react-msaview 5.0.16 → 5.1.0

package/dist/components/header/settingsMenuItems.js

@@ -0,0 +1,59 @@
+export function msaSettingsMenuItems(model) {
+    const { drawMsaLetters, hideGaps, bgColor } = model;
+    return [
+        {
+            label: 'Draw letters',
+            type: 'checkbox',
+            checked: drawMsaLetters,
+            onClick: () => { model.setDrawMsaLetters(!drawMsaLetters); },
+        },
+        {
+            label: 'Color letters instead of background of tiles',
+            type: 'checkbox',
+            checked: !bgColor,
+            onClick: () => { model.setBgColor(!bgColor); },
+        },
+        {
+            label: 'Enable hiding gappy columns?',
+            type: 'checkbox',
+            checked: hideGaps,
+            onClick: () => { model.setHideGaps(!hideGaps); },
+        },
+    ];
+}
+export function treeSettingsMenuItems(model) {
+    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawLabels, } = model;
+    return [
+        {
+            label: 'Show branch length',
+            type: 'checkbox',
+            checked: showBranchLen,
+            onClick: () => { model.setShowBranchLen(!showBranchLen); },
+        },
+        {
+            label: 'Show tree',
+            type: 'checkbox',
+            checked: drawTree,
+            onClick: () => { model.setDrawTree(!drawTree); },
+        },
+        {
+            label: 'Draw clickable bubbles on tree branches',
+            type: 'checkbox',
+            checked: drawNodeBubbles,
+            onClick: () => { model.setDrawNodeBubbles(!drawNodeBubbles); },
+        },
+        {
+            label: 'Tree labels align right',
+            type: 'checkbox',
+            checked: labelsAlignRight,
+            onClick: () => { model.setLabelsAlignRight(!labelsAlignRight); },
+        },
+        {
+            label: 'Draw labels',
+            type: 'checkbox',
+            checked: drawLabels,
+            onClick: () => { model.setDrawLabels(!drawLabels); },
+        },
+    ];
+}
+//# sourceMappingURL=settingsMenuItems.js.map

package/dist/components/header/settingsMenuItems.js.map

@@ -0,0 +1 @@
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package/dist/components/minimap/Minimap.js

@@ -1,9 +1,8 @@
-import React, { useEffect, useRef, useState } from 'react';
+import React, { useCallback, useState } from 'react';
 import { observer } from 'mobx-react';
+import { useDragScroll } from "../../useDragScroll.js";
 const Minimap = observer(function ({ model }) {
-    const [mouseDown, setMouseDown] = useState();
     const [hovered, setHovered] = useState(false);
-    const scheduled = useRef(false);
     const { scrollX, msaAreaWidth, minimapHeight, colWidth, numColumns } = model;
     const unit = msaAreaWidth / numColumns / colWidth;
     const left = -scrollX;
@@ -12,30 +11,9 @@ const Minimap = observer(function ({ model }) {
     const e = right * unit;
     const fill = 'rgba(66, 119, 127, 0.3)';
     const w = Math.max(e - s, 20);
-    useEffect(() => {
-        function fn(event) {
-            if (mouseDown !== undefined) {
-                if (!scheduled.current) {
-                    scheduled.current = true;
-                    window.requestAnimationFrame(() => {
-                        model.setScrollX(mouseDown.scrollX - (event.clientX - mouseDown.clientX) / unit);
-                        scheduled.current = false;
-                    });
-                }
-            }
-        }
-        function fn2() {
-            setMouseDown(undefined);
-        }
-        if (mouseDown !== undefined) {
-            document.addEventListener('mousemove', fn);
-            document.addEventListener('mouseup', fn2);
-            return () => {
-                document.removeEventListener('mousemove', fn);
-                document.removeEventListener('mousemove', fn2);
-            };
-        }
-    }, [model, unit, mouseDown]);
+    const { startDrag } = useDragScroll('x', useCallback((delta, startScroll) => {
+        model.setScrollX(startScroll - delta / unit);
+    }, [model, unit]));
     const barHeight = 12;
     const polygonHeight = minimapHeight - barHeight;
     return (React.createElement("div", { style: {
@@ -62,10 +40,7 @@ const Minimap = observer(function ({ model }) {
             }, onMouseOut: () => {
                 setHovered(false);
             }, onMouseDown: event => {
-                setMouseDown({
-                    clientX: event.clientX,
-                    scrollX: model.scrollX,
-                });
+                startDrag(event, model.scrollX);
             } }),
         React.createElement("svg", { height: polygonHeight, style: { width: '100%' } },
             React.createElement("polygon", { fill: fill, points: [

