react-msaview 3.1.7 → 3.1.8

package/dist/model.js.map

@@ -1 +1 @@
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package/dist/parseGFF.d.ts

@@ -0,0 +1,10 @@
+export declare function parseGFF(str?: string): {
+    seq_id: string;
+    source: string;
+    type: string;
+    start: number;
+    end: number;
+    score: number;
+    strand: string;
+    phase: string;
+}[] | undefined;

package/dist/parseGFF.js

@@ -0,0 +1,29 @@
+export function parseGFF(str) {
+    return str
+        ?.split('\n')
+        .map(f => f.trim())
+        .filter(f => !!f && !f.startsWith('#'))
+        .map(f => {
+        const [seq_id, source, type, start, end, score, strand, phase, col9] = f.split('\t');
+        return {
+            seq_id,
+            source,
+            type,
+            start: +start,
+            end: +end,
+            score: +score,
+            strand,
+            phase,
+            ...Object.fromEntries(col9
+                .split(';')
+                .map(f => f.trim())
+                .filter(f => !!f)
+                .map(f => f.split('='))
+                .map(([key, val]) => [
+                key.trim(),
+                decodeURIComponent(val).trim().split(',').join(' '),
+            ])),
+        };
+    });
+}
+//# sourceMappingURL=parseGFF.js.map

package/dist/parseGFF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"parseGFF.js","sourceRoot":"","sources":["../src/parseGFF.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG;QACR,EAAE,KAAK,CAAC,IAAI,CAAC;SACZ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM;YACN,MAAM;YACN,IAAI;YACJ,KAAK,EAAE,CAAC,KAAK;YACb,GAAG,EAAE,CAAC,GAAG;YACT,KAAK,EAAE,CAAC,KAAK;YACb,MAAM;YACN,KAAK;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI;iBACD,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAG,CAAC,IAAI,EAAE;gBACV,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;aACpD,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/renderToSvg.js

@@ -2,10 +2,11 @@ import React from 'react';
 import { createRoot } from 'react-dom/client';
 import { when } from 'mobx';
 import { renderToStaticMarkup } from '@jbrowse/core/util';
-import { renderTreeCanvas } from './components/TreePanel/renderTreeCanvas';
-import { renderMSABlock } from './components/MSAPanel/renderMSABlock';
+import { renderTreeCanvas } from './components/tree/renderTreeCanvas';
+import { renderMSABlock } from './components/msa/renderMSABlock';
 import { colorContrast } from './util';
-import MinimapSVG from './components/MinimapSVG';
+import MinimapSVG from './components/minimap/MinimapSVG';
+import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock';
 export async function renderToSvg(model, opts) {
     await when(() => !!model.initialized);
     const { width, height, scrollX, scrollY } = model;
@@ -67,11 +68,21 @@ async function render({ width, height, offsetX, offsetY, theme, model, includeMi
 //   )
 // }
 function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context, }) {
-    const clipId = 'tree';
+    const clipId1 = 'tree';
+    const clipId2 = 'msa';
     const { treeAreaWidth, colorScheme } = model;
     const contrastScheme = colorContrast(colorScheme, theme);
     const ctx1 = Context(width, height);
     const ctx2 = Context(width, height);
+    renderBoxFeatureCanvasBlock({
+        ctx: ctx2,
+        offsetX,
+        offsetY,
+        model,
+        blockSizeYOverride: height,
+        highResScaleFactorOverride: 1,
+    });
+    const msaAreaWidth = width - treeAreaWidth;
     renderTreeCanvas({
         model,
         offsetY,
@@ -87,18 +98,21 @@ function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context,
         offsetX,
         contrastScheme,
         ctx: ctx2,
-        blockSizeXOverride: width - treeAreaWidth,
+        blockSizeXOverride: msaAreaWidth,
         blockSizeYOverride: height,
         highResScaleFactorOverride: 1,
     });
     return (React.createElement(React.Fragment, null,
         React.createElement("defs", null,
-            React.createElement("clipPath", { id: clipId },
+            React.createElement("clipPath", { id: clipId1 },
                 React.createElement("rect", { x: 0, y: 0, width: treeAreaWidth, height: height }))),
-        React.createElement("g", { clipPath: `url(#${clipId})`, 
+        React.createElement("defs", null,
+            React.createElement("clipPath", { id: clipId2 },
+                React.createElement("rect", { x: 0, y: 0, width: msaAreaWidth, height: height }))),
+        React.createElement("g", { clipPath: `url(#${clipId1})`, 
             /* eslint-disable-next-line react/no-danger */
             dangerouslySetInnerHTML: { __html: ctx1.getSvg().innerHTML } }),
-        React.createElement("g", { transform: `translate(${treeAreaWidth} 0)`, 
+        React.createElement("g", { clipPath: `url(#${clipId2})`, transform: `translate(${treeAreaWidth} 0)`, 
             /* eslint-disable-next-line react/no-danger */
             dangerouslySetInnerHTML: { __html: ctx2.getSvg().innerHTML } })));
 }
@@ -113,6 +127,6 @@ function SvgWrapper({ width, height, children, }) {
     return (React.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width, height].toString() }, children));
 }
 function NullWrapper({ children }) {
-    return React.createElement(React.Fragment, null, children);
+    return children;
 }
 //# sourceMappingURL=renderToSvg.js.map

