@jbrowse/plugin-linear-genome-view 2.2.1 → 2.3.0

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js.map

@@ -1 +1 @@
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package/esm/BaseLinearDisplay/models/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const baseLinearDisplayConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default baseLinearDisplayConfigSchema;

package/esm/BaseLinearDisplay/models/{baseLinearDisplayConfigSchema.js → configSchema.js}

@@ -1,12 +1,12 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config BaseLinearDisplay
- * BaseLinearDisplay is a "base" config that is extended by classes like
- * "LinearBasicDisplay" (used for feature tracks, etc) and "LinearBareDisplay"
+ * `BaseLinearDisplay` is a "base" config that is extended by classes like
+ * `LinearBasicDisplay` (used for feature tracks, etc) and `LinearBareDisplay`
  * (more stripped down than even the basic display, not commonly used)
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-export const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
+const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisplay', {
     /**
      * #slot
      */
@@ -29,4 +29,5 @@ export const baseLinearDisplayConfigSchema = ConfigurationSchema('BaseLinearDisp
      */
     explicitIdentifier: 'displayId',
 });
-//# sourceMappingURL=baseLinearDisplayConfigSchema.js.map
+export default baseLinearDisplayConfigSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/BaseLinearDisplay/models/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;;;GAKG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,6BAA6B,GAAG,mBAAmB,CACvD,mBAAmB,EACnB;IACE;;OAEG;IACH,uBAAuB,EAAE;QACvB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,qGAAqG;QACvG,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,OAAS;QACvB,WAAW,EACT,4FAA4F;KAC/F;CACF,EACD;IACE;;OAEG;IACH,kBAAkB,EAAE,WAAW;CAChC,CACF,CAAA;AAED,eAAe,6BAA6B,CAAA"}

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -131,7 +131,7 @@ const blockState = types
             const { rpcManager } = getSession(self);
             const { rendererType } = display;
             const { renderArgs } = renderBlockData(cast(self));
-            // renderArgs can be undefined if an error occured in this block
+            // renderArgs can be undefined if an error occurred in this block
             if (renderArgs) {
                 rendererType
                     .freeResourcesInClient(rpcManager, JSON.parse(JSON.stringify(renderArgs)))

