@jbrowse/plugin-linear-comparative-view 2.7.2 → 2.9.0

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -1,6 +1,5 @@
 /// <reference types="react" />
 import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
 /**
  * #stateModel LGVSyntenyDisplay
  * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
@@ -35,7 +34,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        features: Map<string, Feature> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -53,7 +52,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
-            features: Map<string, Feature>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
@@ -70,7 +69,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
         fetchSizeLimit: {
             type: string;
-            defaultValue: number;
+            defaultValue: number; /**
+             * #property
+             */
             description: string;
         };
         height: {
@@ -208,7 +209,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
     featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
 } & {
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
@@ -218,18 +219,18 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly selectedFeatureId: string | undefined;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
-    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
-    readonly featureUnderMouse: Feature | undefined;
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
-    setContextMenuFeature(feature?: Feature | undefined): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
 } & {
     reload(): Promise<void>;
 } & {
@@ -241,7 +242,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    featureUnderMouseVolatile: Feature | undefined;
+    featureUnderMouseVolatile: import("@jbrowse/core/util").Feature | undefined;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
@@ -256,9 +257,9 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
     }): void;
     updateColorTagMap(uniqueTag: string[]): void;
-    setFeatureUnderMouse(feat?: Feature | undefined): void;
-    selectFeature(feature: Feature): void;
-    copyFeatureToClipboard(feature: Feature): void;
+    setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature | undefined): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     setConfig(conf: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -275,7 +276,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
-    readonly featureUnderMouse: Feature | undefined;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     renderReady(): boolean;
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {

package/esm/LGVSyntenyDisplay/model.js

@@ -1,110 +1,9 @@
+import { lazy } from 'react';
 import { ConfigurationReference, } from '@jbrowse/core/configuration';
-import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
-import { MismatchParser, SharedLinearPileupDisplayMixin, } from '@jbrowse/plugin-alignments';
+import { getSession } from '@jbrowse/core/util';
+import { SharedLinearPileupDisplayMixin } from '@jbrowse/plugin-alignments';
 import { types } from 'mobx-state-tree';
-import { when } from 'mobx';
-const { parseCigar } = MismatchParser;
-function findPosInCigar(cigar, startX) {
-    let featX = 0;
-    let mateX = 0;
-    for (let i = 0; i < cigar.length; i++) {
-        const len = +cigar[i];
-        const op = cigar[i + 1];
-        const min = Math.min(len, startX - featX);
-        if (featX >= startX) {
-            break;
-        }
-        else if (op === 'I') {
-            mateX += len;
-        }
-        else if (op === 'D') {
-            featX += min;
-        }
-        else if (op === 'M') {
-            mateX += min;
-            featX += min;
-        }
-    }
-    return [featX, mateX];
-}
-async function navToSynteny(feature, self) {
