jbrowse-plugin-mafviewer 1.0.6 → 1.0.8

package/dist/MafTabixAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;GAGG;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,QAAQ,EAAE;YACR,IAAI,EAAE,cAAc;YACpB,YAAY,EAAE;gBACZ,GAAG,EAAE,wBAAwB;aAC9B;SACF;QACD,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,KAAK;SACpB;KACF,CAAC;CACH,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/MafTabixAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function MafTabixAdapterF(pluginManager: PluginManager): PluginManager;

package/dist/MafTabixAdapter/index.js

@@ -0,0 +1,11 @@
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
+import configSchema from './configSchema';
+import MafTabixAdapter from './MafTabixAdapter';
+export default function MafTabixAdapterF(pluginManager) {
+    return pluginManager.addAdapterType(() => new AdapterType({
+        name: 'MafTabixAdapter',
+        AdapterClass: MafTabixAdapter,
+        configSchema,
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/MafTabixAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafTabixAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AACjE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,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/configSchema.d.ts

@@ -0,0 +1,79 @@
+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<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            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<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        maxDepth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;

package/dist/MafTrack/configSchema.js

@@ -0,0 +1,15 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+export default function configSchemaF(pluginManager) {
+    return ConfigurationSchema('MafTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+        /**
+         * #identifier
+         */
+        explicitIdentifier: 'trackId',
+    });
+}
+//# sourceMappingURL=configSchema.js.map

package/dist/MafTrack/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/MafTrack/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAE3E,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,OAAO,mBAAmB,CACxB,UAAU,EACV,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;QACvD;;WAEG;QACH,kBAAkB,EAAE,SAAS;KAC9B,CACF,CAAA;AACH,CAAC"}

package/dist/MafTrack/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function MafTrackF(pluginManager: PluginManager): PluginManager;

package/dist/MafTrack/index.js

@@ -0,0 +1,14 @@
+import { TrackType, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes';
+import configSchemaF from './configSchema';
+export default function MafTrackF(pluginManager) {
+    return pluginManager.addTrackType(() => {
+        const configSchema = configSchemaF(pluginManager);
+        return new TrackType({
+            name: 'MafTrack',
+            configSchema,
+            displayName: 'MAF track',
+            stateModel: createBaseTrackModel(pluginManager, 'MafTrack', configSchema),
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/MafTrack/index.js.map

@@ -0,0 +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"}

package/dist/TaffyAdapter/TaffyAdapter.d.ts

@@ -0,0 +1,16 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature, Region } from '@jbrowse/core/util';
+interface ByteRange {
+    chrStart: number;
+    fileOffst: number;
+}
+type IndexData = Record<string, ByteRange[]>;
+export default class TaffyAdapter extends BaseFeatureDataAdapter {
+    setupP?: Promise<IndexData>;
+    getRefNames(): Promise<string[]>;
+    setup(): Promise<IndexData>;
+    readTaiFile(): Promise<IndexData>;
+    getFeatures(query: Region): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/dist/TaffyAdapter/TaffyAdapter.js

@@ -0,0 +1,89 @@
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import { openLocation } from '@jbrowse/core/util/io';
+export default class TaffyAdapter extends BaseFeatureDataAdapter {
+    setupP;
+    async getRefNames() {
+        const data = await this.setup();
+        return Object.keys(data);
+    }
+    setup() {
+        if (!this.setupP) {
+            this.setupP = this.readTaiFile().catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async readTaiFile() {
+        const text = await openLocation(this.getConf('taiLocation')).readFile('utf8');
+        const entries = {};
+        let lastChr = '';
+        for (const line of text.split('\n').filter(line => line.trim())) {
+            const [chr, chrStart, fileOffset] = line.split('\t');
+            const ref = chr === '*' ? lastChr : chr;
+            const r2 = ref.split('.').at(-1);
+            if (!entries[r2]) {
+                entries[r2] = [];
+            }
+            entries[r2].push({
+                chrStart: +chrStart,
+                fileOffst: +fileOffset,
+            });
+            lastChr = ref;
+        }
+        return entries;
+    }
+    getFeatures(query) {
+        return ObservableCreate(async (observer) => {
+            try {
+                // const { tafLocation } = getSnapshot(this.config)
+                // const byteRanges = await this.setup()
+                //
+                // for (const range of byteRanges[query.refName] || []) {
+                //   const response = await fetch(tafLocation, {
+                //     headers: {
+                //       Range: `bytes=${range.start}-${range.start + range.length - 1}`,
+                //     },
+                //   })
+                //
+                //   const text = await response.text()
+                //   const lines = text.split('\n').filter(line => line.trim())
+                //
+                //   for (const line of lines) {
+                //     const [chr, start, srcSize, strand, unknown, data] =
+                //       line.split('\t')
+                //
+                //     // Only emit features that overlap with query region
+                //     const featureStart = parseInt(start, 10)
+                //     const featureEnd = featureStart + parseInt(srcSize, 10)
+                //
+                //     if (
+                //       chr === query.refName &&
+                //       featureEnd >= query.start &&
+                //       featureStart <= query.end
+                //     ) {
+                //       observer.next(
+                //         new SimpleFeature({
+                //           uniqueId: `${chr}-${start}-${data}`,
+                //           refName: chr,
+                //           start: featureStart,
+                //           end: featureEnd,
+                //           strand: parseInt(strand, 10),
+                //           data: data,
+                //         }),
+                //       )
+                //     }
+                //   }
+                // }
+                observer.complete();
+            }
+            catch (e) {
+                observer.error(e);
+            }
+        });
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=TaffyAdapter.js.map

package/dist/TaffyAdapter/TaffyAdapter.js.map

@@ -0,0 +1 @@
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package/dist/TaffyAdapter/configSchema.d.ts

@@ -0,0 +1,31 @@
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    samples: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+    /**
+     * #slot
+     */
+    tafLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot
+     */
+    taiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default configSchema;

package/dist/TaffyAdapter/configSchema.js

@@ -0,0 +1,38 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+/**
+ * #config TaffyAdapter
+ * used to configure Taffy adapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const configSchema = ConfigurationSchema('TaffyAdapter', {
+    /**
+     * #slot
+     */
+    samples: {
+        type: 'frozen',
+        description: 'string[] or {id:string,label:string,color?:string}[]',
+        defaultValue: [],
+    },
+    /**
+     * #slot
+     */
+    tafLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.taf',
+            locationType: 'UriLocation',
+        },
+    },
+    /**
+     * #slot
+     */
+    taiLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.taf.tai',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/TaffyAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TaffyAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,mBAAmB,CACtC,cAAc,EACd;IACE;;OAEG;IACH,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,sDAAsD;QACnE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,iBAAiB;YACtB,YAAY,EAAE,aAAa;SAC5B;KACF;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,qBAAqB;YAC1B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,eAAe,YAAY,CAAA"}

package/dist/TaffyAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function TaffyAdapterF(pluginManager: PluginManager): PluginManager;

package/dist/TaffyAdapter/index.js

@@ -0,0 +1,11 @@
+import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
+import configSchema from './configSchema';
+import TaffyAdapter from './TaffyAdapter';
+export default function TaffyAdapterF(pluginManager) {
+    return pluginManager.addAdapterType(() => new AdapterType({
+        name: 'TaffyAdapter',
+        AdapterClass: TaffyAdapter,
+        configSchema,
+    }));
+}
+//# sourceMappingURL=index.js.map

package/dist/TaffyAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TaffyAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AACjE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,aAA4B;IAChE,OAAO,aAAa,CAAC,cAAc,CACjC,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,YAAY;QAC1B,YAAY;KACb,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/index.d.ts

@@ -0,0 +1,8 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class MafViewerPlugin extends Plugin {
+    name: string;
+    version: any;
+    install(pluginManager: PluginManager): void;
+    configure(_pluginManager: PluginManager): void;
+}

package/dist/index.js

@@ -0,0 +1,24 @@
+import Plugin from '@jbrowse/core/Plugin';
+import { version } from '../package.json';
+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';
+export default class MafViewerPlugin extends Plugin {
+    name = 'MafViewerPlugin';
+    version = version;
+    install(pluginManager) {
+        BigMafAdapterF(pluginManager);
+        MafTrackF(pluginManager);
+        LinearMafDisplayF(pluginManager);
+        LinearMafRendererF(pluginManager);
+        MafTabixAdapterF(pluginManager);
+        TaffyAdapterF(pluginManager);
+        MafAddTrackWorkflowF(pluginManager);
+    }
+    configure(_pluginManager) { }
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/jbrowse-plugin-mafviewer.umd.production.min.js

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o.rendererType.configSchema.create({...s,type:"LinearMafRenderer"},(0,Pe.getEnv)(o))}})).views(o=>{let{trackMenuItems:i,renderProps:s}=o;return{renderProps(){let{showAllLetters:f,rendererConfig:p,samples:u,rowHeight:h,rowProportion:x,mismatchRendering:l}=o;return{...s(),config:p,samples:u,rowHeight:h,rowProportion:x,showAllLetters:f,mismatchRendering:l}},trackMenuItems(){return[...i(),{label:"Set row height",onClick:()=>{(0,Pe.getSession)(o).queueDialog(f=>[Gr,{model:o,handleClose:f}])}},{label:"Show all letters",type:"checkbox",checked:o.showAllLetters,onClick:()=>{o.setShowAllLetters(!o.showAllLetters)}},{label:"Draw mismatches as single color",type:"checkbox",checked:!o.mismatchRendering,onClick:()=>{o.setMismatchRendering(!o.mismatchRendering)}}]}}}).actions(o=>{let{renderSvg:i}=o;return{async renderSvg(s){let{renderSvg:f}=await Promise.resolve().then(()=>(et(),Zr));return f(o,s,i)}}})}var Ee=a(R()),rt=a(D()),tt=a(q());Ye();var oo=(0,tt.observer)(function(e){let{model:r}=e,{pluginManager:t}=(0,rt.getEnv)(r),n=t.getPlugin("LinearGenomeViewPlugin"),{BaseLinearDisplayComponent:o}=n.exports;return Ee.default.createElement("div",null,Ee.default.createElement(o,{...e}),Ee.default.createElement(Se,{model:r}))}),ot=oo;function Qe(e){e.addDisplayType(()=>{let r=Ge(e),t=Ke(r,e);return new nt.DisplayType({name:"LinearMafDisplay",configSchema:r,stateModel:t,ReactComponent:ot,viewType:"LinearGenomeView",trackType:"MafTrack",displayName:"MAF display"})})}var it=a(W());var no=(0,it.ConfigurationSchema)("LinearMafRenderer",{},{explicitlyTyped:!0}),at=no;var pt=a(B()),ft=a(ne()),ae=a(D());function st(e){return Object.fromEntries(Object.entries(Xe(e)).map(([r,t])=>[r,e.palette.getContrastText(t)]))}function Xe(e){let{bases:r}=e.palette;return{a:r.A.main,c:r.C.main,g:r.G.main,t:r.T.main}}function io({ctx:e,renderArgs:r}){let{regions:t,bpPerPx:n,rowHeight:o,showAllLetters:i,theme:s,mismatchRendering:f,samples:p,rowProportion:u,features:h}=r,[x]=t,l=o*u,v=(0,ft.createJBrowseTheme)(s),b=Xe(v),d=st(v),A=new Map(p.map((O,N)=>[O.id,N])),c=1/n,C=.4,I=o/2,le=l/2,H=(o-l)/2;e.font="bold 10px Courier New,monospace";for(let O of h.values()){let[N]=(0,ae.featureSpanPx)(O,x,n),Ce=O.get("alignments"),k=O.get("seq").toLowerCase();for(let[X,Fe]of Object.entries(Ce)){let _e=Fe.data,M=_e.toLowerCase(),Z=A.get(X);if(Z===void 0)throw new Error(`unknown sample encountered: ${X}`);let F=o*Z;e.beginPath(),e.fillStyle="black";for(let y=0,S=0;y<M.length;y++)if(k[y]!=="-"){if(M[y]==="-"){let w=N+c*S;e.moveTo(w,F+I),e.lineTo(w+c+C,F+I)}S++}if(e.stroke(),!i){e.beginPath(),e.fillStyle="lightgrey";for(let y=0,S=0;y<M.length;y++)if(k[y]!=="-"){let w=M[y],U=N+c*S;k[y]===w&&w!=="-"&&e.rect(U,H+F,c+C,l),S++}e.fill()}for(let y=0,S=0;y<M.length;y++){let w=M[y];if(k[y]!=="-"){if(w!=="-"){let 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