jbrowse-plugin-msaview 2.1.0 → 2.2.0

package/src/index.ts

@@ -1,7 +1,9 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
 import GridOn from '@mui/icons-material/GridOn'
+import { types } from 'mobx-state-tree'
 
 import { version } from '../package.json'
 import AddHighlightModelF from './AddHighlightModel'
@@ -29,4 +31,25 @@ export default class MsaViewPlugin extends Plugin {
       })
     }
   }
+
+  rootConfigurationSchema = {
+    msa: ConfigurationSchema('MSA', {
+      datasets: types.maybe(
+        types.array(
+          ConfigurationSchema('MSAEntry', {
+            name: {
+              type: 'string',
+              defaultValue: '',
+            },
+            adapter: {
+              type: 'frozen',
+              description:
+                'This can be a data adapter config for a IndexedFasta for example, which has a special way of being interpreted',
+              defaultValue: {},
+            },
+          }),
+        ),
+      ),
+    }),
+  }
 }

package/src/utils/fetch.ts

@@ -15,9 +15,9 @@ export async function textfetch(url: string, args?: RequestInit) {
   return response.text()
 }
 
-export async function jsonfetch(url: string, args?: RequestInit) {
+export async function jsonfetch<T>(url: string, args?: RequestInit) {
   const response = await myfetch(url, args)
-  return response.json()
+  return response.json() as Promise<T>
 }
 
 export function timeout(time: number) {

package/src/utils/ncbiBlast.ts

@@ -1,17 +1,18 @@
 import { jsonfetch, textfetch, timeout } from './fetch'
-
-export const BLAST_URL = `https://blast.ncbi.nlm.nih.gov/blast/Blast.cgi`
+import { BlastResults } from './types'
 
 export async function queryBlast({
   query,
   blastDatabase,
   blastProgram,
+  baseUrl,
   onProgress,
   onRid,
 }: {
   query: string
   blastDatabase: string
   blastProgram: string
+  baseUrl: string
   onProgress: (arg: string) => void
   onRid: (arg: string) => void
 }) {
@@ -20,25 +21,17 @@ export async function queryBlast({
     query,
     blastDatabase,
     blastProgram,
+    baseUrl,
   })
   onRid(rid)
-  await waitForRid({ rid, onProgress })
-  const ret = (await jsonfetch(
-    `${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
-  )) as {
-    BlastOutput2: {
-      report: {
-        results: {
-          search: {
-            hits: {
-              description: { accession: string; id: string; sciname: string }[]
-              hsps: { hseq: string }[]
-            }[]
-          }
-        }
-      }
-    }[]
-  }
+  await waitForRid({
+    rid,
+    onProgress,
+    baseUrl,
+  })
+  const ret = await jsonfetch<BlastResults>(
+    `${baseUrl}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`,
+  )
   return {
     rid,
     hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
@@ -49,16 +42,18 @@ async function initialQuery({
   query,
   blastProgram,
   blastDatabase,
+  baseUrl,
 }: {
   query: string
   blastProgram: string
   blastDatabase: string
+  baseUrl: string
 }) {
-  const res = await textfetch(BLAST_URL, {
+  const res = await textfetch(baseUrl, {
     method: 'POST',
     body: new URLSearchParams({
       CMD: 'Put',
-      PROGRAM: blastProgram,
+      PROGRAM: blastProgram === 'quick-blastp' ? 'blastp' : blastProgram,
       DATABASE: blastDatabase,
       QUERY: query,
       ...(blastDatabase === 'nr_clustered_seq'
@@ -67,6 +62,9 @@ async function initialQuery({
             DB_TYPE: 'Experimental Databases',
           }
         : {}),
+      ...(blastProgram === 'quick-blastp'
+        ? { BLAST_PROGRAMS: 'kmerBlastp' }
+        : {}),
     }),
   })
 
