react-msaview 3.0.0 → 3.0.1

package/src/parsers/ClustalMSA.ts

@@ -12,7 +12,7 @@ export default class ClustalMSA {
   }
 
   getRow(name: string) {
-    return this.MSA.alns.find(aln => aln.id === name)?.seq.split('')
+    return this.MSA.alns.find(aln => aln.id === name)?.seq || ''
   }
 
   getWidth() {

package/src/parsers/FastaMSA.ts

@@ -36,7 +36,7 @@ export default class FastaMSA {
   }
 
   getRow(name: string) {
-    return this.MSA?.seqdata[name]?.split('')
+    return this.MSA?.seqdata[name] || ''
   }
 
   getWidth() {

package/src/parsers/StockholmMSA.ts

@@ -33,7 +33,7 @@ export default class StockholmMSA {
   }
 
   getRow(name: string) {
-    return this.MSA?.seqdata[name]?.split('')
+    return this.MSA?.seqdata[name] || ''
   }
 
   getWidth() {

package/src/util.ts

@@ -109,21 +109,23 @@ export function skipBlanks(blanks: number[], arg: string | string[]) {
   return s
 }
 
+// basically same as setRadius from https://observablehq.com/@d3/tree-of-life
 export function setBrLength(
   d: HierarchyNode<NodeWithIds>,
   y0: number,
   k: number,
 ) {
-  // @ts-expect-error
-  d.len = (y0 += Math.max(d.data.length || 0, 0)) * k
-  d.children?.forEach(d => {
-    setBrLength(d, y0, k)
-  })
+  if (d.children) {
+    d.children.forEach(d => {
+      setBrLength(d, y0, k)
+    })
+  }
 }
 
+// basically same as maxLength from https://observablehq.com/@d3/tree-of-life
 export function maxLength(d: HierarchyNode<NodeWithIds>): number {
   return (
-    (d.data.length || 1) + (d.children ? max(d.children, maxLength) || 0 : 0)
+    (d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0)
   )
 }
 
@@ -140,6 +142,17 @@ export function collapse(d: HierarchyNode<NodeWithIds>) {
   }
 }
 
+// Collapse the node and all it's children, from
+// https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
+export function filterHiddenLeafNodes(
+  d: HierarchyNode<NodeWithIds> | null,
+  hiddenId?: string,
+) {
+  if (d?.children) {
+    d.children = d.children.filter(f => f.id !== hiddenId)
+  }
+}
+
 export function clamp(min: number, num: number, max: number) {
   return Math.min(Math.max(num, min), max)
 }

package/src/version.ts

@@ -1 +1 @@
-export const version = '3.0.0'
+export const version = '3.0.1'

package/dist/components/OverviewRubberband.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../model';
-declare function OverviewRubberband({ model, ControlComponent, }: {
-    model: MsaViewModel;
-    ControlComponent?: React.ReactElement;
-}): React.JSX.Element;
-declare const _default: typeof OverviewRubberband;
-export default _default;

