@jbrowse/plugin-alignments 2.4.2 → 2.5.0

package/esm/HtsgetBamAdapter/configSchema.d.ts

@@ -1,2 +1,27 @@
-declare const HtsgetBamAdapter: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const HtsgetBamAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    htsgetBase: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    htsgetTrackId: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default HtsgetBamAdapter;

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AlignmentsDisplayModel } from '../models/model';
 declare function AlignmentsDisplay({ model }: {
     model: AlignmentsDisplayModel;

package/esm/LinearAlignmentsDisplay/models/configSchema.d.ts

@@ -4,4 +4,42 @@ import PluginManager from '@jbrowse/core/PluginManager';
  * has a "pileup" sub-display, where you can see individual reads and a
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
  */
-export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function configModelFactory(pm: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    pileupDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    /**
+     * #slot
+     */
+    snpCoverageDisplay: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        defaultValue: number;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/esm/LinearAlignmentsDisplay/models/model.d.ts

@@ -3,6 +3,7 @@ import { Instance, IStateTreeNode } from 'mobx-state-tree';
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { MenuItem } from '@jbrowse/core/ui';
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter';
 /**
  * #stateModel LinearAlignmentsDisplay
  * extends `BaseDisplay`
@@ -16,7 +17,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
     snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
@@ -66,7 +67,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: React.FC<any> | undefined;
     trackMenuItems(): MenuItem[];
-    readonly viewMenuActions: MenuItem[];
+    readonly viewMenuActions: MenuItem[]; /**
+     * #action
+     */
     regionCannotBeRendered(): undefined;
 } & {
     setError(error?: unknown): void;
@@ -88,6 +91,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      * #getter
      */
     readonly height: any;
+    readonly featureIdUnderMouse: any;
 } & {
     /**
      * #getter
@@ -125,7 +129,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    updateStatsLimit(stats?: unknown): void;
+    setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;
     /**
      * #action
      */
@@ -164,7 +168,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
     snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;

package/esm/LinearAlignmentsDisplay/models/model.js

@@ -113,6 +113,10 @@ function stateModelFactory(pluginManager, configSchema) {
             var _a;
             return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : getConf(self, 'height');
         },
+        get featureIdUnderMouse() {
+            return (self.PileupDisplay.featureIdUnderMouse ||
+                self.SNPCoverageDisplay.featureIdUnderMouse);
+        },
     }))
         .views(self => ({
         /**
@@ -182,9 +186,9 @@ function stateModelFactory(pluginManager, configSchema) {
         /**
          * #action
          */
-        updateStatsLimit(stats) {
-            self.PileupDisplay.updateStatsLimit(stats);
-            self.SNPCoverageDisplay.updateStatsLimit(stats);
+        setFeatureDensityStatsLimit(stats) {
+            self.PileupDisplay.setFeatureDensityStatsLimit(stats);
+            self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats);
         },
         /**
          * #action

