jbrowse-plugin-mafviewer 1.0.8 → 1.1.1

package/dist/MafTabixAdapter/MafTabixAdapter.js

@@ -1,8 +1,11 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { getSnapshot } from 'mobx-state-tree';
 import { SimpleFeature } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { getSnapshot } from 'mobx-state-tree';
 import { firstValueFrom, toArray } from 'rxjs';
+import parseNewick from '../parseNewick';
+import { normalize } from '../util';
 export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     setupP;
     async setup() {
@@ -39,12 +42,6 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const { adapter } = await this.setup();
             const features = await firstValueFrom(adapter.getFeatures(query).pipe(toArray()));
-            const samples = this.getConf('samples');
-            const sampleStrings = typeof samples[0] === 'string'
-                ? samples
-                : samples.map(s => s.id);
-            const sampleSet = new Set(sampleStrings);
-            let i = 0;
             for (const feature of features) {
                 const data = feature.get('field5').split(',');
                 const alignments = {};
@@ -54,11 +51,8 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                     const idx = ad[0].lastIndexOf('.');
                     const org = ad[0].slice(0, idx);
                     const last = ad[0].slice(idx + 1);
-                    const s = sampleSet.has(org)
-                        ? org
-                        : sampleStrings.find(f => ad[0].startsWith(f));
-                    if (s) {
-                        alignments[s] = {
+                    if (org) {
+                        alignments[org] = {
                             chr: last,
                             start: +ad[1],
                             srcSize: +ad[2],
@@ -67,13 +61,6 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                             data: alns[j],
                         };
                     }
-                    else if (i < 100) {
-                        console.error(`line not processed ${ad[0]}`);
-                        i++;
-                    }
-                    else if (i > 100) {
-                        console.error('too many errors, not printing any more');
-                    }
                 }
                 observer.next(new SimpleFeature({
                     id: feature.id(),
@@ -91,6 +78,18 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
+    async getSamples(_query) {
+        const nhLoc = this.getConf('nhLocation');
+        const nh = nhLoc.uri === '/path/to/my.nh'
+            ? undefined
+            : await openLocation(nhLoc).readFile('utf8');
+        // TODO: we may need to resolve the exact set of rows in the visible region
+        // here
+        return {
+            samples: normalize(this.getConf('samples')),
+            tree: nh ? parseNewick(nh) : undefined,
+        };
+    }
     freeResources() { }
 }
 //# sourceMappingURL=MafTabixAdapter.js.map

package/dist/MafTabixAdapter/MafTabixAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MafTabixAdapter.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/MafTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAmB,aAAa,EAAE,MAAM,oBAAoB,CAAA;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAWnC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,sBAAsB;IAC1D,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QAC1B,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC;YACvC,GAAG,WAAW,CAAC,MAAM,CAAC;YACtB,IAAI,EAAE,iBAAiB;SACxB,CAAC,CAAA;QACF,OAAO;YACL,OAAO,EAAE,OAAO,CAAC,WAAqC;SACvD,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa;QACvB,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACtC,MAAM,QAAQ,GAAG,MAAM,cAAc,CACnC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAC3C,CAAA;YAED,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;gBAC/B,MAAM,IAAI,GAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBACzD,MAAM,UAAU,GAAG,EAAoC,CAAA;gBACvD,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBAE/C,KAAK,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,OAAO,EAAE,EAAE,CAAC;oBACtC,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACzB,MAAM,GAAG,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;oBACnC,MAAM,GAAG,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;oBAChC,MAAM,IAAI,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,CAAC,CAAA;oBAClC,IAAI,GAAG,EAAE,CAAC;wBACR,UAAU,CAAC,GAAG,CAAC,GAAG;4BAChB,GAAG,EAAE,IAAI;4BACT,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;4BACd,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;4BAChB,MAAM,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;4BAC9B,OAAO,EAAE,CAAC,EAAE,CAAC,CAAC,CAAE;4BAChB,IAAI,EAAE,IAAI,CAAC,CAAC,CAAE;yBACf,CAAA;oBACH,CAAC;gBACH,CAAC;gBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;oBAChB,IAAI,EAAE;wBACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;wBAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;wBACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;wBAC/B,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC;wBACzB,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;wBAC3B,UAAU;wBACV,GAAG,EAAE,IAAI,CAAC,CAAC,CAAC;qBACb;iBACF,CAAC,CACH,CAAA;YACH,CAAC;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACxC,MAAM,EAAE,GACN,KAAK,CAAC,GAAG,KAAK,gBAAgB;YAC5B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,MAAM,YAAY,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAEhD,2EAA2E;QAC3E,OAAO;QACP,OAAO;YACL,OAAO,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACvC,CAAA;IACH,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}

package/dist/MafTabixAdapter/configSchema.d.ts

@@ -18,16 +18,33 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.location
+         */
         location: {
             type: string;
             defaultValue: {
                 uri: string;
             };
         };
+        /**
+         * #slot index.indexType
+         */
         indexType: {
             type: string;
             defaultValue: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    nhLocation: {
+        type: string;
+        description: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/MafTabixAdapter/configSchema.js