@@ -79,15 +77,20 @@ async function initialQuery({
   if (!rid) {
     throw new Error('Failed to get RID from BLAST request')
   }
-  return { rid, rtoe }
+  return {
+    rid,
+    rtoe,
+  }
 }
 
 async function waitForRid({
   rid,
   onProgress,
+  baseUrl,
 }: {
   rid: string
   onProgress: (arg: string) => void
+  baseUrl: string
 }) {
   // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
@@ -98,16 +101,23 @@ async function waitForRid({
     }
 
     const res = await textfetch(
-      `${BLAST_URL}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
+      `${baseUrl}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
     )
-    if (/\s+Status=WAITING/m.test(res)) {
+    const isWaiting = /\s+Status=WAITING/m.test(res)
+    const isFailed = /\s+Status=FAILED/m.test(res)
+    const isReady = /\s+Status=READY/m.test(res)
+    const hasHits = /\s+ThereAreHits=yes/m.test(res)
+
+    if (isWaiting) {
       continue
-    } else if (/\s+Status=FAILED/m.test(res)) {
-      throw new Error(
-        `BLAST ${rid} failed; please report to blast-help@ncbi.nlm.nih.gov`,
-      )
-    } else if (/\s+Status=READY/m.test(res)) {
-      if (/\s+ThereAreHits=yes/m.test(res)) {
+    }
+
+    if (isFailed) {
+      throw new Error(`BLAST ${rid} failed`)
+    }
+
+    if (isReady) {
+      if (hasHits) {
         return true
       } else {
         throw new Error('No hits found')

package/src/utils/types.ts

@@ -0,0 +1,14 @@
+export interface BlastResults {
+  BlastOutput2: {
+    report: {
+      results: {
+        search: {
+          hits: {
+            description: { accession: string; id: string; sciname: string }[]
+            hsps: { hseq: string }[]
+          }[]
+        }
+      }
+    }
+  }[]
+}

package/dist/LaunchMsaView/components/MSALoader/MSALoader.js

@@ -1,94 +0,0 @@
-import React, { useEffect, useState } from 'react';
-import { FileSelector } from '@jbrowse/core/ui';
-import { getContainingView, getSession, } from '@jbrowse/core/util';
-import { openLocation } from '@jbrowse/core/util/io';
-import { Button, DialogActions, DialogContent } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { fetchGeneList } from './fetchGeneList';
-import { preCalculatedLaunchView } from './preCalculatedLaunchView';
-import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
-});
-const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClose, }) {
-    const session = getSession(model);
-    const view = getContainingView(model);
-    const { classes } = useStyles();
-    const [, setError] = useState();
-    const [geneNameList, setGeneNameList] = useState();
-    const [fileLocation, setFileLocation] = useState();
-    useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
-            try {
-                const data = await fetchGeneList();
-                setGeneNameList(data);
-                const set = new Set(data);
-                const options = getTranscriptFeatures(feature);
-                const ret = options.find(val => set.has(getId(val)));
-                if (ret) {
-                    setUserSelection(getId(ret));
-                }
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-    }, [feature]);
-    useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-        ;
-        (async () => {
-            try {
-                if (fileLocation) {
-                    await openLocation(fileLocation).readFile();
-                }
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-    }, [fileLocation, feature]);
-    const set = new Set(geneNameList);
-    const options = getTranscriptFeatures(feature);
-    const ret = options.find(val => set.has(getId(val)));
-    const [userSelection, setUserSelection] = useState(getId(options[0]));
-    return (React.createElement(React.Fragment, null,
-        React.createElement(DialogContent, { className: classes.dialogContent },
-            React.createElement(FileSelector, { location: fileLocation, setLocation: setFileLocation })),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            if (!ret) {
-                                return;
-                            }
-                            await preCalculatedLaunchView({
-                                userSelection,
-                                session,
-                                newViewTitle: getGeneDisplayName(ret),
-                                view,
-                                feature: ret,
-                            });
-                            handleClose();
-                        }
-                        catch (e) {
-                            console.error(e);
-                            setError(e);
-                        }
-                    })();
-                } }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
-});
-export default PreLoadedMSA;
-//# sourceMappingURL=MSALoader.js.map

package/dist/LaunchMsaView/components/MSALoader/MSALoader.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.d.ts

@@ -1 +0,0 @@
-export declare function fetchGeneList(): Promise<string[]>;

package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js

@@ -1,12 +0,0 @@
-export async function fetchGeneList() {
-    const res = await fetch('https://jbrowse.org/demos/msaview/knownCanonical/list.txt');
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`);
-    }
-    const result = await res.text();
-    return result
-        .split('\n')
-        .map(f => f.trim())
-        .filter(f => !!f);
-}
-//# sourceMappingURL=fetchGeneList.js.map

package/dist/LaunchMsaView/components/MSALoader/fetchGeneList.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.d.ts