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"serverSideRenderedBlock.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/serverSideRenderedBlock.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,OAAO,EAAE,IAAI,EAAY,MAAM,iBAAiB,CAAA;AAC3E,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EACL,iBAAiB,EACjB,UAAU,EACV,oBAAoB,EACpB,iBAAiB,EACjB,aAAa,EACb,qBAAqB,GAEtB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAA;AACrD,OAAO,EAEL,gBAAgB,GACjB,MAAM,0BAA0B,CAAA;AAEjC,OAAO,EACL,qBAAqB,EACrB,eAAe,GAChB,MAAM,2BAA2B,CAAA;AAElC,OAAO,8BAA8B,MAAM,8CAA8C,CAAA;AAEzF,oEAAoE;AACpE,MAAM,UAAU,GAAG,KAAK;KACrB,KAAK,CAAC,YAAY,EAAE;IACnB,GAAG,EAAE,KAAK,CAAC,MAAM;IACjB,MAAM,EAAE,MAAM;IACd,UAAU,EAAE,CAAC;IACb,0BAA0B,EAAE,KAAK;IACjC,2BAA2B,EAAE,KAAK;CACnC,CAAC;IACF,yFAAyF;KACxF,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;IACf,gBAAgB,EAAE,SAAwC;IAC1D,MAAM,EAAE,KAAK;IACb,YAAY,EAAE,SAA2C;IACzD,QAAQ,EAAE,SAA6C;IACvD,MAAM,EAAE,SAAgB;IACxB,MAAM,EAAE,EAAE;IACV,KAAK,EAAE,SAAoB;IAC3B,OAAO,EAAE,SAA+B;IACxC,gBAAgB,EAAE,KAAK;IACvB,cAAc,EAAE,8BAA8B;IAC9C,WAAW,EAAE,SAAgB;CAC9B,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE;IACd,IAAI,gBAA6C,CAAA;IACjD,OAAO;QACL,QAAQ;YACN,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;QACvC,CAAC;QACD,WAAW;YACT,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,qBAAqB,CACnB,IAAW,EACX,eAAe,EACf,iBAAwB,EAAE,qCAAqC;YAC/D;gBACE,IAAI,EAAE,GAAG,OAAO,CAAC,EAAE,IAAI,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY;gBACjE,KAAK,EAAE,OAAO,CAAC,WAAW;gBAC1B,eAAe,EAAE,IAAI;aACtB,EACD,IAAI,CAAC,UAAU,EACf,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,QAAQ,CACd,CAAA;QACH,CAAC;QACD,SAAS,CAAC,OAAe;YACvB,IAAI,CAAC,MAAM,GAAG,OAAO,CAAA;QACvB,CAAC;QACD,UAAU,CAAC,eAAgC;YACzC,IAAI,gBAAgB,KAAK,SAAS,EAAE;gBAClC,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;oBACpC,gBAAgB,CAAC,KAAK,EAAE,CAAA;iBACzB;aACF;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,eAAe,CAAA;QACpC,CAAC;QACD,UAAU,CAAC,WAAmB;YAC5B,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,WAAW,CAAA;YAC1B,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,WAAW,CACT,KAQa;YAEb,IAAI,CAAC,KAAK,EAAE;gBACV,OAAM;aACP;YACD,MAAM,EACJ,YAAY,EACZ,QAAQ,EACR,MAAM,EACN,gBAAgB,EAChB,WAAW,GACZ,GAAG,KAAK,CAAA;YACT,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;YAClB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;YAChC,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YACxB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;YACpB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;YACxC,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;YAC9B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,QAAQ,CAAC,KAAsB;YAC7B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;YACpB,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,uCAAuC;YACvC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;YAClB,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;YAC5B,IAAI,gBAAgB,CAAC,KAAc,CAAC,EAAE;gBACpC,IAAI,CAAC,MAAM,EAAE,CAAA;aACd;QACH,CAAC;QACD,MAAM;YACJ,IAAI,CAAC,gBAAgB,GAAG,SAAS,CAAA;YACjC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,cAAc,GAAG,8BAA8B,CAAA;YACpD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,SAAS,CAAM,IAAI,EAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAA;QAClC,CAAC;QACD,aAAa;YACX,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YACvC,MAAM,EAAE,YAAY,EAAE,GAAG,OAAO,CAAA;YAChC,MAAM,EAAE,UAAU,EAAE,GAAG,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;YAClD,iEAAiE;YACjE,IAAI,UAAU,EAAE;gBACd,YAAY;qBACT,qBAAqB,CACpB,UAAU,EACV,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CACvC;qBACA,KAAK,CAAC,CAAC,CAAQ,EAAE,EAAE;oBAClB,kEAAkE;oBAClE,OAAO,CAAC,IAAI,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;gBACjD,CAAC,CAAC,CAAA;aACL;QACH,CAAC;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEJ,eAAe,UAAU,CAAA;AAIzB,2EAA2E;AAC3E,mDAAmD;AACnD,MAAM,UAAU,eAAe,CAC7B,IAAgB,EAChB,UAAiC;IAEjC,IAAI;QACF,MAAM,OAAO,GAAG,UAAU,IAAK,oBAAoB,CAAC,IAAI,CAAS,CAAA;QACjE,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,OAAO,CAAC,CAAA;QAC3D,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;QACnE,MAAM,aAAa,GAAG,qBAAqB,CAAC,WAAW,CAAC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package/esm/BaseLinearDisplay/models/util.d.ts

@@ -0,0 +1,18 @@
+export interface RenderProps {
+    rendererType: any;
+    renderArgs: {
+        [key: string]: any;
+    };
+    renderProps: {
+        [key: string]: any;
+    };
+    displayError: unknown;
+    rpcManager: {
+        call: Function;
+    };
+    cannotBeRenderedReason: string;
+}
+export interface ErrorProps {
+    displayError: string;
+}
+export declare function getDisplayStr(totalBytes: number): string;

package/esm/BaseLinearDisplay/models/util.js

@@ -0,0 +1,14 @@
+export function getDisplayStr(totalBytes) {
+    let displayBp;
+    if (Math.floor(totalBytes / 1000000) > 0) {
+        displayBp = `${parseFloat((totalBytes / 1000000).toPrecision(3))} Mb`;
+    }
+    else if (Math.floor(totalBytes / 1000) > 0) {
+        displayBp = `${parseFloat((totalBytes / 1000).toPrecision(3))} Kb`;
+    }
+    else {
+        displayBp = `${Math.floor(totalBytes)} bytes`;
+    }
+    return displayBp;
+}
+//# sourceMappingURL=util.js.map

