jbrowse-plugin-msaview 2.0.6 → 2.1.0

package/dist/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.d.ts

@@ -1,9 +1,5 @@
-import { Feature } from '@jbrowse/core/util';
-export interface SeqState {
-    seq: string;
-    upstream?: string;
-    downstream?: string;
-}
+import type { Feature } from '@jbrowse/core/util';
+import type { SeqState } from './types';
 export interface ErrorState {
     error: string;
 }

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

@@ -1,28 +1,7 @@
 import { useEffect, useState } from 'react';
-import { getConf } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
+import { fetchSeq } from './fetchSeq';
 const BPLIMIT = 500_000;
-async function fetchSeq({ start, end, refName, session, assemblyName, }) {
-    const { assemblyManager, rpcManager } = session;
-    const assembly = await assemblyManager.waitForAssembly(assemblyName);
-    if (!assembly) {
-        throw new Error('assembly not found');
-    }
-    const sessionId = 'getSequence';
-    const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
-        adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-        sessionId,
-        regions: [
-            {
-                start,
-                end,
-                refName: assembly.getCanonicalRefName(refName),
-                assemblyName,
-            },
-        ],
-    }));
-    return feats[0]?.get('seq') ?? '';
-}
 export function useFeatureSequence({ view, feature, upDownBp = 0, forceLoad = true, }) {
     const [sequence, setSequence] = useState();
     const [error, setError] = useState();

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

@@ -1 +1 @@
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+{"version":3,"file":"useFeatureSequence.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE3C,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAQrC,MAAM,OAAO,GAAG,OAAO,CAAA;AAEvB,MAAM,UAAU,kBAAkB,CAAC,EACjC,IAAI,EACJ,OAAO,EACP,QAAQ,GAAG,CAAC,EACZ,SAAS,GAAG,IAAI,GAMjB;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAyB,CAAA;IACjE,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,YAAY,GAAG,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,CAAA;IAC7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,IAAI,EAAE,CAAC;YACT,mEAAmE;YACnE,CAAC;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI,CAAC;oBACH,QAAQ,CAAC,SAAS,CAAC,CAAA;oBACnB,WAAW,CAAC,SAAS,CAAC,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;oBAChC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,MAAM,EAI7C,CAAA;oBACD,IAAI,CAAC,YAAY,EAAE,CAAC;wBAClB,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;oBACtC,CAAC;oBACD,IAAI,CAAC,SAAS,IAAI,GAAG,GAAG,KAAK,GAAG,OAAO,EAAE,CAAC;wBACxC,WAAW,CAAC;4BACV,KAAK,EAAE,gCAAgC,OAAO,wCAAwC;yBACvF,CAAC,CAAA;oBACJ,CAAC;yBAAM,CAAC;wBACN,MAAM,CAAC,GAAG,KAAK,GAAG,QAAQ,CAAA;wBAC1B,MAAM,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;wBACxB,WAAW,CAAC;4BACV,GAAG,EAAE,MAAM,QAAQ,CAAC;gCAClB,KAAK;gCACL,GAAG;gCACH,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;4BACF,QAAQ,EAAE,MAAM,QAAQ,CAAC;gCACvB,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gCACrB,GAAG,EAAE,KAAK;gCACV,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;4BACF,UAAU,EAAE,MAAM,QAAQ,CAAC;gCACzB,KAAK,EAAE,GAAG;gCACV,GAAG,EAAE,CAAC;gCACN,OAAO;gCACP,YAAY;gCACZ,OAAO;6BACR,CAAC;yBACH,CAAC,CAAA;oBACJ,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACb,CAAC;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,YAAY,EAAE,SAAS,CAAC,CAAC,CAAA;IACtD,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;AAC5B,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -49,18 +49,16 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({ model, feature, handleClo
                 ' ',
                 React.createElement("a", { href: "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/alignments/" }, "knownCanonical.multiz100way.protAA.fa.gz")),
             error ? React.createElement(ErrorMessage, { error: error }) : null,
-            geneNameList && !ret ? (React.createElement("div", { style: { color: 'red' } }, "No MSA data for this gene found")) : null,
-            React.createElement(TextField, { value: userSelection, onChange: event => {
+            geneNameList && !ret ? (React.createElement(Typography, { color: "error" }, "No MSA data for this gene found")) : null,
+            React.createElement(TextField, { select: true, label: "Choose isoform to view MSA for", value: userSelection, onChange: event => {
                     setUserSelection(event.target.value);
-                }, label: "Choose isoform to view MSA for", select: true },
-                options
-                    .filter(val => set.has(getId(val)))
-                    .map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id() },
+                } }, options.map(val => {
+                const inSet = set.has(getId(val));
+                return (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: !inSet },
                     getTranscriptDisplayName(val),
-                    " (has data)"))),
-                options
-                    .filter(val => !set.has(getId(val)))
-                    .map(val => (React.createElement(MenuItem, { value: getId(val), key: val.id(), disabled: true }, getTranscriptDisplayName(val)))))),
+                    " ",
+                    inSet ? ' (has data)' : ''));
+            }))),
         React.createElement(DialogActions, null,
             React.createElement(Button, { color: "primary", variant: "contained", onClick: () => {
                     // eslint-disable-next-line @typescript-eslint/no-floating-promises

