jbrowse-plugin-msaview 1.0.17 → 1.0.18

package/CHANGELOG.md

@@ -1,3 +1,7 @@
+# v1.0.18
+
+- Fix clicking on node labels
+
 # v1.0.17
 
 - Avoid Link redirection at react-msaview importform

package/dist/jbrowse-plugin-msaview.cjs.development.js

@@ -113,7 +113,7 @@ function _createSuper(Derived) {
   };
 }
 
-var version = "1.0.17";
+var version = "1.0.18";
 
 var MsaViewPlugin = /*#__PURE__*/function (_Plugin) {
   _inherits(MsaViewPlugin, _Plugin);

package/dist/jbrowse-plugin-msaview.cjs.production.min.js

@@ -1,2 +1,2 @@
-"use strict";function e(e){return e&&"object"==typeof e&&"default"in e?e.default:e}Object.defineProperty(exports,"__esModule",{value:!0});var t=e(require("@jbrowse/core/Plugin")),n=require("@jbrowse/core/util"),r=require("react-msaview"),o=e(require("@jbrowse/core/pluggableElementTypes/ViewType")),i=e(require("@material-ui/icons/GridOn"));function u(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function c(e){return(c=Object.setPrototypeOf?Object.getPrototypeOf:function(e){return e.__proto__||Object.getPrototypeOf(e)})(e)}function a(e,t){return(a=Object.setPrototypeOf||function(e,t){return e.__proto__=t,e})(e,t)}function f(e,t){if(t&&("object"==typeof t||"function"==typeof t))return t;if(void 0!==t)throw new TypeError("Derived constructors may only return object or undefined");return function(e){if(void 0===e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return e}(e)}function l(e){var t=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(e){return!1}}();return function(){var n,r=c(e);if(t){var o=c(this).constructor;n=Reflect.construct(r,arguments,o)}else n=r.apply(this,arguments);return f(this,n)}}exports.default=function(e){!function(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function");e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,writable:!0,configurable:!0}}),t&&a(e,t)}(s,t);var c,f=l(s);function s(){var e;return u(this,s),(e=f.apply(this,arguments)).name="MsaViewPlugin",e.version="1.0.17",e}return(c=[{key:"install",value:function(e){console.log({MSA:r}),e.addViewType((function(){return new o({name:"MsaView",stateModel:r.MSAModel,ReactComponent:r.MSAView})}))}},{key:"configure",value:function(e){n.isAbstractMenuManager(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:i,onClick:function(e){e.addView("MsaView",{})}})}}])&&function(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}(s.prototype,c),s}();
+"use strict";function e(e){return e&&"object"==typeof e&&"default"in e?e.default:e}Object.defineProperty(exports,"__esModule",{value:!0});var t=e(require("@jbrowse/core/Plugin")),n=require("@jbrowse/core/util"),r=require("react-msaview"),o=e(require("@jbrowse/core/pluggableElementTypes/ViewType")),i=e(require("@material-ui/icons/GridOn"));function u(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}function c(e){return(c=Object.setPrototypeOf?Object.getPrototypeOf:function(e){return e.__proto__||Object.getPrototypeOf(e)})(e)}function a(e,t){return(a=Object.setPrototypeOf||function(e,t){return e.__proto__=t,e})(e,t)}function f(e,t){if(t&&("object"==typeof t||"function"==typeof t))return t;if(void 0!==t)throw new TypeError("Derived constructors may only return object or undefined");return function(e){if(void 0===e)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return e}(e)}function l(e){var t=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Boolean.prototype.valueOf.call(Reflect.construct(Boolean,[],(function(){}))),!0}catch(e){return!1}}();return function(){var n,r=c(e);if(t){var o=c(this).constructor;n=Reflect.construct(r,arguments,o)}else n=r.apply(this,arguments);return f(this,n)}}exports.default=function(e){!function(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function");e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,writable:!0,configurable:!0}}),t&&a(e,t)}(s,t);var c,f=l(s);function s(){var e;return u(this,s),(e=f.apply(this,arguments)).name="MsaViewPlugin",e.version="1.0.18",e}return(c=[{key:"install",value:function(e){console.log({MSA:r}),e.addViewType((function(){return new o({name:"MsaView",stateModel:r.MSAModel,ReactComponent:r.MSAView})}))}},{key:"configure",value:function(e){n.isAbstractMenuManager(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:i,onClick:function(e){e.addView("MsaView",{})}})}}])&&function(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}(s.prototype,c),s}();
 //# sourceMappingURL=jbrowse-plugin-msaview.cjs.production.min.js.map

