react-msaview 4.4.4 → 4.4.6

package/dist/StructureModel.js

@@ -1,11 +0,0 @@
-import { types } from 'mobx-state-tree';
-export const StructureModel = types.model({
-    id: types.identifier,
-    structure: types.model({
-        pdb: types.string,
-        startPos: types.number,
-        endPos: types.number,
-    }),
-    range: types.maybe(types.string),
-});
-//# sourceMappingURL=StructureModel.js.map

package/dist/StructureModel.js.map

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

@@ -1,27 +0,0 @@
-export declare const UniprotTrack: import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").ISimpleType<string>;
-    accession: import("mobx-state-tree").ISimpleType<string>;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    associatedRowName: import("mobx-state-tree").ISimpleType<string>;
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-}, {
-    error: unknown;
-    data: string | undefined;
-} & {
-    setError(error: unknown): void;
-    setData(data: string): void;
-} & {
-    afterCreate(): void;
-} & {
-    readonly loading: boolean;
-    readonly features: {
-        seq_id: string;
-        source: string;
-        type: string;
-        start: number;
-        end: number;
-        score: number;
-        strand: string;
-        phase: string;
-    }[] | undefined;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/UniprotTrack.js

@@ -1,53 +0,0 @@
-import { types, addDisposer } from 'mobx-state-tree';
-import { autorun } from 'mobx';
-// locals
-import { parseGFF } from './util';
-export const UniprotTrack = types
-    .model({
-    id: types.string,
-    accession: types.string,
-    name: types.string,
-    associatedRowName: types.string,
-    height: types.optional(types.number, 100),
-})
-    .volatile(() => ({
-    error: undefined,
-    data: undefined,
-}))
-    .actions(self => ({
-    setError(error) {
-        self.error = error;
-    },
-    setData(data) {
-        self.data = data;
-    },
-}))
-    .actions(self => ({
-    afterCreate() {
-        addDisposer(self, autorun(async () => {
-            try {
-                const { accession } = self;
-                const accessionSansVersion = accession?.replace(/\.[^/.]+$/, '');
-                const url = `https://rest.uniprot.org/uniprotkb/${accessionSansVersion}.gff`;
-                const res = await fetch(url);
-                if (!res.ok) {
-                    throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
-                }
-                self.setData(await res.text());
-            }
-            catch (e) {
-                console.error(e);
-                self.setError(e);
-            }
-        }));
-    },
-}))
-    .views(self => ({
-    get loading() {
-        return !self.data;
-    },
-    get features() {
-        return parseGFF(self.data);
-    },
-}));
-//# sourceMappingURL=UniprotTrack.js.map

package/dist/UniprotTrack.js.map

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

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

package/dist/components/BoxTrack.js

@@ -1,15 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-import BoxTrackBlock from './BoxTrackBlock';
-const BoxTrack = observer(function ({ model, track, }) {
-    const { blocksX, msaAreaWidth } = model;
-    const { height } = track.model;
-    return (React.createElement("div", { style: {
-            position: 'relative',
-            height,
-            width: msaAreaWidth,
-            overflow: 'hidden',
-        } }, blocksX.map(bx => (React.createElement(BoxTrackBlock, { track: track, key: bx, model: model, offsetX: bx })))));
-});
-export default BoxTrack;
-//# sourceMappingURL=BoxTrack.js.map

package/dist/components/BoxTrack.js.map

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

@@ -1,8 +0,0 @@
-import React from 'react';
-import { IBoxTrack, MsaViewModel } from '../model';
-declare const BoxTrackBlock: ({ track, model, offsetX, }: {
-    track: IBoxTrack;
-    model: MsaViewModel;
-    offsetX: number;
-}) => React.JSX.Element | null;
-export default BoxTrackBlock;

package/dist/components/BoxTrackBlock.js

@@ -1,136 +0,0 @@
-import React, { useRef, useMemo, useEffect } from 'react';
-import { observer } from 'mobx-react';
-import { getSnapshot, isStateTreeNode } from 'mobx-state-tree';
-import Layout from '../layout';
-const BoxTrackBlock = observer(function ({ track, model, offsetX, }) {
-    const { blockSize, colWidth, blanks, rowHeight, highResScaleFactor, fontSize, scrollX, } = model;
-    const { height, features, associatedRowName } = track.model;
-    const feats = isStateTreeNode(features)
-        ? // @ts-expect-error
-            getSnapshot(features)
-        : features;
-    const layout = useMemo(() => {
-        const temp = new Layout();
-        feats?.forEach((feature, index) => {
-            const { start, end } = feature;
-            if (associatedRowName) {
-                const s = model.rowSpecificBpToPx(associatedRowName, start - 1);
-                const e = model.rowSpecificBpToPx(associatedRowName, end);
-                temp.addRect(`${index}`, s, e, rowHeight, feature);
-            }
-            else {
-                const s = model.globalBpToPx(start - 1);
-                const e = model.globalBpToPx(end);
-                temp.addRect(`${index}`, s, e, rowHeight, feature);
-            }
-        });
-        return temp;
-        // might convert to autorun based drawing
-        // eslint-disable-next-line react-hooks/exhaustive-deps
-    }, [rowHeight, feats, associatedRowName, model, blanks]);
-    const ref = useRef(null);
-    const labelRef = useRef(null);
-    const mouseoverRef = useRef(null);
-    useEffect(() => {
-        if (!ref.current) {
-            return;
-        }
-        const ctx = ref.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.scale(highResScaleFactor, highResScaleFactor);
-        ctx.clearRect(0, 0, blockSize, height);
-        ctx.translate(-offsetX, 0);
-        ctx.textAlign = 'center';
-        ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
-        const xStart = Math.max(0, Math.floor(offsetX / colWidth));
-        ctx.fillStyle = 'goldenrod';
-        layout.rectangles.forEach(value => {
-            const { minX, maxX, minY, maxY } = value;
-            const x1 = (minX - xStart) * colWidth + offsetX - (offsetX % colWidth);
-            const x2 = (maxX - xStart) * colWidth + offsetX - (offsetX % colWidth);
-            if (x2 - x1 > 0) {
-                ctx.fillRect(x1, minY, x2 - x1, (maxY - minY) / 2);
-            }
-        });
-    }, [
-        associatedRowName,
-        fontSize,
-        blockSize,
-        colWidth,
-        layout.rectangles,
-        model,
-        rowHeight,
-        height,
-        offsetX,
-        highResScaleFactor,
-        features,
-        blanks,
-    ]);
-    useEffect(() => {
-        if (!labelRef.current) {
-            return;
-        }
-        const ctx = labelRef.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        // this logic is very similar to MSACanvas
-        ctx.resetTransform();
-        ctx.scale(highResScaleFactor, highResScaleFactor);
-        ctx.clearRect(0, 0, blockSize, height);
-        ctx.translate(-offsetX, 0);
-        ctx.textAlign = 'center';
-        ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
-        ctx.fillStyle = 'black';
-        ctx.textAlign = 'left';
-        for (const value of layout.rectangles.values()) {
-            const { minX, maxX, maxY, minY, data } = value;
-            const x1 = minX * colWidth;
-            const x2 = maxX * colWidth;
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            const feature = data;
-            if (x2 - x1 > 0) {
-                const note = feature.attributes?.Note?.[0];
-                const name = feature.attributes?.Name?.[0];
-                const type = feature.type;
-                ctx.fillText([type, name, note].filter(f => !!f).join(' - '), Math.max(Math.min(-scrollX, x2), x1), minY + (maxY - minY));
-            }
-        }
-    }, [
-        blockSize,
-        colWidth,
-        scrollX,
-        highResScaleFactor,
-        height,
-        layout.rectangles,
-        offsetX,
-        features,
-        model,
-        rowHeight,
-        blanks,
-    ]);
-    return !features ? null : (React.createElement(React.Fragment, null,
-        React.createElement("canvas", { ref: ref, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-                position: 'absolute',
-                left: scrollX + offsetX,
-                width: blockSize,
-                height,
-            } }),
-        React.createElement("canvas", { ref: labelRef, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-                position: 'absolute',
-                left: scrollX + offsetX,
-                width: blockSize,
-                height,
-            } }),
-        React.createElement("canvas", { ref: mouseoverRef, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
-                position: 'absolute',
-                left: scrollX + offsetX,
-                width: blockSize,
-                height,
-            } })));
-});
-export default BoxTrackBlock;
-//# sourceMappingURL=BoxTrackBlock.js.map

package/dist/components/BoxTrackBlock.js.map

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

@@ -1,6 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../model';
-export default function ExportSVGDialog({ model, onClose, }: {
-    model: MsaViewModel;
-    onClose: () => void;
-}): React.JSX.Element;

