jbrowse-plugin-protein3d 0.0.2 → 0.0.4

package/dist/LaunchProteinView/{util.js → components/util.js}

@@ -7,34 +7,13 @@ export function getTranscriptFeatures(feature) {
         : subfeatures;
 }
 export function stripTrailingVersion(s) {
-    return s?.replace(/\.[^/.]+$/, '');
+    return s?.replace(/\.[^./]+$/, '');
 }
 export function z(n) {
     return n.toLocaleString('en-US');
 }
-export function createMapFromData(data) {
-    const map = new Map();
-    if (data) {
-        for (const d of data) {
-            const { pdb_id, transcript_id, refseq_mrna_id, transcript_id_version } = d;
-            if (!pdb_id) {
-                continue;
-            }
-            if (transcript_id) {
-                map.set(transcript_id, pdb_id);
-            }
-            if (refseq_mrna_id) {
-                map.set(refseq_mrna_id, pdb_id);
-            }
-            if (transcript_id_version) {
-                map.set(transcript_id_version, pdb_id);
-            }
-        }
-    }
-    return map;
-}
 export function getDisplayName(f) {
-    return f.get('id');
+    return f.get('name') || f.get('id');
 }
 export function getId(val) {
     return val === undefined ? '' : val.id();
@@ -42,12 +21,12 @@ export function getId(val) {
 export function getTranscriptDisplayName(val) {
     return val === undefined
         ? ''
-        : [val.get('name'), val.get('id')].filter(f => !!f).join(' ');
+        : [val.get('name') || val.get('id')].filter(f => !!f).join(' ');
 }
 export function getGeneDisplayName(val) {
     return val === undefined
         ? ''
-        : [val.get('gene_name') || val.get('name'), val.get('id')]
+        : [val.get('gene_name') || val.get('name') || val.get('id')]
             .filter(f => !!f)
             .join(' ');
 }

package/dist/LaunchProteinView/components/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,qBAAqB,CAAC,OAAgB;IACpD,uEAAuE;IACvE,wEAAwE;IACxE,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,IAAI,EAAE,CAAA;IACpD,OAAO,WAAW,CAAC,IAAI,CACrB,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,KAAK,IAAI,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CACzD;QACC,CAAC,CAAC,CAAC,OAAO,CAAC;QACX,CAAC,CAAC,WAAW,CAAA;AACjB,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,CAAU;IAC7C,OAAO,CAAC,EAAE,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,UAAU,CAAC,CAAC,CAAS;IACzB,OAAO,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AAClC,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,CAAU;IACvC,OAAO,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,GAAa;IACjC,OAAO,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,wBAAwB,CAAC,GAAa;IACpD,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AACnE,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAa;IAC9C,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,WAAW,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;aACvD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,IAAI,CAAC,GAAG,CAAC,CAAA;AAClB,CAAC"}

package/dist/LaunchProteinView/index.js

@@ -7,7 +7,7 @@ function isDisplay(elt) {
     return elt.name === 'LinearBasicDisplay';
 }
 function extendStateModel(stateModel) {
-    return stateModel.views(self => {
+    return stateModel.views((self) => {
         const superContextMenuItems = self.contextMenuItems;
         return {
             contextMenuItems() {
@@ -23,7 +23,11 @@ function extendStateModel(stateModel) {
                                 onClick: () => {
                                     getSession(track).queueDialog(handleClose => [
                                         LaunchProteinViewDialog,
-                                        { model: track, handleClose, feature },
+                                        {
+                                            model: track,
+                                            handleClose,
+                                            feature,
+                                        },
                                     ]);
                                 },
                             },

package/dist/LaunchProteinView/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchProteinView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,UAAU,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAA;AAEnE,QAAQ;AACR,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAE7C,SAAS;AACT,OAAO,uBAAuB,MAAM,sCAAsC,CAAA;AAE1E,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,oBAAoB,CAAA;AAC1C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAAyB;IACjD,OAAO,UAAU,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE;QAC7B,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QACnD,OAAO;YACL,gBAAgB;gBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,OAAO;wBACT,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,qBAAqB;gCAC5B,IAAI,EAAE,OAAO;gCACb,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC3C,uBAAuB;wCACvB,EAAE,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,OAAO,EAAE;qCACvC,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,mBAAmB,CAC/B,6BAA6B,EAC7B,CAAC,GAAyB,EAAE,EAAE;QAC5B,IAAI,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,GAAG,CAAC,UAAU,GAAG,gBAAgB,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QACnD,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC,CACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchProteinView/index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,UAAU,EAAE,kBAAkB,EAAW,MAAM,oBAAoB,CAAA;AAE5E,QAAQ;AACR,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAE7C,SAAS;AACT,OAAO,uBAAuB,MAAM,sCAAsC,CAAA;AAG1E,SAAS,SAAS,CAAC,GAAqB;IACtC,OAAO,GAAG,CAAC,IAAI,KAAK,oBAAoB,CAAA;AAC1C,CAAC;AAED,SAAS,gBAAgB,CAAC,UAAyB;IACjD,OAAO,UAAU,CAAC,KAAK,CACrB,CAAC,IAGA,EAAE,EAAE;QACH,MAAM,qBAAqB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QACnD,OAAO;YACL,gBAAgB;gBACd,MAAM,OAAO,GAAG,IAAI,CAAC,kBAAkB,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,OAAO;oBACL,GAAG,qBAAqB,EAAE;oBAC1B,GAAG,CAAC,OAAO;wBACT,CAAC,CAAC;4BACE;gCACE,KAAK,EAAE,qBAAqB;gCAC5B,IAAI,EAAE,OAAO;gCACb,OAAO,EAAE,GAAG,EAAE;oCACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;wCAC3C,uBAAuB;wCACvB;4CACE,KAAK,EAAE,KAAK;4CACZ,WAAW;4CACX,OAAO;yCACR;qCACF,CAAC,CAAA;gCACJ,CAAC;6BACF;yBACF;wBACH,CAAC,CAAC,EAAE,CAAC;iBACR,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,mBAAmB,CAC/B,6BAA6B,EAC7B,CAAC,GAAyB,EAAE,EAAE;QAC5B,IAAI,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;YACnB,GAAG,CAAC,UAAU,GAAG,gBAAgB,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;QACnD,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/ProteinView/{loadStructureFromData.d.ts → addStructureFromData.d.ts}