package/dist/jbrowse-plugin-msaview.esm.js

@@ -108,7 +108,7 @@ function _createSuper(Derived) {
   };
 }
 
-var version = "1.0.17";
+var version = "1.0.18";
 
 var MsaViewPlugin = /*#__PURE__*/function (_Plugin) {
   _inherits(MsaViewPlugin, _Plugin);

package/dist/jbrowse-plugin-msaview.umd.development.js

@@ -115,7 +115,7 @@
     };
   }
 
-  var version = "1.0.17";
+  var version = "1.0.18";
 
   var smallMSA = "CLUSTAL O(1.2.3) multiple sequence alignment\nUniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM\nUniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI\nUniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM\nUniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM\nUniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM\nUniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------\nUniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS\nUniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV\nUniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP\nUniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------\nUniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST\nUniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------\n";
   var smallMSAOnly = "CLUSTAL O(1.2.4) multiple sequence alignment\n\n\nsp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\t60\nsp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG\t60\nsp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG\t60\n                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**\n\nsp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\t120\nsp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP\t120\nsp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA\t120\n                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**\n\nsp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR\t142\n                           .**: ****: ** ***.***";
@@ -140,7 +140,7 @@
           React__default.createElement("div", { style: { width: '50%' } },
               error ? (React__default.createElement("div", { style: { padding: 20 } },
                   React__default.createElement(core.Typography, { color: "error" },
-                      "Error: ", "" + error))) : null,
+                      "Error: ", "".concat(error)))) : null,
               React__default.createElement(core.Typography, null, "Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),
               React__default.createElement(core.Typography, { color: "error" }, "Note: you can open up just an MSA or just a tree, both are not required. Some MSA files e.g. stockholm format have an embedded tree also and this is fine, and opening a separate tree file is not required.")),
           React__default.createElement(core.Grid, { container: true, spacing: 10, justifyContent: "center", alignItems: "center" },
@@ -165,6 +165,7 @@
                       React__default.createElement(ListItem, { model: model, onClick: function () {
                               model.setTreeFilehandle({
                                   uri: 'https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh',
+                                  locationType: 'UriLocation',
                               });
                           } }, "230k COVID-19 samples (tree only)"),
                       React__default.createElement(ListItem, { model: model, onClick: function () {
@@ -176,30 +177,36 @@
                       React__default.createElement(ListItem, { model: model, onClick: function () {
                               model.setMSAFilehandle({
                                   uri: 'https://ihh.github.io/abrowse/build/pfam-cov2.stock',
+                                  locationType: 'UriLocation',
                               });
                           } }, "PFAM SARS-CoV2 multi-stockholm"),
                       React__default.createElement(ListItem, { model: model, onClick: function () {
                               model.setMSAFilehandle({
                                   uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock',
+                                  locationType: 'UriLocation',
                               });
                           } }, "Lysine stockholm file"),
                       React__default.createElement(ListItem, { model: model, onClick: function () {
                               model.setMSAFilehandle({
                                   uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt',
+                                  locationType: 'UriLocation',
                               });
                           } }, "PF01601 stockholm file (SARS-CoV2 spike protein)"),
                       React__default.createElement(ListItem, { model: model, onClick: function () {
                               model.setMSAFilehandle({
                                   uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa',
+                                  locationType: 'UriLocation',
                               });
                           } }, "Europe COVID full genomes (LR883044.1 and 199 other sequences)"),
                       React__default.createElement(ListItem, { model: model, onClick: function () {
                               mobx.transaction(function () {
                                   model.setMSAFilehandle({
                                       uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.fa',
+                                      locationType: 'UriLocation',
                                   });
                                   model.setTreeFilehandle({
                                       uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh',
+                                      locationType: 'UriLocation',
                                   });
                               });
                           } }, "MAFFT+VeryFastTree(17.9k samples)"))))));
@@ -396,7 +403,7 @@
       var treeAreaWidth = model.treeAreaWidth;
       var classes = useStyles();
       return (React__default.createElement(React__default.Fragment, null,
-          React__default.createElement(core.Tooltip, { open: true, placement: "top", title: "" + (model.pxToBp(coordX) + 1), arrow: true },
+          React__default.createElement(core.Tooltip, { open: true, placement: "top", title: "".concat(model.pxToBp(coordX) + 1), arrow: true },
               React__default.createElement("div", { style: {
                       left: coordX + treeAreaWidth,
                       position: 'absolute',
@@ -1757,7 +1764,7 @@
           ctx.clearRect(0, 0, treeWidth + padding, blockSize);
           ctx.translate(margin.left, -offsetY);
           var font = ctx.font;
-          ctx.font = font.replace(/\d+px/, Math.max(8, rowHeight - 8) + "px");
+          ctx.font = font.replace(/\d+px/, "".concat(Math.max(8, rowHeight - 8), "px"));
           if (!noTree && drawTree) {
               hierarchy.links().forEach(function (_a) {
                   var source = _a.source, target = _a.target;
@@ -1896,6 +1903,7 @@
           labelsAlignRight,
           treeAreaWidth,
           structures,
+          highResScaleFactor,
       ]);
       React.useEffect(function () {
           var canvas = mouseoverRef.current;
@@ -2272,12 +2280,13 @@
   /* MIT license */
 
 
+  var hasOwnProperty = Object.hasOwnProperty;
 
   var reverseNames = {};
 
   // create a list of reverse color names
   for (var name in colorName) {
-  	if (colorName.hasOwnProperty(name)) {
+  	if (hasOwnProperty.call(colorName, name)) {
   		reverseNames[colorName[name]] = name;
   	}
   }
@@ -2320,9 +2329,9 @@
 
   	var abbr = /^#([a-f0-9]{3,4})$/i;
   	var hex = /^#([a-f0-9]{6})([a-f0-9]{2})?$/i;
-  	var rgba = /^rgba?\(\s*([+-]?\d+)\s*,\s*([+-]?\d+)\s*,\s*([+-]?\d+)\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/;
-  	var per = /^rgba?\(\s*([+-]?[\d\.]+)\%\s*,\s*([+-]?[\d\.]+)\%\s*,\s*([+-]?[\d\.]+)\%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/;
-  	var keyword = /(\D+)/;
+  	var rgba = /^rgba?\(\s*([+-]?\d+)(?=[\s,])\s*(?:,\s*)?([+-]?\d+)(?=[\s,])\s*(?:,\s*)?([+-]?\d+)\s*(?:[,|\/]\s*([+-]?[\d\.]+)(%?)\s*)?\)$/;
+  	var per = /^rgba?\(\s*([+-]?[\d\.]+)\%\s*,?\s*([+-]?[\d\.]+)\%\s*,?\s*([+-]?[\d\.]+)\%\s*(?:[,|\/]\s*([+-]?[\d\.]+)(%?)\s*)?\)$/;
+  	var keyword = /^(\w+)$/;
 
   	var rgb = [0, 0, 0, 1];
   	var match;
@@ -2359,7 +2368,11 @@
   		}
 
   		if (match[4]) {
-  			rgb[3] = parseFloat(match[4]);
+  			if (match[5]) {
+  				rgb[3] = parseFloat(match[4]) * 0.01;
+  			} else {
+  				rgb[3] = parseFloat(match[4]);
+  			}
   		}
   	} else if (match = string.match(per)) {
   		for (i = 0; i < 3; i++) {
@@ -2367,19 +2380,22 @@
   		}
 
   		if (match[4]) {
-  			rgb[3] = parseFloat(match[4]);
+  			if (match[5]) {
+  				rgb[3] = parseFloat(match[4]) * 0.01;
+  			} else {
+  				rgb[3] = parseFloat(match[4]);
+  			}
   		}
   	} else if (match = string.match(keyword)) {
   		if (match[1] === 'transparent') {
   			return [0, 0, 0, 0];
   		}
 
-  		rgb = colorName[match[1]];
-
-  		if (!rgb) {
+  		if (!hasOwnProperty.call(colorName, match[1])) {
   			return null;
   		}
 