-    const session = getSession(self);
-    const track = getContainingTrack(self);
-    const view = getContainingView(self);
-    const reg = view.dynamicBlocks.contentBlocks[0];
-    const cigar = feature.get('CIGAR');
-    const strand = feature.get('strand');
-    const regStart = reg.start;
-    const regEnd = reg.end;
-    const featStart = feature.get('start');
-    const featEnd = feature.get('end');
-    const mate = feature.get('mate');
-    const mateStart = mate.start;
-    const mateEnd = mate.end;
-    const mateAsm = mate.assemblyName;
-    const mateRef = mate.refName;
-    const featAsm = reg.assemblyName;
-    const featRef = reg.refName;
-    let rMateStart;
-    let rMateEnd;
-    let rFeatStart;
-    let rFeatEnd;
-    if (cigar) {
-        const p = parseCigar(cigar);
-        const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
-        const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
-        // avoid multiply by 0 with strand undefined
-        const flipper = strand === -1 ? -1 : 1;
-        rFeatStart = featStart + fStartX;
-        rFeatEnd = featStart + fEndX;
-        rMateStart = (strand === -1 ? mateEnd : mateStart) + mStartX * flipper;
-        rMateEnd = (strand === -1 ? mateEnd : mateStart) + mEndX * flipper;
-    }
-    else {
-        rFeatStart = featStart;
-        rFeatEnd = featEnd;
-        rMateStart = mateStart;
-        rMateEnd = mateEnd;
-    }
-    const trackId = track.configuration.trackId;
-    const view2 = session.addView('LinearSyntenyView', {
-        type: 'LinearSyntenyView',
-        views: [
-            {
-                id: `${Math.random()}`,
-                type: 'LinearGenomeView',
-                hideHeader: true,
-            },
-            {
-                id: `${Math.random()}`,
-                type: 'LinearGenomeView',
-                hideHeader: true,
-            },
-        ],
-        tracks: [
-            {
-                configuration: trackId,
-                type: 'SyntenyTrack',
-                displays: [
-                    {
-                        type: 'LinearSyntenyDisplay',
-                        configuration: `${trackId}-LinearSyntenyDisplay`,
-                    },
-                ],
-            },
-        ],
-    });
-    const f = (n) => Math.floor(n);
-    const l1 = `${featRef}:${f(rFeatStart)}-${f(rFeatEnd)}`;
-    const m1 = Math.min(rMateStart, rMateEnd);
-    const m2 = Math.max(rMateStart, rMateEnd);
-    const l2 = `${mateRef}:${f(m1)}-${f(m2)}${strand === -1 ? '[rev]' : ''}`;
-    await when(() => view2.width !== undefined);
-    await Promise.all([
-        view2.views[0].navToLocString(l1, featAsm),
-        view2.views[1].navToLocString(l2, mateAsm),
-    ]);
-}
+const LaunchSyntenyViewDialog = lazy(() => import('./components/LaunchSyntenyViewDialog'));
 /**
  * #stateModel LGVSyntenyDisplay
  * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
@@ -133,7 +32,16 @@ function stateModelFactory(schema) {
                         ? [
                             {
                                 label: 'Open synteny view for this position',
-                                onClick: () => navToSynteny(feature, self),
+                                onClick: () => {
+                                    getSession(self).queueDialog(handleClose => [
+                                        LaunchSyntenyViewDialog,
+                                        {
+                                            model: self,
+                                            handleClose,
+                                            feature,
+                                        },
+                                    ]);
+                                },
                             },
                         ]
                         : []),