@@ -4,7 +4,7 @@ import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-st
 export interface LoadStructureOptions {
     representationParams?: StructureRepresentationPresetProvider.CommonParams;
 }
-export declare function loadStructureFromData({ data, format, options, plugin, }: {
+export declare function addStructureFromData({ data, format, options, plugin, }: {
     data: string;
     format?: BuiltInTrajectoryFormat;
     options?: LoadStructureOptions & {
@@ -13,5 +13,5 @@ export declare function loadStructureFromData({ data, format, options, plugin, }
     };
     plugin: PluginContext;
 }): Promise<{
-    seq: string;
+    model: import("molstar/lib/mol-state").StateObjectSelector<import("molstar/lib/mol-plugin-state/objects").PluginStateObject.Molecule.Model, import("molstar/lib/mol-state").StateTransformer<import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, any>>;
 }>;

package/dist/ProteinView/{loadStructureFromData.js → addStructureFromData.js}

@@ -1,20 +1,15 @@
 // adapted from https://github.com/molstar/molstar/blob/ab4130d42d0ab2591f62460292ade0203207d4d2/src/apps/viewer/app.ts#L255C1-L259C6
-export async function loadStructureFromData({ data, format = 'pdb', options, plugin, }) {
-    await plugin.clear();
+export async function addStructureFromData({ data, format = 'pdb', options, plugin, }) {
     const _data = await plugin.builders.data.rawData({
         data,
         label: options?.dataLabel,
     });
     const trajectory = await plugin.builders.structure.parseTrajectory(_data, format);
     const model = await plugin.builders.structure.createModel(trajectory);
-    const seq = model.obj?.data.sequence.sequences[0].sequence.label
-        .toArray()
-        // @ts-expect-error
-        .join('');
     await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', {
         useDefaultIfSingleModel: true,
         representationPresetParams: options?.representationParams,
     });
-    return { seq: seq };
+    return { model };
 }
-//# sourceMappingURL=loadStructureFromData.js.map
+//# sourceMappingURL=addStructureFromData.js.map

package/dist/ProteinView/addStructureFromData.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"addStructureFromData.js","sourceRoot":"","sources":["../../src/ProteinView/addStructureFromData.ts"],"names":[],"mappings":"AAQA,qIAAqI;AACrI,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,EACzC,IAAI,EACJ,MAAM,GAAG,KAAK,EACd,OAAO,EACP,MAAM,GAMP;IACC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC;QAC/C,IAAI;QACJ,KAAK,EAAE,OAAO,EAAE,SAAS;KAC1B,CAAC,CAAA;IAEF,MAAM,UAAU,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,eAAe,CAChE,KAAK,EACL,MAAM,CACP,CAAA;IACD,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;IAErE,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,SAAS,CAAC,WAAW,CACnD,UAAU,EACV,YAAY,EACZ;QACE,uBAAuB,EAAE,IAAI;QAC7B,0BAA0B,EAAE,OAAO,EAAE,oBAAoB;KAC1D,CACF,CAAA;IAED,OAAO,EAAE,KAAK,EAAE,CAAA;AAClB,CAAC"}

package/dist/ProteinView/{loadStructureFromURL.d.ts → addStructureFromURL.d.ts}

@@ -4,7 +4,7 @@ import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-st
 export interface LoadStructureOptions {
     representationParams?: StructureRepresentationPresetProvider.CommonParams;
 }
-export declare function loadStructureFromURL({ url, format, isBinary, options, plugin, }: {
+export declare function addStructureFromURL({ url, format, isBinary, options, plugin, }: {
     url: string;
     format?: BuiltInTrajectoryFormat;
     isBinary?: boolean;
@@ -13,5 +13,5 @@ export declare function loadStructureFromURL({ url, format, isBinary, options, p
     };
     plugin: PluginContext;
 }): Promise<{
-    seq: string;
+    model: import("molstar/lib/mol-state").StateObjectSelector<import("molstar/lib/mol-plugin-state/objects").PluginStateObject.Molecule.Model, import("molstar/lib/mol-state").StateTransformer<import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, import("molstar/lib/mol-state").StateObject<any, import("molstar/lib/mol-state").StateObject.Type<any>>, any>>;
 }>;

