@jbrowse/plugin-gccontent 2.16.1 → 2.18.0

package/esm/LinearGCContentDisplay/shared.js

@@ -1,25 +1,13 @@
-import { getConf, } from '@jbrowse/core/configuration';
+import { lazy } from 'react';
+import { getConf } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
 import { types } from 'mobx-state-tree';
-import { lazy } from 'react';
 const EditGCContentParamsDialog = lazy(() => import('./components/EditGCContentParams'));
-/**
- * #stateModel SharedGCContentModel
- * #category display
- * extends
- * - [LinearWiggleDisplay](../linearwiggledisplay)
- */
 export default function SharedModelF(pluginManager, configSchema) {
     return types
         .compose('SharedGCContentModel', linearWiggleDisplayModelFactory(pluginManager, configSchema), types.model({
-        /**
-         * #property
-         */
         windowSize: types.maybe(types.number),
-        /**
-         * #property
-         */
         windowDelta: types.maybe(types.number),
     }))
         .actions(self => ({
@@ -39,7 +27,7 @@ export default function SharedModelF(pluginManager, configSchema) {
         },
     }))
         .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
+        const { trackMenuItems: superTrackMenuItems, adapterProps: superAdapterProps, } = self;
         return {
             trackMenuItems() {
                 return [
@@ -55,15 +43,10 @@ export default function SharedModelF(pluginManager, configSchema) {
                     },
                 ];
             },
-            /**
-             * #method
-             * retrieves the sequence adapter from parent track, and puts it as a
-             * subadapter on a GCContentAdapter
-             */
-            renderProps() {
+            adapterProps() {
                 const sequenceAdapter = getConf(self.parentTrack, 'adapter');
                 return {
-                    ...superRenderProps(),
+                    ...superAdapterProps(),
                     adapterConfig: {
                         type: 'GCContentAdapter',
                         sequenceAdapter,

package/esm/LinearGCContentDisplay/stateModel1.d.ts

@@ -1,10 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel LinearGCContentDisplay
- * #category display
- * base model `SharedGCContentModel`
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelF(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): 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>;
@@ -17,21 +12,12 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         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>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -55,15 +41,9 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -210,6 +190,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
@@ -249,19 +230,21 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     }): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -303,6 +286,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -341,7 +325,9 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly rendererTypeName: string;
+    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
 } & {
+    adapterProps(): any;
     readonly ticks: {
         range: number[];
         values: number[];
@@ -352,6 +338,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     renderProps(): any;
     readonly needsScalebar: boolean;
     readonly fillSetting: 1 | 2 | 0;
+    readonly quantitativeStatsReady: boolean;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
@@ -410,5 +397,5 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly windowDeltaSetting: any;
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
+    adapterProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/LinearGCContentDisplay/stateModel1.js

@@ -1,11 +1,5 @@
 import { types } from 'mobx-state-tree';
-// locals
 import SharedModelF from './shared';
-/**
- * #stateModel LinearGCContentDisplay
- * #category display
- * base model `SharedGCContentModel`
- */
 export default function stateModelF(pluginManager, configSchema) {
     return types.compose('LinearGCContentDisplay', SharedModelF(pluginManager, configSchema), types.model({
         type: types.literal('LinearGCContentDisplay'),

package/esm/LinearGCContentDisplay/stateModel2.d.ts

@@ -1,15 +1,5 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel LinearGCContentTrackDisplay
- * #category display
- *
- * used on GCContentTrack, separately from the display type on the
- * ReferenceSequenceTrack
- *
- * extends
- * - [SharedGCContentModel](../sharedgccontentmodel)
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 export default function stateModelF(pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType): 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>;
@@ -22,21 +12,12 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>;
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         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>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -60,15 +41,9 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, import("@jbrowse/core/util").Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -215,6 +190,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
 } & {
@@ -254,19 +230,21 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     message: undefined | string;
     stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     } | undefined;
-    statsFetchInProgress: undefined | AbortController;
+    statsFetchInProgress: undefined | string;
 } & {
     updateQuantitativeStats(stats: {
+        currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
     }): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
     setNegColor(color?: string): void;
-    setLoading(aborter: AbortController): void;
+    setStatsLoading(arg?: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setResolution(res: number): void;
     setFill(fill: number): void;
@@ -308,6 +286,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
+            currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
         } | undefined;
@@ -346,7 +325,9 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
 } & {
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly rendererTypeName: string;
+    readonly quantitativeStatsRelevantToCurrentZoom: boolean;
 } & {
+    adapterProps(): any;
     readonly ticks: {
         range: number[];
         values: number[];
@@ -357,6 +338,7 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     renderProps(): any;
     readonly needsScalebar: boolean;
     readonly fillSetting: 1 | 2 | 0;
+    readonly quantitativeStatsReady: boolean;
 } & {
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
@@ -415,5 +397,5 @@ export default function stateModelF(pluginManager: PluginManager, configSchema:
     readonly windowDeltaSetting: any;
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
-    renderProps(): any;
+    adapterProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/LinearGCContentDisplay/stateModel2.js

@@ -1,16 +1,5 @@
 import { types } from 'mobx-state-tree';
-// locals
 import SharedModelF from './shared';
-/**
- * #stateModel LinearGCContentTrackDisplay
- * #category display
- *
- * used on GCContentTrack, separately from the display type on the
- * ReferenceSequenceTrack
- *
- * extends
- * - [SharedGCContentModel](../sharedgccontentmodel)
- */
 export default function stateModelF(pluginManager, configSchema) {
     return types.compose('LinearGCContentTrackDisplay', SharedModelF(pluginManager, configSchema), types.model({
         type: types.literal('LinearGCContentTrackDisplay'),

package/esm/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class GCContentPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,5 +1,4 @@
 import Plugin from '@jbrowse/core/Plugin';
-// locals
 import GCContentAdapterF from './GCContentAdapter';
 import GCContentTrackF from './GCContentTrack';
 import LinearGCContentDisplayF from './LinearGCContentDisplay';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gccontent",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 gccontent concepts",
   "keywords": [
     "jbrowse",
@@ -53,5 +53,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }