react-msaview 2.0.0 → 2.1.1

package/dist/components/TreeBranchMenu.d.ts

@@ -0,0 +1,14 @@
+import React from 'react';
+import { MsaViewModel } from '../model';
+interface Node {
+    x: number;
+    y: number;
+    name: string;
+    id: string;
+}
+declare const TreeBranchMenu: ({ node, model, onClose, }: {
+    node: Node;
+    model: MsaViewModel;
+    onClose: () => void;
+}) => React.JSX.Element;
+export default TreeBranchMenu;

package/dist/components/TreeBranchMenu.js

@@ -0,0 +1,26 @@
+import React from 'react';
+import { Menu, MenuItem } from '@mui/material';
+import { observer } from 'mobx-react';
+const TreeBranchMenu = observer(function ({ node, model, onClose, }) {
+    return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+            left: node.x,
+            top: node.y,
+        }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
+        React.createElement(MenuItem, { dense: true, disabled: true }, node.name),
+        React.createElement(MenuItem, { dense: true, onClick: () => {
+                model.toggleCollapsed(node.id);
+                onClose();
+            } }, model.collapsed.includes(node.id)
+            ? 'Expand this node'
+            : 'Collapse this node'),
+        React.createElement(MenuItem, { dense: true, onClick: () => {
+                model.showOnly === node.id
+                    ? model.setShowOnly(undefined)
+                    : model.setShowOnly(node.id);
+                onClose();
+            } }, model.showOnly === node.id
+            ? 'Disable show only this node'
+            : 'Show only this node')));
+});
+export default TreeBranchMenu;
+//# sourceMappingURL=TreeBranchMenu.js.map

package/dist/components/TreeBranchMenu.js.map

@@ -0,0 +1 @@
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package/dist/components/TreeCanvas.d.ts

@@ -1,5 +1,6 @@
+import React from 'react';
 import { MsaViewModel } from '../model';
 declare const TreeCanvas: ({ model }: {
     model: MsaViewModel;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default TreeCanvas;