package/dist/components/minimap/Minimap.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Minimap.js","sourceRoot":"","sources":["../../../src/components/minimap/Minimap.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEpD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAA;AAItD,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAC5E,MAAM,IAAI,GAAG,YAAY,GAAG,UAAU,GAAG,QAAQ,CAAA;IACjD,MAAM,IAAI,GAAG,CAAC,OAAO,CAAA;IACrB,MAAM,KAAK,GAAG,IAAI,GAAG,YAAY,CAAA;IACjC,MAAM,CAAC,GAAG,IAAI,GAAG,IAAI,CAAA;IACrB,MAAM,CAAC,GAAG,KAAK,GAAG,IAAI,CAAA;IACtB,MAAM,IAAI,GAAG,yBAAyB,CAAA;IACtC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;IAE7B,MAAM,EAAE,SAAS,EAAE,GAAG,aAAa,CACjC,GAAG,EACH,WAAW,CACT,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,CAAC,CAAA;IAC9C,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,CAAC,CACd,CACF,CAAA;IAED,MAAM,SAAS,GAAG,EAAE,CAAA;IACpB,MAAM,aAAa,GAAG,aAAa,GAAG,SAAS,CAAA;IAC/C,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,aAAa;YACrB,KAAK,EAAE,MAAM;SACd;QAED,6BACE,KAAK,EAAE;gBACL,MAAM,EAAE,SAAS;gBACjB,SAAS,EAAE,YAAY;gBACvB,MAAM,EAAE,gBAAgB;aACzB,GACD;QACF,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACpB,UAAU,EAAE,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,IAAI;gBACnD,MAAM,EAAE,SAAS;gBACjB,MAAM,EAAE,SAAS;gBACjB,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;aACZ,EACD,WAAW,EAAE,GAAG,EAAE;gBAChB,UAAU,CAAC,IAAI,CAAC,CAAA;YAClB,CAAC,EACD,UAAU,EAAE,GAAG,EAAE;gBACf,UAAU,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,SAAS,CAAC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAA;YACjC,CAAC,GACD;QAEF,6BAAK,MAAM,EAAE,aAAa,EAAE,KAAK,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE;YAClD,iCACE,IAAI,EAAE,IAAI,EACV,MAAM,EAAE;oBACN,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;oBACV,CAAC,CAAC,EAAE,CAAC,CAAC;oBACN,CAAC,CAAC,EAAE,aAAa,CAAC;oBAClB,CAAC,YAAY,EAAE,aAAa,CAAC;iBAC9B,CAAC,QAAQ,EAAE,GACZ,CACE,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/msa/MSACanvasBlock.js

