react-msaview 1.3.2 → 2.1.0

package/dist/components/AnnotationDlg.js

@@ -1,77 +0,0 @@
-var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogTitle, DialogContent, IconButton, TextField, Typography, } from '@material-ui/core';
-import DeleteIcon from '@material-ui/icons/Delete';
-var specialFromEntries = function (val) {
-    var ret = {};
-    val.forEach(function (_a) {
-        var key = _a[0], val = _a[1];
-        if (!ret[key])
-            ret[key] = [];
-        ret[key].push(val);
-    });
-    return ret;
-};
-var Row = observer(function (_a) {
-    var name = _a.name, value = _a.value, setValue = _a.setValue, setName = _a.setName, onDelete = _a.onDelete;
-    return (React.createElement("div", null,
-        React.createElement(IconButton, { onClick: onDelete, style: { margin: 10 } },
-            React.createElement(DeleteIcon, null)),
-        React.createElement(TextField, { value: name, onChange: function (event) { return setName(event.target.value); }, label: "Key" }),
-        React.createElement(TextField, { value: value, onChange: function (event) { return setValue(event.target.value); }, label: "Value" })));
-});
-export default observer(function (_a) {
-    var onClose = _a.onClose, data = _a.data, model = _a.model;
-    var blanks = model.blanks;
-    var l = data.left, r = data.right;
-    var _b = useState([
-        ['Name', ''],
-        ['ID', ''],
-        ['Note', ''],
-    ]), rows = _b[0], setRows = _b[1];
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: true },
-        React.createElement(DialogTitle, null, "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 ".concat(model.getPos(l), "..").concat(model.getPos(r))
-                    : ''),
-            rows.map(function (_a, index) {
-                var key = _a[0], val = _a[1];
-                return (React.createElement(Row, { key: index, name: key, value: val, setValue: function (newValue) {
-                        var newRows = __spreadArray([], rows, true);
-                        newRows[index][1] = newValue;
-                        setRows(newRows);
-                    }, setName: function (newName) {
-                        var newRows = __spreadArray([], rows, true);
-                        newRows[index][0] = newName;
-                        setRows(newRows);
-                    }, onDelete: function () {
-                        rows.splice(index, 1);
-                        setRows(__spreadArray([], rows, true));
-                    } }));
-            }),
-            React.createElement(Button, { onClick: function () {
-                    setRows(__spreadArray(__spreadArray([], rows, true), [['', '']], false));
-                } }, "Add row"),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: function () {
-                        model.addAnnotation(l, r, specialFromEntries(rows));
-                        onClose();
-                    }, variant: "contained", color: "primary" }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: function () { return onClose(); } }, "Cancel")))));
-});

package/dist/components/DetailsDlg.d.ts

@@ -1,8 +0,0 @@
-/// <reference types="react" />
-import { MsaViewModel } from '../model';
-declare const _default: ({ model, onClose, open, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    open: boolean;
-}) => JSX.Element;
-export default _default;

package/dist/components/DetailsDlg.js

@@ -1,12 +0,0 @@
-import React from 'react';
-import { Dialog, DialogTitle, DialogContent } from '@material-ui/core';
-import { observer } from 'mobx-react';
-import { Attributes } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-export default observer(function (_a) {
-    var model = _a.model, onClose = _a.onClose, open = _a.open;
-    var alignmentDetails = model.alignmentDetails;
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: open },
-        React.createElement(DialogTitle, null, "Metadata"),
-        React.createElement(DialogContent, null,
-            React.createElement(Attributes, { attributes: alignmentDetails }))));
-});

package/dist/components/MoreInfoDlg.d.ts

@@ -1,6 +0,0 @@
-/// <reference types="react" />
-declare const _default: ({ info, onClose }: {
-    info: any;
-    onClose: () => void;
-}) => JSX.Element;
-export default _default;

package/dist/components/MoreInfoDlg.js

@@ -1,11 +0,0 @@
-import React from 'react';
-import { Dialog, DialogTitle, DialogContent } from '@material-ui/core';
-import { observer } from 'mobx-react';
-import { Attributes } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
-export default observer(function (_a) {
-    var info = _a.info, onClose = _a.onClose;
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: true },
-        React.createElement(DialogTitle, null, "Metadata"),
-        React.createElement(DialogContent, null,
-            React.createElement(Attributes, { attributes: info }))));
-});