package/dist/components/OverviewRubberband.js

@@ -1,185 +0,0 @@
-import React, { useRef, useEffect, useState, lazy } from 'react';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { Popover, Typography, alpha } from '@mui/material';
-import { Menu } from '@jbrowse/core/ui';
-// icons
-import AssignmentIcon from '@mui/icons-material/Assignment';
-import VerticalGuide from './VerticalGuide';
-const AnnotationDialog = lazy(() => import('./dialogs/AnnotationDialog'));
-const useStyles = makeStyles()(theme => {
-    const background = 'tertiary' in theme.palette && theme.palette.tertiary
-        ? alpha(theme.palette.tertiary.main, 0.7)
-        : alpha(theme.palette.primary.main, 0.7);
-    return {
-        rubberband: {
-            height: '100%',
-            background,
-            position: 'absolute',
-            zIndex: 10,
-            textAlign: 'center',
-            overflow: 'hidden',
-        },
-        rubberbandControl: {
-            cursor: 'crosshair',
-            width: '100%',
-            minHeight: 8,
-        },
-        rubberbandText: {
-            color: theme.palette.tertiary
-                ? theme.palette.tertiary.contrastText
-                : theme.palette.primary.contrastText,
-        },
-        popover: {
-            mouseEvents: 'none',
-            cursor: 'crosshair',
-        },
-        paper: {
-            paddingLeft: theme.spacing(1),
-            paddingRight: theme.spacing(1),
-        },
-    };
-});
-function OverviewRubberband({ model, ControlComponent = React.createElement("div", null), }) {
-    const { treeAreaWidth } = model;
-    const [startX, setStartX] = useState();
-    const [currentX, setCurrentX] = useState();
-    // clientX and clientY used for anchorPosition for menu
-    // offsetX used for calculations about width of selection
-    const [anchorPosition, setAnchorPosition] = useState();
-    const [guideX, setGuideX] = useState();
-    const controlsRef = useRef(null);
-    const rubberbandRef = useRef(null);
-    const { classes } = useStyles();
-    const mouseDragging = startX !== undefined && anchorPosition === undefined;
-    useEffect(() => {
-        function globalMouseMove(event) {
-            if (controlsRef.current && mouseDragging) {
-                const relativeX = event.clientX - controlsRef.current.getBoundingClientRect().left;
-                setCurrentX(relativeX);
-            }
-        }
-        function globalMouseUp(event) {
-            if (startX !== undefined && controlsRef.current) {
-                const { clientX, clientY } = event;
-                const ref = controlsRef.current;
-                const offsetX = clientX - ref.getBoundingClientRect().left;
-                // as stated above, store both clientX/Y and offsetX for different
-                // purposes
-                setAnchorPosition({
-                    offsetX,
-                    clientX,
-                    clientY,
-                });
-                setGuideX(undefined);
-            }
-        }
-        if (mouseDragging) {
-            window.addEventListener('mousemove', globalMouseMove);
-            window.addEventListener('mouseup', globalMouseUp);
-            return () => {
-                window.removeEventListener('mousemove', globalMouseMove);
-                window.removeEventListener('mouseup', globalMouseUp);
-            };
-        }
-        return () => { };
-    }, [startX, mouseDragging, anchorPosition]);
-    useEffect(() => {
-        if (!mouseDragging &&
-            currentX !== undefined &&
-            startX !== undefined &&
-            Math.abs(currentX - startX) <= 3) {
-            handleClose();
-        }
-    }, [mouseDragging, currentX, startX, model.colWidth]);
-    function mouseDown(event) {
-        event.preventDefault();
-        event.stopPropagation();
-        const relativeX = event.clientX -
-            event.target.getBoundingClientRect().left;
-        setStartX(relativeX);
-        setCurrentX(relativeX);
-    }
-    function mouseMove(event) {
-        const target = event.target;
-        setGuideX(event.clientX - target.getBoundingClientRect().left);
-    }
-    function mouseOut() {
-        setGuideX(undefined);
-        model.clearAnnotationClickBoundaries();
-    }
-    function handleClose() {
-        setAnchorPosition(undefined);
-        setStartX(undefined);
-        setCurrentX(undefined);
-    }
-    function handleMenuItemClick(_, callback) {
-        callback();
-        handleClose();
-    }
-    if (startX === undefined) {
-        return (React.createElement(React.Fragment, null,
-            guideX !== undefined ? (React.createElement(VerticalGuide, { model: model, coordX: guideX })) : null,
-            React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
-    }
-    const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
-    const left = right < startX ? right : startX;
-    const width = Math.abs(right - startX);
-    const leftBpOffset = model.pxToBp(left);
-    const rightBpOffset = model.pxToBp(left + width);
-    const numOfBpSelected = Math.ceil(width / model.colWidth);
-    const menuItems = [
-        {
-            label: 'Create annotation',
-            icon: AssignmentIcon,
-            onClick: () => {
-                model.setAnnotationClickBoundaries(leftBpOffset, rightBpOffset);
-                model.queueDialog(onClose => [
-                    AnnotationDialog,
-                    {
-                        data: model.annotPos,
-                        model,
-                        onClose: () => {
-                            model.clearAnnotationClickBoundaries();
-                            onClose();
-                        },
-                    },
-                ]);
-                handleClose();
-            },
-        },
-    ];
-    return (React.createElement(React.Fragment, null,
-        rubberbandRef.current ? (React.createElement(React.Fragment, null,
-            React.createElement(Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'left',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'right',
-                }, keepMounted: true, disableRestoreFocus: true },
-                React.createElement(Typography, null, leftBpOffset + 1)),
-            React.createElement(Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'right',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'left',
-                }, keepMounted: true, disableRestoreFocus: true },
-                React.createElement(Typography, null, rightBpOffset + 1)))) : null,
-        React.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left: left + treeAreaWidth, width } },
-            React.createElement(Typography, { variant: "h6", className: classes.rubberbandText },
-                numOfBpSelected.toLocaleString('en-US'),
-                " bp")),
-        React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
-        anchorPosition ? (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-                left: anchorPosition.clientX,
-                top: anchorPosition.clientY,
-            }, onMenuItemClick: handleMenuItemClick, open: Boolean(anchorPosition), onClose: handleClose, menuItems: menuItems })) : null));
-}
-export default observer(OverviewRubberband);
-//# sourceMappingURL=OverviewRubberband.js.map

