px; text-align: center;">Bifurcation Fun
         </div>
     </div>
 
+</div>
+
+    <!-- Do not change it here, this is a placeholder. -->
+    <span id="version">v0.0.0</span>
+
 </div>
 </body>
 </html>
diff --git a/fe/explorer.html b/fe/explorer.html
@@ -2,7 +2,7 @@
 
 <html lang="en">
 <head>
-    <title>[Aeon] Attractor Explorer</title>
+    <title>Biodivine/Aeon - Attractor Explorer</title>
     <meta charset="utf-8">
     <link rel="stylesheet" href="style.css" type="text/css">
 
@@ -40,10 +40,11 @@
     <script src="script/UI.js"></script>
     <script src="script/CytoscapeEditor.js"></script>
     <script src="script/ModelEditor.js"></script>
-    <script src="script/endpoints/ComputationResultsEndpoints.js"></script>
+    <script src="script/tauriCommands/ComputationResultsCommands.js"></script>
     <script src="script/explorerMain.js"></script>
     <script src="script/events/ExplorerWindowEvent.js"></script>
     <script src="script/Windows.js"></script>
+    <script src="script/Menu.js"></script>
 
     <style>
         .vis-network:focus, canvas:focus {
@@ -54,8 +55,17 @@
 
 <body onload="init()">
 
+<div id="loading-indicator" class="invisible">
+    <img src="img/progress.gif"/><br><br>Loading...
+</div>
+
+<div id="content">
+
 <h1 id='logo'>Aeon/<span id='title'>BIODIVINE</span></h1>
 
+<!-- Do not change it here, this is a placeholder. -->
+<span id="version">v0.0.0</span>
+
 <div style="position:absolute" id="explorer-witness-panel" class="main-panel gone">
     <img alt="close" src="img/close-24px.svg" class="panel-close-button" onclick="witnessPanelVisible(false)">
     <h2 style="margin: 0 auto; font-size: 20px; text-align: center;">Witness update functions</h2>
@@ -75,9 +85,6 @@ <h2 style="margin: 0 auto; font-size: 20px; text-align: center;">Witness update
     <div id="explorer-witness-text">
         <div></div>
 
-        <!-- engine address  -->
-        <div id="engine-address" style="display:none">http://localhost:8000/</div>
-
         <div style="position: absolute;">
             <div id="side-menu">
                 <div class="button-group" onclick='witnessPanelVisible()'>
@@ -90,5 +97,7 @@ <h2 style="margin: 0 auto; font-size: 20px; text-align: center;">Witness update
     </div>
 </div>
 
+</div>
+
 </body>
 </html>
diff --git a/fe/help-window.html b/fe/help-window.html
@@ -25,6 +25,9 @@
 
   <link rel="stylesheet" href="style.css" type="text/css">
 
+  <script src="script/common/const.js"></script>
+  <script src="script/Menu.js"></script>
+
 </head>
 
 <body style="background-color: #f5f5f5; overflow-y: hidden;">

diff --git a/fe/index.html b/fe/index.html
@@ -2,7 +2,7 @@
 
 <html>
     <head>
-        <title>Biodivine/Aeon</title>
+        <title>Biodivine/Aeon - Model editor</title>
         <meta charset="utf-8">
 
         <!-- Favicon -->
@@ -34,10 +34,12 @@
 
         <script src="script/common/const.js"></script>
         <script src="script/common/Strings.js"></script>
+        <script src="script/common/Model.js"></script>
         <script src="script/Results.js"></script>
         <script src="script/Computation.js"></script>
+        <script src="script/tauriCommands/WindowsCommands.js"></script>
         <script src="script/Windows.js"></script>
-        <script src="script/endpoints/ModelEndpoints.js"></script>
+        <script src="script/tauriCommands/ModelCommands.js"></script>
         <script src="script/common/Examples.js"></script>
         <script src="script/LiveModel.js"></script>
         <script src="script/UI.js"></script>
@@ -62,13 +64,19 @@
 
     <body onload="init()">
 
+        <div id="loading-indicator" class="invisible">
+            <img src="img/progress.gif"/><br><br>Loading...
+        </div>
+
+        <div id="content">
+
         <!-- Hosts the interactive model editor -->        
         <div id="cytoscape-editor">
         </div>
 
         <h1 id='logo'>Aeon/<span id='title'>BIODIVINE</span></h1>
 
-        <!-- Do not change it here, this is a placeholder. Change it in const.js -->
+        <!-- Do not change it here, this is a placeholder. -->
         <span id="version">v0.0.0</span>
 
         <!-- A menu element that is shown for selected graph nodes in the editor. -->
@@ -174,7 +182,7 @@ <h4> ● Update Function</h4>
             <div id="side-menu">
                 <div class="button-group-fake">
                     <img alt="Compute Bifurcation" id="side-menu-compute" src="img/play_circle_filled-48px.svg"
-                         onclick="LiveModel.startAnalysis(LiveModel.exportAeon());" class="button-fake">
+                         onclick="UI.startAnalysis(LiveModel.exportAeon());" class="button-fake">
                     <span class="hint invisible">Start Analysis</span>
                 </div>
 
@@ -189,8 +197,8 @@ <h4> ● Update Function</h4>
                     <span class="hint invisible">Apply Layout</span>
                 </div>
             </div>
+        </div>
 
-            <div id="loading-indicator" class="invisible"><img src="img/progress.gif"/><br><br>Waiting for server...</div>
         </div>
 
     </body>

diff --git a/fe/manual/book.toml b/fe/manual/book.toml
@@ -0,0 +1,6 @@
+[book]
+authors = ["Samuel Pastva"]
+language = "en"
+multilingual = false
+src = "src"
+title = "AEON 2021: Manual"
diff --git a/fe/manual/book/.nojekyll b/fe/manual/book/.nojekyll
@@ -0,0 +1 @@
+This file makes sure that Github Pages doesn't process mdBook's output.
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		This file makes sure that Github Pages doesn't process mdBook's output.