@@ -1,15 +1,20 @@
-import React, { useEffect, useMemo, useRef, useState } from 'react';
+import React, { useEffect, useRef, useState } from 'react';
 import { BaseTooltip } from '@jbrowse/core/ui';
-import { useTheme } from '@mui/material';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
 import { renderBoxFeatureCanvasBlock } from "./renderBoxFeatureCanvasBlock.js";
 import { renderMSABlock } from "./renderMSABlock.js";
-import { colorContrast } from "../../util.js";
+import { useColorContrast } from "../../useColorContrast.js";
+function eventToColRow(event, el, offsetX, offsetY, colWidth, rowHeight) {
+    const { left, top } = el.getBoundingClientRect();
+    return {
+        col: Math.floor((event.clientX - left + offsetX) / colWidth),
+        row: Math.floor((event.clientY - top + offsetY) / rowHeight),
+    };
+}
 const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
     const { colWidth, rowHeight, scrollY, scrollX, colorScheme, blockSize, mouseClickCol, mouseClickRow, highResScaleFactor, } = model;
-    const theme = useTheme();
-    const contrastScheme = useMemo(() => colorContrast(colorScheme, theme), [colorScheme, theme]);
+    const { theme, contrastScheme } = useColorContrast(colorScheme);
     const ref = useRef(null);
     useEffect(() => {
         const ctx = ref.current?.getContext('2d');
@@ -49,36 +54,29 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
     const { hoveredInsertion } = model;
     return (React.createElement(React.Fragment, null,
         React.createElement("canvas", { ref: ref, onMouseMove: event => {
-                if (!ref.current) {
-                    return;
-                }
-                setMousePosition({ x: event.clientX, y: event.clientY });
-                const { left, top } = ref.current.getBoundingClientRect();
-                const mouseX = event.clientX - left + offsetX;
-                const mouseY = event.clientY - top + offsetY;
-                const x = Math.floor(mouseX / colWidth);
-                const y = Math.floor(mouseY / rowHeight);
-                // Only set mouse position if within valid MSA bounds
-                if (x >= 0 && x < model.numColumns && y >= 0 && y < model.numRows) {
-                    model.setMousePos(x, y);
-                }
-                else {
-                    model.setMousePos(undefined, undefined);
+                if (ref.current) {
+                    setMousePosition({ x: event.clientX, y: event.clientY });
+                    const { col, row } = eventToColRow(event, ref.current, offsetX, offsetY, colWidth, rowHeight);
+                    // Only set mouse position if within valid MSA bounds
+                    if (col >= 0 &&
+                        col < model.numColumns &&
+                        row >= 0 &&
+                        row < model.numRows) {
+                        model.setMousePos(col, row);
+                    }
+                    else {
+                        model.setMousePos(undefined, undefined);
+                    }
                 }
             }, onClick: event => {
-                if (!ref.current) {
-                    return;
-                }
-                const { left, top } = ref.current.getBoundingClientRect();
-                const mouseX = event.clientX - left + offsetX;
-                const mouseY = event.clientY - top + offsetY;
-                const x = Math.floor(mouseX / colWidth);
-                const y = Math.floor(mouseY / rowHeight);
-                if (x === mouseClickCol && y === mouseClickRow) {
-                    model.setMouseClickPos(undefined, undefined);
-                }
-                else {
-                    model.setMouseClickPos(x, y);
+                if (ref.current) {
+                    const { col, row } = eventToColRow(event, ref.current, offsetX, offsetY, colWidth, rowHeight);
+                    if (col === mouseClickCol && row === mouseClickRow) {
+                        model.setMouseClickPos(undefined, undefined);
+                    }
+                    else {
+                        model.setMouseClickPos(col, row);
+                    }
                 }
             }, onMouseLeave: () => {
                 model.setMousePos();