package/dist/components/SettingsDlg.d.ts

@@ -1,8 +0,0 @@
-/// <reference types="react" />
-import { MsaViewModel } from '../model';
-declare const _default: ({ model, onClose, open, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    open: boolean;
-}) => JSX.Element;
-export default _default;

package/dist/components/SettingsDlg.js

@@ -1,40 +0,0 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, Checkbox, Dialog, DialogActions, DialogTitle, DialogContent, FormControlLabel, MenuItem, TextField, } from '@material-ui/core';
-import colorSchemes from '../colorSchemes';
-export default observer(function (_a) {
-    var model = _a.model, onClose = _a.onClose, open = _a.open;
-    var rowHeightInit = model.rowHeight, colWidthInit = model.colWidth, treeWidthInit = model.treeWidth, colorSchemeName = model.colorSchemeName, noTree = model.noTree;
-    var _b = useState("".concat(rowHeightInit)), rowHeight = _b[0], setRowHeight = _b[1];
-    var _c = useState("".concat(colWidthInit)), colWidth = _c[0], setColWidth = _c[1];
-    var _d = useState("".concat(treeWidthInit)), treeWidth = _d[0], setTreeWidth = _d[1];
-    function error(n) {
-        return Number.isNaN(+n) || +n < 0;
-    }
-    var rowHeightError = error(rowHeight);
-    var colWidthError = error(colWidth);
-    var treeWidthError = error(treeWidth);
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: open },
-        React.createElement(DialogTitle, null, "Settings"),
-        React.createElement(DialogContent, null,
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.showBranchLen, onChange: function () { return model.toggleBranchLen(); } }), label: "Show branch length" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.bgColor, onChange: function () { return model.toggleBgColor(); } }), label: "Color background" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.drawNodeBubbles, onChange: function () { return model.toggleNodeBubbles(); } }), label: "Draw node bubbles" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.drawTree, onChange: function () { return model.toggleDrawTree(); } }), label: "Draw tree (if available)" }),
-            React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: model.labelsAlignRight, onChange: function () { return model.toggleLabelsAlignRight(); } }), label: "Labels align right (note: labels may draw over tree, but can adjust tree width or tree area width in UI)" }),
-            React.createElement(TextField, { label: "Row height (px)", value: rowHeight, error: rowHeightError, onChange: function (event) { return setRowHeight(event.target.value); } }),
-            React.createElement(TextField, { label: "Column width (px)", value: colWidth, error: colWidthError, onChange: function (event) { return setColWidth(event.target.value); } }),
-            React.createElement("br", null),
-            !noTree ? (React.createElement(TextField, { label: "Tree width (px)", value: treeWidth, error: treeWidthError, onChange: function (event) { return setTreeWidth(event.target.value); } })) : null,
-            React.createElement("br", null),
-            React.createElement(TextField, { select: true, label: "Color scheme", value: colorSchemeName, onChange: function (event) { return model.setColorSchemeName(event.target.value); } }, Object.keys(colorSchemes).map(function (option) { return (React.createElement(MenuItem, { key: option, value: option }, option)); })),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { disabled: rowHeightError || colWidthError || treeWidthError, onClick: function () {
-                        model.setRowHeight(+rowHeight);
-                        model.setColWidth(+colWidth);
-                        if (!noTree) {
-                            model.setTreeWidth(+treeWidth);
-                        }
-                        onClose();
-                    }, variant: "contained", color: "primary" }, "Submit")))));
-});

package/dist/components/TrackInfoDlg.d.ts

@@ -1,6 +0,0 @@
-/// <reference types="react" />
-declare const TrackInfoDialog: ({ model, onClose }: {
-    model: any;
-    onClose: () => void;
-}) => JSX.Element;
-export default TrackInfoDialog;

package/dist/components/TrackInfoDlg.js

@@ -1,33 +0,0 @@
-import React, { useState } from 'react';
-import copy from 'copy-to-clipboard';
-import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogTitle, DialogContent, makeStyles, } from '@material-ui/core';
-var useStyles = makeStyles(function (theme) { return ({
-    textArea: {
-        padding: theme.spacing(2),
-        overflow: 'auto',
-        background: '#ddd',
-        wordBreak: 'break-word',
-    },
-}); });
-var TrackInfoDialog = observer(function (_a) {
-    var model = _a.model, onClose = _a.onClose;
-    var _b = useState('Copy to clipboard'), label = _b[0], setLabel = _b[1];
-    var classes = useStyles();
-    return (React.createElement(Dialog, { open: true, onClose: onClose, fullWidth: true, maxWidth: "lg" },
-        React.createElement(DialogTitle, null,
-            "Track info - ",
-            model.name),
-        React.createElement(DialogContent, null,
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: function () {
-                    copy(model.data);
-                    setLabel('Copied!');
-                    setTimeout(function () {
-                        setLabel('Copy to clipboard');
-                    }, 300);
-                } }, label),
-            React.createElement("pre", { className: classes.textArea }, model.data)),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", onClick: onClose, color: "secondary" }, "Close"))));
-});
-export default TrackInfoDialog;