package/dist/ProteinView/{loadStructureFromURL.js → addStructureFromURL.js}

@@ -1,17 +1,19 @@
 // adapted from https://github.com/molstar/molstar/blob/ab4130d42d0ab2591f62460292ade0203207d4d2/src/apps/viewer/app.ts#L230
-export async function loadStructureFromURL({ url, format = 'mmcif', isBinary, options, plugin, }) {
-    await plugin.clear();
-    const data = await plugin.builders.data.download({ url, isBinary }, { state: { isGhost: true } });
+export async function addStructureFromURL({ url, format = 'mmcif', isBinary, options, plugin, }) {
+    const data = await plugin.builders.data.download({
+        url,
+        isBinary,
+    }, {
+        state: {
+            isGhost: true,
+        },
+    });
     const trajectory = await plugin.builders.structure.parseTrajectory(data, format);
     const model = await plugin.builders.structure.createModel(trajectory);
-    const seq = model.obj?.data.sequence.sequences[0].sequence.label
-        .toArray()
-        // @ts-expect-error
-        .join('');
     await plugin.builders.structure.hierarchy.applyPreset(trajectory, 'all-models', {
         useDefaultIfSingleModel: true,
         representationPresetParams: options?.representationParams,
     });
-    return { seq: seq };
+    return { model };
 }
-//# sourceMappingURL=loadStructureFromURL.js.map
+//# sourceMappingURL=addStructureFromURL.js.map

package/dist/ProteinView/addStructureFromURL.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"addStructureFromURL.js","sourceRoot":"","sources":["../../src/ProteinView/addStructureFromURL.ts"],"names":[],"mappings":"AAQA,4HAA4H;AAC5H,MAAM,CAAC,KAAK,UAAU,mBAAmB,CAAC,EACxC,GAAG,EACH,MAAM,GAAG,OAAO,EAChB,QAAQ,EACR,OAAO,EACP,MAAM,GAOP;IACC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAC9C;QACE,GAAG;QACH,QAAQ;KACT,EACD;QACE,KAAK,EAAE;YACL,OAAO,EAAE,IAAI;SACd;KACF,CACF,CAAA;IAED,MAAM,UAAU,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,eAAe,CAChE,IAAI,EACJ,MAAM,CACP,CAAA;IACD,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;IAErE,MAAM,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,SAAS,CAAC,WAAW,CACnD,UAAU,EACV,YAAY,EACZ;QACE,uBAAuB,EAAE,IAAI;QAC7B,0BAA0B,EAAE,OAAO,EAAE,oBAAoB;KAC1D,CACF,CAAA;IACD,OAAO,EAAE,KAAK,EAAE,CAAA;AAClB,CAAC"}

package/dist/ProteinView/clearSelection.js

@@ -1,4 +1,4 @@
 export default function clearSelection({ plugin }) {
-    plugin?.managers.interactivity.lociSelects.deselectAll();
+    plugin.managers.interactivity.lociSelects.deselectAll();
 }
 //# sourceMappingURL=clearSelection.js.map

package/dist/ProteinView/clearSelection.js.map

@@ -1 +1 @@
-{"version":3,"file":"clearSelection.js","sourceRoot":"","sources":["../../src/ProteinView/clearSelection.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,MAAM,EAA6B;IAC1E,MAAM,EAAE,QAAQ,CAAC,aAAa,CAAC,WAAW,CAAC,WAAW,EAAE,CAAA;AAC1D,CAAC"}
+{"version":3,"file":"clearSelection.js","sourceRoot":"","sources":["../../src/ProteinView/clearSelection.ts"],"names":[],"mappings":"AAEA,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,MAAM,EAA6B;IAC1E,MAAM,CAAC,QAAQ,CAAC,aAAa,CAAC,WAAW,CAAC,WAAW,EAAE,CAAA;AACzD,CAAC"}

