Merge branch 'master' of https://github.com/sulcgroup/oxdna-viewer

dist/UI/UI.js

@@ -994,7 +994,7 @@ class fluxGraph {
                 //    this.chart.toBase64Image();
                 //}
             },
-            responsiveAnimationDuration: 0,
+            responsiveAnimationDuration: 0, // animation duration after a resize
             responsive: true,
             title: {
                 display: true,

dist/api/plugin_api.js

@@ -0,0 +1,33 @@
+// let's define a storage structure for the plugin API
+// it will sit in local storage and load the code for the individual plugins named as key 
+// and the code as value packed away in a JSON object hidden at the key "plugins" in local storage
+// this is the object that will be stored in local storage
+// it will contain the code for the individual plugins
+// the key will be the name of the plugin, the value will be the code
+let plugins = {};
+// this function will load the plugins from local storage
+// it will be called at the beginning of the program
+function loadPlugins() {
+    let pluginsString = localStorage.getItem("plugins");
+    if (pluginsString) {
+        plugins = JSON.parse(pluginsString);
+    }
+    // if there are no plugins in local storage, we will create an empty object
+    else {
+        plugins = {}; //"test": plugin_code};
+    }
+    //iterate over all the plugins and load them
+    for (let plugin in plugins) {
+        eval(plugins[plugin]);
+    }
+}
+// this function will save the plugins to local storage (it will be called any time we add a new plugin)
+function savePlugins() {
+    localStorage.setItem("plugins", JSON.stringify(plugins));
+}
+function addPlugin(name, plugin_code) {
+    plugins[name] = plugin_code;
+    eval(plugin_code);
+    savePlugins();
+}
+loadPlugins();

dist/file_handling/aux_readers.js

@@ -99,34 +99,47 @@ const handleCSV = (file) => {
         render();
     });
 };
-//parse a trap file
-function readTrap(trapFile) {
-    trapFile.text().then(text => {
+function readForce(forceFile) {
+    forceFile.text().then(text => {
         //{ can be replaced with \n to make sure no parameter is lost
         while (text.indexOf("{") >= 0)
             text = text.replace("{", "\n");
-        // traps can be split by } because everything between {} is one trap
-        let traps = text.split("}");
+        // forces can be split by } because everything between {} is one force
+        let forces = text.split("}");
         let trap_objs = [];
-        traps.forEach((trap) => {
-            let lines = trap.split('\n');
+        forces.forEach((force) => {
+            let lines = force.split('\n');
             //empty lines and empty traps need not be processed as well as comments
             lines = lines.filter((line) => line !== "" && !line.startsWith("#"));
             if (lines.length == 0)
                 return;
             let trap_obj = {};
             lines.forEach((line) => {
+                // remove comments
                 let com_pos = line.indexOf("#");
                 if (com_pos >= 0)
                     line = line.slice(0, com_pos).trim();
-                //another chance an empty line can be encountered. Remove whitespace
+                // another chance an empty line can be encountered. Remove whitespace
                 if (line.trim().length == 0)
                     return;
-                //split into option name and value
+                // split into option name and value
                 let options = line.split("=");
                 let lft = options[0].trim();
                 let rght = options[1].trim();
-                trap_obj[lft] = Number.isNaN(parseFloat(rght)) ? rght : parseFloat(rght);
+                // Check if the string represents a list of floats (numbers separated by commas)
+                if (rght.includes(',')) {
+                    // Split the string by commas and convert each part to a float
+                    let floatList = rght.split(',').map(Number);
+                    trap_obj[lft] = floatList;
+                }
+                else if (/^-?\d+(\.\d+)?$/.test(rght)) {
+                    // Check if the entire string is a valid number
+                    trap_obj[lft] = parseFloat(rght);
+                }
+                else {
+                    // Otherwise, treat it as a string
+                    trap_obj[lft] = rght;
+                }
             });
             if (Object.keys(trap_obj).length > 0)
                 trap_objs.push(trap_obj);
@@ -146,8 +159,20 @@ function readTrap(trapFile) {
                     skewTrap.update();
                     forces.push(skewTrap);
                     break;
+                case "repulsion_plane":
+                    let repPlane = new RepulsionPlane();
+                    repPlane.setFromParsedJson(f);
+                    repPlane.update();
+                    forces.push(repPlane);
+                    break;
+                case "attraction_plane":
+                    let attrPlane = new AttractionPlane();
+                    attrPlane.setFromParsedJson(f);
+                    attrPlane.update();
+                    forces.push(attrPlane);
+                    break;
                 default:
-                    notify(`External force ${f["type"]} type not supported yet, feel free to implement in aux_readers.ts and force.ts`);
+                    notify(`External force -${f["type"]}- type not supported yet, feel free to implement in aux_readers.ts and force.ts`);
                     break;
             }
         });

dist/file_handling/file_handling.js

@@ -88,7 +88,7 @@ async function handleFiles(files) {
             auxFiles.push(new File2reader(files[i], 'json', readJson));
         }
         else if (ext === "txt" && (fileName.includes("trap") || fileName.includes("force"))) {
-            auxFiles.push(new File2reader(files[i], 'force', readTrap));
+            auxFiles.push(new File2reader(files[i], 'force', readForce));
         }
         else if (ext === "txt" && (fileName.includes("_m"))) {
             auxFiles.push(new File2reader(files[i], 'mass', readMassFile));

dist/file_handling/order_parameter_selector.js

@@ -58,12 +58,12 @@ let loadHyperSelector = () => {
                 // mode:"dataset", // it is possible to remove the line view from the plot 
                 // intersect:true  // on hover, but i find it to distracting 
             },
-            responsiveAnimationDuration: 0,
+            responsiveAnimationDuration: 0, // animation duration after a resize
             scales: {
                 xAxes: [{ display: true, scaleLabel: { display: true, labelString: 'Time' }, gridLines: { drawOnChartArea: false } }],
                 yAxes: [{ display: true, gridLines: { drawOnChartArea: false } }],
             },
-            spanGaps: true,
+            spanGaps: true, // handle null in the chart data
             annotation: {
                 events: ["click"],
                 annotations: [
@@ -143,7 +143,7 @@ let handleParameterDrop = (files) => {
             else {
                 console.log("adding new axis");
                 myChart.options.scales.yAxes.push({
-                    type: 'linear',
+                    type: 'linear', // only linear but allow scale type registration. This allows extensions to exist solely for log scale for instance
                     display: true,
                     position: 'left',
                     id: `y-axis-id${axis_counter}`,
@@ -159,7 +159,7 @@ let handleParameterDrop = (files) => {
                         labels: labels,
                         datasets: [
                             {
-                                label: parameter_name,
+                                label: parameter_name, //files[0].name.split(".")[0],
                                 data: data,
                                 fill: false,
                                 borderColor: chartColorMap.get(),
@@ -170,7 +170,7 @@ let handleParameterDrop = (files) => {
                 }
                 else {
                     myChart.data.datasets.push({
-                        label: parameter_name,
+                        label: parameter_name, //files[i].name.split(".")[0],
                         data: data,
                         fill: false,
                         borderColor: chartColorMap.get(),