package/dist/components/TreeCanvas.js

@@ -1,326 +1,8 @@
 import React, { useEffect, useRef, useState } from 'react';
-import { Menu, MenuItem } from '@mui/material';
 import normalizeWheel from 'normalize-wheel';
 import { observer } from 'mobx-react';
-import RBush from 'rbush';
-import MoreInfoDlg from './MoreInfoDlg';
-const extendBounds = 5;
-const radius = 3.5;
-const d = radius * 2;
+import TreeCanvasBlock from './TreeCanvasBlock';
 const padding = 600;
-const TreeMenu = observer(function ({ node, onClose, model, }) {
-    var _a, _b;
-    const { structures } = model;
-    const nodeDetails = node ? model.getRowData(node.name) : undefined;
-    return (React.createElement(React.Fragment, null,
-        React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-                top: node.y,
-                left: node.x,
-            }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
-            React.createElement(MenuItem, { dense: true, disabled: true }, node.name),
-            React.createElement(MenuItem, { dense: true, onClick: () => {
-                    model.setDialogComponent(MoreInfoDlg, {
-                        info: model.getRowData(node.name),
-                    });
-                    onClose();
-                } }, "More info..."), (_a = structures[node.name]) === null || _a === void 0 ? void 0 :
-            _a.map(entry => {
-                return !model.selectedStructures.some(n => n.id === node.name) ? (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
-                        model.addStructureToSelection({
-                            structure: entry,
-                            id: node.name,
-                        });
-                        onClose();
-                    } },
-                    "Add PDB to selection (",
-                    entry.pdb,
-                    ")")) : (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
-                        model.removeStructureFromSelection({
-                            structure: entry,
-                            id: node.name,
-                        });
-                        onClose();
-                    } },
-                    "Remove PDB from selection (",
-                    entry.pdb,
-                    ")"));
-            }), 
-        // @ts-expect-error
-        (_b = nodeDetails === null || nodeDetails === void 0 ? void 0 : nodeDetails.data.accession) === null || _b === void 0 ? void 0 :
-            _b.map((accession) => (React.createElement(MenuItem, { dense: true, key: accession, onClick: () => {
-                    model.addUniprotTrack({
-                        // @ts-expect-error
-                        name: nodeDetails === null || nodeDetails === void 0 ? void 0 : nodeDetails.data.name,
-                        accession,
-                    });
-                    onClose();
-                } },
-                "Open UniProt track (",
-                accession,
-                ")"))))));
-});
-const TreeBranchMenu = observer(function ({ node, model, onClose, }) {
-    return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-            left: node.x,
-            top: node.y,
-        }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
-        React.createElement(MenuItem, { dense: true, disabled: true }, node.name),
-        React.createElement(MenuItem, { dense: true, onClick: () => {
-                model.toggleCollapsed(node.id);
-                onClose();
-            } }, model.collapsed.includes(node.id)
-            ? 'Expand this node'
-            : 'Collapse this node'),
-        React.createElement(MenuItem, { dense: true, onClick: () => {
-                model.showOnly === node.id
-                    ? model.setShowOnly(undefined)
-                    : model.setShowOnly(node.id);
-                onClose();
-            } }, model.showOnly === node.id
-            ? 'Disable show only this node'
-            : 'Show only this node')));
-});
-const TreeBlock = observer(function ({ model, offsetY, }) {
-    const ref = useRef(null);
-    const clickMap = useRef(new RBush());
-    const mouseoverRef = useRef(null);
-    const [branchMenu, setBranchMenu] = useState();
-    const [toggleNodeMenu, setToggleNodeMenu] = useState();
-    const [hoverElt, setHoverElt] = useState();
-    const { hierarchy, rowHeight, scrollY, treeWidth, showBranchLen, collapsed, margin, labelsAlignRight, noTree, blockSize, drawNodeBubbles, drawTree, treeAreaWidth, structures, highResScaleFactor, } = model;
-    useEffect(() => {
-        clickMap.current.clear();
-        if (!ref.current) {
-            return;
-        }
-        const ctx = ref.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.scale(highResScaleFactor, highResScaleFactor);
-        ctx.clearRect(0, 0, treeWidth + padding, blockSize);
-        ctx.translate(margin.left, -offsetY);
-        const font = ctx.font;
-        ctx.font = font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
-        if (!noTree && drawTree) {
-            hierarchy.links().forEach(({ source, target }) => {
-                const y = showBranchLen ? 'len' : 'y';
-                // @ts-expect-error
-                const { x: sy, [y]: sx } = source;
-                // @ts-expect-error
-                const { x: ty, [y]: tx } = target;
-                const y1 = Math.min(sy, ty);
-                const y2 = Math.max(sy, ty);
-                // 1d line intersection to check if line crosses block at all, this is
-                // an optimization that allows us to skip drawing most tree links
-                // outside the block
-                if (offsetY + blockSize >= y1 && y2 >= offsetY) {
-                    ctx.beginPath();
-                    ctx.moveTo(sx, sy);
-                    ctx.lineTo(sx, ty);
-                    ctx.lineTo(tx, ty);
-                    ctx.stroke();
-                }
-            });
-            if (drawNodeBubbles) {
-                hierarchy.descendants().forEach(node => {
-                    const val = showBranchLen ? 'len' : 'y';
-                    const { 
-                    // @ts-expect-error
-                    x: y, 
-                    // @ts-expect-error
-                    [val]: x, data, } = node;
-                    const { id = '', name = '' } = data;
-                    if (y > offsetY - extendBounds &&
-                        y < offsetY + blockSize + extendBounds) {
-                        ctx.strokeStyle = 'black';
-                        ctx.fillStyle = collapsed.includes(id) ? 'black' : 'white';
-                        ctx.beginPath();
-                        ctx.arc(x, y, radius, 0, 2 * Math.PI);
-                        ctx.fill();
-                        ctx.stroke();
-                        clickMap.current.insert({
-                            minX: x - radius,
-                            maxX: x - radius + d,
-                            minY: y - radius,
-                            maxY: y - radius + d,
-                            branch: true,
-                            id,
-                            name,
-                        });
-                    }
-                });
-            }
-        }
-        if (rowHeight >= 10) {
-            if (labelsAlignRight) {
-                ctx.textAlign = 'right';
-                ctx.setLineDash([1, 3]);