package/dist/ProteinView/components/ProteinAlignment.d.ts

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

package/dist/ProteinView/components/ProteinAlignment.js

@@ -1,35 +1,46 @@
-import React from 'react';
+import React, { useEffect, useState } from 'react';
 import { observer } from 'mobx-react';
 import { Tooltip, Typography } from '@mui/material';
 import ProteinAlignmentHelpButton from './ProteinAlignmentHelpButton';
 import { clickProteinToGenome, hoverProteinToGenome, } from '../proteinToGenomeMapping';
 import SplitString from './SplitString';
 const ProteinAlignment = observer(function ({ model, }) {
-    const { structureSeqHoverPos, alignment, structurePositionToAlignmentMap, alignmentToStructurePosition, showHighlight, } = model;
-    const a0 = alignment.alns[0].seq;
-    const a1 = alignment.alns[1].seq;
-    const con = alignment.consensus;
-    const set = new Set();
+    const { pairwiseAlignment, pairwiseAlignmentToStructurePosition, structurePositionToAlignmentMap, structureSeqHoverPos, showHighlight, } = model;
+    const [pairwiseAlignmentHoverPos, setPairwiseAlignmentHoverPos] = useState();
+    useEffect(() => {
+        setPairwiseAlignmentHoverPos(structureSeqHoverPos === undefined
+            ? undefined
+            : structurePositionToAlignmentMap?.[structureSeqHoverPos]);
+    }, [structurePositionToAlignmentMap, structureSeqHoverPos]);
+    if (!pairwiseAlignment) {
+        return React.createElement("div", null, "No pairwiseAlignment");
+    }
+    const a0 = pairwiseAlignment.alns[0].seq;
+    const a1 = pairwiseAlignment.alns[1].seq;
+    const con = pairwiseAlignment.consensus;
+    const gapSet = new Set();
     // eslint-disable-next-line unicorn/no-for-loop
     for (let i = 0; i < con.length; i++) {
         const letter = con[i];
         if (letter === '|') {
-            set.add(i);
+            gapSet.add(i);
         }
     }
-    const alignmentHoverPos = structureSeqHoverPos !== undefined
-        ? structurePositionToAlignmentMap?.[structureSeqHoverPos]
-        : undefined;
-    function onMouseOver(alignmentPos) {
-        const structureSeqPos = alignmentToStructurePosition[alignmentPos];
-        model.setHoveredPosition({ structureSeqPos });
-        hoverProteinToGenome({ model, structureSeqPos });
+    function onMouseOver(p) {
+        setPairwiseAlignmentHoverPos(p);
+        if (pairwiseAlignmentToStructurePosition) {
+            const structureSeqPos = pairwiseAlignmentToStructurePosition[p];
+            model.setHoveredPosition({ structureSeqPos });
+            hoverProteinToGenome({ model, structureSeqPos });
+        }
     }
-    function onClick(alignmentPos) {
-        const structureSeqPos = alignmentToStructurePosition[alignmentPos];
-        clickProteinToGenome({ model, structureSeqPos }).catch(e => {
-            console.error(e);
-        });
+    function onClick(pairwiseAlignmentPos) {
+        if (pairwiseAlignmentToStructurePosition) {
+            const structureSeqPos = pairwiseAlignmentToStructurePosition[pairwiseAlignmentPos];
+            clickProteinToGenome({ model, structureSeqPos }).catch((e) => {
+                console.error(e);
+            });
+        }
     }
     return (React.createElement("div", null,
         React.createElement(ProteinAlignmentHelpButton, { model: model }),
@@ -47,16 +58,16 @@ const ProteinAlignment = observer(function ({ model, }) {
                 model.clearHoverGenomeHighlights();
             } },
             React.createElement("div", null,
-                React.createElement(Tooltip, { title: "This is the sequence of the protein from the structure file" },
-                    React.createElement("span", null, "STRUCT\u00A0")),
-                React.createElement(SplitString, { str: a0, showHighlight: showHighlight, col: alignmentHoverPos, set: set, onMouseOver: onMouseOver, onClick: onClick })),
+                React.createElement(Tooltip, { title: "This is the sequence of the protein from the reference genome transcript" },
+                    React.createElement("span", null, "GENOME\u00A0")),
+                React.createElement(SplitString, { str: a0, showHighlight: showHighlight, hoveredPosition: pairwiseAlignmentHoverPos, gapSet: gapSet, onMouseOver: onMouseOver, onClick: onClick })),
             React.createElement("div", null,
                 React.createElement("span", null, "\u00A0\u00A0\u00A0\u00A0\u00A0\u00A0\u00A0"),
-                React.createElement(SplitString, { showHighlight: showHighlight, str: con, col: alignmentHoverPos, set: set, onMouseOver: onMouseOver, onClick: onClick })),
+                React.createElement(SplitString, { showHighlight: showHighlight, str: con, hoveredPosition: pairwiseAlignmentHoverPos, gapSet: gapSet, onMouseOver: onMouseOver, onClick: onClick })),
             React.createElement("div", null,
-                React.createElement(Tooltip, { title: "This is the sequence of the protein from the reference genome transcript" },
-                    React.createElement("span", null, "GENOME\u00A0")),
-                React.createElement(SplitString, { str: a1, col: alignmentHoverPos, showHighlight: showHighlight, set: set, onMouseOver: onMouseOver, onClick: onClick })))));
+                React.createElement(Tooltip, { title: "This is the sequence of the protein from the structure file" },
+                    React.createElement("span", null, "STRUCT\u00A0")),
+                React.createElement(SplitString, { str: a1, hoveredPosition: pairwiseAlignmentHoverPos, showHighlight: showHighlight, gapSet: gapSet, onMouseOver: onMouseOver, onClick: onClick })))));
 });
 export default ProteinAlignment;
 //# sourceMappingURL=ProteinAlignment.js.map

package/dist/ProteinView/components/ProteinAlignment.js.map

@@ -1 +1 @@
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package/dist/ProteinView/components/ProteinAlignmentHelpButton.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { JBrowsePluginProteinViewModel } from '../model';
+import { JBrowsePluginProteinStructureModel } from '../model';
 export default function ProteinAlignmentHelpButton({ model, }: {
-    model: JBrowsePluginProteinViewModel;
+    model: JBrowsePluginProteinStructureModel;
 }): React.JSX.Element;