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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+{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAKzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oCAAoC,CAAA;AACrE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAA;AAChE,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAA;AAEtC,OAAO,UAAU,MAAM,iCAAiC,CAAA;AACxD,OAAO,EAAE,2BAA2B,EAAE,MAAM,8CAA8C,CAAA;AAE1F,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,KAAmB,EACnB,IAAoE;IAEpE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACrC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACjD,MAAM,EAAE,UAAU,EAAE,KAAK,EAAE,cAAc,EAAE,GAAG,IAAI,CAAA;IAElD,IAAI,UAAU,KAAK,QAAQ,EAAE,CAAC;QAC5B,OAAO,MAAM,CAAC;YACZ,KAAK,EAAE,KAAK,CAAC,UAAU,GAAG,KAAK,CAAC,aAAa;YAC7C,MAAM,EAAE,KAAK,CAAC,WAAW;YACzB,KAAK;YACL,KAAK;YACL,OAAO,EAAE,CAAC;YACV,OAAO,EAAE,CAAC;YACV,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;SAAM,IAAI,UAAU,KAAK,UAAU,EAAE,CAAC;QACrC,OAAO,MAAM,CAAC;YACZ,KAAK;YACL,MAAM;YACN,KAAK;YACL,KAAK;YACL,OAAO,EAAE,OAAO;YAChB,OAAO,EAAE,CAAC,OAAO;YACjB,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAA;IACxC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,MAAM,CAAC,EACpB,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,KAAK,EACL,KAAK,EACL,cAAc,GASf;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,OAAO,GAAG,cAAc,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,WAAW,CAAA;IAE7D,OAAO,oBAAoB,CACzB,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM;QACtC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK;YACnB,oBAAC,aAAa,IACZ,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,OAAO,EAChB,OAAO,EAAE,OAAO,EAChB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,GACd,CACM,CACC,EACb,UAAU,CACX,CAAA;AACH,CAAC;AAED,iEAAiE;AACjE,4CAA4C;AAC5C,0BAA0B;AAC1B,aAAa;AACb,8BAA8B;AAC9B,eAAe;AACf,iCAAiC;AACjC,uEAAuE;AACvE,sBAAsB;AACtB,gBAAgB;AAChB,WAAW;AACX,uCAAuC;AACvC,yDAAyD;AACzD,wEAAwE;AACxE,WAAW;AACX,WAAW;AACX,sDAAsD;AACtD,yDAAyD;AACzD,wEAAwE;AACxE,WAAW;AACX,iBAAiB;AACjB,MAAM;AACN,IAAI;AAEJ,SAAS,aAAa,CAAC,EACrB,KAAK,EACL,KAAK,EACL,KAAK,EACL,MAAM,EACN,OAAO,EACP,OAAO,EACP,OAAO,GAYR;IACC,MAAM,OAAO,GAAG,MAAM,CAAA;IACtB,MAAM,OAAO,GAAG,KAAK,CAAA;IACrB,MAAM,EAAE,aAAa,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,CAAA;IACxD,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,2BAA2B,CAAC;QAC1B,GAAG,EAAE,IAAI;QACT,OAAO;QACP,OAAO;QACP,KAAK;QACL,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,MAAM,YAAY,GAAG,KAAK,GAAG,aAAa,CAAA;IAC1C,gBAAgB,CAAC;QACf,KAAK;QACL,OAAO;QACP,GAAG,EAAE,IAAI;QACT,KAAK;QACL,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,cAAc,CAAC;QACb,KAAK;QACL,KAAK;QACL,OAAO;QACP,OAAO;QACP,cAAc;QACd,GAAG,EAAE,IAAI;QACT,kBAAkB,EAAE,YAAY;QAChC,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,OAAO;gBACnB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,MAAM,EAAE,MAAM,GAAI,CACjD,CACN;QACP;YACE,kCAAU,EAAE,EAAE,OAAO;gBACnB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,GAAI,CAChD,CACN;QAEP,2BACE,QAAQ,EAAE,QAAQ,OAAO,GAAG;YAC5B,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D;QACF,2BACE,QAAQ,EAAE,QAAQ,OAAO,GAAG,EAC5B,SAAS,EAAE,aAAa,aAAa,KAAK;YAC1C,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D,CACD,CACJ,CAAA;AACH,CAAC;AAED,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,QAAQ,GAIT;IACC,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAE9C,OAAO,CACL;QACE,2BAAG,SAAS,EAAE,aAAa,aAAa,KAAK;YAC3C,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B;QAEJ,2BAAG,SAAS,EAAE,eAAe,aAAa,GAAG,IAAG,QAAQ,CAAK,CAC5D,CACJ,CAAA;AACH,CAAC;AAED,SAAS,UAAU,CAAC,EAClB,KAAK,EACL,MAAM,EACN,QAAQ,GAKT;IACC,OAAO,CACL,6BACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAC,4BAA4B,EAClC,UAAU,EAAC,8BAA8B,EACzC,OAAO,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,QAAQ,EAAE,IAExC,QAAQ,CACL,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EAAE,QAAQ,EAAiC;IAC9D,OAAO,QAAQ,CAAA;AACjB,CAAC"}

