@jbrowse/plugin-alignments 2.1.7 → 2.2.0

package/dist/CramAdapter/CramSlightlyLazyFeature.js

@@ -3,7 +3,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 class CramSlightlyLazyFeature {
     // uses parameter properties to automatically create fields on the class
     // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     constructor(record, _store) {
         this.record = record;
         this._store = _store;
@@ -15,7 +14,8 @@ class CramSlightlyLazyFeature {
         return this.record.alignmentStart - 1;
     }
     _get_end() {
-        return this.record.alignmentStart + this.record.lengthOnRef - 1;
+        var _a;
+        return this.record.alignmentStart + ((_a = this.record.lengthOnRef) !== null && _a !== void 0 ? _a : 1) - 1;
     }
     _get_cram_read_features() {
         return this.record.readFeatures;
@@ -85,12 +85,16 @@ class CramSlightlyLazyFeature {
         let cigar = '';
         let op = 'M';
         let oplen = 0;
+        if (!this.record._refRegion) {
+            return '';
+        }
         // not sure I should access these, but...
         const ref = this.record._refRegion.seq;
         const refStart = this.record._refRegion.start;
         let last_pos = this.record.alignmentStart;
         let sublen = 0;
         if (typeof this.record.readFeatures !== 'undefined') {
+            let insLen = 0;
             // @ts-ignore
             for (let i = 0; i < this.record.readFeatures.length; i++) {
                 const { code, refPos, sub, data } = this.record.readFeatures[i];
@@ -105,6 +109,10 @@ class CramSlightlyLazyFeature {
                     op = 'M';
                     oplen += sublen;
                 }
+                if (insLen > 0 && code !== 'i') {
+                    cigar += `${insLen}I`;
+                    insLen = 0;
+                }
                 if (code === 'b') {
                     // An array of bases stored verbatim
                     const ret = data.split(',');
@@ -145,11 +153,11 @@ class CramSlightlyLazyFeature {
                 }
                 else if (code === 'i') {
                     // Single base insertion
-                    seq += data;
+                    // seq += data
                     if (oplen) {
                         cigar += oplen + op;
                     }
-                    cigar += `${1}I`;
+                    insLen++;
                     oplen = 0;
                 }
                 else if (code === 'P') {
@@ -231,18 +239,10 @@ class CramSlightlyLazyFeature {
         return 0;
     }
     toJSON() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const tags = {};
-        this.tags().forEach((t) => {
-            const val = this.get(t);
-            if (val !== undefined) {
-                tags[t] = val;
-            }
-        });
         return {
-            ...tags,
-            name: this.get('name'),
-            type: this.get('type'),
+            ...Object.fromEntries(this.tags()
+                .map(t => [t, this.get(t)])
+                .filter(elt => elt[1] !== undefined)),
             uniqueId: this.id(),
         };
     }
@@ -255,10 +255,21 @@ class CramSlightlyLazyFeature {
         const start = this.get('start');
         const mismatches = new Array(readFeatures.length);
         let j = 0;
+        let insLen = 0;
+        let refPos = 0;
         for (let i = 0; i < readFeatures.length; i++) {
             const f = readFeatures[i];
             const { code, pos, data, sub, ref } = f;
-            const refPos = f.refPos - 1 - start;
+            if (insLen > 0 && code !== 'i') {
+                mismatches[j++] = {
+                    start: refPos,
+                    type: 'insertion',
+                    base: `${insLen}`,
+                    length: 0,
+                };
+                insLen = 0;
+            }
+            refPos = f.refPos - 1 - start;
             if (code === 'X') {
                 // substitution
                 mismatches[j++] = {
@@ -334,12 +345,7 @@ class CramSlightlyLazyFeature {
             else if (code === 'i') {
                 // single-base insertion
                 // insertion
-                mismatches[j++] = {
-                    start: refPos,
-                    type: 'insertion',
-                    base: data,
-                    length: 1,
-                };
+                insLen++;
             }
             else if (code === 'Q') {
                 // single quality value

package/dist/CramAdapter/CramSlightlyLazyFeature.js.map

@@ -1 +1 @@
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package/dist/CramAdapter/configSchema.d.ts