package/dist/components/OverviewRubberband.js.map

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package/dist/components/Rubberband.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../model';
-declare function Rubberband({ model, ControlComponent, }: {
-    model: MsaViewModel;
-    ControlComponent?: React.ReactElement;
-}): React.JSX.Element;
-declare const _default: typeof Rubberband;
-export default _default;

package/dist/components/Rubberband.js

@@ -1,185 +0,0 @@
-import React, { useRef, useEffect, useState, lazy } from 'react';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { Popover, Typography, alpha } from '@mui/material';
-import { Menu } from '@jbrowse/core/ui';
-// icons
-import AssignmentIcon from '@mui/icons-material/Assignment';
-import VerticalGuide from './VerticalGuide';
-const AnnotationDialog = lazy(() => import('./dialogs/AnnotationDialog'));
-const useStyles = makeStyles()(theme => {
-    const background = 'tertiary' in theme.palette && theme.palette.tertiary
-        ? alpha(theme.palette.tertiary.main, 0.7)
-        : alpha(theme.palette.primary.main, 0.7);
-    return {
-        rubberband: {
-            height: '100%',
-            background,
-            position: 'absolute',
-            zIndex: 10,
-            textAlign: 'center',
-            overflow: 'hidden',
-        },
-        rubberbandControl: {
-            cursor: 'crosshair',
-            width: '100%',
-            minHeight: 8,
-        },
-        rubberbandText: {
-            color: theme.palette.tertiary
-                ? theme.palette.tertiary.contrastText
-                : theme.palette.primary.contrastText,
-        },
-        popover: {
-            mouseEvents: 'none',
-            cursor: 'crosshair',
-        },
-        paper: {
-            paddingLeft: theme.spacing(1),
-            paddingRight: theme.spacing(1),
-        },
-    };
-});
-function Rubberband({ model, ControlComponent = React.createElement("div", null), }) {
-    const { treeAreaWidth } = model;
-    const [startX, setStartX] = useState();
-    const [currentX, setCurrentX] = useState();
-    // clientX and clientY used for anchorPosition for menu
-    // offsetX used for calculations about width of selection
-    const [anchorPosition, setAnchorPosition] = useState();
-    const [guideX, setGuideX] = useState();
-    const controlsRef = useRef(null);
-    const rubberbandRef = useRef(null);
-    const { classes } = useStyles();
-    const mouseDragging = startX !== undefined && anchorPosition === undefined;
-    useEffect(() => {
-        function globalMouseMove(event) {
-            if (controlsRef.current && mouseDragging) {
-                const relativeX = event.clientX - controlsRef.current.getBoundingClientRect().left;
-                setCurrentX(relativeX);
-            }
-        }
-        function globalMouseUp(event) {
-            if (startX !== undefined && controlsRef.current) {
-                const { clientX, clientY } = event;
-                const ref = controlsRef.current;
-                const offsetX = clientX - ref.getBoundingClientRect().left;
-                // as stated above, store both clientX/Y and offsetX for different
-                // purposes
-                setAnchorPosition({
-                    offsetX,
-                    clientX,
-                    clientY,
-                });
-                setGuideX(undefined);
-            }
-        }
-        if (mouseDragging) {
-            window.addEventListener('mousemove', globalMouseMove);
-            window.addEventListener('mouseup', globalMouseUp);
-            return () => {
-                window.removeEventListener('mousemove', globalMouseMove);
-                window.removeEventListener('mouseup', globalMouseUp);
-            };
-        }
-        return () => { };
-    }, [startX, mouseDragging, anchorPosition]);
-    useEffect(() => {
-        if (!mouseDragging &&
-            currentX !== undefined &&
-            startX !== undefined &&
-            Math.abs(currentX - startX) <= 3) {
-            handleClose();
