jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/dist/MafTabixAdapter/MafTabixAdapter.js

@@ -2,10 +2,11 @@ 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';
+import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { firstValueFrom, toArray } from 'rxjs';
 import parseNewick from '../parseNewick';
 import { normalize } from '../util';
+import { parseAssemblyAndChr, selectReferenceSequence, } from '../util/parseAssemblyName';
 export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     setupP;
     async setupPre() {
@@ -62,38 +63,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                         if (!assemblyAndChr || !seq) {
                             continue;
                         }
-                        // Optimized assembly name parsing with simplified logic
-                        let assemblyName;
-                        let chr;
-                        const firstDotIndex = assemblyAndChr.indexOf('.');
-                        if (firstDotIndex === -1) {
-                            // No dot found, entire string is assembly name
-                            assemblyName = assemblyAndChr;
-                            chr = '';
-                        }
-                        else {
-                            const secondDotIndex = assemblyAndChr.indexOf('.', firstDotIndex + 1);
-                            if (secondDotIndex === -1) {
-                                // Only one dot: assembly.chr
-                                assemblyName = assemblyAndChr.slice(0, Math.max(0, firstDotIndex));
-                                chr = assemblyAndChr.slice(Math.max(0, firstDotIndex + 1));
-                            }
-                            else {
-                                // Multiple dots: check if second part is numeric (version number)
-                                const secondPart = assemblyAndChr.slice(firstDotIndex + 1, secondDotIndex);
-                                const isNumeric = secondPart.length > 0 && !Number.isNaN(+secondPart);
-                                if (isNumeric) {
-                                    // assembly.version.chr format
-                                    assemblyName = assemblyAndChr.slice(0, Math.max(0, secondDotIndex));
-                                    chr = assemblyAndChr.slice(Math.max(0, secondDotIndex + 1));
-                                }
-                                else {
-                                    // assembly.chr.more format
-                                    assemblyName = assemblyAndChr.slice(0, Math.max(0, firstDotIndex));
-                                    chr = assemblyAndChr.slice(Math.max(0, firstDotIndex + 1));
-                                }
-                            }
-                        }
+                        const { assemblyName, chr } = parseAssemblyAndChr(assemblyAndChr);
                         if (assemblyName) {
                             // Set first assembly name found (only once)
                             if (!firstAssemblyNameFound) {
@@ -119,8 +89,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
                             name: feature.get('name'),
                             score: feature.get('score'),
                             alignments,
-                            seq: alignments[refAssemblyName || query.assemblyName]?.seq ||
-                                alignments[firstAssemblyNameFound]?.seq,
+                            seq: selectReferenceSequence(alignments, refAssemblyName, query.assemblyName, firstAssemblyNameFound),
                         },
                     }));
                 }