@@ -1,7 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 /**
  * #config MafTabixAdapter
- * used to configure MafTabix adapter
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const configSchema = ConfigurationSchema('MafTabixAdapter', {
@@ -24,17 +23,34 @@ const configSchema = ConfigurationSchema('MafTabixAdapter', {
         },
     },
     index: ConfigurationSchema('Index', {
+        /**
+         * #slot index.location
+         */
         location: {
             type: 'fileLocation',
             defaultValue: {
                 uri: '/path/to/my.bed.gz.tbi',
             },
         },
+        /**
+         * #slot index.indexType
+         */
         indexType: {
             type: 'string',
             defaultValue: 'TBI',
         },
     }),
+    /**
+     * #slot
+     */
+    nhLocation: {
+        type: 'fileLocation',
+        description: 'newick tree',
+        defaultValue: {
+            uri: '/path/to/my.nh',
+            locationType: 'UriLocation',
+        },
+    },
 }, { explicitlyTyped: true });
 export default configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/MafTabixAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,iBAAiB,EACjB;IACE;;OAEG;IACH,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,sDAAsD;QACnE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,KAAK,EAAE,mBAAmB,CAAC,OAAO,EAAE;QAClC;;WAEG;QACH,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;aAC9B;SACF;QACD;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,KAAK;SACpB;KACF,CAAC;IACF;;OAEG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,cAAc;QACpB,WAAW,EAAE,aAAa;QAC1B,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/MafTabixAdapter/index.js

@@ -1,6 +1,6 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
 import MafTabixAdapter from './MafTabixAdapter';
+import configSchema from './configSchema';
 export default function MafTabixAdapterF(pluginManager) {
     return pluginManager.addAdapterType(() => new AdapterType({
         name: 'MafTabixAdapter',

package/dist/MafTabixAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,aAA4B;IACnE,OAAO,aAAa,CAAC,cAAc,CACjC,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,iBAAiB;QACvB,YAAY,EAAE,eAAe;QAC7B,YAAY;KACb,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/MafTrack/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,EACL,SAAS,EACT,oBAAoB,GACrB,MAAM,qCAAqC,CAAA;AAC5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,aAA4B;IAC5D,OAAO,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QACrC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,UAAU;YAChB,YAAY;YACZ,WAAW,EAAE,WAAW;YACxB,UAAU,EAAE,oBAAoB,CAAC,aAAa,EAAE,UAAU,EAAE,YAAY,CAAC;SAC1E,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,EACL,SAAS,EACT,oBAAoB,GACrB,MAAM,qCAAqC,CAAA;AAE5C,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,MAAM,CAAC,OAAO,UAAU,SAAS,CAAC,aAA4B;IAC5D,OAAO,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QACrC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,UAAU;YAChB,YAAY;YACZ,WAAW,EAAE,WAAW;YACxB,UAAU,EAAE,oBAAoB,CAAC,aAAa,EAAE,UAAU,EAAE,YAAY,CAAC;SAC1E,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/index.js

@@ -1,12 +1,13 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { version } from '../package.json';
+import BgzipTaffyAdapterF from './BgzipTaffyAdapter';
 import BigMafAdapterF from './BigMafAdapter';
-import MafTrackF from './MafTrack';
 import LinearMafDisplayF from './LinearMafDisplay';
 import LinearMafRendererF from './LinearMafRenderer';
-import MafTabixAdapterF from './MafTabixAdapter';
-import TaffyAdapterF from './TaffyAdapter';
 import MafAddTrackWorkflowF from './MafAddTrackWorkflow';
+import MafRPCF from './MafRPC';
+import MafTabixAdapterF from './MafTabixAdapter';
+import MafTrackF from './MafTrack';
 export default class MafViewerPlugin extends Plugin {
     name = 'MafViewerPlugin';
     version = version;
@@ -16,8 +17,9 @@ export default class MafViewerPlugin extends Plugin {
         LinearMafDisplayF(pluginManager);
         LinearMafRendererF(pluginManager);
         MafTabixAdapterF(pluginManager);
-        TaffyAdapterF(pluginManager);
+        BgzipTaffyAdapterF(pluginManager);
         MafAddTrackWorkflowF(pluginManager);
+        MafRPCF(pluginManager);
     }
     configure(_pluginManager) { }
 }

package/dist/index.js.map

@@ -1 +1 @@
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