package/esm/LinearAlignmentsDisplay/models/model.js.map

@@ -1 +1 @@
-{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/model.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AACpC,OAAO,EACL,WAAW,EACX,WAAW,EACX,OAAO,EACP,KAAK,GAGN,MAAM,iBAAiB,CAAA;AACxB,OAAO,SAAS,MAAM,iBAAiB,CAAA;AAEvC,UAAU;AACV,OAAO,EACL,sBAAsB,EAGtB,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,WAAW,EAAE,MAAM,4CAA4C,CAAA;AAIxE,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAE3B,SAAS,qBAAqB,CAAC,aAA4B;IACzD,OAAO,CACL,aAAa;SACV,kBAAkB,EAAE;QACrB,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,CAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,IAAI,MAAK,yBAAyB,CAAA,EAAA,CAAC;QAC9D,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,UAAU,CAAA,EAAA,CAAC,CACzC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CACf,EAAK,EACL,EAAK;IAEL,OAAO,SAAS,CACd,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,EAChC,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CACjC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,IAA4B;IAC5C,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,OAAO,CACL,aAAa;QACb,OAAO,CAAC,aAAa,CAAC;QACtB,kBAAkB;QAClB,OAAO,CAAC,kBAAkB,CAAC,CAC5B,CAAA;AACH,CAAC;AAED,SAAS,gBAAgB,CAAC,IAA4B;IACpD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,EAAE;QAC7C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,kBAAkB,CAAC,OAAO,CAAC,EAAE;QAChE,kBAAkB,CAAC,UAAU,CAAC,WAAW,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAA;KAClE;AACH,CAAC;AAED,SAAS,iBAAiB,CAAC,IAA4B;IACrD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,QAAQ,EAAE;QAC9C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,QAAQ,EAAE,kBAAkB,CAAC,QAAQ,CAAC,EAAE;QAClE,kBAAkB,CAAC,WAAW,CAAC,WAAW,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAA;KACpE;AACH,CAAC;AAED,SAAS,eAAe,CACtB,aAA4B,EAC5B,YAAwC;IAExC,MAAM,kBAAkB,GAAG,qBAAqB,CAAC,aAAa,CAAC,CAAC,GAAG,CACjE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAClB,CAAA;IAED,OAAO,KAAK,CAAC,KAAK,CAAC;QACjB;;;WAGG;QACH,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,kBAAkB,CAAC,CAAC;QAC9D;;;WAGG;QACH,kBAAkB,EAAE,KAAK,CAAC,KAAK,CAC7B,aAAa,CAAC,cAAc,CAAC,0BAA0B,CAAC,CAAC,UAAU,CACpE;QACD;;WAEG;QACH,YAAY,EAAE,EAAE;QAChB;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,yBAAyB,CAAC;QAC9C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD;;WAEG;QACH,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,wBAAwB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACnD;;WAEG;QACH,cAAc,EAAE,qBAAqB;KACtC,CAAC,CAAA;AACJ,CAAC;AAED;;;GAGG;AACH,SAAS,iBAAiB,CACxB,aAA4B,EAC5B,YAAwC;IAExC,OAAO,KAAK;SACT,OAAO,CACN,yBAAyB,EACzB,WAAW,EACX,eAAe,CAAC,aAAa,EAAE,YAAY,CAAC,CAC7C;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,CAAC;KACb,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,SAAiB;YAC5B,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QAED;;WAEG;QACH,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,MAAM;;YACR,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAI,OAAO,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;QACxD,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,UAAU;YACZ,