package/dist/components/ExportSVGDialog.js

@@ -1,39 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
-import { Button, Checkbox, DialogContent, DialogActions, FormControlLabel, FormControl, FormLabel, RadioGroup, Radio, Typography, useTheme, } from '@mui/material';
-export default function ExportSVGDialog({ model, onClose, }) {
-    const [includeMinimap, setIncludeMinimap] = useState(true);
-    const [exportType, setExportType] = useState('viewport');
-    const [error, setError] = useState();
-    const theme = useTheme();
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Export SVG" },
-        React.createElement(DialogContent, null,
-            error ? React.createElement(ErrorMessage, { error: error }) : null,
-            React.createElement(Typography, null, "Settings:"),
-            React.createElement("div", null,
-                React.createElement(FormControl, null,
-                    React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: includeMinimap, onChange: event => setIncludeMinimap(event.target.checked) }), disabled: exportType === 'entire', label: "Include minimap?" }))),
-            React.createElement("div", null,
-                React.createElement(FormControl, null,
-                    React.createElement(FormLabel, null, "Export type"),
-                    React.createElement(RadioGroup, { value: exportType, onChange: event => setExportType(event.target.value) },
-                        React.createElement(FormControlLabel, { value: "entire", control: React.createElement(Radio, null), label: "Entire MSA" }),
-                        React.createElement(FormControlLabel, { value: "viewport", control: React.createElement(Radio, null), label: "Current viewport only" }))))),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: async () => {
-                    try {
-                        await model.exportSVG({
-                            theme,
-                            includeMinimap: exportType === 'entire' ? false : includeMinimap,
-                            exportType,
-                        });
-                    }
-                    catch (e) {
-                        console.error(e);
-                        setError(e);
-                    }
-                    onClose();
-                } }, "Submit"),
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"))));
-}
-//# sourceMappingURL=ExportSVGDialog.js.map

package/dist/components/ExportSVGDialog.js.map

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

@@ -1,6 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../model';
-declare const Header: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default Header;

package/dist/components/Header.js

@@ -1,62 +0,0 @@
-import React, { Suspense, lazy, useState } from 'react';
-import { IconButton } from '@mui/material';
-import { observer } from 'mobx-react';
-// icons
-import FolderOpen from '@mui/icons-material/FolderOpen';
-import Settings from '@mui/icons-material/Settings';
-import Help from '@mui/icons-material/Help';
-import Assignment from '@mui/icons-material/Assignment';
-import List from '@mui/icons-material/List';
-// locals
-import ZoomControls from './ZoomControls';
-import MultiAlignmentSelector from './MultiAlignmentSelector';
-import HeaderInfoArea from './HeaderInfoArea';
-const SettingsDialog = lazy(() => import('./dialogs/SettingsDialog'));
-const AboutDialog = lazy(() => import('./dialogs/AboutDialog'));
-const MetadataDialog = lazy(() => import('./dialogs/MetadataDialog'));
-const TracklistDialog = lazy(() => import('./dialogs/TracklistDialog'));
-const Header = observer(function ({ model }) {
-    const [settingsDialogViz, setSettingsDialogViz] = useState(false);
-    const [aboutDialogViz, setAboutDialogViz] = useState(false);
-    const [detailsDialogViz, setMetadataDialogViz] = useState(false);
-    const [tracklistDialogViz, setTracklistDialogViz] = useState(false);
-    return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement(IconButton, { onClick: async () => {
-                try {
-                    model.setData({ tree: '', msa: '' });
-                    model.clearSelectedStructures();
-                    model.setScrollY(0);
-                    model.setScrollX(0);
-                    model.setCurrentAlignment(0);
-                    await model.setTreeFilehandle(undefined);
-                    await model.setMSAFilehandle(undefined);
-                }
-                catch (e) {
-                    console.error(e);
-                    model.setError(e);
-                }
-            } },
-            React.createElement(FolderOpen, null)),
-        React.createElement(IconButton, { onClick: () => setSettingsDialogViz(true) },
-            React.createElement(Settings, null)),
-        React.createElement(IconButton, { onClick: () => setMetadataDialogViz(true) },
-            React.createElement(Assignment, null)),
-        React.createElement(IconButton, { onClick: () => setTracklistDialogViz(true) },
-            React.createElement(List, null)),
-        React.createElement(Suspense, { fallback: null },
-            settingsDialogViz ? (React.createElement(SettingsDialog, { model: model, onClose: () => setSettingsDialogViz(false) })) : null,
-            aboutDialogViz ? (React.createElement(AboutDialog, { onClose: () => setAboutDialogViz(false) })) : null,
-            detailsDialogViz ? (React.createElement(MetadataDialog, { model: model, onClose: () => setMetadataDialogViz(false) })) : null,
-            tracklistDialogViz ? (React.createElement(TracklistDialog, { model: model, onClose: () => setTracklistDialogViz(false) })) : null),
-        React.createElement(MultiAlignmentSelector, { model: model }),
-        React.createElement(ZoomControls, { model: model }),
-        React.createElement(HeaderInfoArea, { model: model }),
-        React.createElement(Spacer, null),
-        React.createElement(IconButton, { onClick: () => setAboutDialogViz(true) },
-            React.createElement(Help, null))));
-});
-function Spacer() {
-    return React.createElement("div", { style: { flex: 1 } });
-}
-export default Header;
-//# sourceMappingURL=Header.js.map