package/dist/components/msa/MSACanvasBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSACanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE1D,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAC9C,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,2BAA2B,EAAE,MAAM,kCAAkC,CAAA;AAC9E,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAI5D,SAAS,aAAa,CACpB,KAAuB,EACvB,EAAqB,EACrB,OAAe,EACf,OAAe,EACf,QAAgB,EAChB,SAAiB;IAEjB,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,CAAC,qBAAqB,EAAE,CAAA;IAChD,OAAO;QACL,GAAG,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,GAAG,OAAO,CAAC,GAAG,QAAQ,CAAC;QAC5D,GAAG,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,OAAO,GAAG,GAAG,GAAG,OAAO,CAAC,GAAG,SAAS,CAAC;KAC7D,CAAA;AACH,CAAC;AAED,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,EACP,OAAO,GAKR;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,OAAO,EACP,OAAO,EACP,WAAW,EACX,SAAS,EACT,aAAa,EACb,aAAa,EACb,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,KAAK,EAAE,cAAc,EAAE,GAAG,gBAAgB,CAAC,WAAW,CAAC,CAAA;IAE/D,MAAM,GAAG,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAC3C,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QACD,OAAO,OAAO,CAAC,GAAG,EAAE;YAClB,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CACX,CAAC,EACD,CAAC,EACD,SAAS,GAAG,kBAAkB,EAC9B,SAAS,GAAG,kBAAkB,CAC/B,CAAA;YACD,IAAI,KAAK,CAAC,mBAAmB,EAAE,CAAC;gBAC9B,2BAA2B,CAAC;oBAC1B,GAAG;oBACH,OAAO;oBACP,OAAO;oBACP,KAAK;iBACN,CAAC,CAAA;YACJ,CAAC;YACD,cAAc,CAAC;gBACb,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO;gBACP,cAAc;gBACd,KAAK;aACN,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC,EAAE;QACD,KAAK;QACL,OAAO;QACP,OAAO;QACP,KAAK;QACL,SAAS;QACT,kBAAkB;QAClB,cAAc;KACf,CAAC,CAAA;IAEF,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,EAA4B,CAAA;IAC9E,MAAM,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAElC,OAAO,CACL;QACE,gCACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,gBAAgB,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,CAAA;oBACxD,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,aAAa,CAChC,KAAK,EACL,GAAG,CAAC,OAAO,EACX,OAAO,EACP,OAAO,EACP,QAAQ,EACR,SAAS,CACV,CAAA;oBACD,qDAAqD;oBACrD,IACE,GAAG,IAAI,CAAC;wBACR,GAAG,GAAG,KAAK,CAAC,UAAU;wBACtB,GAAG,IAAI,CAAC;wBACR,GAAG,GAAG,KAAK,CAAC,OAAO,EACnB,CAAC;wBACD,KAAK,CAAC,WAAW,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;oBAC7B,CAAC;yBAAM,CAAC;wBACN,KAAK,CAAC,WAAW,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;oBACzC,CAAC;gBACH,CAAC;YACH,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,aAAa,CAChC,KAAK,EACL,GAAG,CAAC,OAAO,EACX,OAAO,EACP,OAAO,EACP,QAAQ,EACR,SAAS,CACV,CAAA;oBACD,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE,CAAC;wBACnD,KAAK,CAAC,gBAAgB,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;oBAC9C,CAAC;yBAAM,CAAC;wBACN,KAAK,CAAC,gBAAgB,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;gBACH,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,KAAK,CAAC,WAAW,EAAE,CAAA;gBACnB,gBAAgB,CAAC,SAAS,CAAC,CAAA;YAC7B,CAAC,EACD,KAAK,EAAE,SAAS,GAAG,kBAAkB,EACrC,MAAM,EAAE,SAAS,GAAG,kBAAkB,EACtC,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,OAAO,GAAG,OAAO;gBACtB,IAAI,EAAE,OAAO,GAAG,OAAO;gBACvB,KAAK,EAAE,SAAS;gBAChB,MAAM,EAAE,SAAS;aAClB,GACD;QACD,gBAAgB,IAAI,aAAa,CAAC,CAAC,CAAC,CACnC,oBAAC,WAAW,IACV,WAAW,EAAE,EAAE,CAAC,EAAE,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,aAAa,CAAC,CAAC,GAAG,EAAE,EAAE;;YAEhD,gBAAgB,CAAC,OAAO,CAAC,MAAM;YAC1C,KAAK,CAAC,YAAY,KAAK,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI;;YAAI,GAAG;YACnD,gBAAgB,CAAC,OAAO,CAAC,MAAM,GAAG,EAAE;gBACnC,CAAC,CAAC,GAAG,gBAAgB,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK;gBAC/C,CAAC,CAAC,gBAAgB,CAAC,OAAO,CAChB,CACf,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/msa/renderMSABlock.js