-        }
-    }, [mouseDragging, currentX, startX, model.colWidth]);
-    function mouseDown(event) {
-        event.preventDefault();
-        event.stopPropagation();
-        const relativeX = event.clientX -
-            event.target.getBoundingClientRect().left;
-        setStartX(relativeX);
-        setCurrentX(relativeX);
-    }
-    function mouseMove(event) {
-        const target = event.target;
-        setGuideX(event.clientX - target.getBoundingClientRect().left);
-    }
-    function mouseOut() {
-        setGuideX(undefined);
-        model.clearAnnotationClickBoundaries();
-    }
-    function handleClose() {
-        setAnchorPosition(undefined);
-        setStartX(undefined);
-        setCurrentX(undefined);
-    }
-    function handleMenuItemClick(_, callback) {
-        callback();
-        handleClose();
-    }
-    if (startX === undefined) {
-        return (React.createElement(React.Fragment, null,
-            guideX !== undefined ? (React.createElement(VerticalGuide, { model: model, coordX: guideX })) : null,
-            React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent)));
-    }
-    const right = anchorPosition ? anchorPosition.offsetX : currentX || 0;
-    const left = right < startX ? right : startX;
-    const width = Math.abs(right - startX);
-    const leftBpOffset = model.pxToBp(left);
-    const rightBpOffset = model.pxToBp(left + width);
-    const numOfBpSelected = Math.ceil(width / model.colWidth);
-    const menuItems = [
-        {
-            label: 'Create annotation',
-            icon: AssignmentIcon,
-            onClick: () => {
-                model.setAnnotationClickBoundaries(leftBpOffset, rightBpOffset);
-                model.queueDialog(onClose => [
-                    AnnotationDialog,
-                    {
-                        data: model.annotPos,
-                        model,
-                        onClose: () => {
-                            model.clearAnnotationClickBoundaries();
-                            onClose();
-                        },
-                    },
-                ]);
-                handleClose();
-            },
-        },
-    ];
-    return (React.createElement(React.Fragment, null,
-        rubberbandRef.current ? (React.createElement(React.Fragment, null,
-            React.createElement(Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'left',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'right',
-                }, keepMounted: true, disableRestoreFocus: true },
-                React.createElement(Typography, null, leftBpOffset + 1)),
-            React.createElement(Popover, { className: classes.popover, classes: {
-                    paper: classes.paper,
-                }, open: true, anchorEl: rubberbandRef.current, anchorOrigin: {
-                    vertical: 'top',
-                    horizontal: 'right',
-                }, transformOrigin: {
-                    vertical: 'bottom',
-                    horizontal: 'left',
-                }, keepMounted: true, disableRestoreFocus: true },
-                React.createElement(Typography, null, rightBpOffset + 1)))) : null,
-        React.createElement("div", { ref: rubberbandRef, className: classes.rubberband, style: { left: left + treeAreaWidth, width } },
-            React.createElement(Typography, { variant: "h6", className: classes.rubberbandText },
-                numOfBpSelected.toLocaleString('en-US'),
-                " bp")),
-        React.createElement("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, role: "presentation", ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove }, ControlComponent),
-        anchorPosition ? (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-                left: anchorPosition.clientX,
-                top: anchorPosition.clientY,
-            }, onMenuItemClick: handleMenuItemClick, open: Boolean(anchorPosition), onClose: handleClose, menuItems: menuItems })) : null));
-}
-export default observer(Rubberband);
-//# sourceMappingURL=Rubberband.js.map