package/dist/ProteinView/components/ProteinAlignmentHelpButton.js

@@ -5,10 +5,12 @@ import { getSession } from '@jbrowse/core/util';
 import Help from '@mui/icons-material/Help';
 const ProteinAlignmentHelpDialog = lazy(() => import('./ProteinAlignmentHelpDialog'));
 export default function ProteinAlignmentHelpButton({ model, }) {
-    return (React.createElement(IconButton, { style: { float: 'right' }, onClick: () => getSession(model).queueDialog(handleClose => [
-            ProteinAlignmentHelpDialog,
-            { handleClose },
-        ]) },
+    return (React.createElement(IconButton, { style: { float: 'right' }, onClick: () => {
+            getSession(model).queueDialog(handleClose => [
+                ProteinAlignmentHelpDialog,
+                { handleClose },
+            ]);
+        } },
         React.createElement(Help, null)));
 }
 //# sourceMappingURL=ProteinAlignmentHelpButton.js.map

package/dist/ProteinView/components/ProteinAlignmentHelpButton.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ProteinAlignmentHelpButton.js","sourceRoot":"","sources":["../../../src/ProteinView/components/ProteinAlignmentHelpButton.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAK/C,QAAQ;AACR,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAE3C,MAAM,0BAA0B,GAAG,IAAI,CACrC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA8B,CAAC,CAC7C,CAAA;AAED,MAAM,CAAC,OAAO,UAAU,0BAA0B,CAAC,EACjD,KAAK,GAGN;IACC,OAAO,CACL,oBAAC,UAAU,IACT,KAAK,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,EACzB,OAAO,EAAE,GAAG,EAAE;YACZ,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC3C,0BAA0B;gBAC1B,EAAE,WAAW,EAAE;aAChB,CAAC,CAAA;QACJ,CAAC;QAED,oBAAC,IAAI,OAAG,CACG,CACd,CAAA;AACH,CAAC"}

package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Button, DialogActions, DialogContent, Divider, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, Typography, } from '@mui/material';
 import { Dialog } from '@jbrowse/core/ui';
 function Typography2({ children }) {
     return (React.createElement(Typography, { style: {
@@ -10,11 +10,12 @@ function Typography2({ children }) {
 export default function ProteinAlignmentHelpDialog({ handleClose, }) {
     return (React.createElement(Dialog, { open: true, maxWidth: "lg", onClose: handleClose, title: "Protein alignment" },
         React.createElement(DialogContent, null,
-            React.createElement(Typography2, null, "This panel shows the computed alignment of the reference genome sequence to the structure sequence. The structure file (PDB file, mmCIF file, etc) has a stored representation of the e.g. amino acid sequence but the sequence in the structure file can differ from the sequence from the gene on the genome browser"),
-            React.createElement(Typography2, null, "In order to resolve this, we align the two sequences together (using EMBOSS needle) to get alignment of the genome's representation of the protein and the structure file's representation of the protein."),
+            React.createElement(Typography2, null, "This panel shows the computed pairwise alignment of the reference genome sequence to the structure sequence. The structure file (PDB file, mmCIF file, etc) has a stored representation of the e.g. amino acid sequence but the sequence in the structure file can differ from the sequence from the gene on the genome browser"),
+            React.createElement(Typography2, null, "In order to resolve this, we align the two sequences together (using EMBOSS needle) to get pairwise alignment of the genome's representation of the protein and the structure file's representation of the protein."),
             React.createElement(Typography2, null, "If you need a 100% fidelity protein, you can do a folding with e.g. AlphaFold to make sure the structure you are using matches exactly the sequence of the transcript")),
-        React.createElement(Divider, null),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { onClick: () => handleClose(), color: "primary" }, "Close"))));
+            React.createElement(Button, { onClick: () => {
+                    handleClose();
+                }, variant: "contained", color: "primary" }, "Close"))));
 }
 //# sourceMappingURL=ProteinAlignmentHelpDialog.js.map

package/dist/ProteinView/components/ProteinAlignmentHelpDialog.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ProteinAlignmentHelpDialog.js","sourceRoot":"","sources":["../../../src/ProteinView/components/ProteinAlignmentHelpDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,UAAU,GAEX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,WAAW,CAAC,EAAE,QAAQ,EAAmB;IAChD,OAAO,CACL,oBAAC,UAAU,IACT,KAAK,EAAE;YACL,MAAM,EAAE,CAAC;YACT,YAAY,EAAE,EAAE;SACjB,IAEA,QAAQ,CACE,CACd,CAAA;AACH,CAAC;AACD,MAAM,CAAC,OAAO,UAAU,0BAA0B,CAAC,EACjD,WAAW,GAGZ;IACC,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,QAAQ,EAAC,IAAI,EAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,mBAAmB;QACxE,oBAAC,aAAa;YACZ,oBAAC,WAAW,0UAME;YACd,oBAAC,WAAW,8NAKE;YACd,oBAAC,WAAW,gLAIE,CACA;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,YAGR,CACK,CACT,CACV,CAAA;AACH,CAAC"}

