react-msaview 4.4.6 → 4.5.0

package/dist/parsers/ClustalMSA.d.ts

@@ -5,12 +5,12 @@ export default class ClustalMSA {
     getMSA(): {
         consensus: string;
         alns: {
-            id: string;
+            id: string | undefined;
             seq: string;
         }[];
         header: {
             info: string;
-            version: string;
+            version: string | undefined;
         };
     };
     getRow(name: string): string;
@@ -18,9 +18,9 @@ export default class ClustalMSA {
     getRowData(): undefined;
     getHeader(): {
         info: string;
-        version: string;
+        version: string | undefined;
     };
-    getNames(): string[];
+    getNames(): (string | undefined)[];
     getStructures(): {};
     get alignmentNames(): never[];
     getTree(): NodeWithIds;

package/dist/parsers/ClustalMSA.js

@@ -33,7 +33,9 @@ export default class ClustalMSA {
             id: 'root',
             name: 'root',
             noTree: true,
-            children: this.getNames().map(name => ({
+            children: this.getNames()
+                .filter((name) => name !== undefined)
+                .map(name => ({
                 id: name,
                 name,
                 children: [],

package/dist/parsers/ClustalMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/parsers/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAIlC,MAAM,CAAC,OAAO,OAAO,UAAU;IACrB,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAE,CAAC,GAAG,CAAC,MAAM,CAAA;IACrC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE;iBACtB,MAAM,CAAC,CAAC,IAAI,EAAkB,EAAE,CAAC,IAAI,KAAK,SAAS,CAAC;iBACpD,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACZ,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,QAAQ,EAAE,EAAE;aACb,CAAC,CAAC;SACN,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/parsers/FastaMSA.js

@@ -1,22 +1,23 @@
-function parseSmallFasta(text) {
-    return text
-        .split('>')
-        .filter(t => /\S/.test(t))
-        .map(entryText => {
-        const [defLine, ...seqLines] = entryText.split('\n');
-        const [id, ...description] = defLine.split(' ');
-        const descriptionStr = description.join(' ');
-        const seqLinesStr = seqLines.join('');
-        const sequence = seqLinesStr.replaceAll(/\s/g, '');
-        return { id, description: descriptionStr, sequence };
-    });
-}
 export default class FastaMSA {
     MSA;
     constructor(text) {
-        this.MSA = {
-            seqdata: Object.fromEntries(parseSmallFasta(text).map(m => [m.id, m.sequence])),
-        };
+        const seqdata = {};
+        for (const entry of text.split('>')) {
+            if (!/\S/.test(entry)) {
+                continue;
+            }
+            const newlineIdx = entry.indexOf('\n');
+            if (newlineIdx === -1) {
+                continue;
+            }
+            const defLine = entry.slice(0, newlineIdx);
+            const spaceIdx = defLine.indexOf(' ');
+            const id = spaceIdx === -1 ? defLine : defLine.slice(0, spaceIdx);
+            if (id) {
+                seqdata[id] = entry.slice(newlineIdx + 1).replaceAll(/\s/g, '');
+            }
+        }
+        this.MSA = { seqdata };
     }
     getMSA() {
         return this.MSA;

package/dist/parsers/FastaMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/parsers/FastaMSA.ts"],"names":[],"mappings":"AAEA,SAAS,eAAe,CAAC,IAAY;IACnC,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,CAAC,EAAE,EAAE,GAAG,WAAW,CAAC,GAAG,OAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAChD,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrC,MAAM,QAAQ,GAAG,WAAW,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QAClD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,cAAc,EAAE,QAAQ,EAAE,CAAA;IACtD,CAAC,CAAC,CAAA;AACN,CAAC;AACD,MAAM,CAAC,OAAO,OAAO,QAAQ;IACnB,GAAG,CAAqC;IAChD,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG;YACT,OAAO,EAAE,MAAM,CAAC,WAAW,CACzB,eAAe,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CACnD;SACF,CAAA;IACH,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}
+{"version":3,"file":"FastaMSA.js","sourceRoot":"","sources":["../../src/parsers/FastaMSA.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,OAAO,QAAQ;IACnB,GAAG,CAAqC;IAEhD,YAAY,IAAY;QACtB,MAAM,OAAO,GAA2B,EAAE,CAAA;QAC1C,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;YACtC,IAAI,UAAU,KAAK,CAAC,CAAC,EAAE,CAAC;gBACtB,SAAQ;YACV,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;YAC1C,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACrC,MAAM,EAAE,GAAG,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjE,IAAI,EAAE,EAAE,CAAC;gBACP,OAAO,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;YACjE,CAAC;QACH,CAAC;QACD,IAAI,CAAC,GAAG,GAAG,EAAE,OAAO,EAAE,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,SAAS;QACP,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,IAAI;gBACR,QAAQ,EAAE,EAAE;gBACZ,IAAI;aACL,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