package/dist/reparseTree.d.ts

@@ -0,0 +1,2 @@
+import { NodeWithIds } from './util';
+export declare function reparseTree(tree: NodeWithIds): NodeWithIds;

package/dist/reparseTree.js

@@ -0,0 +1,13 @@
+export function reparseTree(tree) {
+    return {
+        ...tree,
+        branchset: tree.branchset.map(r => r.branchset.length
+            ? reparseTree(r)
+            : {
+                branchset: [r],
+                id: `${r.id}-leafnode`,
+                name: `${r.name}-hidden`,
+            }),
+    };
+}
+//# sourceMappingURL=reparseTree.js.map

package/dist/reparseTree.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"reparseTree.js","sourceRoot":"","sources":["../src/reparseTree.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,WAAW,CAAC,IAAiB;IAC3C,OAAO;QACL,GAAG,IAAI;QACP,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAChC,CAAC,CAAC,SAAS,CAAC,MAAM;YAChB,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC;YAChB,CAAC,CAAC;gBACE,SAAS,EAAE,CAAC,CAAC,CAAC;gBACd,EAAE,EAAE,GAAG,CAAC,CAAC,EAAE,WAAW;gBACtB,IAAI,EAAE,GAAG,CAAC,CAAC,IAAI,SAAS;aACzB,CACN;KACF,CAAA;AACH,CAAC"}

package/dist/util.d.ts

@@ -26,19 +26,13 @@ export declare function generateNodeIds(tree: Node, parent?: string, depth?: num
 export declare function colorContrast(colorScheme: Record<string, string>, theme: Theme): {
     [k: string]: string;
 };
-export declare function parseGFF(str?: string): {
-    seq_id: string;
-    source: string;
-    type: string;
-    start: number;
-    end: number;
-    score: number;
-    strand: string;
-    phase: string;
-}[] | undefined;
 export declare function skipBlanks(blanks: number[], arg: string | string[]): string;
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function collapse(d: HierarchyNode<NodeWithIds>): void;
 export declare function clamp(min: number, num: number, max: number): number;
+export declare function len(a: {
+    end: number;
+    start: number;
+}): number;
 export {};