package/esm/BaseLinearDisplay/models/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/util.ts"],"names":[],"mappings":"AAaA,MAAM,UAAU,aAAa,CAAC,UAAkB;IAC9C,IAAI,SAAS,CAAA;IACb,IAAI,IAAI,CAAC,KAAK,CAAC,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE;QACxC,SAAS,GAAG,GAAG,UAAU,CAAC,CAAC,UAAU,GAAG,OAAO,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;KACtE;SAAM,IAAI,IAAI,CAAC,KAAK,CAAC,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE;QAC5C,SAAS,GAAG,GAAG,UAAU,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;KACnE;SAAM;QACL,SAAS,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,QAAQ,CAAA;KAC9C;IACD,OAAO,SAAS,CAAA;AAClB,CAAC"}

package/esm/FeatureTrack/index.d.ts

@@ -1,3 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
+declare const _default: (pm: PluginManager) => void;
 export default _default;

package/esm/FeatureTrack/index.js

@@ -1,12 +1,13 @@
 import { createBaseTrackModel, TrackType, } from '@jbrowse/core/pluggableElementTypes';
 import configSchemaF from './configSchema';
-export default (pluginManager) => {
-    pluginManager.addTrackType(() => {
-        const configSchema = configSchemaF(pluginManager);
+export default (pm) => {
+    pm.addTrackType(() => {
+        const configSchema = configSchemaF(pm);
         return new TrackType({
             name: 'FeatureTrack',
+            displayName: 'Feature track',
             configSchema,
-            stateModel: createBaseTrackModel(pluginManager, 'FeatureTrack', configSchema),
+            stateModel: createBaseTrackModel(pm, 'FeatureTrack', configSchema),
         });
     });
 };

package/esm/FeatureTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/FeatureTrack/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,oBAAoB,EACpB,SAAS,GACV,MAAM,qCAAqC,CAAA;AAE5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAC9B,aAAa,EACb,cAAc,EACd,YAAY,CACb;SACF,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/FeatureTrack/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,oBAAoB,EACpB,SAAS,GACV,MAAM,qCAAqC,CAAA;AAE5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,WAAW,EAAE,eAAe;YAC5B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,cAAc,EAAE,YAAY,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/LaunchLinearGenomeView/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LaunchLinearGenomeView/index.js

@@ -0,0 +1,42 @@
+import { when } from '@jbrowse/core/util';
+export default (pluginManager) => {
+    pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
+    // @ts-ignore
+    async ({ session, assembly, loc, tracks = [], }) => {
+        try {
+            const { assemblyManager } = session;
+            const view = session.addView('LinearGenomeView', {});
+            await when(() => !!view.volatileWidth);
+            if (!assembly) {
+                throw new Error('No assembly provided when launching linear genome view');
+            }
+            const asm = await assemblyManager.waitForAssembly(assembly);
+            if (!asm) {
+                throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
+            }
+            await view.navToLocString(loc, assembly);
+            const idsNotFound = [];
+            tracks.forEach(track => {
+                try {
+                    view.showTrack(track);
+                }
+                catch (e) {
+                    if (`${e}`.match('Could not resolve identifier')) {
+                        idsNotFound.push(track);
+                    }
+                    else {
+                        throw e;
+                    }
+                }
+            });
+            if (idsNotFound.length) {
+                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
+            }
+        }
+        catch (e) {
+            session.notify(`${e}`, 'error');
+            throw e;
+        }
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/LaunchLinearGenomeView/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LaunchLinearGenomeView/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAwB,IAAI,EAAE,MAAM,oBAAoB,CAAA;AAK/D,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,mBAAmB,CAC/B,6BAA6B;IAC7B,aAAa;IACb,KAAK,EAAE,EACL,OAAO,EACP,QAAQ,EACR,GAAG,EACH,MAAM,GAAG,EAAE,GAMZ,EAAE,EAAE;QACH,IAAI;YACF,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;YACnC,MAAM,IAAI,GAAG,OAAO,CAAC,OAAO,CAAC,kBAAkB,EAAE,EAAE,CAAQ,CAAA;YAE3D,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAEtC,IAAI,CAAC,QAAQ,EAAE;gBACb,MAAM,IAAI,KAAK,CACb,wDAAwD,CACzD,CAAA;aACF;YAED,MAAM,GAAG,GAAG,MAAM,eAAe,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAA;YAC3D,IAAI,CAAC,GAAG,EAAE;gBACR,MAAM,IAAI,KAAK,CACb,aAAa,QAAQ,+CAA+C,CACrE,CAAA;aACF;YAED,MAAM,IAAI,CAAC,cAAc,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;YAExC,MAAM,WAAW,GAAG,EAAc,CAAA;YAClC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;gBACrB,IAAI;oBACF,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;iBACtB;gBAAC,OAAO,CAAC,EAAE;oBACV,IAAI,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,8BAA8B,CAAC,EAAE;wBAChD,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;qBACxB;yBAAM;wBACL,MAAM,CAAC,CAAA;qBACR;iBACF;YACH,CAAC,CAAC,CAAA;YACF,IAAI,WAAW,CAAC,MAAM,EAAE;gBACtB,MAAM,IAAI,KAAK,CACb,kCAAkC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAC1D,CAAA;aACF;SACF;QAAC,OAAO,CAAC,EAAE;YACV,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;YAC/B,MAAM,CAAC,CAAA;SACR;IACH,CAAC,CACF,CAAA;AACH,CAAC,CAAA"}

