@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/esm/GuessAlignmentsTypes/index.js

@@ -0,0 +1,54 @@
+import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
+export default (pluginManager) => {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.cram$/i;
+            const adapterName = 'CramAdapter';
+            const fileName = getFileName(file);
+            const obj = {
+                type: adapterName,
+                cramLocation: file,
+                craiLocation: index || makeIndex(file, '.crai'),
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.bam$/i;
+            const adapterName = 'BamAdapter';
+            const fileName = getFileName(file);
+            const indexName = index && getFileName(index);
+            const obj = {
+                type: adapterName,
+                bamLocation: file,
+                index: {
+                    location: index || makeIndex(file, '.bai'),
+                    indexType: makeIndexType(indexName, 'CSI', 'BAI'),
+                },
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
+                return 'AlignmentsTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/GuessAlignmentsTypes/index.js.map

@@ -0,0 +1 @@
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package/esm/HtsgetBamAdapter/index.js

@@ -1,16 +1,16 @@
 import configSchema from './configSchema';
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 export default (pluginManager) => {
-    pluginManager.addAdapterType(() => new AdapterType({
-        name: 'HtsgetBamAdapter',
-        adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-        },
-        configSchema,
-        getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
-    }));
+    pluginManager.addAdapterType(() => {
+        return new AdapterType({
+            name: 'HtsgetBamAdapter',
+            displayName: 'Htsget BAM adapter',
+            adapterMetadata: {
+                hiddenFromGUI: true,
+            },
+            configSchema,
+            getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
+        });
+    });
 };
 //# sourceMappingURL=index.js.map

package/esm/HtsgetBamAdapter/index.js.map

@@ -1 +1 @@
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package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -11,24 +11,21 @@ const useStyles = makeStyles()(() => ({
     },
 }));
 function AlignmentsDisplay({ model }) {
-    const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model;
+    const { PileupDisplay, SNPCoverageDisplay } = model;
     const { classes } = useStyles();
     const top = SNPCoverageDisplay.height;
     return (React.createElement("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' } },
-        showCoverage ? (React.createElement(React.Fragment, null,
-            React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
-                React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
-            React.createElement(ResizeHandle, { onDrag: delta => {
-                    SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
-                    return delta;
-                }, className: classes.resizeHandle, style: {
-                    top,
-                } }))) : null,
-        showPileup ? (React.createElement("div", { "data-testid": "Blockset-pileup", style: {
+        React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
+            React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
+        React.createElement(ResizeHandle, { onDrag: delta => {
+                SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
+                return delta;
+            }, className: classes.resizeHandle, style: { top } }),
+        React.createElement("div", { "data-testid": "Blockset-pileup", style: {
                 position: 'absolute',
-                top: showCoverage ? SNPCoverageDisplay.height : 0,
+                top,
             } },
-            React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))) : null));
+            React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
 }
 export default observer(AlignmentsDisplay);
 //# sourceMappingURL=AlignmentsDisplay.js.map

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAK/C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,GAAG,EAAE,CAAC,CAAC;IACpC,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,4CACe,WAAW,OAAO,CAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE/B,4CAAiB,sBAAsB;YACrC,oBAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;QACN,oBAAC,YAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;gBAC/D,OAAO,KAAK,CAAA;YACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,GAAG,EAAE,GACd;QAEF,4CACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG;aACJ;YAED,oBAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACF,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,iBAAiB,CAAC,CAAA"}

package/esm/LinearAlignmentsDisplay/index.js

@@ -8,6 +8,7 @@ export default function (pluginManager) {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
             name: 'LinearAlignmentsDisplay',
+            displayName: 'Alignments display (combination)',
             configSchema,
             stateModel: modelFactory(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',

package/esm/LinearAlignmentsDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearAlignmentsDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,SAAS;AACT,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,gCAAgC,CAAA;AAE3D,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,yBAAyB;YAC/B,WAAW,EAAE,kCAAkC;YAC/C,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc;SACf,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

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

@@ -1,4 +1,7 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configModelFactory: (pm: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export type AlignmentsConfigModel = ReturnType<typeof configModelFactory>;
-export default configModelFactory;
+/**
+ * #config LinearAlignmentsDisplay
+ * 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;

package/esm/LinearAlignmentsDisplay/models/configSchema.js

@@ -5,8 +5,7 @@ import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-vie
  * has a "pileup" sub-display, where you can see individual reads and a
  * quantitative "snpcoverage" sub-display track showing SNP frequencies
  */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configModelFactory = (pm) => {
+export default function configModelFactory(pm) {
     return ConfigurationSchema('LinearAlignmentsDisplay', {
         /**
          * #slot
@@ -24,6 +23,5 @@ const configModelFactory = (pm) => {
         baseConfiguration: baseLinearDisplayConfigSchema,
         explicitlyTyped: true,
     });
-};
-export default configModelFactory;
+}
 //# sourceMappingURL=configSchema.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAGlF;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EAAiB;IAC1D,OAAO,mBAAmB,CACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QAEpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;KAChB,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}

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

@@ -1,8 +1,8 @@
 import React from 'react';
+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 { Instance } from 'mobx-state-tree';
 /**
  * #stateModel LinearAlignmentsDisplay
  * extends `BaseDisplay`
@@ -12,15 +12,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
+    PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
     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>;
     height: import("mobx-state-tree").IType<number | undefined, number, number>;
-    showCoverage: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    showPileup: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -33,11 +32,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+        } & 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>; /**
-             * #property
-             */
+            type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -54,16 +51,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             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]>; /**
-             * #action
-             */
+        } & 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>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>; /**
+         * #property
+         */
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
@@ -80,14 +77,6 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     scrollTop: number;
 } & {
-    /**
-     * #action
-     */
-    toggleCoverage(): void;
-    /**
-     * #action
-     */
-    togglePileup(): void;
     /**
      * #action
      */
@@ -100,7 +89,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly pileupDisplayConfig: any;
+    readonly pileupConf: any;
     /**
      * #method
      */
@@ -124,19 +113,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly sortedByPosition: any;
-    /**
-     * #getter
-     */
-    readonly sortedByRefName: any;
-    /**
-     * #getter
-     */
-    readonly snpCoverageDisplayConfig: any;
-    /**
-     * #method
-     */
-    trackMenuItems(): MenuItem[];
+    readonly coverageConf: any;
 } & {
     /**
      * #action
@@ -153,7 +130,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #action
      */
-    setHeight(displayHeight: number): number;
+    setHeight(n: number): number;
+    /**
+     * #action
+     */
+    setLowerPanelType(type: string): void;
     /**
      * #action
      */
@@ -166,6 +147,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<JSX.Element>;
+} & {
+    /**
+     * #method
+     */
+    trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;
 export type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;