+  		rgb = colorName[match[1]];
   		rgb[3] = 1;
 
   		return rgb;
@@ -2400,12 +2416,12 @@
   		return null;
   	}
 
-  	var hsl = /^hsla?\(\s*([+-]?(?:\d{0,3}\.)?\d+)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/;
+  	var hsl = /^hsla?\(\s*([+-]?(?:\d{0,3}\.)?\d+)(?:deg)?\s*,?\s*([+-]?[\d\.]+)%\s*,?\s*([+-]?[\d\.]+)%\s*(?:[,|\/]\s*([+-]?(?=\.\d|\d)(?:0|[1-9]\d*)?(?:\.\d*)?(?:[eE][+-]?\d+)?)\s*)?\)$/;
   	var match = string.match(hsl);
 
   	if (match) {
   		var alpha = parseFloat(match[4]);
-  		var h = (parseFloat(match[1]) + 360) % 360;
+  		var h = ((parseFloat(match[1]) % 360) + 360) % 360;
   		var s = clamp(parseFloat(match[2]), 0, 100);
   		var l = clamp(parseFloat(match[3]), 0, 100);
   		var a = clamp(isNaN(alpha) ? 1 : alpha, 0, 1);
@@ -2421,7 +2437,7 @@
   		return null;
   	}
 
-  	var hwb = /^hwb\(\s*([+-]?\d{0,3}(?:\.\d+)?)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/;
+  	var hwb = /^hwb\(\s*([+-]?\d{0,3}(?:\.\d+)?)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?(?=\.\d|\d)(?:0|[1-9]\d*)?(?:\.\d*)?(?:[eE][+-]?\d+)?)\s*)?\)$/;
   	var match = string.match(hwb);
 
   	if (match) {
@@ -2500,7 +2516,7 @@
   }
 
   function hexDouble(num) {
-  	var str = num.toString(16).toUpperCase();
+  	var str = Math.round(num).toString(16).toUpperCase();
   	return (str.length < 2) ? '0' + str : str;
   }
   });
@@ -4194,9 +4210,9 @@
       var _a;
       if (parent === void 0) { parent = 'node'; }
       if (depth === void 0) { depth = 0; }
-      var id = parent + "-" + depth;
+      var id = "".concat(parent, "-").concat(depth);
       return __assign$1(__assign$1({}, tree), { id: id, branchset: ((_a = tree.branchset) === null || _a === void 0 ? void 0 : _a.map(function (b, i) {
-              return generateNodeIds(b, id + "-" + i, depth + 1);
+              return generateNodeIds(b, "".concat(id, "-").concat(i), depth + 1);
           })) || [] });
   }
   function colorContrast(colorScheme, theme) {
@@ -4655,7 +4671,7 @@
           }
       }
       var proportion = ent / total;
-      var thresh = "hsl(240, 30%, " + 100 * Math.max(1 - ent / total / 3, 0.3) + "%)";
+      var thresh = "hsl(240, 30%, ".concat(100 * Math.max(1 - ent / total / 3, 0.3), "%)");
       if (proportion > 0.4) {
           if (l === letter) {
               return thresh;
@@ -4682,7 +4698,7 @@
           ctx.clearRect(0, 0, blockSize, blockSize);
           ctx.translate(-offsetX, rowHeight / 2 - offsetY);
           ctx.textAlign = 'center';
-          ctx.font = ctx.font.replace(/\d+px/, Math.max(8, rowHeight - 8) + "px");
+          ctx.font = ctx.font.replace(/\d+px/, "".concat(Math.max(8, rowHeight - 8), "px"));
           var leaves = hierarchy.leaves();
           var b = blockSize;
           // slice vertical rows, e.g. tree leaves, avoid negative slice
@@ -4863,7 +4879,7 @@
           React__default.createElement(core.CircularProgress, null),
           React__default.createElement(core.Typography, null, "Loading..."))) : (blocks2d.map(function (_a) {
           var bx = _a[0], by = _a[1];
-          return (React__default.createElement(MSABlock, { key: bx + "_" + by, model: model, offsetX: bx, offsetY: by }));
+          return (React__default.createElement(MSABlock, { key: "".concat(bx, "_").concat(by), model: model, offsetX: bx, offsetY: by }));
       }))));
   });
 
@@ -4934,7 +4950,7 @@
       if (num < 999) {
           return String(num);
       }
-      return mathPower(~~(num / 1000)) + "," + ("00" + ~~(num % 1000)).substr(-3, 3);
+      return "".concat(mathPower(~~(num / 1000)), ",").concat("00".concat(~~(num % 1000)).substr(-3, 3));
   }
   var useStyles$1 = core.makeStyles(function ( /* theme */) { return ({
       majorTickLabel: {
@@ -4960,7 +4976,7 @@
               .filter(function (tick) { return tick.type === 'major'; })
               .map(function (tick) {
               var x = (reversed ? end - tick.base : tick.base - start) / bpPerPx;
-              return (React__default.createElement("text", { x: x, y: 10, key: "label-" + tick.base, textAnchor: "middle", style: { fontSize: '11px' }, className: classes.majorTickLabel }, mathPower(tick.base + 1)));
+              return (React__default.createElement("text", { x: x, y: 10, key: "label-".concat(tick.base), textAnchor: "middle", style: { fontSize: '11px' }, className: classes.majorTickLabel }, mathPower(tick.base + 1)));
           })));
   }
   var Ruler = mobxReact.observer(function (_a) {
@@ -4994,9 +5010,9 @@
   var SettingsDialog = mobxReact.observer(function (_a) {
       var model = _a.model, onClose = _a.onClose, open = _a.open;
       var rowHeightInit = model.rowHeight, colWidthInit = model.colWidth, treeWidthInit = model.treeWidth, colorSchemeName = model.colorSchemeName, noTree = model.noTree;
-      var _b = React.useState("" + rowHeightInit), rowHeight = _b[0], setRowHeight = _b[1];
-      var _c = React.useState("" + colWidthInit), colWidth = _c[0], setColWidth = _c[1];
-      var _d = React.useState("" + treeWidthInit), treeWidth = _d[0], setTreeWidth = _d[1];
+      var _b = React.useState("".concat(rowHeightInit)), rowHeight = _b[0], setRowHeight = _b[1];
+      var _c = React.useState("".concat(colWidthInit)), colWidth = _c[0], setColWidth = _c[1];
+      var _d = React.useState("".concat(treeWidthInit)), treeWidth = _d[0], setTreeWidth = _d[1];
       function error(n) {
           return Number.isNaN(+n) || +n < 0;
       }
@@ -5028,7 +5044,7 @@
                       }, variant: "contained", color: "primary" }, "Submit")))));
   });
 
-  var version$1 = "1.2.10";
+  var version$1 = "1.3.1";
 