package/dist/ProteinView/components/ProteinView.js

@@ -1,78 +1,36 @@
 import React, { useEffect } from 'react';
 import { observer } from 'mobx-react';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import Header from './Header';
+import { ErrorMessage, ResizeHandle } from '@jbrowse/core/ui';
+import ProteinViewHeader from './ProteinViewHeader';
 // hooks
 import useProteinView from '../useProteinView';
-import useProteinViewClickBehavior from '../useProteinViewClickBehavior';
-import useProteinViewHoverBehavior from '../useProteinViewHoverBehavior';
-// utils
-import selectResidue from '../selectResidue';
-import highlightResidue from '../highlightResidue';
-import clearSelection from '../clearSelection';
 // css
 import css from '../css/molstar';
-if (document?.head) {
-    const style = document.createElement('style');
-    style.append(css);
-    document.head?.append(style);
-}
+const style = document.createElement('style');
+style.append(css);
+document.head.append(style);
 const ProteinView = observer(function ({ model, }) {
-    const { url, data, showControls } = model;
-    const { plugin, seq, parentRef, error } = useProteinView({
-        url,
-        data,
+    const { showControls } = model;
+    const { plugin, parentRef, error } = useProteinView({
         showControls,
     });
-    return error ? (React.createElement(ErrorMessage, { error: error })) : (React.createElement(ProteinViewContainer, { model: model, plugin: plugin, seq: seq, parentRef: parentRef }));
-});
-const ProteinViewContainer = observer(function ({ model, plugin, seq, parentRef, }) {
-    const { width, height, structureSeqToTranscriptSeqPosition, seq2, structureSeqHoverPos, showHighlight, alignment, } = model;
-    const { error } = useProteinViewClickBehavior({ plugin, model });
-    useProteinViewHoverBehavior({ plugin, model });
-    const structure = plugin?.managers.structure.hierarchy.current.structures[0]?.cell.obj?.data;
-    useEffect(() => {
-        model.setSeqs(seq, seq2);
-    }, [seq, model, seq2]);
     useEffect(() => {
-        if (!plugin || !structureSeqToTranscriptSeqPosition || !structure) {
-            return;
-        }
-        if (showHighlight) {
-            for (const coord of Object.keys(structureSeqToTranscriptSeqPosition)) {
-                selectResidue({
-                    structure,
-                    plugin,
-                    selectedResidue: +coord + 1,
-                });
-            }
-        }
-        else {
-            clearSelection({ plugin });
-        }
-    }, [plugin, structure, showHighlight, structureSeqToTranscriptSeqPosition]);
-    useEffect(() => {
-        if (!plugin || !structure || structureSeqHoverPos === undefined) {
-            return;
-        }
-        if (structureSeqHoverPos !== undefined) {
-            highlightResidue({
-                structure,
-                plugin,
-                selectedResidue: structureSeqHoverPos,
-            });
-        }
-        else {
-            console.warn('not found');
-        }
-    }, [plugin, structure, structureSeqHoverPos]);
-    return (React.createElement("div", { style: { background: !alignment ? '#ccc' : undefined } },
+        model.setMolstarPluginContext(plugin);
+    }, [plugin, model]);
+    return error ? (React.createElement(ErrorMessage, { error: error })) : (React.createElement(ProteinViewContainer, { model: model, parentRef: parentRef }));
+});
+const ProteinViewContainer = observer(function ({ model, parentRef, }) {
+    const { width, height, error } = model;
+    return (React.createElement("div", { style: { background: '#ccc' } },
         error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement(Header, { model: model }),
+        React.createElement(ProteinViewHeader, { model: model }),
         React.createElement("div", { ref: parentRef, style: {
                 position: 'relative',
                 width,
                 height,
+            } }),
+        React.createElement(ResizeHandle, { style: { height: 4, background: 'grey' }, onDrag: delta => {
+                model.setHeight(model.height + delta);
             } })));
 });
 export default ProteinView;