@@ -7,7 +7,10 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
     ctx.scale(k, k);
     ctx.translate(-offsetX, rowHeight / 2 - offsetY);
     ctx.textAlign = 'center';
-    ctx.font = ctx.font.replace(/\d+px/, `${bgColor ? '' : 'bold '}${fontSize}px`);
+    // match an optional existing "bold " so re-renders don't accumulate it
+    // (an invalid "bold bold 16px" string would be silently ignored by canvas,
+    // freezing the font size against zoom changes)
+    ctx.font = ctx.font.replace(/(?:bold )?\d+px/, `${bgColor ? '' : 'bold '}${fontSize}px`);
     const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
     const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight));
     const xStart = Math.max(0, Math.floor(offsetX / colWidth));
@@ -61,14 +64,17 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
                 const letter = str[j];
                 // Use a muted background for positions that match reference
                 const isMatchingReference = referenceSeq && name !== relativeTo && letter === referenceSeq[j];
-                const color = isClustalX
-                    ? model.colClustalX[xStart + j][letter]
-                    : isPercentIdentity
-                        ? (() => {
-                            const consensus = model.colConsensus[xStart + j];
-                            return letter === consensus.letter ? consensus.color : undefined;
-                        })()
-                        : colorScheme[letter.toUpperCase()];
+                let color;
+                if (isClustalX) {
+                    color = model.colClustalX[xStart + j][letter];
+                }
+                else if (isPercentIdentity) {
+                    const consensus = model.colConsensus[xStart + j];
+                    color = letter === consensus.letter ? consensus.color : undefined;
+                }
+                else {
+                    color = colorScheme[letter.toUpperCase()];
+                }
                 if (bgColor || isClustalX || isPercentIdentity) {
                     // Use a very light background for matching positions in relative mode
                     const finalColor = isMatchingReference

package/dist/components/msa/renderMSABlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"renderMSABlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSABlock.ts"],"names":[],"mappings":"AAKA,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,GAAG,EACH,KAAK,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,kBAAkB,GAWnB;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,SAAS,EACT,QAAQ,EACR,kBAAkB,EAClB,mBAAmB,EACnB,MAAM,EACN,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;IAChD,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,uEAAuE;IACvE,2EAA2E;IAC3E,+CAA+C;IAC/C,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CACzB,iBAAiB,EACjB,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,GAAG,QAAQ,IAAI,CACzC,CAAA;IAED,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IAC3E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC1D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC9D,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAEhD,IAAI,CAAC,mBAAmB,EAAE,CAAC;QACzB,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,KAAK;YACL,OAAO;YACP,MAAM;YACN,IAAI;YACJ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;IACD,QAAQ,CAAC;QACP,KAAK;QACL,GAAG;QACH,OAAO;QACP,cAAc;QACd,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,uBAAuB,CAAC;QACtB,KAAK;QACL,GAAG;QACH,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,OAAO,EACP,GAAG,EACH,aAAa,EACb,KAAK,EACL,MAAM,EACN,IAAI,GASL;IACC,MAAM,EACJ,OAAO,EACP,eAAe,EACf,WAAW,EACX,OAAO,EACP,QAAQ,EACR,SAAS,EACT,UAAU,GACX,GAAG,KAAK,CAAA;IAET,8CAA8C;IAC9C,MAAM,YAAY,GAAG,UAAU;QAC7B,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;QAC1C,CAAC,CAAC,IAAI,CAAA;IAER,MAAM,UAAU,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACjE,MAAM,iBAAiB,GAAG,eAAe,KAAK,0BAA0B,CAAA;IACxE,MAAM,cAAc,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;IAErD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAC9C,IAAI,GAAG,EAAE,CAAC;YACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;gBAEtB,4DAA4D;gBAC5D,MAAM,mBAAmB,GACvB,YAAY,IAAI,IAAI,KAAK,UAAU,IAAI,MAAM,KAAK,YAAY,CAAC,CAAC,CAAC,CAAA;gBAEnE,IAAI,KAAyB,CAAA;gBAC7B,IAAI,UAAU,EAAE,CAAC;oBACf,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAE,CAAC,MAAM,CAAC,CAAA;gBAChD,CAAC;qBAAM,IAAI,iBAAiB,EAAE,CAAC;oBAC7B,MAAM,SAAS,GAAG,KAAK,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,CAAA;oBACjD,KAAK,GAAG,MAAM,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;gBACnE,CAAC;qBAAM,CAAC;oBACN,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;gBAC3C,CAAC;gBACD,IAAI,OAAO,IAAI,UAAU,IAAI,iBAAiB,EAAE,CAAC;oBAC/C,sEAAsE;oBACtE,MAAM,UAAU,GAAG,mBAAmB;wBACpC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;wBAC5B,CAAC,CAAC,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAA;oBAC7C,GAAG,CAAC,SAAS,GAAG,UAAU,CAAA;oBAC1B,GAAG,CAAC,QAAQ,CACV,CAAC,GAAG,QAAQ,GAAG,cAAc,EAC7B,CAAC,GAAG,SAAS,EACb,QAAQ,EACR,SAAS,CACV,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,OAAO,EACP,cAAc,EACd,GAAG,EACH,aAAa,EACb,MAAM,EACN,IAAI,GASL;IACC,MAAM,EACJ,OAAO,EACP,mBAAmB,EACnB,cAAc,EACd,WAAW,EACX,OAAO,EACP,QAAQ,EACR,SAAS,EACT,UAAU,GACX,GAAG,KAAK,CAAA;IAET,8CAA8C;IAC9C,MAAM,YAAY,GAAG,UAAU;QAC7B,CAAC,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC;QAC1C,CAAC,CAAC,IAAI,CAAA;IAER,IAAI,cAAc,EAAE,CAAC;QACnB,MAAM,cAAc,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;QACrD,MAAM,YAAY,GAAG,QAAQ,GAAG,CAAC,CAAA;QACjC,MAAM,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;YAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;YACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,GAAG,gBAAgB,CAAA;YACpC,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,GAAG,EAAE,CAAC;gBACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;oBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;oBAEtB,+CAA+C;oBAC/C,MAAM,mBAAmB,GACvB,YAAY,IAAI,IAAI,KAAK,UAAU,IAAI,MAAM,KAAK,YAAY,CAAC,CAAC,CAAC,CAAA;oBAEnE,mEAAmE;oBACnE,MAAM,aAAa,GAAG,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAA;oBAExD,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE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package/dist/components/tree/TreeCanvas.js

@@ -23,30 +23,28 @@ const TreeCanvas = observer(function ({ model }) {
                     const { relativeTo, leaves, rowHeight, hoveredTreeNode, treeAreaWidth: w, height: h, scrollY: sy, mouseOverRowName, } = model;
                     ctx.resetTransform();
                     ctx.clearRect(0, 0, w, h);
-                    if (relativeTo) {
-                        const referenceLeaf = leaves.find(leaf => leaf.data.name === relativeTo);
-                        if (referenceLeaf) {
-                            ctx.fillStyle = referenceColor;
-                            ctx.fillRect(0, referenceLeaf.x + sy - rowHeight / 2, w, rowHeight);
+                    const leafByName = new Map(leaves.map(leaf => [leaf.data.name, leaf]));
+                    const fillRow = (name) => {
+                        const leaf = leafByName.get(name);
+                        if (leaf) {
+                            ctx.fillRect(0, leaf.x + sy - rowHeight / 2, w, rowHeight);
                         }
+                    };
+                    if (relativeTo) {
+                        ctx.fillStyle = referenceColor;
+                        fillRow(relativeTo);
                     }
                     if (hoveredTreeNode) {
                         ctx.fillStyle = treeHoverColor;
                         for (const descendantName of hoveredTreeNode.descendantNames) {
-                            const matchingLeaf = leaves.find(leaf => leaf.data.name === descendantName);
-                            if (matchingLeaf) {
-                                ctx.fillRect(0, matchingLeaf.x + sy - rowHeight / 2, w, rowHeight);
-                            }
+                            fillRow(descendantName);
                         }
                     }
                     if (mouseOverRowName &&
                         mouseOverRowName !== relativeTo &&
                         !hoveredTreeNode?.descendantNames.includes(mouseOverRowName)) {
-                        const matchingLeaf = leaves.find(leaf => leaf.data.name === mouseOverRowName);
-                        if (matchingLeaf) {
-                            ctx.fillStyle = treeHoverColor;
-                            ctx.fillRect(0, matchingLeaf.x + sy - rowHeight / 2, w, rowHeight);
-                        }
+                        ctx.fillStyle = treeHoverColor;
+                        fillRow(mouseOverRowName);
                     }
                 }
             })