   function LicenseDialog(_a) {
       var onClose = _a.onClose, open = _a.open;
@@ -5046,7 +5062,7 @@
               React__default.createElement(core.DialogTitle, null, "About this plugin"),
               React__default.createElement(core.DialogContent, null,
                   React__default.createElement(core.Typography, null,
-                      "JBrowse 2 MSAView plugin ",
+                      "MSAView ",
                       version$1,
                       " (",
                       React__default.createElement(core.Link, { href: "https://github.com/gmod/jbrowse-plugin-msaview" }, "Github"),
@@ -5242,7 +5258,7 @@
                   model.setCurrentAlignment(+event.target.value);
                   model.setScrollX(0);
                   model.setScrollY(0);
-              } }, alignmentNames.map(function (option, index) { return (React__default.createElement("option", { key: option + "-" + index, value: index }, option)); }))) : null,
+              } }, alignmentNames.map(function (option, index) { return (React__default.createElement("option", { key: "".concat(option, "-").concat(index), value: index }, option)); }))) : null,
           React__default.createElement(InfoArea, { model: model }),
           React__default.createElement("div", { style: { flex: 1 } }),
           React__default.createElement(core.IconButton, { onClick: function () { return setAboutDialogVisible(true); } },
@@ -5596,7 +5612,7 @@
                   r,
                   ' ',
                   blanks.length
-                      ? " (gapped " + model.getPos(l) + ".." + model.getPos(r)
+                      ? " (gapped ".concat(model.getPos(l), "..").concat(model.getPos(r))
                       : ''),
               rows.map(function (_a, index) {
                   var key = _a[0], val = _a[1];
@@ -7229,7 +7245,7 @@
       };
       Object.defineProperty(StockholmMSA.prototype, "alignmentNames", {
           get: function () {
-              return this.data.map(function (aln, index) { var _a; return ((_a = aln.gf.DE) === null || _a === void 0 ? void 0 : _a[0]) || "Alignment " + (index + 1); });
+              return this.data.map(function (aln, index) { var _a; return ((_a = aln.gf.DE) === null || _a === void 0 ? void 0 : _a[0]) || "Alignment ".concat(index + 1); });
           },
           enumerable: false,
           configurable: true
@@ -7437,7 +7453,7 @@
           ctx.clearRect(0, 0, blockSize, rowHeight);
           ctx.translate(-offsetX, 0);
           ctx.textAlign = 'center';
-          ctx.font = ctx.font.replace(/\d+px/, Math.max(8, rowHeight - 8) + "px");
+          ctx.font = ctx.font.replace(/\d+px/, "".concat(Math.max(8, rowHeight - 8), "px"));
           var xStart = Math.max(0, Math.floor(offsetX / colWidth));
           var xEnd = Math.max(0, Math.ceil((offsetX + blockSize) / colWidth));
           var str = data === null || data === void 0 ? void 0 : data.slice(xStart, xEnd);
@@ -7549,12 +7565,12 @@
               if (associatedRowName) {
                   var s = model.rowSpecificBpToPx(associatedRowName, start - 1);
                   var e = model.rowSpecificBpToPx(associatedRowName, end);
-                  temp.addRect("" + index, s, e, rowHeight, feature);
+                  temp.addRect("".concat(index), s, e, rowHeight, feature);
               }
               else {
                   var s = model.globalBpToPx(start - 1);
                   var e = model.globalBpToPx(end);
-                  temp.addRect("" + index, s, e, rowHeight, feature);
+                  temp.addRect("".concat(index), s, e, rowHeight, feature);
               }
           });
           return temp;
@@ -7575,7 +7591,7 @@
           ctx.clearRect(0, 0, blockSize, height);
           ctx.translate(-offsetX, 0);
           ctx.textAlign = 'center';
-          ctx.font = ctx.font.replace(/\d+px/, Math.max(8, rowHeight - 8) + "px");
+          ctx.font = ctx.font.replace(/\d+px/, "".concat(Math.max(8, rowHeight - 8), "px"));
           var xStart = Math.max(0, Math.floor(offsetX / colWidth));
           ctx.fillStyle = 'goldenrod';
           layout.rectangles.forEach(function (value) {
@@ -7613,7 +7629,7 @@
           ctx.clearRect(0, 0, blockSize, height);
           ctx.translate(-offsetX, 0);
           ctx.textAlign = 'center';
-          ctx.font = ctx.font.replace(/\d+px/, Math.max(8, rowHeight - 8) + "px");
+          ctx.font = ctx.font.replace(/\d+px/, "".concat(Math.max(8, rowHeight - 8), "px"));
           ctx.fillStyle = 'black';
           ctx.textAlign = 'left';
           layout.rectangles.forEach(function (value) {
@@ -7819,12 +7835,12 @@
                       case 0:
                           _a.trys.push([0, 3, , 4]);
                           accession = self.accession;
-                          url = "https://www.uniprot.org/uniprot/" + accession + ".gff";
+                          url = "https://www.uniprot.org/uniprot/".concat(accession, ".gff");
                           return [4 /*yield*/, fetch(url)];
                       case 1:
                           response = _a.sent();
                           if (!response.ok) {
-                              throw new Error("HTTP " + response.status + " " + response.statusText + " fetching " + url);
+                              throw new Error("HTTP ".concat(response.status, " ").concat(response.statusText, " fetching ").concat(url));
                           }
                           return [4 /*yield*/, response.text()];
                       case 2:
@@ -7955,7 +7971,9 @@
           self.selectedStructures = [];
       },
       setError: function (error) {
-          console.error(error);
+          if (error) {
+              console.error(error);
+          }
           self.error = error;
       },
       setMousePos: function (col, row) {
@@ -8161,9 +8179,9 @@
           return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getDetails()) || {};
       },
       getRowDetails: function (name) {
-          var _a;
+          var _a, _b;
           //@ts-ignore
-          var details = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getRowDetails(name);
+          var details = (_b = (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getRowDetails) === null || _b === void 0 ? void 0 : _b.call(_a, name);
           var matches = name.match(/\S+\/(\d+)-(\d+)/);
           return __assign$3(__assign$3({}, details), (matches && { range: { start: +matches[1], end: +matches[2] } }));
       },
@@ -8432,7 +8450,7 @@
                                   ? Object.entries(region.attributes)
                                       .map(function (_a) {
                                       var k = _a[0], v = _a[1];
-                                      return k + "=" + v.join(',');
+                                      return "".concat(k, "=").concat(v.join(','));
                                   })
                                       .join(';')
                                   : '.';