package/dist/util.js

@@ -20,34 +20,6 @@ export function colorContrast(colorScheme, theme) {
         theme.palette.getContrastText(colord(color).toHex()),
     ]);
 }
-export function parseGFF(str) {
-    return str
-        ?.split('\n')
-        .map(f => f.trim())
-        .filter(f => !!f && !f.startsWith('#'))
-        .map(f => {
-        const [seq_id, source, type, start, end, score, strand, phase, col9] = f.split('\t');
-        return {
-            seq_id,
-            source,
-            type,
-            start: +start,
-            end: +end,
-            score: +score,
-            strand,
-            phase,
-            ...Object.fromEntries(col9
-                .split(';')
-                .map(f => f.trim())
-                .filter(f => !!f)
-                .map(f => f.split('='))
-                .map(([key, val]) => [
-                key.trim(),
-                decodeURIComponent(val).trim().split(',').join(' '),
-            ])),
-        };
-    });
-}
 export function skipBlanks(blanks, arg) {
     let s = '';
     let b = 0;
@@ -90,4 +62,7 @@ export function collapse(d) {
 export function clamp(min, num, max) {
     return Math.min(Math.max(num, min), max);
 }
+export function len(a) {
+    return a.end - a.start;
+}
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAE9B,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAE9C,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,MAAM,UAAU,SAAS,CACvB,GAAsB,EACtB,EAAsC;IAEtC,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAwBD,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,SAAS,EACP,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC3B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,WAAmC,EACnC,KAAY;IAEZ,OAAO,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QACjD,MAAM;QACN,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;KACrD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,MAAgB,EAAE,GAAsB;IACjE,IAAI,CAAC,GAAG,EAAE,CAAA;IACV,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpC,IAAI,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,CAA6B;IACpD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,mBAAmB;QACnB,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,QAAQ,CAAA;QACxB,mBAAmB;QACnB,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAC7B,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,GAAW,EAAE,GAAW,EAAE,GAAW;IACzD,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.1.7";
+export declare const version = "3.1.8";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.7';
+export const version = '3.1.8';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,9 +1,10 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.7",
+  "version": "3.1.8",
   "license": "MIT",
   "main": "dist/index.js",
+  "module": "dist/index.js",
   "files": [
     "dist",
     "bundle",
@@ -15,6 +16,7 @@
   "scripts": {
     "clean": "rimraf dist",
     "prebuild": "npm run clean",
+    "test": "jest",
     "prepublishOnly": "node output-version.js > src/version.ts && git add -A src && git commit -m '[skip ci] Bump version.ts'",
     "build:esm": "tsc",
     "build:bundle": "rollup -c --bundleConfigAsCjs",
@@ -35,6 +37,10 @@
     "react-dom": ">=16.8.0"
   },
   "dependencies": {
+    "@types/react": "^18.2.55",
+    "@types/react-dom": "^18.2.19",
+    "@typescript-eslint/eslint-plugin": "^7.1.0",
+    "@typescript-eslint/parser": "^7.1.0",
     "clustal-js": "^2.0.0",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",
@@ -43,8 +49,12 @@
     "file-saver": "^2.0.5",
     "normalize-wheel": "^1.0.1",
     "rbush": "^3.0.1",
+    "react-error-boundary": "^4.0.13",
+    "rollup": "^4.9.1",
     "stockholm-js": "^1.0.10",
     "svgcanvas": "^2.5.0",
-    "tss-react": "^4.8.3"
+    "tss-react": "^4.8.3",
+    "typescript": "^5.3.3",
+    "vite": "^5.0.10"
   }
 }

package/src/components/Checkbox2.tsx

@@ -0,0 +1,34 @@
+import React from 'react'
+import {
+  Checkbox,
+  FormControlLabel,
+  FormControlLabelProps,
+} from '@mui/material'
+
+function FormControlLabel2(rest: FormControlLabelProps) {
+  return (
+    <div>
+      <FormControlLabel {...rest} />
+    </div>
+  )
+}
+export default function Checkbox2({
+  checked,
+  label,
+  disabled,
+  onChange,
+}: {
+  checked: boolean
+  label: string
+  disabled?: boolean
+  onChange: () => void
+}) {
+  return (
+    <FormControlLabel2
+      control={
+        <Checkbox disabled={disabled} checked={checked} onChange={onChange} />
+      }
+      label={label}
+    />
+  )
+}

package/src/components/Loading.tsx

@@ -1,25 +1,41 @@
 import React from 'react'
-
 import { observer } from 'mobx-react'
-import { Typography } from '@mui/material'
+import { Button, Typography } from '@mui/material'
+import { ErrorBoundary } from 'react-error-boundary'
+import { ErrorMessage } from '@jbrowse/core/ui'
 