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,CAAA;YAC3C,OAAO;gBACL,GAAG,IAAI;gBACP,IAAI,EAAE,IAAI,CAAC,cAAc;gBACzB,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,IAAI,IAAI,CAAC,cAAc,MAAM,EAAE,yEAAyE;aACnJ,CAAA;QACH,CAAC;QAED;;WAEG;QACH,cAAc,CAAC,QAAgB,EAAE,EAAU;YACzC,OAAO,IAAI,CAAC,aAAa,CAAC,cAAc,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;QACxD,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,EAAU;YAC1B,OAAO,IAAI,CAAC,aAAa,CAAC,iBAAiB,CAAC,EAAE,CAAC,CAAA;QACjD,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;;YACd,OAAO,MAAA,IAAI,CAAC,aAAa,0CAAE,YAAY,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;YACd,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,EAAE,oBAAoB,CAAC,CAAA;YAChD,OAAO;gBACL,GAAG,IAAI;gBACP,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,kBAAkB,EAAE,yEAAyE;aACxI,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,qBAAqB,CAAC,aAAoC;YACxD,IAAI,CAAC,kBAAkB,GAAG;gBACxB,IAAI,EAAE,0BAA0B;gBAChC,aAAa;gBACb,MAAM,EAAE,IAAI,CAAC,YAAY;aAC1B,CAAA;QACH,CAAC;QACD;;WAEG;QACH,gBAAgB,CAAC,KAAe;YAC9B,IAAI,CAAC,aAAa,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,CAAC,kBAAkB,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;QACjD,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,aAAoC;YACnD,IAAI,CAAC,aAAa,GAAG;gBACnB,IAAI,EAAE,aAAa,CAAC,IAAI,IAAI,qBAAqB;gBACjD,aAAa;aACd,CAAA;QACH,CAAC;QACD;;WAEG;QACH,SAAS,CAAC,CAAS;YACjB,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,gBAAgB,CAAC,CAAA;YACpD,OAAO,IAAI,CAAC,eAAe,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,IAAY;YAC5B,IAAI,CAAC,cAAc,GAAG,IAAI,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,QAAgB;YAC3B,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAA;YAC7B,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;YACxD,OAAO,SAAS,GAAG,SAAS,CAAA;QAC9B,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,EACJ,kBAAkB,EAClB,aAAa,EACb,YAAY,EACZ,UAAU,GACX,GAAG,IAAI,CAAA;gBAER,IAAI,CAAC,kBAAkB,EAAE;oBACvB,IAAI,CAAC,qBAAqB,CAAC,YAAY,CAAC,CAAA;iBACzC;qBAAM,IACL,CAAC,SAAS,CACR,YAAY,EACZ,WAAW,CAAC,kBAAkB,CAAC,aAAa,CAAC,CAC9C,EACD;oBACA,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;oBAC/C,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;iBAChD;gBAED,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,cAAc,KAAK,aAAa,CAAC,IAAI,EAAE;oBAChE,IAAI,CAAC,gBAAgB,CAAC,UAAU,CAAC,CAAA;iBAClC;qBAAM,IACL,CAAC,SAAS,CAAC,UAAU,EAAE,WAAW,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,EAChE;oBACA,aAAa,CAAC,SAAS,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;iBACzC;gBAED,gBAAgB,CAAC,IAA8B,CAAC,CAAA;gBAChD,iBAAiB,CAAC,IAA8B,CAAC,CAAA;YACnD,CAAC,CAAC,CACH,CAAA;YAED,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;YAC3D,CAAC,CAAC,CACH,CAAA;YAED,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,aAAa,CAAC,SAAS,CAC1B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAC7C,CAAA;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;QACD;;WAEG;QACH,KAAK,CAAC,SAAS,CAAC,IAAmC;YACjD,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAA;YACjE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;YAC1C,OAAO,CACL;gBACE,+BAAI,MAAM,