package/esm/LinearBareDisplay/index.d.ts

@@ -1,2 +1,6 @@
-export { configSchemaFactory } from './configSchema';
-export { stateModelFactory } from './model';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { configSchemaFactory } from './configSchema';
+import { stateModelFactory } from './model';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { configSchemaFactory, stateModelFactory };

package/esm/LinearBareDisplay/index.js

@@ -1,3 +1,20 @@
-export { configSchemaFactory } from './configSchema';
-export { stateModelFactory } from './model';
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
+// locals
+import { configSchemaFactory } from './configSchema';
+import { stateModelFactory } from './model';
+import { BaseLinearDisplayComponent } from '../BaseLinearDisplay/';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        return new DisplayType({
+            name: 'LinearBareDisplay',
+            configSchema,
+            stateModel: stateModelFactory(configSchema),
+            trackType: 'BasicTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplayComponent,
+        });
+    });
+};
+export { configSchemaFactory, stateModelFactory };
 //# sourceMappingURL=index.js.map

package/esm/LinearBareDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,SAAS;AACT,OAAO,EAAE,mBAAmB,EAAE,MAAM,gBAAgB,CAAA;AACpD,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAC3C,OAAO,EAAE,0BAA0B,EAAE,MAAM,uBAAuB,CAAA;AAElE,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,YAAY;YACvB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,OAAO,EAAE,mBAAmB,EAAE,iBAAiB,EAAE,CAAA"}

package/esm/LinearBareDisplay/model.d.ts

@@ -121,10 +121,10 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {

package/esm/LinearBasicDisplay/components/SetMaxHeight.js

@@ -1,18 +1,12 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, Typography, TextField, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, Typography, TextField, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
 const useStyles = makeStyles()(theme => ({
     root: {
         width: 500,
     },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
     field: {
         margin: theme.spacing(2),
     },
@@ -21,11 +15,7 @@ function SetMaxHeightDlg({ model, handleClose, }) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = useState(`${maxHeight}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, "aria-labelledby": "alert-dialog-title", "aria-describedby": "alert-dialog-description" },
-        React.createElement(DialogTitle, { id: "alert-dialog-title" },
-            "Filter options",
-            React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose, size: "large" },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         React.createElement(DialogContent, { className: classes.root },
             React.createElement(Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
             React.createElement(TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" }),

package/esm/LinearBasicDisplay/components/SetMaxHeight.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearBasicDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,UAAU,EACV,SAAS,GACV,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;IAED,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,EACvB,KAAK,EACL,WAAW,GAOZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,UAAU,qHAGE;YACb,oBAAC,SAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,iBAAiB,GAC7B;YACF,oBAAC,aAAa;gBACZ,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,eAAe,CAAC,CAAA"}

package/esm/LinearBasicDisplay/index.d.ts

@@ -1,2 +1,6 @@
-export { default as modelFactory } from './model';
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import configSchema from './configSchema';
+import modelFactory from './model';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { modelFactory, configSchema };