-            }
-            else {
-                ctx.textAlign = 'start';
-            }
-            hierarchy.leaves().forEach(node => {
-                const { 
-                // @ts-expect-error
-                x: y, 
-                // @ts-expect-error
-                y: x, data: { name, id }, 
-                // @ts-expect-error
-                len, } = node;
-                if (y > offsetY - extendBounds &&
-                    y < offsetY + blockSize + extendBounds) {
-                    // note: +rowHeight/4 matches with -rowHeight/4 in msa
-                    const yp = y + rowHeight / 4;
-                    const xp = showBranchLen ? len : x;
-                    const { width } = ctx.measureText(name);
-                    const height = ctx.measureText('M').width; // use an 'em' for height
-                    const hasStructure = structures[name];
-                    ctx.fillStyle = hasStructure ? 'blue' : 'black';
-                    if (!drawTree && !labelsAlignRight) {
-                        ctx.fillText(name, 0, yp);
-                        clickMap.current.insert({
-                            minX: 0,
-                            maxX: width,
-                            minY: yp - height,
-                            maxY: yp,
-                            name,
-                            id,
-                        });
-                    }
-                    else if (labelsAlignRight) {
-                        const smallPadding = 2;
-                        const offset = treeAreaWidth - smallPadding - margin.left;
-                        if (drawTree && !noTree) {
-                            const { width } = ctx.measureText(name);
-                            ctx.moveTo(xp + radius + 2, y);
-                            ctx.lineTo(offset - smallPadding - width, y);
-                            ctx.stroke();
-                        }
-                        ctx.fillText(name, offset, yp);
-                        clickMap.current.insert({
-                            minX: treeAreaWidth - margin.left - width,
-                            maxX: treeAreaWidth - margin.left,
-                            minY: yp - height,
-                            maxY: yp,
-                            name,
-                            id,
-                        });
-                    }
-                    else {
-                        ctx.fillText(name, xp + d, yp);
-                        clickMap.current.insert({
-                            minX: xp + d,
-                            maxX: xp + d + width,
-                            minY: yp - height,
-                            maxY: yp,
-                            name,
-                            id,
-                        });
-                    }
-                }
-            });
-            ctx.setLineDash([]);
-        }
-    }, [
-        collapsed,
-        rowHeight,
-        margin.left,
-        hierarchy,
-        offsetY,
-        treeWidth,
-        showBranchLen,
-        noTree,
-        blockSize,
-        drawNodeBubbles,
-        drawTree,
-        labelsAlignRight,
-        treeAreaWidth,
-        structures,
-        highResScaleFactor,
-    ]);
-    useEffect(() => {
-        const canvas = mouseoverRef.current;
-        if (!canvas) {
-            return;
-        }
-        const ctx = canvas.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.clearRect(0, 0, treeWidth + padding, blockSize);
-        ctx.translate(margin.left, -offsetY);
-        if (hoverElt) {
-            const { minX, maxX, minY, maxY } = hoverElt;
-            ctx.fillStyle = 'rgba(0,0,0,0.1)';
-            ctx.fillRect(minX, minY, maxX - minX, maxY - minY);
-        }
-    }, [hoverElt, margin.left, offsetY, blockSize, treeWidth]);
-    function hoverBranchClickMap(event) {
-        const x = event.nativeEvent.offsetX - margin.left;
-        const y = event.nativeEvent.offsetY;
-        const [entry] = clickMap.current.search({
-            minX: x,
-            maxX: x + 1,
-            minY: y + offsetY,
-            maxY: y + 1 + offsetY,
-        });
-        return entry && entry.branch
-            ? { ...entry, x: event.clientX, y: event.clientY }
-            : undefined;
-    }
-    function hoverNameClickMap(event) {
-        const x = event.nativeEvent.offsetX - margin.left;
-        const y = event.nativeEvent.offsetY;
-        const [entry] = clickMap.current.search({
-            minX: x,
-            maxX: x + 1,
-            minY: y + offsetY,
-            maxY: y + 1 + offsetY,
-        });
-        return entry && !entry.branch
-            ? { ...entry, x: event.clientX, y: event.clientY }
-            : undefined;
-    }
-    return (React.createElement(React.Fragment, null,
-        (branchMenu === null || branchMenu === void 0 ? void 0 : branchMenu.id) ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => setBranchMenu(undefined) })) : null,
-        (toggleNodeMenu === null || toggleNodeMenu === void 0 ? void 0 : toggleNodeMenu.id) ? (React.createElement(TreeMenu, { node: toggleNodeMenu, model: model, onClose: () => setToggleNodeMenu(undefined) })) : null,
-        React.createElement("canvas", { width: (treeWidth + padding) * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
-                width: treeWidth + padding,
-                height: blockSize,
-                top: scrollY + offsetY,
-                left: 0,
-                position: 'absolute',
-            }, onMouseMove: event => {
-                if (!ref.current) {
-                    return;
-                }
-                const ret = hoverNameClickMap(event) || hoverBranchClickMap(event);
-                ref.current.style.cursor = ret ? 'pointer' : 'default';
-                setHoverElt(hoverNameClickMap(event));
-            }, onClick: event => {
-                const { clientX: x, clientY: y } = event;
-                const data = hoverBranchClickMap(event);
-                if (data === null || data === void 0 ? void 0 : data.id) {
-                    setBranchMenu({ ...data, x, y });
-                }
-                const data2 = hoverNameClickMap(event);
-                if (data2 === null || data2 === void 0 ? void 0 : data2.id) {
-                    setToggleNodeMenu({ ...data2, x, y });
-                }
-            }, ref: ref }),
-        React.createElement("canvas", { style: {
-                width: treeWidth + padding,
-                height: blockSize,
-                top: scrollY + offsetY,
-                left: 0,
-                position: 'absolute',
-                pointerEvents: 'none',
-                zIndex: 100,
-            }, width: treeWidth + padding, height: blockSize, ref: mouseoverRef })));
-});
 const TreeCanvas = observer(function ({ model }) {
     const ref = useRef(null);
     const scheduled = useRef(false);
@@ -412,7 +94,7 @@ const TreeCanvas = observer(function ({ model }) {
             position: 'relative',
             overflow: 'hidden',
             width: treeWidth + padding,
-        } }, blocksY.map(block => (React.createElement(TreeBlock, { key: block, model: model, offsetY: block })))));
+        } }, blocksY.map(block => (React.createElement(TreeCanvasBlock, { key: block, model: model, offsetY: block })))));
 });
 export default TreeCanvas;
 //# sourceMappingURL=TreeCanvas.js.map