package/esm/LaunchLinearSyntenyView.js

@@ -24,8 +24,12 @@ export default function LaunchLinearSyntenyView(pluginManager) {
             const idsNotFound = [];
             await Promise.all(views.map(async (data, idx) => {
                 const view = model.views[idx];
-                const { loc, tracks = [] } = data;
-                await view.navToLocString(loc);
+                const { assembly, loc, tracks = [] } = data;
+                const asm = await assemblyManager.waitForAssembly(assembly);
+                if (!asm) {
+                    throw new Error(`Assembly ${data.assembly} failed to load`);
+                }
+                await view.navToSearchString({ input: loc, assembly: asm });
                 tracks.forEach(track => tryTrack(view, track, idsNotFound));
             }));
             tracks.forEach(track => tryTrack(model, track, idsNotFound));

package/esm/LinearComparativeView/model.d.ts

@@ -123,7 +123,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     } & {
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
-        toggleTrack(trackId: string): void;
+        toggleTrack(trackId: string): boolean;
         setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
         toggleCenterLine(): void;
         setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
@@ -173,6 +173,126 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     } & {
         moveTo(start?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, end?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
         navToLocString(input: string, optAssemblyName?: string | undefined): Promise<void>;
+        navToSearchString({ input, assembly, }: {
+            input: string;
+            assembly: {
+                configuration: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+                error: unknown;
+                loaded: boolean;
+                loadingP: Promise<void> | undefined;
+                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                lowerCaseRefNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly initialized: boolean; /**
+                 * #property
+                 */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                readonly aliases: string[];
+                readonly displayName: string | undefined;
+                hasName(name: string): boolean;
+                readonly allAliases: string[];
+                readonly allRefNames: string[] | undefined;
+                readonly lowerCaseRefNames: string[] | undefined;
+                readonly allRefNamesWithLowerCase: string[] | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+                readonly refNameColors: string[];
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                isValidRefName(refName: string): boolean;
+            } & {
+                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+                setError(e: unknown): void;
+                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+                setRefNameAliases(aliases: {
+                    [x: string]: string | undefined;
+                }, lcAliases: {
+                    [x: string]: string | undefined;
+                }): void;
+                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setLoadingP(p?: Promise<void> | undefined): void;
+                load(): Promise<void>;
+                loadPre(): Promise<void>;
+            } & {
+                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+            } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+                configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+            }, {
+                error: unknown;
+                loaded: boolean;
+                loadingP: Promise<void> | undefined;
+                volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                refNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                lowerCaseRefNameAliases: {
+                    [x: string]: string | undefined;
+                } | undefined;
+                cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+            } & {
+                getConf(arg: string): any;
+            } & {
+                readonly initialized: boolean; /**
+                 * #property
+                 */
+                readonly name: string;
+                readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+                readonly aliases: string[];
+                readonly displayName: string | undefined;
+                hasName(name: string): boolean;
+                readonly allAliases: string[];
+                readonly allRefNames: string[] | undefined;
+                readonly lowerCaseRefNames: string[] | undefined;
+                readonly allRefNamesWithLowerCase: string[] | undefined;
+                readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
+                readonly refNameColors: string[];
+            } & {
+                readonly refNames: string[] | undefined;
+            } & {
+                getCanonicalRefName(refName: string): string | undefined;
+                getRefNameColor(refName: string): string | undefined;
+                isValidRefName(refName: string): boolean;
+            } & {
+                setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+                setError(e: unknown): void;
+                setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+                setRefNameAliases(aliases: {
+                    [x: string]: string | undefined;
+                }, lcAliases: {
+                    [x: string]: string | undefined;
+                }): void;
+                setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+                setLoadingP(p?: Promise<void> | undefined): void;
+                load(): Promise<void>;
+                loadPre(): Promise<void>;
+            } & {
+                getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+                getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+                getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+                    [x: string]: string | undefined;
+                }>;
+            }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }): Promise<void>;
         navToLocations(parsedLocStrings: import("@jbrowse/core/util").ParsedLocString[], assemblyName?: string | undefined): Promise<void>;
         navTo(query: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation): void;
         navToMultiple(locations: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").NavLocation[]): void;
@@ -277,7 +397,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
     /**
      * #action
      */
-    toggleTrack(trackId: string): void;
+    toggleTrack(trackId: string): boolean;
     /**
      * #action
      */

package/esm/LinearComparativeView/model.js

@@ -186,12 +186,12 @@ function stateModelFactory(pluginManager) {
          * #action
          */
         toggleTrack(trackId) {
-            // if we have any tracks with that configuration, turn them off
             const hiddenCount = this.hideTrack(trackId);
-            // if none had that configuration, turn one on
             if (!hiddenCount) {
                 this.showTrack(trackId);
+                return true;
             }
+            return false;
         },
         /**
          * #action

package/esm/LinearReadVsRef/LinearReadVsRef.js

@@ -144,7 +144,7 @@ export default function ReadVsRefDialog({ track, feature: preFeature, handleClos
                             {
                                 start: 0,
                                 end: totalLength,
-                                seq: featSeq || '',
+                                seq: featSeq || '', // can be empty if user clicks secondary read
                                 refName: readName,
                                 uniqueId: `${Math.random()}`,
                             },

package/esm/LinearSyntenyView/components/ImportForm/index.js

@@ -17,7 +17,7 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 function TrackSelector({ setSessionTrackData, setShowTrackId, sessionTrackData, assembly1, assembly2, model, }) {
-    const [choice, setChoice] = useState('none');
+    const [choice, setChoice] = useState('tracklist');
     useEffect(() => {
         if (choice === 'none') {
             setSessionTrackData(undefined);