package/esm/LinearBasicDisplay/index.js

@@ -1,3 +1,21 @@
-export { default as modelFactory } from './model';
-export { default as configSchema } from './configSchema';
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
+import { BaseLinearDisplayComponent } from '../BaseLinearDisplay';
+// locals
+import configSchema from './configSchema';
+import modelFactory from './model';
+export default (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const config = configSchema(pluginManager);
+        return new DisplayType({
+            name: 'LinearBasicDisplay',
+            displayName: 'Basic deature display',
+            configSchema: config,
+            stateModel: modelFactory(config),
+            trackType: 'FeatureTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplayComponent,
+        });
+    });
+};
+export { modelFactory, configSchema };
 //# sourceMappingURL=index.js.map

package/esm/LinearBasicDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AACjE,OAAO,EAAE,0BAA0B,EAAE,MAAM,sBAAsB,CAAA;AAEjE,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,YAAY,MAAM,SAAS,CAAA;AAElC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,MAAM,GAAG,YAAY,CAAC,aAAa,CAAC,CAAA;QAC1C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,uBAAuB;YACpC,YAAY,EAAE,MAAM;YACpB,UAAU,EAAE,YAAY,CAAC,MAAM,CAAC;YAChC,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,CAAA"}

package/esm/LinearBasicDisplay/model.d.ts

@@ -4,7 +4,8 @@ import { MenuItem } from '@jbrowse/core/ui';
 import { Instance } from 'mobx-state-tree';
 /**
  * #stateModel LinearBasicDisplay
- * used by `FeatureTrack`, has simple settings like "show/hide feature labels", etc.
+ * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
+ * etc.
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -34,14 +35,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
-        /**
-         * #property
-         */
         layout: any;
         status: string;
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean;
+        maxHeightReached: boolean; /**
+         * #getter
+         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -49,7 +49,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & {
         doReload(): void;
         afterAttach(): void;
-        setStatus(message: string): void; /**
+        setStatus(message: string): void;
+        /**
          * #getter
          */
         setLoading(abortController: AbortController): void;
@@ -58,7 +59,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
-            maxHeightReached: boolean;
+            maxHeightReached: boolean; /**
+             * #method
+             */
             renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
@@ -107,9 +110,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
              */
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
-             * #property
-             */
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -135,12 +136,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    }> | null;
+    }> | null; /**
+     * #action
+     */
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined; /**
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    /**
      * #method
      */
     trackMenuItems(): MenuItem[];
@@ -152,10 +156,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {

package/esm/LinearBasicDisplay/model.js

@@ -9,7 +9,8 @@ import { BaseLinearDisplay } from '../BaseLinearDisplay';
 const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'));
 /**
  * #stateModel LinearBasicDisplay
- * used by `FeatureTrack`, has simple settings like "show/hide feature labels", etc.
+ * used by `FeatureTrack`, has simple settings like "show/hide feature labels",
+ * etc.
  */
 function stateModelFactory(configSchema) {
     return types

package/esm/LinearBasicDisplay/model.js.map

@@ -1 +1 @@
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package/esm/LinearGenomeView/components/ExportSvgDialog.js

@@ -1,16 +1,6 @@
 import React, { useState } from 'react';
-import { makeStyles } from 'tss-react/mui';
-import { Button, Checkbox, CircularProgress, Dialog, DialogActions, DialogContent, DialogTitle, FormControlLabel, IconButton, TextField, Typography, } from '@mui/material';
-import { ErrorMessage } from '@jbrowse/core/ui';
-import CloseIcon from '@mui/icons-material/Close';
-const useStyles = makeStyles()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+import { Button, Checkbox, CircularProgress, DialogActions, DialogContent, FormControlLabel, TextField, Typography, } from '@mui/material';
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 function LoadingMessage() {
     return (React.createElement("div", null,
         React.createElement(CircularProgress, { size: 20, style: { marginRight: 20 } }),
@@ -23,12 +13,7 @@ export default function ExportSvgDlg({ model, handleClose, }) {
     const [loading, setLoading] = useState(false);
     const [filename, setFilename] = useState('jbrowse.svg');
     const [error, setError] = useState();
-    const { classes } = useStyles();
-    return (React.createElement(Dialog, { open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Export SVG",
-            React.createElement(IconButton, { className: classes.closeButton, onClick: handleClose },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         React.createElement(DialogContent, null,
             error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
             React.createElement(TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),

package/esm/LinearGenomeView/components/ExportSvgDialog.js.map

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