npm - jbrowse-plugin-mafviewer - Versions diffs - 1.1.3 → 1.2.0 - Mend

jbrowse-plugin-mafviewer 1.1.3 → 1.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (62) hide show

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/MafTabixAdapter/MafTabixAdapter.d.ts CHANGED Viewed

@@ -1,18 +1,21 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Feature, Region } from '@jbrowse/core/util';
 export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     setupP?: Promise<{
         adapter: BaseFeatureDataAdapter;
     }>;
-    setup(): Promise<{
+    setupPre(): Promise<{
         adapter: BaseFeatureDataAdapter;
     }>;
-    setupPre(): Promise<{
+    setupPre2(): Promise<{
+        adapter: BaseFeatureDataAdapter;
+    }>;
+    setup(opts?: BaseOptions): Promise<{
         adapter: BaseFeatureDataAdapter;
     }>;
-    getRefNames(): Promise<string[]>;
-    getHeader(): Promise<unknown>;
-    getFeatures(query: Region): import("rxjs").Observable<Feature>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<unknown>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;

package/dist/MafTabixAdapter/MafTabixAdapter.js CHANGED Viewed

@@ -1,5 +1,5 @@
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, updateStatus, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { getSnapshot } from 'mobx-state-tree';
@@ -8,7 +8,7 @@ import parseNewick from '../parseNewick';
 import { normalize } from '../util';
 export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     setupP;
-    async setup() {
+    async setupPre() {
         const config = this.config;
         if (!this.getSubAdapter) {
             throw new Error('no getSubAdapter available');
@@ -21,60 +21,91 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
             adapter: adapter.dataAdapter,
         };
     }
-    async setupPre() {
+    async setupPre2() {
         if (!this.setupP) {
-            this.setupP = this.setup().catch((e) => {
+            this.setupP = this.setupPre().catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });
         }
         return this.setupP;
     }
-    async getRefNames() {
-        const { adapter } = await this.setup();
+    async setup(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.setupPre2());
+    }
+    async getRefNames(opts) {
+        const { adapter } = await this.setup(opts);
         return adapter.getRefNames();
     }
-    async getHeader() {
-        const { adapter } = await this.setup();
+    async getHeader(opts) {
+        const { adapter } = await this.setup(opts);
         return adapter.getHeader();
     }
-    getFeatures(query) {
+    getFeatures(query, opts) {
+        const { statusCallback = () => { } } = opts || {};
         return ObservableCreate(async (observer) => {
-            const { adapter } = await this.setup();
-            const features = await firstValueFrom(adapter.getFeatures(query).pipe(toArray()));
-            for (const feature of features) {
-                const data = feature.get('field5').split(',');
-                const alignments = {};
-                const alns = data.map(elt => elt.split(':')[5]);
-                for (const [j, elt] of data.entries()) {
-                    const ad = elt.split(':');
-                    const idx = ad[0].lastIndexOf('.');
-                    const org = ad[0].slice(0, idx);
-                    const last = ad[0].slice(idx + 1);
-                    if (org) {
-                        alignments[org] = {
-                            chr: last,
-                            start: +ad[1],
-                            srcSize: +ad[2],
-                            strand: ad[3] === '-' ? -1 : 1,
-                            unknown: +ad[4],
-                            data: alns[j],
-                        };
+            const { adapter } = await this.setup(opts);
+            const features = await updateStatus('Downloading alignments', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
+            await updateStatus('Processing alignments', statusCallback, () => {
+                let firstAssemblyNameFound = '';
+                const refAssemblyName = this.getConf('refAssemblyName');
+                for (const feature of features) {
+                    const data = feature.get('field5').split(',');
+                    const alignments = {};
+                    for (let j = 0; j < data.length; j++) {
+                        const elt = data[j];
+                        const seq = elt.split(':')[5];
+                        const ad = elt.split(':');
+                        const ag = ad[0].split('.');
+                        const [n1, n2 = '', ...rest] = ag;
+                        let assemblyName;
+                        let last = '';
+                        if (ag.length === 2) {
+                            assemblyName = n1;
+                            last = n2;
+                        }
+                        else if (!Number.isNaN(+n2)) {
+                            assemblyName = `${n1}.${n2}`;
+                            last = rest.join('.');
+                        }
+                        else {
+                            assemblyName = n1;
+                            last = [n2, ...rest].join('.');
+                        }
+                        if (assemblyName) {
+                            firstAssemblyNameFound = firstAssemblyNameFound || assemblyName;
+                            alignments[assemblyName] = {
+                                chr: last,
+                                start: +ad[1],
+                                srcSize: +ad[2],
+                                strand: ad[3] === '-' ? -1 : 1,
+                                unknown: +ad[4],
+                                data: seq,
+                            };
+                        }
                     }
-                }
-                observer.next(new SimpleFeature({
-                    id: feature.id(),
-                    data: {
-                        start: feature.get('start'),
-                        end: feature.get('end'),
-                        refName: feature.get('refName'),
-                        name: feature.get('name'),
-                        score: feature.get('score'),
+                    console.log({
                         alignments,
-                        seq: alns[0],
-                    },
-                }));
-            }
+                        firstAssemblyNameFound,
+                        refAssemblyName,
+                        q: query.assemblyName,
+                    }, alignments[refAssemblyName], alignments[query.assemblyName], alignments[firstAssemblyNameFound]);
+                    observer.next(new SimpleFeature({
+                        id: feature.id(),
+                        data: {
+                            start: feature.get('start'),
+                            end: feature.get('end'),
+                            refName: feature.get('refName'),
+                            name: feature.get('name'),
+                            score: feature.get('score'),
+                            alignments,
+                            seq: alignments[refAssemblyName || query.assemblyName]?.data ||
+                                alignments[firstAssemblyNameFound]?.data,
+                        },
+                    }));
+                }
+            });
             observer.complete();
         });
     }

package/dist/MafTabixAdapter/MafTabixAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/MafTabixAdapter/configSchema.d.ts CHANGED Viewed

@@ -17,6 +17,13 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
+    /**
+     * #slot
+     */
+    refAssemblyName: {
+        type: string;
+        defaultValue: string;
+    };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         /**
          * #slot index.location

package/dist/MafTabixAdapter/configSchema.js CHANGED Viewed

@@ -22,6 +22,13 @@ const configSchema = ConfigurationSchema('MafTabixAdapter', {
             locationType: 'UriLocation',
         },
     },
+    /**
+     * #slot
+     */
+    refAssemblyName: {
+        type: 'string',
+        defaultValue: '',
+    },
     index: ConfigurationSchema('Index', {
         /**
          * #slot index.location

package/dist/MafTabixAdapter/configSchema.js.map CHANGED Viewed

	@@ -1 +1 @@
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