@@ -1,9 +0,0 @@
-import { AbstractSessionModel, Feature } from '@jbrowse/core/util';
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }: {
-    session: AbstractSessionModel;
-    userSelection: string;
-    newViewTitle: string;
-    view: LinearGenomeViewModel;
-    feature: Feature;
-}): Promise<void>;

package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js

@@ -1,36 +0,0 @@
-import { ungzip } from 'pako';
-async function myfetch(url) {
-    const res = await fetch(url);
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching ${await res.text()}`);
-    }
-    const data = await res.arrayBuffer();
-    return new TextDecoder().decode(ungzip(data));
-}
-export async function preCalculatedLaunchView({ userSelection, session, newViewTitle, view, feature, }) {
-    const d = await myfetch(`https://jbrowse.org/demos/msaview/knownCanonical/${userSelection}.mfa.gz`);
-    session.addView('MsaView', {
-        type: 'MsaView',
-        displayName: newViewTitle,
-        treeAreaWidth: 200,
-        treeWidth: 100,
-        drawNodeBubbles: false,
-        labelsAlignRight: true,
-        showBranchLen: false,
-        colWidth: 10,
-        rowHeight: 12,
-        colorSchemeName: 'percent_identity_dynamic',
-        treeFilehandle: {
-            uri: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.nh',
-        },
-        treeMetadataFilehandle: {
-            uri: 'https://s3.amazonaws.com/jbrowse.org/demos/app/species.json',
-        },
-        data: {
-            msa: d,
-        },
-        connectedViewId: view.id,
-        connectedFeature: feature.toJSON(),
-    });
-}
-//# sourceMappingURL=preCalculatedLaunchView.js.map

package/dist/LaunchMsaView/components/MSALoader/preCalculatedLaunchView.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js

@@ -1,85 +0,0 @@
-import React, { useState } from 'react';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import { getContainingView, } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, MenuItem } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { getProteinSequence } from './calculateProteinSequence';
-import { ncbiBlastLaunchView } from './ncbiBlastLaunchView';
-import { useFeatureSequence } from './useFeatureSequence';
-import TextField2 from '../../../TextField2';
-import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, } from '../../util';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-});
-const NcbiBlastPanel = observer(function NcbiBlastPanel2({ handleClose, feature, model, }) {
-    const { classes } = useStyles();
-    const view = getContainingView(model);
-    const [blastDatabase, setBlastDatabase] = useState('nr');
-    const [msaAlgorithm, setMsaAlgorithm] = useState('clustalo');
-    const options = getTranscriptFeatures(feature);
-    const [userSelection, setUserSelection] = useState(getId(options[0]));
-    const selectedTranscript = options.find(val => getId(val) === userSelection);
-    const { sequence, error } = useFeatureSequence({
-        view,
-        feature: selectedTranscript,
-    });
-    const proteinSequence = sequence && !('error' in sequence)
-        ? getProteinSequence({
-            seq: sequence.seq,
-            selectedTranscript,
-        })
-        : '';
-    const blastDatabaseOptions = ['nr', 'nr_cluster_seq'];
-    const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'];
-    return (React.createElement(DialogContent, { className: classes.dialogContent },
-        error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement(TextField2, { value: blastDatabase, onChange: event => {
-                setBlastDatabase(event.target.value);
-            }, label: "BLAST blastDatabase", select: true }, blastDatabaseOptions.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-        React.createElement(TextField2, { value: msaAlgorithm, onChange: event => {
-                setMsaAlgorithm(event.target.value);
-            }, label: "MSA Algorithm", select: true }, msaAlgorithms.map(val => (React.createElement(MenuItem, { value: val, key: val }, val)))),
-        React.createElement(TextField2, { value: userSelection, onChange: event => {
-                setUserSelection(event.target.value);
-            }, label: "Choose isoform to BLAST", select: true }, options.map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
-            getGeneDisplayName(feature),
-            " - ",
-            getTranscriptDisplayName(val))))),
-        React.createElement(TextField2, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, fullWidth: true, value: proteinSequence
-                ? `>${getTranscriptDisplayName(selectedTranscript)}\n${proteinSequence}`
-                : 'Loading...', slotProps: {
-                input: {
-                    readOnly: true,
-                    classes: {
-                        input: classes.textAreaFont,
-                    },
-                },
-            } }),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
-                    const newView = ncbiBlastLaunchView({
-                        feature: selectedTranscript,
-                        view,
-                        newViewTitle: `NCBI BLAST - ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)} - ${msaAlgorithm}`,
-                    });
-                    newView.setBlastParams({
-                        blastProgram: 'blastp',
-                        blastDatabase,
-                        msaAlgorithm,
-                        selectedTranscript,
-                        proteinSequence,
-                    });
-                    handleClose();
-                }, disabled: !proteinSequence }, "Submit"),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
-});
-export default NcbiBlastPanel;
-//# sourceMappingURL=NcbiBlastPanel.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js