package/dist/renderToSvg.d.ts

@@ -3,6 +3,7 @@ import type { Theme } from '@mui/material';
 export interface ExportSvgOptions {
     theme: Theme;
     includeMinimap?: boolean;
+    includeTracks?: boolean;
     exportType: string;
 }
 export declare function renderToSvg(model: MsaViewModel, opts: ExportSvgOptions): Promise<string>;

package/dist/renderToSvg.js

@@ -5,56 +5,66 @@ import { when } from 'mobx';
 import MinimapSVG from './components/minimap/MinimapSVG';
 import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock';
 import { renderMSABlock } from './components/msa/renderMSABlock';
+import { renderAllTracks } from './components/tracks/renderTracksSvg';
 import { renderTreeCanvas } from './components/tree/renderTreeCanvas';
 import { colorContrast } from './util';
 export async function renderToSvg(model, opts) {
     await when(() => !!model.dataInitialized);
-    const { width, height, scrollX, scrollY } = model;
-    const { exportType, theme, includeMinimap } = opts;
+    const { width, height, scrollX, scrollY, totalTrackAreaHeight } = model;
+    const { exportType, theme, includeMinimap, includeTracks } = opts;
+    const trackHeight = includeTracks ? totalTrackAreaHeight : 0;
     if (exportType === 'entire') {
         return render({
             width: model.totalWidth + model.treeAreaWidth,
-            height: model.totalHeight,
+            height: model.totalHeight + trackHeight,
+            contentHeight: model.totalHeight,
+            trackHeight,
             theme,
             model,
             offsetY: 0,
             offsetX: 0,
             includeMinimap,
+            includeTracks,
         });
     }
     if (exportType === 'viewport') {
         return render({
             width,
-            height,
+            height: height + (includeMinimap ? model.minimapHeight : 0) + trackHeight,
+            contentHeight: height,
+            trackHeight,
             theme,
             model,
-            offsetY: scrollY,
+            offsetY: -scrollY,
             offsetX: -scrollX,
             includeMinimap,
+            includeTracks,
         });
     }
     throw new Error('unknown export type');
 }
-async function render({ width, height, offsetX, offsetY, theme, model, includeMinimap, }) {
+async function render({ width, height, contentHeight, trackHeight, offsetX, offsetY, theme, model, includeMinimap, includeTracks, }) {
     const { Context } = await import('svgcanvas');
     const Wrapper = includeMinimap ? MinimapWrapper : NullWrapper;
     return renderToStaticMarkup(React.createElement(SvgWrapper, { width: width, height: height },
         React.createElement(Wrapper, { model: model },
-            React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, height: height }))));
+            includeTracks && trackHeight > 0 ? (React.createElement(TrackRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, width: width, trackHeight: trackHeight })) : null,
+            React.createElement("g", { transform: trackHeight > 0 ? `translate(0 ${trackHeight})` : undefined },
+                React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, contentHeight: contentHeight })))));
 }
-function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context, }) {
-    const clipId1 = 'tree';
-    const clipId2 = 'msa';
-    const { treeAreaWidth, colorScheme } = model;