dist/file_handling/output_file.js

@@ -128,9 +128,9 @@ function getNewIds(useNew = false) {
     });
     // these subtypes are not implemented in the CG-oxDNA model, just used for a 'relative' subtype that oxDNA will take as input
     let gsSubtypes = {
-        subtypelist: [],
-        masses: [],
-        radii: [],
+        subtypelist: [], // per particle subtype assignment
+        masses: [], //
+        radii: [], //
         subtype: -1
     };
     // Next, generic sphere objects
@@ -477,9 +477,9 @@ function makeUNFOutput(name) {
             let naStrandsSchema = {
                 "id": strand.id,
                 "name": strand.label,
-                "isScaffold": strand.getLength() > 1000 ? true : false,
-                "naType": strand.end5.isDNA() ? "DNA" : "RNA",
-                "color": strand.end5.color ? '#'.concat(strand.end5.color.getHexString()) : '',
+                "isScaffold": strand.getLength() > 1000 ? true : false, //entirely arbitrary, but generally right.
+                "naType": strand.end5.isDNA() ? "DNA" : "RNA", // Nucleotide type is actually pretty poorly defined in oxView, so this is the best I can do
+                "color": strand.end5.color ? '#'.concat(strand.end5.color.getHexString()) : '', // OxView defines colors on a per-nucleotide level while UNF defines it at the strand level.
                 "fivePrimeId": strand.end5.id,
                 "threePrimeId": strand.end3.id,
                 "pdbFileId": 0,
@@ -504,7 +504,7 @@ function makeUNFOutput(name) {
             let aaChainSchema = {
                 "id": strand.id,
                 "chainName": strand.label,
-                "color": strand.end5.color ? '#'.concat(strand.end5.color.getHexString()) : '',
+                "color": strand.end5.color ? '#'.concat(strand.end5.color.getHexString()) : '', // OxView defines colors on a per-nucleotide level while UNF defines it at the strand level.
                 "pdbFileId": 0,
                 "nTerm": strand.end5.id,
                 "cTerm": strand.end3.id,

dist/file_handling/pdb_worker.js

@@ -20,48 +20,48 @@ this.onmessage = function (e) {
     postMessage(ret, undefined);
 };
 var backboneColors = [
-    new THREE.Color(0xfdd291),
-    new THREE.Color(0xffb322),
-    new THREE.Color(0x437092),
+    new THREE.Color(0xfdd291), //light yellow
+    new THREE.Color(0xffb322), //goldenrod
+    new THREE.Color(0x437092), //dark blue
     new THREE.Color(0x6ea4cc), //light blue
 ];
 var nucleosideColors = [
-    new THREE.Color(0x4747B8),
-    new THREE.Color(0xFFFF33),
+    new THREE.Color(0x4747B8), //A or K; Royal Blue
+    new THREE.Color(0xFFFF33), //G or C; Medium Yellow
     //C or A
-    new THREE.Color(0x8CFF8C),
+    new THREE.Color(0x8CFF8C), //Medium green
     //T/U or T
-    new THREE.Color(0xFF3333),
+    new THREE.Color(0xFF3333), //Red
     //E
-    new THREE.Color(0x660000),
+    new THREE.Color(0x660000), //Dark Brown
     //S
-    new THREE.Color(0xFF7042),
+    new THREE.Color(0xFF7042), //Medium Orange
     //D
-    new THREE.Color(0xA00042),
+    new THREE.Color(0xA00042), //Dark Rose
     //N
-    new THREE.Color(0xFF7C70),
+    new THREE.Color(0xFF7C70), //Light Salmon
     //Q
-    new THREE.Color(0xFF4C4C),
+    new THREE.Color(0xFF4C4C), //Dark Salmon
     //H
-    new THREE.Color(0x7070FF),
+    new THREE.Color(0x7070FF), //Medium Blue
     //G
-    new THREE.Color(0xEBEBEB),
+    new THREE.Color(0xEBEBEB), // light GREY
     //P
-    new THREE.Color(0x525252),
+    new THREE.Color(0x525252), //Dark Grey
     //R
-    new THREE.Color(0x00007C),
+    new THREE.Color(0x00007C), //Dark Blue
     //V
-    new THREE.Color(0x5E005E),
+    new THREE.Color(0x5E005E), //Dark Purple
     //I
-    new THREE.Color(0x004C00),
+    new THREE.Color(0x004C00), //Dark Green
     //L
-    new THREE.Color(0x455E45),
+    new THREE.Color(0x455E45), //Olive Green
     //M
-    new THREE.Color(0xB8A042),
+    new THREE.Color(0xB8A042), //Light Brown
     //F
-    new THREE.Color(0x534C42),
+    new THREE.Color(0x534C42), //Olive Grey
     //Y
-    new THREE.Color(0x8C704C),
+    new THREE.Color(0x8C704C), //Medium Brown
     //W
     new THREE.Color(0x4F4600), //Olive Brown
 ];