@@ -1,47 +0,0 @@
-import { defaultCodonTable, generateCodonTable, revcom, } from '@jbrowse/core/util';
-export function stitch(subfeats, sequence) {
-    return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
-}
-export function calculateProteinSequence({ cds, sequence, codonTable, }) {
-    const str = stitch(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
-        // use & symbol for undefined codon, or partial slice
-        protein += codonTable[str.slice(i, i + 3)] ?? '&';
-    }
-    return protein;
-}
-export function revlist(list, seqlen) {
-    return list
-        .map(sub => ({
-        ...sub,
-        start: seqlen - sub.end,
-        end: seqlen - sub.start,
-    }))
-        .sort((a, b) => a.start - b.start);
-}
-// filter items if they have the same "ID" or location
-function getItemId(feat) {
-    return `${feat.start}-${feat.end}`;
-}
-// filters if successive elements share same start/end
-export function dedupe(list) {
-    return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
-}
-export function getProteinSequence({ selectedTranscript, seq, }) {
-    const f = selectedTranscript.toJSON();
-    const cds = dedupe(f.subfeatures
-        ?.sort((a, b) => a.start - b.start)
-        .map(sub => ({
-        ...sub,
-        start: sub.start - f.start,
-        end: sub.end - f.start,
-    }))
-        .filter(f => f.type === 'CDS') || []);
-    return calculateProteinSequence({
-        cds: f.strand === -1 ? revlist(cds, seq.length) : cds,
-        sequence: f.strand === -1 ? revcom(seq) : seq,
-        codonTable: generateCodonTable(defaultCodonTable),
-    });
-}
-//# sourceMappingURL=calculateProteinSequence.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/fetchSeq.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.d.ts

@@ -1 +0,0 @@
-export { default } from './NcbiBlastPanel';

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js

@@ -1,2 +0,0 @@
-export { default } from './NcbiBlastPanel';
-//# sourceMappingURL=index.js.map

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/index.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAA"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"ncbiBlastLaunchView.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/ncbiBlastLaunchView.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAKxD,MAAM,UAAU,mBAAmB,CAAC,EAClC,YAAY,EACZ,IAAI,EACJ,OAAO,GAKR;IACC,OAAO,UAAU,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,SAAS,EAAE;QACzC,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,YAAY;QACzB,eAAe,EAAE,IAAI,CAAC,EAAE;QACxB,gBAAgB,EAAE,OAAO,CAAC,MAAM,EAAE;QAClC,aAAa,EAAE,GAAG;QAClB,SAAS,EAAE,GAAG;QACd,eAAe,EAAE,IAAI;QACrB,gBAAgB,EAAE,IAAI;QACtB,QAAQ,EAAE,EAAE;QACZ,SAAS,EAAE,EAAE;QACb,eAAe,EAAE,0BAA0B;KAC5C,CAA8B,CAAA;AACjC,CAAC"}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/types.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/types.ts"],"names":[],"mappings":""}

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.js.map

@@ -1 +0,0 @@
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package/dist/LaunchMsaView/components/NewNCBIBlastQuery/util.js.map

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package/dist/OpenInNewIcon.d.ts

@@ -1,3 +0,0 @@
-import React from 'react';
-import type { SvgIconProps } from '@mui/material';
-export default function OpenInNewIcon(props: SvgIconProps): React.JSX.Element;

package/dist/OpenInNewIcon.js

@@ -1,8 +0,0 @@
-import React from 'react';
-import { SvgIcon } from '@mui/material';
-export default function OpenInNewIcon(props) {
-    return (React.createElement(SvgIcon, { ...props },
-        React.createElement("path", { d: "M0 0h24v24H0z", fill: "none" }),
-        React.createElement("path", { d: "M19 19H5V5h7V3H5c-1.11 0-2 .9-2 2v14c0 1.1.89 2 2 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z" })));
-}
-//# sourceMappingURL=OpenInNewIcon.js.map

package/dist/OpenInNewIcon.js.map

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