@@ -1,3 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/dist/CramAdapter/configSchema.js

@@ -1,28 +1,50 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = (pluginManager) => {
-    return mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('CramAdapter', {
-        fetchSizeLimit: {
-            type: 'number',
-            defaultValue: 3000000,
+/**
+ * #config CramAdapter
+ * used to configure CRAM adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = (0, configuration_1.ConfigurationSchema)('CramAdapter', {
+    /**
+     * #slot fetchSizeLimit
+     */
+    fetchSizeLimit: {
+        type: 'number',
+        description: 'used to determine when to display a warning to the user that too much data will be fetched',
+        defaultValue: 3000000,
+    },
+    /**
+     * #slot cramLocation
+     */
+    cramLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.cram',
+            locationType: 'UriLocation',
         },
-        cramLocation: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.cram',
-                locationType: 'UriLocation',
-            },
+    },
+    /**
+     * #slot craiLocation
+     */
+    craiLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.cram.crai',
+            locationType: 'UriLocation',
         },
-        craiLocation: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.cram.crai',
-                locationType: 'UriLocation',
-            },
-        },
-        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
-    }, { explicitlyTyped: true }));
-};
+    },
+    /**
+     * #slot sequenceAdapter
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: 'frozen',
+        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
+        defaultValue: null,
+    },
+}, { explicitlyTyped: true });
+exports.default = configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/CramAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/CramAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,aAAa,EACb;IACE;;OAEG;IACH,cAAc,EAAE;QACd,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,4FAA4F;QAC9F,YAAY,EAAE,OAAS;KACxB;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,kBAAkB;YACvB,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;OAEG;IACH,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,uBAAuB;YAC5B,YAAY,EAAE,aAAa;SAC5B;KACF;IAED;;;;OAIG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,kBAAe,YAAY,CAAA"}

package/dist/CramAdapter/index.js

@@ -32,7 +32,7 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'CramAdapter',
-        configSchema: pluginManager.load(configSchema_1.default),
+        configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
     }));
 };

package/dist/CramAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/CramAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,SAAS;AACT,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -2,8 +2,11 @@ import { BamFile } from '@gmod/bam';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import BamAdapter from '../BamAdapter/BamAdapter';
 export default class HtsgetBamAdapter extends BamAdapter {
-    protected configure(): Promise<{
+    protected configurePre(): Promise<{
         bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+        sequenceAdapter: BaseFeatureDataAdapter;
+    } | {
+        bam: BamFile;
+        sequenceAdapter?: undefined;
     }>;
 }