+function CoreRendering({ model, theme, width, contentHeight, offsetX, offsetY, Context, }) {
+    const { treeAreaWidth, colorScheme, id } = model;
+    const clipId1 = `tree-${id}`;
+    const clipId2 = `msa-${id}`;
     const contrastScheme = colorContrast(colorScheme, theme);
-    const ctx1 = Context(width, height);
-    const ctx2 = Context(width, height);
+    const ctx1 = Context(width, contentHeight);
+    const ctx2 = Context(width, contentHeight);
     renderBoxFeatureCanvasBlock({
         ctx: ctx2,
         offsetX,
         offsetY,
         model,
-        blockSizeYOverride: height,
+        blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });
     const msaAreaWidth = width - treeAreaWidth;
@@ -63,7 +73,7 @@ function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context,
         offsetY,
         ctx: ctx1,
         theme,
-        blockSizeYOverride: height,
+        blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });
     renderMSABlock({
@@ -74,19 +84,39 @@ function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context,
         contrastScheme,
         ctx: ctx2,
         blockSizeXOverride: msaAreaWidth,
-        blockSizeYOverride: height,
+        blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });
     return (React.createElement(React.Fragment, null,
         React.createElement("defs", null,
             React.createElement("clipPath", { id: clipId1 },
-                React.createElement("rect", { x: 0, y: 0, width: treeAreaWidth, height: height }))),
+                React.createElement("rect", { x: 0, y: 0, width: treeAreaWidth, height: contentHeight }))),
         React.createElement("defs", null,
             React.createElement("clipPath", { id: clipId2 },
-                React.createElement("rect", { x: 0, y: 0, width: msaAreaWidth, height: height }))),
+                React.createElement("rect", { x: 0, y: 0, width: msaAreaWidth, height: contentHeight }))),
         React.createElement("g", { clipPath: `url(#${clipId1})`, dangerouslySetInnerHTML: { __html: ctx1.getSvg().innerHTML } }),
         React.createElement("g", { clipPath: `url(#${clipId2})`, transform: `translate(${treeAreaWidth} 0)`, dangerouslySetInnerHTML: { __html: ctx2.getSvg().innerHTML } })));
 }
+function TrackRendering({ model, theme, width, trackHeight, offsetX, Context, }) {
+    const { treeAreaWidth, colorScheme, id } = model;
+    const clipId = `tracks-${id}`;
+    const contrastScheme = colorContrast(colorScheme, theme);
+    const msaAreaWidth = width - treeAreaWidth;
+    const ctx = Context(msaAreaWidth, trackHeight);
+    renderAllTracks({
+        model,
+        ctx,
+        offsetX,
+        contrastScheme,
+        blockSizeXOverride: msaAreaWidth,
+        highResScaleFactorOverride: 1,
+    });
+    return (React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
+        React.createElement("defs", null,
+            React.createElement("clipPath", { id: clipId },
+                React.createElement("rect", { x: 0, y: 0, width: msaAreaWidth, height: trackHeight }))),
+        React.createElement("g", { clipPath: `url(#${clipId})`, dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML } })));
+}
 function MinimapWrapper({ model, children, }) {
     const { minimapHeight, treeAreaWidth } = model;
     return (React.createElement(React.Fragment, null,

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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package/dist/rowCoordinateCalculations.js

@@ -7,6 +7,8 @@ export function mouseOverCoordToGlobalCoord(blanks, position) {
     // Iterate until we reach the target mouse position
     while (mousePosition < position) {
         // Skip any blank positions in the sequence
+        // Check if the next position (globalPosition + 1) is blank by comparing
+        // blanks[blankArrayIndex] - 1 with current globalPosition
         while (blankArrayIndex < blanksLen &&
             blanks[blankArrayIndex] - 1 === globalPosition) {
             blankArrayIndex++;

package/dist/rowCoordinateCalculations.js.map

@@ -1 +1 @@
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+{"version":3,"file":"rowCoordinateCalculations.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC,MAAM,UAAU,2BAA2B,CACzC,MAAgB,EAChB,QAAgB;IAEhB,IAAI,aAAa,GAAG,CAAC,CAAA,CAAC,wCAAwC;IAC9D,IAAI,eAAe,GAAG,CAAC,CAAA,CAAC,oCAAoC;IAC5D,IAAI,cAAc,GAAG,CAAC,CAAA,CAAC,gDAAgD;IACvE,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAA;IAE/B,mDAAmD;IACnD,OAAO,aAAa,GAAG,QAAQ,EAAE,CAAC;QAChC,2CAA2C;QAC3C,wEAAwE;QACxE,0DAA0D;QAC1D,OACE,eAAe,GAAG,SAAS;YAC3B,MAAM,CAAC,eAAe,CAAE,GAAG,CAAC,KAAK,cAAc,EAC/C,CAAC;YACD,eAAe,EAAE,CAAA;YACjB,cAAc,EAAE,CAAA;QAClB,CAAC;QAED,wBAAwB;QACxB,aAAa,EAAE,CAAA;QACf,cAAc,EAAE,CAAA;IAClB,CAAC;IAED,OAAO,cAAc,CAAA;AACvB,CAAC;AAED,MAAM,UAAU,6BAA6B,CAAC,GAAW,EAAE,QAAgB;IACzE,4CAA4C;IAC5C,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,8BAA8B;IAC9B,IAAI,eAAe,GAAG,CAAC,CAAA;IACvB,MAAM,cAAc,GAAG,GAAG,CAAC,MAAM,CAAA;IAEjC,gEAAgE;IAChE,OAAO,eAAe,GAAG,QAAQ,IAAI,eAAe,GAAG,cAAc,EAAE,CAAC;QACtE,mEAAmE;QACnE,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,eAAe,CAAC,CAAC,EAAE,CAAC;YACnC,WAAW,EAAE,CAAA;QACf,CAAC;QACD,eAAe,EAAE,CAAA;IACnB,CAAC;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,MAAM,UAAU,kCAAkC,CAAC,EACjD,OAAO,EACP,QAAQ,EACR,MAAM,EACN,MAAM,GAMP;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAC/B,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,+BAA+B,CAAC;YAC9B,GAAG;YACH,QAAQ;YACR,MAAM;SACP,CAAC;QACJ,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,MAAM,UAAU,+BAA+B,CAAC,EAC9C,GAAG,EACH,MAAM,EACN,QAAQ,GAKT;IACC,yDAAyD;IACzD,MAAM,SAAS,GAAG,2BAA2B,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IAC/D,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAA;IAEzB,iDAAiD;IACjD,IAAI,SAAS,GAAG,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC;QAClD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,qDAAqD;IACrD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACjD,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,WAAW,EAAE,CAAA;QACf,CAAC;IACH,CAAC;IAED,uEAAuE;IACvE,OAAO,SAAS,GAAG,MAAM,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAA;AACrD,CAAC"}

package/dist/types.d.ts

@@ -11,13 +11,12 @@ export interface BasicTrackModel {
 }
 export interface TextTrackModel extends BasicTrackModel {
     customColorScheme?: Record<string, string>;
-    data: string;
+    data?: string;
 }
-export interface ITextTrack {
+export interface BasicTrack {
     ReactComponent: React.FC<any>;
     model: TextTrackModel;
 }
-export type BasicTrack = ITextTrack;
 export interface Node {
     children?: Node[];
     name?: string;

package/dist/util.js

@@ -21,17 +21,25 @@ export function colorContrast(colorScheme, theme) {
     ]);
 }
 export function skipBlanks(blanks, arg) {
-    let s = '';
-    let b = 0;
-    for (let j = 0, l = arg.length; j < l; j++) {
-        if (j === blanks[b]) {
-            b++;
-        }
-        else {
-            s += arg[j];
+    if (blanks.length === 0) {
+        return typeof arg === 'string' ? arg : arg.join('');
+    }
+    const chunks = [];
+    let lastEnd = 0;
+    for (const blankIdx of blanks) {
+        if (blankIdx > lastEnd) {
+            chunks.push(typeof arg === 'string'
+                ? arg.slice(lastEnd, blankIdx)
+                : arg.slice(lastEnd, blankIdx).join(''));
         }
+        lastEnd = blankIdx + 1;
+    }
+    if (lastEnd < arg.length) {
+        chunks.push(typeof arg === 'string'
+            ? arg.slice(lastEnd)
+            : arg.slice(lastEnd).join(''));
     }
-    return s;
+    return chunks.join('');
 }
 // basically same as setRadius from https://observablehq.com/@d3/tree-of-life
 export function setBrLength(d, y0, k) {