package/dist/ProteinView/components/ProteinView.js.map

@@ -1 +1 @@
-{"version":3,"file":"ProteinView.js","sourceRoot":"","sources":["../../../src/ProteinView/components/ProteinView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAK/C,OAAO,MAAM,MAAM,UAAU,CAAA;AAE7B,QAAQ;AACR,OAAO,cAAc,MAAM,mBAAmB,CAAA;AAC9C,OAAO,2BAA2B,MAAM,gCAAgC,CAAA;AACxE,OAAO,2BAA2B,MAAM,gCAAgC,CAAA;AAExE,QAAQ;AACR,OAAO,aAAa,MAAM,kBAAkB,CAAA;AAC5C,OAAO,gBAAgB,MAAM,qBAAqB,CAAA;AAClD,OAAO,cAAc,MAAM,mBAAmB,CAAA;AAE9C,MAAM;AACN,OAAO,GAAG,MAAM,gBAAgB,CAAA;AAEhC,IAAI,QAAQ,EAAE,IAAI,EAAE,CAAC;IACnB,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IAC7C,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;IACjB,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC,KAAK,CAAC,CAAA;AAC9B,CAAC;AAED,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IACzC,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,cAAc,CAAC;QACvD,GAAG;QACH,IAAI;QACJ,YAAY;KACb,CAAC,CAAA;IACF,OAAO,KAAK,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,CACF,oBAAC,oBAAoB,IACnB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,GAAG,EAAE,GAAG,EACR,SAAS,EAAE,SAAS,GACpB,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,EACL,MAAM,EACN,GAAG,EACH,SAAS,GAMV;IACC,MAAM,EACJ,KAAK,EACL,MAAM,EACN,mCAAmC,EACnC,IAAI,EACJ,oBAAoB,EACpB,aAAa,EACb,SAAS,GACV,GAAG,KAAK,CAAA;IAET,MAAM,EAAE,KAAK,EAAE,GAAG,2BAA2B,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC,CAAA;IAChE,2BAA2B,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,CAAC,CAAA;IAE9C,MAAM,SAAS,GACb,MAAM,EAAE,QAAQ,CAAC,SAAS,CAAC,SAAS,CAAC,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,EAAE,IAAI,CAAA;IAE5E,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAC1B,CAAC,EAAE,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;IAEtB,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC,MAAM,IAAI,CAAC,mCAAmC,IAAI,CAAC,SAAS,EAAE,CAAC;YAClE,OAAM;QACR,CAAC;QACD,IAAI,aAAa,EAAE,CAAC;YAClB,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,IAAI,CAAC,mCAAmC,CAAC,EAAE,CAAC;gBACrE,aAAa,CAAC;oBACZ,SAAS;oBACT,MAAM;oBACN,eAAe,EAAE,CAAC,KAAK,GAAG,CAAC;iBAC5B,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;aAAM,CAAC;YACN,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;QAC5B,CAAC;IACH,CAAC,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,aAAa,EAAE,mCAAmC,CAAC,CAAC,CAAA;IAE3E,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC,MAAM,IAAI,CAAC,SAAS,IAAI,oBAAoB,KAAK,SAAS,EAAE,CAAC;YAChE,OAAM;QACR,CAAC;QACD,IAAI,oBAAoB,KAAK,SAAS,EAAE,CAAC;YACvC,gBAAgB,CAAC;gBACf,SAAS;gBACT,MAAM;gBACN,eAAe,EAAE,oBAAoB;aACtC,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;QAC3B,CAAC;IACH,CAAC,EAAE,CAAC,MAAM,EAAE,SAAS,EAAE,oBAAoB,CAAC,CAAC,CAAA;IAE7C,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,EAAE;QACxD,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,GAAI;QACxB,6BACE,GAAG,EAAE,SAAS,EACd,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,KAAK;gBACL,MAAM;aACP,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}
+{"version":3,"file":"ProteinView.js","sourceRoot":"","sources":["../../../src/ProteinView/components/ProteinView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAI7D,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AAEnD,QAAQ;AACR,OAAO,cAAc,MAAM,mBAAmB,CAAA;AAE9C,MAAM;AACN,OAAO,GAAG,MAAM,gBAAgB,CAAA;AAEhC,MAAM,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;AAC7C,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACjB,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;AAE3B,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC9B,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,GAAG,cAAc,CAAC;QAClD,YAAY;KACb,CAAC,CAAA;IAEF,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,uBAAuB,CAAC,MAAM,CAAC,CAAA;IACvC,CAAC,EAAE,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,CAAA;IAEnB,OAAO,KAAK,CAAC,CAAC,CAAC,CACb,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,CACF,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,EAAE,SAAS,EAAE,SAAS,GAAI,CAC7D,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,EACL,SAAS,GAIV;IACC,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAEtC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,MAAM,EAAE;QAC/B,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QAC9C,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI;QACnC,6BACE,GAAG,EAAE,SAAS,EACd,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,KAAK;gBACL,MAAM;aACP,GACD;QACF,oBAAC,YAAY,IACX,KAAK,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,UAAU,EAAE,MAAM,EAAE,EACxC,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;YACvC,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}