 // locals
-import ImportForm from './ImportForm'
+import ImportForm from './import/ImportForm'
 import MSAView from './MSAView'
 import { MsaViewModel } from '../model'
 
+function Reset({ model, error }: { model: MsaViewModel; error: unknown }) {
+  return (
+    <div>
+      <ErrorMessage error={error} />
+      <Button variant="contained" color="primary" onClick={() => model.reset()}>
+        Return to import form
+      </Button>
+    </div>
+  )
+}
+
 const Loading = observer(function ({ model }: { model: MsaViewModel }) {
-  const { done, initialized } = model
+  const { isLoading, initialized } = model
 
   return (
     <div>
-      {!initialized ? (
-        <ImportForm model={model} />
-      ) : !done ? (
-        <Typography variant="h4">Loading...</Typography>
-      ) : (
-        <MSAView model={model} />
-      )}
+      <ErrorBoundary
+        fallbackRender={props => <Reset model={model} error={props.error} />}
+      >
+        {!initialized ? (
+          <ImportForm model={model} />
+        ) : isLoading ? (
+          <Typography variant="h4">Loading...</Typography>
+        ) : (
+          <MSAView model={model} />
+        )}
+      </ErrorBoundary>
     </div>
   )
 })

package/src/components/MSAView.tsx

@@ -4,12 +4,11 @@ import { observer } from 'mobx-react'
 // locals
 import { HorizontalResizeHandle, VerticalResizeHandle } from './ResizeHandles'
 import { MsaViewModel } from '../model'
-import TreeRuler from './TreePanel/TreeRuler'
-import Header from './Header'
-import Track from './Track'
-import MSAPanel from './MSAPanel'
-import TreePanel from './TreePanel'
-import Minimap from './Minimap'
+import TreeRuler from './tree/TreeRuler'
+import Header from './header/Header'
+import MSAPanel from './msa/MSAPanel'
+import TreePanel from './tree/TreePanel'
+import Minimap from './minimap/Minimap'
 
 function TopArea({ model }: { model: MsaViewModel }) {
   return (
@@ -30,13 +29,10 @@ function MainArea({ model }: { model: MsaViewModel }) {
 }
 
 const View = observer(function ({ model }: { model: MsaViewModel }) {
-  const { turnedOnTracks } = model
   return (
     <div style={{ position: 'relative' }}>
       <TopArea model={model} />
-      {turnedOnTracks?.map(track => (
-        <Track key={track.model.id} model={model} track={track} />
-      ))}
+
       <MainArea model={model} />
     </div>
   )

package/src/components/SequenceTextArea.tsx

@@ -0,0 +1,63 @@
+import React, { useState } from 'react'
+import { Button, TextField } from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+import copy from 'copy-to-clipboard'
+
+// locals
+import Checkbox2 from './Checkbox2'
+
+const useStyles = makeStyles()({
+  textAreaFont: {
+    fontFamily: 'Courier New',
+  },
+  dialogContent: {
+    background: 'lightgrey',
+    margin: 4,
+    minWidth: '80em',
+  },
+})
+
+export default function SequenceTextArea({ str }: { str: [string, string][] }) {
+  const { classes } = useStyles()
+  const [copied, setCopied] = useState(false)
+  const [showGaps, setShowGaps] = useState(false)
+
+  const disp = str
+    .map(([s1, s2]) => `>${s1}\n${showGaps ? s2 : s2.replaceAll('-', '')}`)
+    .join('\n')
+  return (
+    <>
+      <Button
+        color="primary"
+        variant="contained"
+        onClick={() => {
+          copy(disp)
+          setCopied(true)
+          setTimeout(() => setCopied(false), 500)
+        }}
+      >
+        {copied ? 'Copied!' : 'Copy to clipboard'}
+      </Button>
+      <Checkbox2
+        label="Show gaps"
+        checked={showGaps}
+        onChange={() => setShowGaps(!showGaps)}
+      />
+      <TextField
+        variant="outlined"
+        multiline
+        className={classes.dialogContent}
+        minRows={5}
+        maxRows={10}
+        fullWidth
+        value={disp}
+        InputProps={{
+          readOnly: true,
+          classes: {
+            input: classes.textAreaFont,
+          },
+        }}
+      />
+    </>
+  )
+}