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAM9B,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;AAED,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,QAAQ,EACN,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC1B,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,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACrD,CAAC;IACD,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,KAAK,MAAM,QAAQ,IAAI,MAAM,EAAE,CAAC;QAC9B,IAAI,QAAQ,GAAG,OAAO,EAAE,CAAC;YACvB,MAAM,CAAC,IAAI,CACT,OAAO,GAAG,KAAK,QAAQ;gBACrB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,QAAQ,CAAC;gBAC9B,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,QAAQ,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAC1C,CAAA;QACH,CAAC;QACD,OAAO,GAAG,QAAQ,GAAG,CAAC,CAAA;IACxB,CAAC;IACD,IAAI,OAAO,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;QACzB,MAAM,CAAC,IAAI,CACT,OAAO,GAAG,KAAK,QAAQ;YACrB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC;YACpB,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAChC,CAAA;IACH,CAAC;IACD,OAAO,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACxB,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,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC;AAED,8CAA8C;AAC9C,oCAAoC;AACpC,MAAM,UAAU,OAAO,CAAC,CAAU;IAChC,OAAO,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAA;AAC/B,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.4.6";
+export declare const version = "4.4.7";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '4.4.6';
+export const version = '4.4.7';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "4.4.6",
+  "version": "4.5.0",
   "license": "MIT",
   "repository": {
     "type": "git",
@@ -22,15 +22,15 @@
     "clean": "rimraf dist",
     "watch": "yarn build:esm --watch",
     "format": "prettier --write .",
-    "prebuild": "npm run clean",
-    "prepublishOnly": "node output-version.js > src/version.ts && git add -A src && git commit -m '[skip ci] Bump version.ts'",
+    "prebuild": "yarn clean",
+    "preversion": "node output-version.js > src/version.ts && git add -A src && git commit -m '[skip ci] Bump version.ts'",
     "build:esm": "tsc",
     "build:bundle": "webpack",
-    "build": "npm run build:esm && npm run build:bundle",
-    "prepack": "npm run build",
+    "build": "yarn build:esm && yarn build:bundle",
+    "prepack": "yarn build",
     "postversion": "git push --follow-tags",
     "statedocs": "rm -rf apidocs && mkdir apidocs && node --experimental-strip-types docgen/generateStateModelDocs.ts",
-    "poststatedocs": "npm run format",
+    "poststatedocs": "yarn format",
     "test": "vitest"
   },
   "peerDependencies": {

package/src/colorSchemes.ts

@@ -2,7 +2,7 @@ import { blue, green, orange, red } from '@mui/material/colors'
 import { colord, extend } from 'colord'
 import namesPlugin from 'colord/plugins/names'
 
-import { isBlank, transform } from './util'
+import { transform } from './util'
 
 extend([namesPlugin])
 