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js

@@ -4,29 +4,24 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bam_1 = require("@gmod/bam");
-const configuration_1 = require("@jbrowse/core/configuration");
 const BamAdapter_1 = __importDefault(require("../BamAdapter/BamAdapter"));
 class HtsgetBamAdapter extends BamAdapter_1.default {
-    async configure() {
-        if (!this.configured) {
-            const htsgetBase = (0, configuration_1.readConfObject)(this.config, 'htsgetBase');
-            const htsgetTrackId = (0, configuration_1.readConfObject)(this.config, 'htsgetTrackId');
-            const bam = new bam_1.HtsgetFile({
-                baseUrl: htsgetBase,
-                trackId: htsgetTrackId,
-            });
-            const adapterConfig = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
-            if (adapterConfig && this.getSubAdapter) {
-                this.configured = this.getSubAdapter(adapterConfig).then(({ dataAdapter }) => {
-                    return {
-                        bam,
-                        sequenceAdapter: dataAdapter,
-                    };
-                });
-            }
-            this.configured = Promise.resolve({ bam });
+    async configurePre() {
+        const htsgetBase = this.getConf('htsgetBase');
+        const htsgetTrackId = this.getConf('htsgetTrackId');
+        const bam = new bam_1.HtsgetFile({
+            baseUrl: htsgetBase,
+            trackId: htsgetTrackId,
+        });
+        const adapterConfig = this.getConf('sequenceAdapter');
+        if (adapterConfig && this.getSubAdapter) {
+            const adapter = await this.getSubAdapter(adapterConfig);
+            return {
+                bam,
+                sequenceAdapter: adapter.dataAdapter,
+            };
         }
-        return this.configured;
+        return { bam };
     }
 }
 exports.default = HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAA+C;AAC/C,+DAA4D;AAE5D,0EAAiD;AAEjD,MAAqB,gBAAiB,SAAQ,oBAAU;IAC5C,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,MAAM,UAAU,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,YAAY,CAAC,CAAA;YAC5D,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;YAClE,MAAM,GAAG,GAAG,IAAI,gBAAU,CAAC;gBACzB,OAAO,EAAE,UAAU;gBACnB,OAAO,EAAE,aAAa;aACvB,CAAuB,CAAA;YAExB,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,iBAAiB,CAAC,CAAA;YACpE,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;gBACvC,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAC,IAAI,CACtD,CAAC,EAAE,WAAW,EAAE,EAAE,EAAE;oBAClB,OAAO;wBACL,GAAG;wBACH,eAAe,EAAE,WAAqC;qBACvD,CAAA;gBACH,CAAC,CACF,CAAA;aACF;YACD,IAAI,CAAC,UAAU,GAAG,OAAO,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;SAC3C;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;CACF;AAzBD,mCAyBC"}
+{"version":3,"file":"HtsgetBamAdapter.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/HtsgetBamAdapter.ts"],"names":[],"mappings":";;;;;AAAA,mCAA+C;AAE/C,0EAAiD;AAEjD,MAAqB,gBAAiB,SAAQ,oBAAU;IAC5C,KAAK,CAAC,YAAY;QAC1B,MAAM,UAAU,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,GAAG,GAAG,IAAI,gBAAU,CAAC;YACzB,OAAO,EAAE,UAAU;YACnB,OAAO,EAAE,aAAa;SACvB,CAAuB,CAAA;QAExB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QACrD,IAAI,aAAa,IAAI,IAAI,CAAC,aAAa,EAAE;YACvC,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,aAAa,CAAC,CAAA;YACvD,OAAO;gBACL,GAAG;gBACH,eAAe,EAAE,OAAO,CAAC,WAAqC;aAC/D,CAAA;SACF;QACD,OAAO,EAAE,GAAG,EAAE,CAAA;IAChB,CAAC;CACF;AAnBD,mCAmBC"}

package/dist/HtsgetBamAdapter/configSchema.d.ts

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

package/dist/HtsgetBamAdapter/configSchema.js

@@ -1,19 +1,36 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-exports.default = mobx_state_tree_1.types.late(() => (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
+/**
+ * #config HtsgetBamAdapter
+ * Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const HtsgetBamAdapter = (0, configuration_1.ConfigurationSchema)('HtsgetBamAdapter', {
+    /**
+     * #slot
+     */
     htsgetBase: {
         type: 'string',
+        description: 'the base URL to fetch from',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
     htsgetTrackId: {
         type: 'string',
+        description: 'the trackId, which is appended to the base URL',
         defaultValue: '',
     },
+    /**
+     * #slot
+     */
     sequenceAdapter: {
         type: 'frozen',
+        description: 'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
         defaultValue: null,
     },
-}, { explicitlyTyped: true }));
+}, { explicitlyTyped: true });
+exports.default = HtsgetBamAdapter;
 //# sourceMappingURL=configSchema.js.map

package/dist/HtsgetBamAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,qDAAuC;AAEvC,kBAAe,uBAAK,CAAC,IAAI,CAAC,GAAG,EAAE,CAC7B,IAAA,mCAAmB,EACjB,kBAAkB,EAClB;IACE,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CACF,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HtsgetBamAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,gBAAgB,GAAG,IAAA,mCAAmB,EAC1C,kBAAkB,EAClB;IACE;;OAEG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,4BAA4B;QACzC,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,gDAAgD;QAC7D,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,8EAA8E;QAChF,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,gBAAgB,CAAA"}