package/dist/components/TreeCanvas.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvas.js","sourceRoot":"","sources":["../../src/components/TreeCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAC1D,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,MAAM,OAAO,GAAG,GAAG,CAAA;AAEnB,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,KAAK,GAAG,MAAM,CAAS,CAAC,CAAC,CAAA;IAC/B,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEzD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAA;QACxB,IAAI,CAAC,IAAI,EAAE;YACT,OAAM;SACP;QACD,SAAS,OAAO,CAAC,SAAqB;YACpC,MAAM,KAAK,GAAG,cAAc,CAAC,SAAS,CAAC,CAAA;YACvC,MAAM,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;YAE9B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE;gBACtB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;gBACxB,qBAAqB,CAAC,GAAG,EAAE;oBACzB,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;oBAChC,MAAM,CAAC,OAAO,GAAG,CAAC,CAAA;oBAClB,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;gBAC3B,CAAC,CAAC,CAAA;aACH;YACD,SAAS,CAAC,cAAc,EAAE,CAAA;QAC5B,CAAC;QACD,IAAI,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QACvC,OAAO,GAAG,EAAE;YACV,IAAI,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,OAAO,GAAG,GAAG,EAAE,GAAE,CAAC,CAAA;QAEtB,SAAS,eAAe,CAAC,KAAiB;YACxC,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YAC3B,MAAM,SAAS,GAAG,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YACvC,IAAI,SAAS,EAAE;gBACb,uEAAuE;gBACvE,8EAA8E;gBAC9E,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE;oBACtB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;oBACxB,MAAM,CAAC,qBAAqB,CAAC,GAAG,EAAE;wBAChC,KAAK,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;wBAC1B,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;wBACzB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;oBAC/B,CAAC,CAAC,CAAA;iBACH;aACF;QACH,CAAC;QAED,SAAS,aAAa;YACpB,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA;YACjB,IAAI,aAAa,EAAE;gBACjB,gBAAgB,CAAC,KAAK,CAAC,CAAA;aACxB;QACH,CAAC;QAED,IAAI,aAAa,EAAE;YACjB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,GAAG,EAAE;gBACb,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;SACF;QACD,OAAO,OAAO,CAAA;IAChB,CAAC,EAAE,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC,CAAA;IAE1B,SAAS,SAAS,CAAC,KAAuB;QACxC,2DAA2D;QAC3D,MAAM,MAAM,GAAG,KAAK,CAAC,MAAqB,CAAA;QAC1C,IAAI,MAAM,CAAC,SAAS,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE;YAC9C,OAAM;SACP;QAED,qCAAqC;QACrC,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE;YACtB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;YAC7B,gBAAgB,CAAC,IAAI,CAAC,CAAA;SACvB;IACH,CAAC;IAED,yEAAyE;IACzE,wEAAwE;IACxE,SAAS,OAAO,CAAC,KAAuB;QACtC,KAAK,CAAC,cAAc,EAAE,CAAA;QACtB,gBAAgB,CAAC,KAAK,CAAC,CAAA;IACzB,CAAC;IAED,SAAS,UAAU,CAAC,KAAuB;QACzC,KAAK,CAAC,cAAc,EAAE,CAAA;IACxB,CAAC;IAED,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,SAAS,EACtB,SAAS,EAAE,OAAO,EAClB,YAAY,EAAE,UAAU,EACxB,KAAK,EAAE;YACL,MAAM;YACN,QAAQ,EAAE,UAAU;YACpB,QAAQ,EAAE,QAAQ;YAClB,KAAK,EAAE,SAAS,GAAG,OAAO;SAC3B,IAEA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACpB,oBAAC,eAAe,IAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,GAAI,CAC9D,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/TreeCanvasBlock.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { MsaViewModel } from '../model';
+declare const TreeCanvasBlock: ({ model, offsetY, }: {
+    model: MsaViewModel;
+    offsetY: number;
+}) => React.JSX.Element;
+export default TreeCanvasBlock;