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,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AACtD,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EACL,mBAAmB,EACnB,uBAAuB,GACxB,MAAM,2BAA2B,CAAA;AAWlC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,sBAAsB;IAC1D,MAAM,CAA+C;IAE5D,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,iBAAiB;aACxB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,SAAS;QACb,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACjD,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,KAAK,CAAC,IAAkB;QAC5B,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,YAAY,CAAC,mBAAmB,EAAE,cAAc,EAAE,GAAG,EAAE,CAC5D,IAAI,CAAC,SAAS,EAAE,CACjB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAkB;QAC3C,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,QAAQ,GAAG,MAAM,YAAY,CACjC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CACjE,CAAA;YAED,MAAM,YAAY,CAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC/D,IAAI,sBAAsB,GAAG,EAAE,CAAA;gBAC/B,MAAM,eAAe,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;gBAEvD,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;oBAC/B,MAAM,IAAI,GAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBACzD,MAAM,UAAU,GAAG,EAAoC,CAAA;oBACvD,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAA;oBAE9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAE,CAAA;wBACpB,mDAAmD;wBACnD,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;wBAE5B,sEAAsE;wBACtE,MAAM,CACJ,cAAc,EACd,QAAQ,EACR,UAAU,EACV,SAAS,EACT,UAAU,EACV,GAAG,EACJ,GAAG,KAAK,CAAA;wBAET,2CAA2C;wBAC3C,IAAI,CAAC,cAAc,IAAI,CAAC,GAAG,EAAE,CAAC;4BAC5B,SAAQ;wBACV,CAAC;wBAED,MAAM,EAAE,YAAY,EAAE,GAAG,EAAE,GAAG,mBAAmB,CAAC,cAAc,CAAC,CAAA;wBAEjE,IAAI,YAAY,EAAE,CAAC;4BACjB,4CAA4C;4BAC5C,IAAI,CAAC,sBAAsB,EAAE,CAAC;gCAC5B,sBAAsB,GAAG,YAAY,CAAA;4BACvC,CAAC;4BAED,2DAA2D;4BAC3D,UAAU,CAAC,YAAY,CAAC,GAAG;gCACzB,GAAG;gCACH,KAAK,EAAE,CAAC,QAAS;gCACjB,OAAO,EAAE,CAAC,UAAW;gCACrB,MAAM,EAAE,SAAS,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gCAClC,OAAO,EAAE,CAAC,UAAW;gCACrB,GAAG;6BACJ,CAAA;wBACH,CAAC;oBACH,CAAC;oBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;wBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;wBAChB,IAAI,EAAE;4BACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;4BACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;4BAC/B,IAAI,EAAE,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC;4BACzB,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,UAAU;4BACV,GAAG,EAAE,uBAAuB,CAC1B,UAAU,EACV,eAAe,EACf,KAAK,CAAC,YAAY,EAClB,sBAAsB,CACvB;yBACF;qBACF,CAAC,CACH,CAAA;gBACH,CAAC;YACH,CAAC,CAAC,CAAA;YACF,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

@@ -1,4 +1,4 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
@@ -24,7 +24,7 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
         type: string;
         defaultValue: string;
     };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         /**
          * #slot index.location
          */
@@ -41,7 +41,7 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             type: string;
             defaultValue: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     /**
      * #slot
      */
@@ -53,5 +53,5 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/MafTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -25,8 +25,13 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
         description: string;
         defaultValue: {};
     };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -37,10 +42,10 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
             description: string;
             defaultValue: string[];
         };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -63,8 +68,8 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
             defaultValue: number;
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -75,5 +80,5 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;
+    }, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;

package/dist/index.js

@@ -6,6 +6,7 @@ import LinearMafRendererF from './LinearMafRenderer';
 import MafAddTrackWorkflowF from './MafAddTrackWorkflow';
 import MafGetSamplesF from './MafGetSamples';
 import MafGetSequencesF from './MafGetSequences';
+import MafSequenceWidgetF from './MafSequenceWidget';
 import MafTabixAdapterF from './MafTabixAdapter';
 import MafTrackF from './MafTrack';
 export default class MafViewerPlugin extends Plugin {
@@ -20,6 +21,7 @@ export default class MafViewerPlugin extends Plugin {
         MafAddTrackWorkflowF(pluginManager);
         MafGetSequencesF(pluginManager);
         MafGetSamplesF(pluginManager);
+        MafSequenceWidgetF(pluginManager);
     }
     configure(_pluginManager) { }
 }

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAGzC,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,oBAAoB,MAAM,uBAAuB,CAAA;AACxD,OAAO,cAAc,MAAM,iBAAiB,CAAA;AAC5C,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,kBAAkB,MAAM,qBAAqB,CAAA;AACpD,OAAO,gBAAgB,MAAM,mBAAmB,CAAA;AAChD,OAAO,SAAS,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,MAAM;IACjD,IAAI,GAAG,iBAAiB,CAAA;IACxB,OAAO,GAAG,OAAO,CAAA;IAEjB,OAAO,CAAC,aAA4B;QAClC,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,SAAS,CAAC,aAAa,CAAC,CAAA;QACxB,iBAAiB,CAAC,aAAa,CAAC,CAAA;QAChC,kBAAkB,CAAC,aAAa,CAAC,CAAA;QACjC,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,oBAAoB,CAAC,aAAa,CAAC,CAAA;QACnC,gBAAgB,CAAC,aAAa,CAAC,CAAA;QAC/B,cAAc,CAAC,aAAa,CAAC,CAAA;QAC7B,kBAAkB,CAAC,aAAa,CAAC,CAAA;IACnC,CAAC;IAED,SAAS,CAAC,cAA6B,IAAG,CAAC;CAC5C"}