package/dist/ProteinView/components/{Header.js → ProteinViewHeader.js}

@@ -1,24 +1,35 @@
 import React from 'react';
 import { observer } from 'mobx-react';
+import { LoadingEllipses } from '@jbrowse/core/ui';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 // icons
 import MenuIcon from '@mui/icons-material/Menu';
 import Visibility from '@mui/icons-material/Visibility';
 import ProteinAlignment from './ProteinAlignment';
-import { LoadingEllipses } from '@jbrowse/core/ui';
 const ProteinViewHeader = observer(function ({ model, }) {
-    const { alignment, showAlignment } = model;
+    const { structures, showAlignment } = model;
     return (React.createElement("div", null,
         React.createElement(InformativeHeaderArea, { model: model }),
-        showAlignment && alignment ? (React.createElement(ProteinAlignment, { model: model })) : (React.createElement(LoadingEllipses, { message: "Loading pairwise alignment" }))));
+        showAlignment
+            ? structures.map((structure, idx) => {
+                const { pairwiseAlignment } = structure;
+                return (React.createElement("div", { key: idx }, pairwiseAlignment ? (React.createElement(ProteinAlignment, { key: idx, model: structure })) : (React.createElement(LoadingEllipses, { message: "Loading pairwise alignment" }))));
+            })
+            : null));
 });
-const InformativeHeaderArea = observer(function ({ model, }) {
-    const { showAlignment, clickString, hoverString, showHighlight, zoomToBaseLevel, } = model;
-    return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement("span", null, [
+const StructureInfoHeaderArea = observer(function ({ model, }) {
+    return model.structures.map((s, id) => {
+        const { clickString, hoverString } = s;
+        return (React.createElement("span", { key: id }, [
             clickString ? `Click: ${clickString}` : '',
             hoverString ? `Hover: ${hoverString}` : '',
-        ].join(' ')),
+        ].join(' ')));
+    });
+});
+const InformativeHeaderArea = observer(function ({ model, }) {
+    const { showAlignment, showHighlight, zoomToBaseLevel } = model;
+    return (React.createElement("div", { style: { display: 'flex' } },
+        React.createElement(StructureInfoHeaderArea, { model: model }),
         React.createElement("span", { style: { flexGrow: 1 } }),
         React.createElement(CascadingMenuButton, { menuItems: [
                 {
@@ -26,24 +37,30 @@ const InformativeHeaderArea = observer(function ({ model, }) {
                     type: 'checkbox',
                     checked: showAlignment,
                     icon: Visibility,
-                    onClick: () => model.setShowAlignment(!showAlignment),
+                    onClick: () => {
+                        model.setShowAlignment(!showAlignment);
+                    },
                 },
                 {
                     label: 'Show pairwise alignment as highlight',
                     type: 'checkbox',
                     checked: showHighlight,
                     icon: Visibility,
-                    onClick: () => model.setShowHighlight(!showHighlight),
+                    onClick: () => {
+                        model.setShowHighlight(!showHighlight);
+                    },
                 },
                 {
                     label: 'Zoom to base level on click',
                     type: 'checkbox',
                     checked: zoomToBaseLevel,
                     icon: Visibility,
-                    onClick: () => model.setZoomToBaseLevel(!zoomToBaseLevel),
+                    onClick: () => {
+                        model.setZoomToBaseLevel(!zoomToBaseLevel);
+                    },
                 },
             ] },
             React.createElement(MenuIcon, null))));
 });
 export default ProteinViewHeader;
-//# sourceMappingURL=Header.js.map
+//# sourceMappingURL=ProteinViewHeader.js.map

package/dist/ProteinView/components/ProteinViewHeader.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ProteinViewHeader.js","sourceRoot":"","sources":["../../../src/ProteinView/components/ProteinViewHeader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AAEtE,QAAQ;AACR,OAAO,QAAQ,MAAM,0BAA0B,CAAA;AAC/C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AAIvD,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AAEjD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,KAAK,GAGN;IACC,MAAM,EAAE,UAAU,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC3C,OAAO,CACL;QACE,oBAAC,qBAAqB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,aAAa;YACZ,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,SAAS,EAAE,GAAG,EAAE,EAAE;gBAChC,MAAM,EAAE,iBAAiB,EAAE,GAAG,SAAS,CAAA;gBACvC,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,IACV,iBAAiB,CAAC,CAAC,CAAC,CACnB,oBAAC,gBAAgB,IAAC,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,SAAS,GAAI,CACjD,CAAC,CAAC,CAAC,CACF,oBAAC,eAAe,IAAC,OAAO,EAAC,4BAA4B,GAAG,CACzD,CACG,CACP,CAAA;YACH,CAAC,CAAC;YACJ,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,uBAAuB,GAAG,QAAQ,CAAC,UAAU,EACjD,KAAK,GAGN;IACC,OAAO,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE;QACpC,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,CAAC,CAAA;QAEtC,OAAO,CACL,8BAAM,GAAG,EAAE,EAAE,IACV;YACC,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;YAC1C,WAAW,CAAC,CAAC,CAAC,UAAU,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE;SAC3C,CAAC,IAAI,CAAC,GAAG,CAAC,CACN,CACR,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,MAAM,qBAAqB,GAAG,QAAQ,CAAC,UAAU,EAC/C,KAAK,GAGN;IACC,MAAM,EAAE,aAAa,EAAE,aAAa,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC/D,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,uBAAuB,IAAC,KAAK,EAAE,KAAK,GAAI;QACzC,8BAAM,KAAK,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,GAAI;QAChC,oBAAC,mBAAmB,IAClB,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,8BAA8B;oBACrC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;oBACxC,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,sCAAsC;oBAC7C,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,aAAa;oBACtB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;oBACxC,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,6BAA6B;oBACpC,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,eAAe;oBACxB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC,CAAA;oBAC5C,CAAC;iBACF;aACF;YAED,oBAAC,QAAQ,OAAG,CACQ,CAClB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/ProteinView/components/SplitString.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
-export default function SplitString({ str, col, set, onMouseOver, onClick, showHighlight, }: {
+export default function SplitString({ str, gapSet, hoveredPosition, showHighlight, onMouseOver, onClick, }: {
     str: string;
-    col?: number;
-    set?: Set<number>;
+    gapSet?: Set<number>;
+    hoveredPosition?: number;
+    showHighlight: boolean;
     onMouseOver?: (arg: number) => void;
     onClick?: (arg: number) => void;
-    showHighlight: boolean;
 }): React.JSX.Element[];