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

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

package/dist/LinearAlignmentsDisplay/models/configSchema.js

@@ -2,13 +2,30 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const configModelFactory = (pluginManager) => {
-    const PileupDisplayConfigSchema = pluginManager.getDisplayType('LinearPileupDisplay').configSchema;
-    const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType('LinearSNPCoverageDisplay').configSchema;
+/**
+ * #config LinearAlignmentsDisplay
+ * 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) => {
     return (0, configuration_1.ConfigurationSchema)('LinearAlignmentsDisplay', {
-        pileupDisplay: PileupDisplayConfigSchema,
-        snpCoverageDisplay: SNPCoverageDisplayConfigSchema,
-    }, { baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema, explicitlyTyped: true });
+        /**
+         * #slot
+         */
+        pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
+        /**
+         * #slot
+         */
+        snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
+            .configSchema,
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
+        explicitlyTyped: true,
+    });
 };
 exports.default = configModelFactory;
 //# sourceMappingURL=configSchema.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAAkF;AAGlF,MAAM,kBAAkB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC1D,MAAM,yBAAyB,GAAG,aAAa,CAAC,cAAc,CAC5D,qBAAqB,CACtB,CAAC,YAAY,CAAA;IACd,MAAM,8BAA8B,GAAG,aAAa,CAAC,cAAc,CACjE,0BAA0B,CAC3B,CAAC,YAAY,CAAA;IAEd,OAAO,IAAA,mCAAmB,EACxB,yBAAyB,EACzB;QACE,aAAa,EAAE,yBAAyB;QACxC,kBAAkB,EAAE,8BAA8B;KACnD,EACD,EAAE,iBAAiB,EAAE,yDAA6B,EAAE,eAAe,EAAE,IAAI,EAAE,CAC5E,CAAA;AACH,CAAC,CAAA;AAGD,kBAAe,kBAAkB,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAAkF;AAGlF;;;;GAIG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,kBAAkB,GAAG,CAAC,EAAiB,EAAE,EAAE;IAC/C,OAAO,IAAA,mCAAmB,EACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QACpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;KAChB,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,yDAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC,CAAA;AAGD,kBAAe,kBAAkB,CAAA"}

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

@@ -1,10 +1,13 @@
 import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+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';
-import { AlignmentsConfigModel } from './configSchema';
-declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AlignmentsConfigModel) => import("mobx-state-tree").IModelType<{
+/**
+ * #stateModel LinearAlignmentsDisplay
+ * extends `BaseDisplay`
+ */
+declare function stateModelFactory(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>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -32,7 +35,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             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]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
+            type: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             */
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
@@ -50,7 +55,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
             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]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
+             * #action
+             */
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
@@ -73,29 +80,89 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
 } & {
     scrollTop: number;
 } & {
+    /**
+     * #action
+     */
     toggleCoverage(): void;
+    /**
+     * #action
+     */
     togglePileup(): void;
+    /**
+     * #action
+     */
     setScrollTop(scrollTop: number): void;
+    /**
+     * #action
+     */
     setSNPCoverageHeight(n: number): void;
 } & {
+    /**
+     * #getter
+     */
     readonly pileupDisplayConfig: any;
+    /**
+     * #method
+     */
     getFeatureByID(blockKey: string, id: string): any;
+    /**
+     * #method
+     */
     searchFeatureByID(id: string): any;
+    /**
+     * #getter
+     */
     readonly features: any;
+    /**
+     * #getter
+     */
     readonly DisplayBlurb: any;
+    /**
+     * #getter
+     */
     readonly sortedBy: any;
+    /**
+     * #getter
+     */
     readonly sortedByPosition: any;
+    /**
+     * #getter
+     */
     readonly sortedByRefName: any;
+    /**
+     * #getter
+     */
     readonly snpCoverageDisplayConfig: any;
+    /**
+     * #method
+     */
     trackMenuItems(): MenuItem[];
 } & {
+    /**
+     * #action
+     */
     setSNPCoverageDisplay(displayConfig: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
     setUserFeatureScreenDensity(limit: number): void;
+    /**
+     * #action
+     */
     setPileupDisplay(displayConfig: AnyConfigurationModel): void;
+    /**
+     * #action
+     */
     setHeight(displayHeight: number): number;
+    /**
+     * #action
+     */
     resizeHeight(distance: number): number;
 } & {
     afterAttach(): void;
+    /**
+     * #action
+     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<JSX.Element>;