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"PreLoadedMSADataPanel.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAGL,iBAAiB,EACjB,UAAU,GACX,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,QAAQ,EACR,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAA;AAC/C,OAAO,EAAE,uBAAuB,EAAE,MAAM,2BAA2B,CAAA;AACnE,OAAO,EACL,kBAAkB,EAClB,KAAK,EACL,wBAAwB,EACxB,qBAAqB,GACtB,MAAM,YAAY,CAAA;AAInB,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;CACF,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,aAAa,CAAC,EACnD,KAAK,EACL,OAAO,EACP,WAAW,GAKZ;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,EAAY,CAAA;IAC5D,SAAS,CAAC,GAAG,EAAE;QACb,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,MAAM,IAAI,GAAG,MAAM,aAAa,EAAE,CAAA;gBAClC,eAAe,CAAC,IAAI,CAAC,CAAA;gBACrB,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,CAAA;gBACzB,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;gBAC9C,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;gBACpD,IAAI,GAAG,EAAE,CAAC;oBACR,gBAAgB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAA;gBAC9B,CAAC;YACH,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAA;IACb,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,YAAY,CAAC,CAAA;IACjC,MAAM,OAAO,GAAG,qBAAqB,CAAC,OAAO,CAAC,CAAA;IAC9C,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;IACpD,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAErE,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC7C,oBAAC,UAAU;;gBACsD,GAAG;gBAClE,2BAAG,IAAI,EAAC,0EAA0E,+CAE9E,CACO;YACZ,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC7C,YAAY,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CACtB,oBAAC,UAAU,IAAC,KAAK,EAAC,OAAO,sCAA6C,CACvE,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,SAAS,IACR,MAAM,QACN,KAAK,EAAC,gCAAgC,EACtC,KAAK,EAAE,aAAa,EACpB,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBACtC,CAAC,IAEA,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACjB,MAAM,KAAK,GAAG,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAA;gBACjC,OAAO,CACL,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,KAAK;oBACzD,wBAAwB,CAAC,GAAG,CAAC;;oBAAG,KAAK,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,CAClD,CACZ,CAAA;YACH,CAAC,CAAC,CACQ,CACE;QAEhB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,KAAK,EAAC,SAAS,EACf,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,mEAAmE;oBACnE,CAAC;oBAAA,CAAC,KAAK,IAAI,EAAE;wBACX,IAAI,CAAC;4BACH,IAAI,CAAC,GAAG,EAAE,CAAC;gCACT,OAAM;4BACR,CAAC;4BACD,MAAM,uBAAuB,CAAC;gCAC5B,aAAa;gCACb,OAAO;gCACP,YAAY,EAAE,kBAAkB,CAAC,GAAG,CAAC;gCACrC,IAAI;gCACJ,OAAO,EAAE,GAAG;6BACb,CAAC,CAAA;4BACF,WAAW,EAAE,CAAA;wBACf,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACb,CAAC;oBACH,CAAC,CAAC,EAAE,CAAA;gBACN,CAAC,aAGM;YACT,oBAAC,MAAM,IACL,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,aAGM,CACK,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/LaunchMsaView/components/TabPanel.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+export default function TabPanel({ children, value, index, ...other }: {
+    children?: React.ReactNode;
+    index: number;
+    value: number;
+}): React.JSX.Element;

package/dist/LaunchMsaView/components/TabPanel.js

@@ -0,0 +1,6 @@
+import React from 'react';
+// this is from MUI example
+export default function TabPanel({ children, value, index, ...other }) {
+    return (React.createElement("div", { role: "tabpanel", hidden: value !== index, ...other }, value === index && React.createElement("div", null, children)));
+}
+//# sourceMappingURL=TabPanel.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"TabPanel.js","sourceRoot":"","sources":["../../../src/LaunchMsaView/components/TabPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,2BAA2B;AAC3B,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAC/B,QAAQ,EACR,KAAK,EACL,KAAK,EACL,GAAG,KAAK,EAKT;IACC,OAAO,CACL,6BAAK,IAAI,EAAC,UAAU,EAAC,MAAM,EAAE,KAAK,KAAK,KAAK,KAAM,KAAK,IACpD,KAAK,KAAK,KAAK,IAAI,iCAAM,QAAQ,CAAO,CACrC,CACP,CAAA;AACH,CAAC"}

package/dist/MsaViewPanel/model.d.ts

@@ -269,6 +269,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         url?: string;
     } | undefined;
     highResScaleFactor: number;
+    showZoomStar: boolean;
     loadingMSA: boolean;
     loadingTree: boolean;
     volatileWidth: number | undefined;
@@ -293,6 +294,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setAllowedGappyness(arg: number): void;
     setContrastLettering(arg: boolean): void;
     setLoadingMSA(arg: boolean): void;
+    setShowZoomStar(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
     setHeight(height: number): void;
@@ -334,10 +336,10 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly treeMetadata: any;
     readonly MSA: import("react-msaview/dist/parsers/StockholmMSA").default | import("react-msaview/dist/parsers/FastaMSA").default | import("react-msaview/dist/parsers/EmfMSA").default | import("react-msaview/dist/parsers/ClustalMSA").default | null;
     readonly numColumns: number;
-    readonly tree: import("react-msaview/dist/util").NodeWithIds;
+    readonly tree: import("react-msaview/dist/types").NodeWithIds;
     readonly rowNames: string[];
     readonly mouseOverRowName: string | undefined;
-    readonly root: HierarchyNode<import("react-msaview/dist/util").NodeWithIds>;
+    readonly root: HierarchyNode<import("react-msaview/dist/types").NodeWithIds>;
     readonly msaAreaWidth: number;
     readonly treeAreaWidthMinusMargin: number;
     readonly blanks: number[];
@@ -354,9 +356,10 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly colStatsSums: {
         [k: string]: number;
     };
-    readonly hierarchy: HierarchyNode<import("react-msaview/dist/util").NodeWithIdsAndLength>;
+    readonly hierarchy: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>;
     readonly totalHeight: number;
-    readonly leaves: HierarchyNode<import("react-msaview/dist/util").NodeWithIdsAndLength>[];
+    readonly leaves: HierarchyNode<import("react-msaview/dist/types").NodeWithIdsAndLength>[];
+    readonly allBranchesLength0: boolean;
 } & {
     readonly totalWidth: number;
 } & {
@@ -371,6 +374,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly showTreeText: boolean;
 } & {
     setDrawMsaLetters(arg: boolean): void;
+    resetZoom(): void;
     zoomOutHorizontal(): void;
     zoomInHorizontal(): void;
     zoomInVertical(): void;
@@ -391,9 +395,9 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly secondaryStructureConsensus: string | undefined;
     readonly seqConsensus: string | undefined;
     readonly conservation: string[];
-    readonly adapterTrackModels: import("react-msaview/dist/model").BasicTrack[];
-    readonly tracks: import("react-msaview/dist/model").BasicTrack[];
-    readonly turnedOnTracks: import("react-msaview/dist/model").ITextTrack[];
+    readonly adapterTrackModels: import("react-msaview/dist/types").BasicTrack[];
+    readonly tracks: import("react-msaview/dist/types").BasicTrack[];
+    readonly turnedOnTracks: import("react-msaview/dist/types").ITextTrack[];
     readonly showHorizontalScrollbar: boolean;
     readonly rowNamesSet: Map<string, number>;
     mouseOverCoordToRowLetter(rowName: string, position: number): string | undefined;
@@ -402,7 +406,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
 } & {
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview/dist/model").Accession>;
+    readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview/dist/types").Accession>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;