package/dist/components/TracklistDlg.d.ts

@@ -1,8 +0,0 @@
-/// <reference types="react" />
-import { MsaViewModel } from '../model';
-declare const _default: ({ model, onClose, open, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-    open: boolean;
-}) => JSX.Element;
-export default _default;

package/dist/components/TracklistDlg.js

@@ -1,18 +0,0 @@
-import React from 'react';
-import { Dialog, DialogTitle, DialogContent, FormControlLabel, FormGroup, Checkbox, DialogActions, Button, Typography, } from '@material-ui/core';
-import { observer } from 'mobx-react';
-export default observer(function (_a) {
-    var model = _a.model, onClose = _a.onClose, open = _a.open;
-    var tracks = model.tracks;
-    return (React.createElement(Dialog, { onClose: function () { return onClose(); }, open: open },
-        React.createElement(DialogTitle, null, "Add track"),
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "Open relevant per-alignment tracks e.g. protein domains"),
-            React.createElement(FormGroup, null, tracks.map(function (track) {
-                return (React.createElement(FormControlLabel, { key: track.model.id, control: React.createElement(Checkbox, { checked: !model.turnedOffTracks.has(track.model.id), onChange: function () {
-                            model.toggleTrack(track.model.id);
-                        } }), label: track.model.name }));
-            })),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { onClick: function () { return onClose(); }, variant: "contained", color: "primary" }, "Close")))));
-});

package/dist/components/package.json

@@ -1,62 +0,0 @@
-{
-    "version": "1.3.1",
-    "license": "MIT",
-    "main": "dist/index.js",
-    "typings": "dist/index.d.ts",
-    "files": [
-        "dist",
-        "bundle"
-    ],
-    "engines": {
-        "node": ">=10"
-    },
-    "scripts": {
-        "lint": "eslint src",
-        "clean": "rimraf dist",
-        "prestart": "npm run clean",
-        "prebuild": "npm run clean",
-        "start": "yarn tsc --watch",
-        "build": "yarn tsc && rollup -c",
-        "preversion": "npm run build",
-        "postversion": "git push --follow-tags"
-    },
-    "peerDependencies": {
-        "@jbrowse/core": ">=1.5.1",
-        "@material-ui/core": ">=4.12.2",
-        "react": ">=16.8.0",
-        "react-dom": ">=16.8.0"
-    },
-    "name": "react-msaview",
-    "author": "Colin",
-    "devDependencies": {
-        "@rollup/plugin-commonjs": "^21.0.1",
-        "@rollup/plugin-json": "^4.1.0",
-        "@rollup/plugin-node-resolve": "^13.0.6",
-        "@rollup/plugin-typescript": "^8.3.0",
-        "@types/color": "^3.0.1",
-        "@types/d3": "^6.7.0",
-        "@types/lodash": "^4.14.170",
-        "@types/react": "^17.0.3",
-        "@types/react-dom": "^17.0.2",
-        "concurrently": "^6.2.0",
-        "eslint-config-react-app": "^6.0.0",
-        "react": "^17.0.1",
-        "react-dom": "^17.0.1",
-        "rollup": "^2.60.2",
-        "rollup-plugin-node-builtins": "^2.1.2",
-        "rollup-plugin-node-polyfills": "^0.2.1",
-        "rollup-plugin-polyfill-node": "^0.7.0",
-        "tslib": "^2.1.0",
-        "typescript": "^4.2.3"
-    },
-    "dependencies": {
-        "clustal-js": "^1.0.3",
-        "color": "^3.1.3",
-        "copy-to-clipboard": "^3.3.1",
-        "d3-array": "^2.12.0",
-        "d3-hierarchy": "^2.0.0",
-        "normalize-wheel": "^1.0.1",
-        "rbush": "^3.0.1",
-        "stockholm-js": "^1.0.10"
-    }
-}