package/dist/components/tree/TreeCanvas.js.map

@@ -1 +1 @@
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package/dist/components/tree/renderTreeCanvas.d.ts

@@ -21,26 +21,32 @@ interface ClickMapIndex {
         maxY: number;
     }): ClickEntry[];
 }
-export declare function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, }: {
+export declare function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
     offsetY: number;
     ctx: CanvasRenderingContext2D;
     model: MsaViewModel;
     theme: Theme;
+    maxBranchLen: number;
+    maxDepthToLeaf: number;
     blockSizeYOverride?: number;
 }): void;
-export declare function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOverride, }: {
+export declare function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
     ctx: CanvasRenderingContext2D;
     clickMap?: ClickMapIndex;
     offsetY: number;
     model: MsaViewModel;
+    maxBranchLen: number;
+    maxDepthToLeaf: number;
     blockSizeYOverride?: number;
 }): void;
-export declare function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }: {
+export declare function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }: {
     model: MsaViewModel;
     offsetY: number;
     ctx: CanvasRenderingContext2D;
     clickMap?: ClickMapIndex;
     theme: Theme;
+    maxBranchLen: number;
+    maxDepthToLeaf: number;
     blockSizeYOverride?: number;
 }): void;
 export declare function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }: {

package/dist/components/tree/renderTreeCanvas.js

@@ -1,37 +1,8 @@
-import { descendants, links } from "../../hierarchy.js";
+import { calcDepthToLeaf, descendants, links } from "../../hierarchy.js";
 export const padding = 600;
 const extendBounds = 5;
 const radius = 2.5;
 const d = radius * 2;
-// Cladogram positioning algorithm based on ape package's plot.phylo
-// Uses topological depth (steps to tips) instead of branch length for x-positioning
-// This ensures all leaf nodes align at the same x-coordinate (rightmost position)
-// See: https://github.com/emmanuelparadis/ape/blob/master/R/plot.phylo.R
-function calcDepthToLeaf(node) {
-    if (node.depthToLeaf !== undefined) {
-        return node.depthToLeaf;
-    }
-    if (!node.children || node.children.length === 0) {
-        node.depthToLeaf = 0;
-    }
-    else {
-        let maxDepth = 0;
-        for (const child of node.children) {
-            maxDepth = Math.max(maxDepth, 1 + calcDepthToLeaf(child));
-        }
-        node.depthToLeaf = maxDepth;
-    }
-    return node.depthToLeaf;
-}
-function findMaxBranchLen(node) {
-    let maxLen = node.len || 0;
-    if (node.children) {
-        for (const child of node.children) {
-            maxLen = Math.max(maxLen, findMaxBranchLen(child));
-        }
-    }
-    return maxLen;
-}
 // Calculate node x-coordinate for both phylogram (with branch lengths) and cladogram (topology only) modes
 // For cladograms: x = (maxDepthToLeaf - nodeDepthToLeaf) / maxDepthToLeaf * maxWidth
 // This positions: leaves at maxWidth (rightmost), root at 0 (leftmost), internal nodes proportionally in between
@@ -43,12 +14,10 @@ function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
     const depthToLeaf = calcDepthToLeaf(node);
     return ((maxDepthToLeaf - depthToLeaf) / maxDepthToLeaf) * maxBranchLen;
 }
-export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, }) {
+export function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, blockSize } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
-    const maxBranchLen = findMaxBranchLen(hierarchy);
-    const maxDepthToLeaf = calcDepthToLeaf(hierarchy);
     for (const link of links(hierarchy)) {
         const { source, target } = link;
         const sy = source.x;
@@ -72,11 +41,9 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
         }
     }
 }
-export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOverride, }) {
+export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
     const by = blockSizeYOverride || blockSize;
-    const maxBranchLen = findMaxBranchLen(hierarchy);
-    const maxDepthToLeaf = calcDepthToLeaf(hierarchy);
     for (const node of descendants(hierarchy)) {
         const x = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf);
         if (x === undefined) {
@@ -106,8 +73,8 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
         }
     }
 }
-export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, hierarchy, } = model;
+export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
+    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
     const by = blockSizeYOverride || blockSize;
     const emHeight = ctx.measureText('M').width;
     if (labelsAlignRight) {
@@ -117,8 +84,6 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
     else {
         ctx.textAlign = 'start';
     }
-    const maxBranchLen = findMaxBranchLen(hierarchy);
-    const maxDepthToLeaf = calcDepthToLeaf(hierarchy);
     for (const node of leaves) {
         const { data: { name, id }, } = node;
         const y = node.x;
@@ -186,12 +151,17 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     ctx.translate(marginLeft, -offsetY);
     const font = ctx.font;
     ctx.font = font.replace(/\d+px/, `${fontSize}px`);
+    // memoized on the model and shared across the tree/bubble/label passes (and
+    // across all tree blocks) rather than re-traversing the hierarchy in each
+    const { maxBranchLength: maxBranchLen, maxDepthToLeaf } = model;
     if (!noTree && drawTree) {
         renderTree({
             ctx,
             offsetY,
             model,
             theme,
+            maxBranchLen,
+            maxDepthToLeaf,
             blockSizeYOverride,
         });
         if (drawNodeBubbles) {
@@ -200,6 +170,8 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
                 offsetY,
                 clickMap,
                 model,
+                maxBranchLen,
+                maxDepthToLeaf,
                 blockSizeYOverride,
             });
         }
@@ -211,6 +183,8 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             model,
             clickMap,
             theme,
+            maxBranchLen,
+            maxDepthToLeaf,
             blockSizeYOverride,
         });
     }

package/dist/components/tree/renderTreeCanvas.js.map

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

@@ -1,4 +1,5 @@
 export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
 export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
 export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
-export declare function timeout(time: number): Promise<unknown>;
+export declare function timeout(time: number, signal?: AbortSignal): Promise<void>;
+export declare function isAbortError(e: unknown): boolean;

package/dist/fetchUtils.js

@@ -13,7 +13,21 @@ export async function jsonfetch(url, args) {
     const response = await myfetch(url, args);
     return response.json();
 }
-export function timeout(time) {
-    return new Promise(res => setTimeout(res, time));
+export function timeout(time, signal) {
+    return new Promise((resolve, reject) => {
+        if (signal?.aborted) {
+            reject(new DOMException('Aborted', 'AbortError'));
+        }
+        else {
+            const id = setTimeout(resolve, time);
+            signal?.addEventListener('abort', () => {
+                clearTimeout(id);
+                reject(new DOMException('Aborted', 'AbortError'));
+            });
+        }
+    });
+}
+export function isAbortError(e) {
+    return e instanceof DOMException && e.name === 'AbortError';
 }
 //# sourceMappingURL=fetchUtils.js.map

package/dist/fetchUtils.js.map

@@ -1 +1 @@
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