package/dist/components/Header.js.map

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

@@ -1,6 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../model';
-declare const HeaderInfoArea: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default HeaderInfoArea;

package/dist/components/HeaderInfoArea.js

@@ -1,12 +0,0 @@
-import React from 'react';
-import { Typography } from '@mui/material';
-import { observer } from 'mobx-react';
-const HeaderInfoArea = observer(({ model }) => {
-    const { mouseOverRowName, mouseCol } = model;
-    return (React.createElement("div", null, mouseOverRowName && mouseCol !== undefined ? (React.createElement(Typography, null,
-        mouseOverRowName,
-        ":",
-        model.relativePxToBp(mouseOverRowName, mouseCol))) : null));
-});
-export default HeaderInfoArea;
-//# sourceMappingURL=HeaderInfoArea.js.map

package/dist/components/HeaderInfoArea.js.map

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

@@ -1,6 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../../model';
-declare const ImportFormExamples: ({ model, }: {
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default ImportFormExamples;

package/dist/components/ImportForm/ImportFormExamples.js

@@ -1,50 +0,0 @@
-import React from 'react';
-import { Typography, Link } from '@mui/material';
-import { observer } from 'mobx-react';
-import { smallTree, smallMSA, smallMSAOnly } from './data/seq2';
-import { load } from './util';
-const ListItem = ({ onClick, model, children, }) => (React.createElement("li", null,
-    React.createElement(Link, { onClick: event => {
-            model.setError(undefined);
-            event.preventDefault();
-            onClick();
-        }, href: "#" },
-        React.createElement(Typography, { display: "inline" }, children))));
-const ImportFormExamples = observer(function ({ model, }) {
-    return (React.createElement("ul", null,
-        React.createElement(ListItem, { model: model, onClick: () => load(model, undefined, {
-                uri: 'https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh',
-                locationType: 'UriLocation',
-            }) }, "230k COVID-19 samples (tree only)"),
-        React.createElement(ListItem, { model: model, onClick: () => {
-                model.setData({ msa: smallMSA, tree: smallTree });
-            } }, "Small protein MSA+tree"),
-        React.createElement(ListItem, { model: model, onClick: () => {
-                model.setData({ msa: smallMSAOnly });
-            } }, "Small MSA only"),
-        React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/pfam-cov2.stock',
-                locationType: 'UriLocation',
-            }) }, "PFAM SARS-CoV2 multi-stockholm"),
-        React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock',
-                locationType: 'UriLocation',
-            }) }, "Lysine stockholm file"),
-        React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt',
-                locationType: 'UriLocation',
-            }) }, "PF01601 stockholm file (SARS-CoV2 spike protein)"),
-        React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa',
-                locationType: 'UriLocation',
-            }) }, "Europe COVID full genomes (LR883044.1 and 199 other sequences)"),
-        React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                uri: '/rhv_test-only.aligned_with_mafft_auto.fa',
-                locationType: 'UriLocation',
-            }, {
-                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh',
-                locationType: 'UriLocation',
-            }) }, "MAFFT+VeryFastTree(17.9k samples)")));
-});
-export default ImportFormExamples;
-//# sourceMappingURL=ImportFormExamples.js.map

package/dist/components/ImportForm/ImportFormExamples.js.map

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package/dist/components/ImportForm/data/seq2.d.ts