@@ -353,181 +353,3 @@ export default transform(colorSchemes, ([key, val]) => [
   key,
   transform(val, ([letter, color]) => [letter, colord(color).toHex()]),
 ])
-
-// info http://www.jalview.org/help/html/colourSchemes/clustal.html
-// modifications:
-// reference to clustalX source code scheme modifies what the jalview.org
-// scheme says there the jalview.org colorscheme says WLVIMAFCHP but it
-// should be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
-export function getClustalXColor(
-  stats: Record<string, number>,
-  total: number,
-  model: { columns: Record<string, string> },
-  row: string,
-  col: number,
-) {
-  const l = model.columns[row]![col]!
-  const {
-    W = 0,
-    L = 0,
-    V = 0,
-    I = 0,
-    M = 0,
-    A = 0,
-    F = 0,
-    C = 0,
-    H = 0,
-    P = 0,
-    R = 0,
-    K = 0,
-    Q = 0,
-    E = 0,
-    D = 0,
-    T = 0,
-    S = 0,
-    G = 0,
-    Y = 0,
-    N = 0,
-  } = stats
-
-  const WLVIMAFCHP = W + L + V + I + M + A + F + C + H + P + Y
-
-  const KR = K + R
-  const QE = Q + E
-  const ED = E + D
-  const TS = T + S
-
-  if (WLVIMAFCHP / total > 0.6) {
-    if (
-      l === 'W' ||
-      l === 'L' ||
-      l === 'V' ||
-      l === 'A' ||
-      l === 'I' ||
-      l === 'M' ||
-      l === 'F' ||
-      l === 'C'
-    ) {
-      // blue from jalview.org docs
-      return 'rgb(128,179,230)'
-    }
-  }
-
-  if (
-    (l === 'K' || l === 'R') &&
-    (KR / total > 0.6 || K / total > 0.8 || R / total > 0.8 || Q / total > 0.8)
-  ) {
-    return '#d88'
-  }
-
-  if (
-    l === 'E' &&
-    (KR / total > 0.6 ||
-      QE / total > 0.5 ||
-      E / total > 0.8 ||
-      Q / total > 0.8 ||
-      D / total > 0.8)
-  ) {
-    return 'rgb(192, 72, 192)'
-  }
-
-  if (
-    l === 'D' &&
-    (KR / total > 0.6 ||
-      ED / total > 0.5 ||
-      K / total > 0.8 ||
-      R / total > 0.8 ||
-      Q / total > 0.8)
-  ) {
-    return 'rgb(204, 77, 204)'
-  }
-
-  if (l === 'N' && (N / total > 0.5 || Y / total > 0.85)) {
-    return '#8f8'
-  }
-  if (
-    l === 'Q' &&
-    (KR / total > 0.6 ||
-      QE / total > 0.6 ||
-      Q / total > 0.85 ||
-      E / total > 0.85 ||
-      K / total > 0.85 ||
-      R / total > 0.85)
-  ) {
-    return '#8f8'
-  }
-
-  if (
-    (l === 'S' || l === 'T') &&
-    // WLVIMAFCHP modified from 0.6 to 0.55 on page to match what i see in jalview
-    (WLVIMAFCHP / total > 0.6 ||
-      TS / total > 0.5 ||
-      S / total > 0.85 ||
-      T / total > 0.85)
-  ) {
-    return 'rgb(26,204,26)'
-  }
-
-  if (l === 'C' && C / total > 0.85) {
-    return 'rgb(240, 128, 128)'
-  }
-
-  if (l === 'G' && G / total > 0) {
-    return 'rgb(240, 144, 72)'
-  }
-  if (l === 'P' && P / total > 0) {
-    return 'rgb(204, 204, 0)'
-  }
-
-  if (
-    (l === 'H' || l === 'Y') &&
-    (WLVIMAFCHP / total > 0.6 ||
-      W > 0.85 ||
-      Y > 0.85 ||
-      A > 0.85 ||
-      C > 0.85 ||
-      P > 0.85 ||
-      Q > 0.85 ||
-      F > 0.85 ||
-      H > 0.85 ||
-      I > 0.85 ||
-      L > 0.85 ||
-      M > 0.85 ||
-      V > 0.85)
-  ) {
-    // cyan from jalview.org docs
-    return 'rgb(26, 179, 179)'
-  }
-  return undefined
-}
-
-// info http://www.jalview.org/help/html/colourSchemes/clustal.html
-// modifications:
-// reference to clustalX source code scheme modifies what the jalview.org
-// scheme says there the jalview.org colorscheme says WLVIMAFCHP but it should
-// be WLVIMAFCHPY, colprot.xml says e.g. %#ACFHILMVWYPp" which has Y
-export function getPercentIdentityColor(
-  stats: Record<string, number>,
-  total: number,
-  model: { columns: Record<string, string> },
-  row: string,
-  col: number,
-) {
-  const l = model.columns[row]![col]!
-  const entries = Object.entries(stats)
-  let ent = 0
-  let letter = ''
-  for (const entry of entries) {
-    if (entry[1] > ent && !isBlank(entry[0])) {
-      letter = entry[0]
-      ent = entry[1]
-    }
-  }
-  const proportion = ent / total
-  const thresh = `hsl(240, 30%, ${100 * Math.max(1 - ent / total / 3, 0.3)}%)`
-  if (proportion > 0.4) {
-    if (l === letter) {
-      return thresh
-    }
-  }
-}