package/dist/components/Rubberband.js.map

@@ -1 +0,0 @@
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package/dist/components/TreePanel/TreeMenu.js.map

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package/dist/components/TreePanel/dialogs/TreeNodeInfoDlg.js.map

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

@@ -1,11 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../../model';
-declare const _default: ({ onClose, data, model, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    data: {
-        left: number;
-        right: number;
-    };
-}) => React.JSX.Element;
-export default _default;

package/dist/components/dialogs/AnnotationDialog.js

@@ -1,65 +0,0 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, DialogActions, DialogContent, IconButton, TextField, Typography, } from '@mui/material';
-import { Dialog } from '@jbrowse/core/ui';
-// icons
-import DeleteIcon from '@mui/icons-material/Delete';
-const specialFromEntries = (val) => {
-    const ret = {};
-    val.forEach(([key, val]) => {
-        if (!ret[key]) {
-            ret[key] = [];
-        }
-        ret[key].push(val);
-    });
-    return ret;
-};
-const Row = observer(function ({ name, value, setValue, setName, onDelete, }) {
-    return (React.createElement("div", null,
-        React.createElement(IconButton, { onClick: onDelete, style: { margin: 10 } },
-            React.createElement(DeleteIcon, null)),
-        React.createElement(TextField, { value: name, onChange: event => setName(event.target.value), label: "Key" }),
-        React.createElement(TextField, { value: value, onChange: event => setValue(event.target.value), label: "Value" })));
-});
-export default observer(({ onClose, data, model, }) => {
-    const { blanks } = model;
-    const { left: l, right: r } = data;
-    const [rows, setRows] = useState([
-        ['Name', ''],
-        ['ID', ''],
-        ['Note', ''],
-    ]);
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Create new region annotation" },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null,
-                "Do you want to add an annotation to the MSA at ",
-                l,
-                "..",
-                r,
-                ' ',
-                blanks.length
-                    ? ` (gapped ${model.getPos(l)}..${model.getPos(r)}`
-                    : ''),
-            rows.map(([key, val], index) => (React.createElement(Row, { key: index, name: key, value: val, setValue: newValue => {
-                    const newRows = [...rows];
-                    newRows[index][1] = newValue;
-                    setRows(newRows);
-                }, setName: newName => {
-                    const newRows = [...rows];
-                    newRows[index][0] = newName;
-                    setRows(newRows);
-                }, onDelete: () => {
-                    rows.splice(index, 1);
-                    setRows([...rows]);
-                } }))),
-            React.createElement(Button, { onClick: () => {
-                    setRows([...rows, ['', '']]);
-                } }, "Add row"),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: () => {
-                        model.addAnnotation(l, r, specialFromEntries(rows));
-                        onClose();
-                    }, variant: "contained", color: "primary" }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel")))));
-});
-//# sourceMappingURL=AnnotationDialog.js.map

package/dist/components/dialogs/AnnotationDialog.js.map

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