@@ -1,3 +0,0 @@
-export declare const smallMSA = "CLUSTAL O(1.2.3) multiple sequence alignment\nUniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM\nUniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI\nUniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM\nUniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM\nUniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM\nUniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------\nUniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS\nUniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV\nUniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP\nUniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------\nUniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST\nUniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------\n";
-export declare const smallMSAOnly = "CLUSTAL O(1.2.4) multiple sequence alignment\n\n\nsp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\t60\nsp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG\t60\nsp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG\t60\n                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**\n\nsp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\t120\nsp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP\t120\nsp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA\t120\n                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**\n\nsp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR\t142\n                           .**: ****: ** ***.***";
-export declare const smallTree = "(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)";

package/dist/components/ImportForm/data/seq2.js

@@ -1,33 +0,0 @@
-export const smallMSA = `CLUSTAL O(1.2.3) multiple sequence alignment
-UniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
-UniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
-UniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
-UniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM
-UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM
-UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------
-UniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS
-UniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV
-UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP
-UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
-UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
-UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
-`;
-export const smallMSAOnly = `CLUSTAL O(1.2.4) multiple sequence alignment
-
-
-sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
-sp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG	60
-sp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG	60
-                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**
-
-sp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP	120
-sp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP	120
-sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA	120
-                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**
-
-sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
-sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
-sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
-                           .**: ****: ** ***.***`;
-export const smallTree = '(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)';
-//# sourceMappingURL=seq2.js.map

package/dist/components/ImportForm/data/seq2.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"seq2.js","sourceRoot":"","sources":["../../../../src/components/ImportForm/data/seq2.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,QAAQ,GAAG;;;;;;;;;;;;;CAavB,CAAA;AAED,MAAM,CAAC,MAAM,YAAY,GAAG;;;;;;;;;;;;;;;;iDAgBqB,CAAA;AAEjD,MAAM,CAAC,MAAM,SAAS,GACpB,+nBAA+nB,CAAA"}

package/dist/components/ImportForm/index.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../../model';
-declare const _default: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default _default;

package/dist/components/ImportForm/index.js

@@ -1,31 +0,0 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, Container, Grid, Typography } from '@mui/material';
-import { FileSelector } from '@jbrowse/core/ui';
-import { load } from './util';
-import ImportFormExamples from './ImportFormExamples';
-export default observer(({ model }) => {
-    const [msaFile, setMsaFile] = useState();
-    const [treeFile, setTreeFile] = useState();
-    const { error } = model;
-    return (React.createElement(Container, null,
-        React.createElement("div", { style: { width: '50%' } },
-            error ? (React.createElement("div", { style: { padding: 20 } },
-                React.createElement(Typography, { color: "error" },
-                    "Error: ",
-                    `${error}`))) : null,
-            React.createElement(Typography, null, "Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),
-            React.createElement(Typography, { color: "error" }, "Note: you can open up just an MSA or just a tree, both are not required. Some MSA files e.g. stockholm format have an embedded tree also and this is fine, and opening a separate tree file is not required.")),
-        React.createElement(Grid, { container: true, spacing: 10, justifyContent: "center", alignItems: "center" },
-            React.createElement(Grid, { item: true },
-                React.createElement(Typography, null, "MSA file or URL"),
-                React.createElement(FileSelector, { location: msaFile, setLocation: setMsaFile }),
-                React.createElement(Typography, null, "Tree file or URL"),
-                React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile })),
-            React.createElement(Grid, { item: true },
-                React.createElement(Button, { onClick: () => load(model, msaFile, treeFile), variant: "contained", color: "primary", disabled: !msaFile && !treeFile }, "Open")),
-            React.createElement(Grid, { item: true },
-                React.createElement(Typography, null, "Examples"),
-                React.createElement(ImportFormExamples, { model: model })))));
-});
-//# sourceMappingURL=index.js.map

package/dist/components/ImportForm/index.js.map

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package/dist/components/ImportForm/util.d.ts

@@ -1,3 +0,0 @@
-import { FileLocation } from '@jbrowse/core/util';
-import { MsaViewModel } from '../../model';
-export declare function load(model: MsaViewModel, msaFile?: FileLocation, treeFile?: FileLocation): Promise<void>;