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,CAAK;gBACtD,2BAAG,SAAS,EAAE,eAAe,IAAI,CAAC,kBAAkB,CAAC,MAAM,GAAG,IAC3D,MAAM,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC;oBAClC,GAAG,IAAI;oBACP,cAAc,EAAE,YAAY;iBAC7B,CAAC,CACA,CACH,CACJ,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,cAAc,EAAE,mBAAmB,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO;YACL;;eAEG;YACH,cAAc;gBACZ,MAAM,KAAK,GAAG,qBAAqB,CAAC,aAAa,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;oBAC3D,IAAI,EAAE,OAAO;oBACb,KAAK,EAAE,CAAC,CAAC,WAAW;oBACpB,OAAO,EAAE,CAAC,CAAC,IAAI,KAAK,IAAI,CAAC,aAAa,CAAC,IAAI;oBAC3C,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC,IAAI,CAAC;iBAC9C,CAAC,CAAC,CAAA;gBACH,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,iBAAiB;wBACxB,OAAO,EAAE,IAAI,CAAC,aAAa,CAAC,cAAc,EAAE;qBAC7C;oBACD;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,sBAAsB;wBAC7B,OAAO,EAAE,IAAI,CAAC,kBAAkB,CAAC,cAAc,EAAE;qBAClD;oBACD;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,6BAA6B;wBACpC,OAAO,EAAE,KAAK;qBACf;iBACF,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,kBAAkB,CAAC,IAAI,CAAC,EAAE;QACzB,IAAI,CAAC,IAAI,EAAE;YACT,OAAO,IAAI,CAAA;SACZ;QACD,mBAAmB;QACnB,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;QAChC,OAAO,EAAE,eAAe,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,CAAA;IAC7C,CAAC,CAAC,CAAA;AACN,CAAC;AAED,eAAe,iBAAiB,CAAA"}
+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/model.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AACpC,OAAO,EACL,WAAW,EACX,WAAW,EACX,OAAO,EACP,KAAK,GAGN,MAAM,iBAAiB,CAAA;AACxB,OAAO,SAAS,MAAM,iBAAiB,CAAA;AAEvC,UAAU;AACV,OAAO,EACL,sBAAsB,EAGtB,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,WAAW,EAAE,MAAM,4CAA4C,CAAA;AAKxE,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAE3B,SAAS,qBAAqB,CAAC,aAA4B;IACzD,OAAO,CACL,aAAa;SACV,kBAAkB,EAAE;QACrB,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,CAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,IAAI,MAAK,yBAAyB,CAAA,EAAA,CAAC;QAC9D,mBAAmB;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,MAAA,CAAC,CAAC,UAAU,0CAAE,UAAU,CAAA,EAAA,CAAC,CACzC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CACf,EAAK,EACL,EAAK;IAEL,OAAO,SAAS,CACd,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,EAChC,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CACjC,CAAA;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,IAA4B;IAC5C,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,OAAO,CACL,aAAa;QACb,OAAO,CAAC,aAAa,CAAC;QACtB,kBAAkB;QAClB,OAAO,CAAC,kBAAkB,CAAC,CAC5B,CAAA;AACH,CAAC;AAED,SAAS,gBAAgB,CAAC,IAA4B;IACpD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,EAAE;QAC7C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,kBAAkB,CAAC,OAAO,CAAC,EAAE;QAChE,kBAAkB,CAAC,UAAU,CAAC,WAAW,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAA;KAClE;AACH,CAAC;AAED,SAAS,iBAAiB,CAAC,IAA4B;IACrD,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,IAAI,CAAA;IAClD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,QAAQ,EAAE;QAC9C,OAAM;KACP;IACD,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,QAAQ,EAAE,kBAAkB,CAAC,QAAQ,CAAC,EAAE;QAClE,kBAAkB,CAAC,WAAW,CAAC,WAAW,CAAC,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAA;KACpE;AACH,CAAC;AAED,SAAS,eAAe,CACtB,aAA4B,EAC5B,YAAwC;IAExC,MAAM,kBAAkB,GAAG,qBAAqB,CAAC,aAAa,CAAC,CAAC,GAAG,CACjE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAClB,CAAA;IAED,OAAO,KAAK,CAAC,KAAK,CAAC;QACjB;;;WAGG;QACH,aAAa,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,kBAAkB,CAAC,CAAC;QAC9D;;;WAGG;QACH,kBAAkB,EAAE,KAAK,CAAC,KAAK,CAC7B,aAAa,CAAC,cAAc,CAAC,0BAA0B,CAAC,CAAC,UAAU,CACpE;QACD;;WAEG;QACH,YAAY,EAAE,EAAE;QAChB;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,yBAAyB,CAAC;QAC9C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD;;WAEG;QACH,eAAe,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC1C;;WAEG;QACH,wBAAwB,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACnD;;WAEG;QACH,cAAc,EAAE,qBAAqB;KACtC,CAAC,CAAA;AACJ,CAAC;AAED;;;GAGG;AACH,SAAS,iBAAiB,CACxB,aAA4B,EAC5B,YAAwC;IAExC,OAAO,KAAK;SACT,OAAO,CACN,yBAAyB,EACzB,WAAW,EACX,eAAe,CAAC,aAAa,EAAE,YAAY,CAAC,CAC7C;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,CAAC;KACb,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,YAAY,CAAC,SAAiB;YAC5B,IAAI,CAAC,SAAS,GAAG,SAAS,CAAA;QAC5B,CAAC;QAED;;WAEG;QACH,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACvB,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,MAAM;;YACR,OAAO,MAAA,IAAI,CAAC,eAAe,mCAAI,OAAO,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;QACxD,CAAC;QAED,IAAI,mBAAmB;YACrB,OAAO,CACL,IAAI,CAAC,aAAa,CAAC,mBAAmB;gBACtC,IAAI,CAAC,kBAAkB,CAAC,mBAAmB,CAC5C,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,UAAU;YACZ,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,EAAE,eAAe,CAAC,CAAA;YAC3C,OAAO;gBACL,GAAG,IAAI;gBACP,IAAI,EAAE,IAAI,CAAC,cAAc;gBACzB,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,IAAI,IAAI,CAAC,cAAc,MAAM,EAAE,yEAAyE;aACnJ,CAAA;QACH,CAAC;QAED;;WAEG;QACH,cAAc,CAAC,QAAgB,EAAE,EAAU;YACzC,OAAO,IAAI,CAAC,aAAa,CAAC,cAAc,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;QACxD,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,EAAU;YAC1B,OAAO,IAAI,CAAC,aAAa,CAAC,iBAAiB,CAAC,EAAE,CAAC,CAAA;QACjD,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;;YACd,OAAO,MAAA,IAAI,CAAC,aAAa,0CAAE,YAAY,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,IAAI,QAAQ;YACV,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAA;QACpC,CAAC;QAED;;WAEG;QACH,IAAI,YAAY;YACd,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,EAAE,oBAAoB,CAAC,CAAA;YAChD,OAAO;gBACL,GAAG,IAAI;gBACP,SAAS,EAAE,GAAG,IAAI,CAAC,aAAa,CAAC,SAAS,kBAAkB,EAAE,yEAAyE;aACxI,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,qBAAqB,CAAC,aAAoC;YACxD,IAAI,CAAC,kBAAkB,GAAG;gBACxB,IAAI,EAAE,0BAA0B;gBAChC,aAAa;gBACb,MAAM,EAAE,IAAI,CAAC,YAAY;aAC1B,CAAA;QACH,CAAC;QACD;;WAEG;QACH,2BAA2B,CAAC,KAA2B;YACrD,IAAI,CAAC,aAAa,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;YACrD,IAAI,CAAC,kBAAkB,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;QAC5D,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,aAAoC;YACnD,IAAI,CAAC,aAAa,GAAG;gBACnB,IAAI,EAAE,aAAa,CAAC,IAAI,IAAI,qBAAqB;gBACjD,aAAa;aACd,CAAA;QACH,CAAC;QACD;;WAEG;QACH,SAAS,CAAC,CAAS;YACjB,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,gBAAgB,CAAC,CAAA;YACpD,OAAO,IAAI,CAAC,eAAe,CAAA;QAC7B,CAAC;QACD;;WAEG;QACH,iBAAiB,CAAC,IAAY;YAC5B,IAAI,CAAC,cAAc,GAAG,IAAI,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,YAAY,CAAC,QAAgB;YAC3B,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAA;YAC7B,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;YACxD,OAAO,SAAS,GAAG,SAAS,CAAA;QAC9B,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,EACJ,kBAAkB,EAClB,aAAa,EACb,YAAY,EACZ,UAAU,GACX,GAAG,IAAI,CAAA;gBAER,IAAI,CAAC,kBAAkB,EAAE;oBACvB,IAAI,CAAC,qBAAqB,CAAC,YAAY,CAAC,CAAA;iBACzC;qBAAM,IACL,CAAC,SAAS,CACR,YAAY,EACZ,WAAW,CAAC,kBAAkB,CAAC,aAAa,CAAC,CAC9C,EACD;oBACA,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;oBAC/C,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;iBAChD;gBAED,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,cAAc,KAAK,aAAa,CAAC,IAAI,EAAE;oBAChE,IAAI,CAAC,gBAAgB,CAAC,UAAU,CAAC,CAAA;iBAClC;qBAAM,IACL,CAAC,SAAS,CAAC,UAAU,EAAE,WAAW,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,EAChE;oBACA,aAAa,CAAC,SAAS,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;iBACzC;gBAED,gBAAgB,CAAC,IAA8B,CAAC,CAAA;gBAChD,iBAAiB,CAAC,IAA8B,CAAC,CAAA;YACnD,CAAC,CAAC,CACH,CAAA;YAED,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;YAC3D,CAAC,CAAC,CACH,CAAA;YAED,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,aAAa,CAAC,SAAS,CAC1B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAC7C,CAAA;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;QACD;;WAEG;QACH,KAAK,CAAC,SAAS,CAAC,IAAmC;YACjD,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAA;YACjE,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;YAC1C,OAAO,CACL;gBACE,+BAAI,MAAM,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,IAAI,CAAC,CAAK;gBACtD,2BAAG,SAAS,EAAE,eAAe,IAAI,CAAC,kBAAkB,CAAC,MAAM,GAAG,IAC3D,MAAM,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC;oBAClC,GAAG,IAAI;oBACP,cAAc,EAAE,YAAY;iBAC7B,CAAC,CACA,CACH,CACJ,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,cAAc,EAAE,mBAAmB,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO;YACL;;eAEG;YACH,cAAc;gBACZ,MAAM,KAAK,GAAG,qBAAqB,CAAC,aAAa,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;oBAC3D,IAAI,EAAE,OAAO;oBACb,KAAK,EAAE,CAAC,CAAC,WAAW;oBACpB,OAAO,EAAE,CAAC,CAAC,IAAI,KAAK,IAAI,CAAC,aAAa,CAAC,IAAI;oBAC3C,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,CAAC,IAAI,CAAC;iBAC9C,CAAC,CAAC,CAAA;gBACH,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,iBAAiB;wBACxB,OAAO,EAAE,IAAI,CAAC,aAAa,CAAC,cAAc,EAAE;qBAC7C;oBACD;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,sBAAsB;wBAC7B,OAAO,EAAE,IAAI,CAAC,kBAAkB,CAAC,cAAc,EAAE;qBAClD;oBACD;wBACE,IAAI,EAAE,SAAS;wBACf,KAAK,EAAE,6BAA6B;wBACpC,OAAO,EAAE,KAAK;qBACf;iBACF,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,kBAAkB,CAAC,IAAI,CAAC,EAAE;QACzB,IAAI,CAAC,IAAI,EAAE;YACT,OAAO,IAAI,CAAA;SACZ;QACD,mBAAmB;QACnB,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;QAChC,OAAO,EAAE,eAAe,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,CAAA;IAC7C,CAAC,CAAC,CAAA;AACN,CAAC;AAED,eAAe,iBAAiB,CAAA"}

package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { ObservableMap } from 'mobx';
 declare function ColorByTagDlg(props: {
     model: {

package/esm/LinearPileupDisplay/components/ColorByTag.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function ColorByTagDlg(props: {
     model: {
         setColorScheme: Function;

package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export interface LinearPileupDisplayBlurbProps {
     model: {
         sortedBy?: {

package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function SetFeatureHeightDlg(props: {
     model: {
         setFeatureHeight: (arg?: number) => void;

package/esm/LinearPileupDisplay/components/SetMaxHeight.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function SetMaxHeightDlg(props: {
     model: {
         maxHeight?: number;

package/esm/LinearPileupDisplay/components/SetMaxHeight.js

@@ -3,11 +3,11 @@ import { observer } from 'mobx-react';
 import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
 import { Dialog } from '@jbrowse/core/ui';
 import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
+const useStyles = makeStyles()({
     root: {
         width: 500,
     },
-}));
+});
 function SetMaxHeightDlg(props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
@@ -16,9 +16,7 @@ function SetMaxHeightDlg(props) {
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
         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 height for layout" }),
+            React.createElement(TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max height for layout" }),
             React.createElement(DialogActions, null,
                 React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
                         model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);

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

@@ -1 +1 @@
-{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/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,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,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;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,KAMxB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,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;oBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,EACD,WAAW,EAAC,6BAA6B,GACzC;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"}
+{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/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,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAA;AAEF,SAAS,eAAe,CAAC,KAMxB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,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,6BAA6B,GACzC;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/LinearPileupDisplay/components/SortByTag.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function SortByTagDlg(props: {
     model: {
         setSortedBy: Function;

package/esm/LinearPileupDisplay/configSchema.d.ts

@@ -1,3 +1,59 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    colorScheme: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    fetchSizeLimit: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    height: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    mouseover: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>;
 export default configSchemaF;

package/esm/LinearPileupDisplay/model.d.ts

@@ -3,6 +3,15 @@ import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
+export interface Filter {
+    flagInclude: number;
+    flagExclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
 /**
  * #stateModel LinearPileupDisplay
  * extends `BaseLinearDisplay`
@@ -25,6 +34,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        /**
+         * #stateModel LinearPileupDisplay
+         * extends `BaseLinearDisplay`
+         */
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -34,15 +47,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
-        status: string; /**
-         * #property
-         */
+        status: string;
         error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
-        /**
-         * #property
-         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -52,13 +60,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
+        setMessage(messageText: string): void; /**
+         * #property
+         */
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any;
+            renderProps: any; /**
+             * #property
+             */
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
@@ -66,9 +78,32 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    configuration: AnyConfigurationSchemaType;
     showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -103,6 +138,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
+            /**
+             * #action
+             */
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -126,7 +164,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
-            error: unknown;
+            error: unknown; /**
+             * #action
+             */
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
             id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
@@ -154,8 +194,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
 } & {
     readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
@@ -174,31 +214,34 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
     readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
+    readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
 } & {
     setMessage(message: string): void;
 } & {
     afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
     readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
+    readonly regionTooLargeReason: string; /**
+     * #action
+     * uses copy-to-clipboard and generates notification
+     */
 } & {
     reload(): Promise<void>;
 } & {
@@ -286,30 +329,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #action
      */
-    setConfig(configuration: AnyConfigurationModel): void;
+    setConfig(conf: AnyConfigurationModel): void;
     /**
      * #action
      */
     setSortedBy(type: string, tag?: string): void;
-    setFilterBy(filter: {
-        flagInclude: number;
-        flagExclude: number;
-        readName?: string;
-        tagFilter?: {
-            tag: string;
-            value: string;
-        };
-    }): void;
+    setFilterBy(filter: Filter): void;
 } & {
     /**
      * #action
      */
     reload(): void;
 } & {
-    /**
-     * #getter
-     */
-    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -318,6 +349,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+} & {
+    /**
+     * #getter
+     */
+    readonly maxHeight: any;
     /**
      * #getter
      */
@@ -422,12 +458,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    /**
-     * #action
-     */
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
-     * #action
-     */
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -444,23 +475,21 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined; /**
-         * #action
-         */
+        renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
-        message: string | undefined;
+        message: string | undefined; /**
+         * #getter
+         */
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
-        renderProps: any; /**
-         * #getter
-         */
+        renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
@@ -471,10 +500,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, Feature>;
             layout: any;
-            maxHeightReached: boolean;
-            renderProps: any; /**
-             * #getter
+            maxHeightReached: boolean; /**
+             * #method
              */
+            renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
@@ -482,9 +511,37 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number; /**
+             * #getter
+             */
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number; /**
+             * #method
+             */
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
     id: string;
+    configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
     rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;