npm - jbrowse-plugin-mafviewer - Versions diffs - 1.2.2 → 1.2.4 - Mend

jbrowse-plugin-mafviewer 1.2.2 → 1.2.4

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 (78) hide show

package/README.md CHANGED Viewed

@@ -94,7 +94,12 @@ can use nhLocation or samples array on adapter
 ### Example BgzipTaffyAdapter config
-can use nhLocation or samples array on adapter
+Note: TAF files are actually significantly slower and has known bugs...will
+update once fixed
+This notice will be removed it it is improved
+As with other adapters, you can use nhLocation or samples array on adapter
 ```json
 {

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts CHANGED Viewed

@@ -1,9 +1,18 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { Feature, Region } from '@jbrowse/core/util';
-import type { IndexData } from './types';
+import type { IndexData, OrganismRecord } from './types';
 export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     setupP?: Promise<IndexData>;
+    private cache;
     getRefNames(): Promise<string[]>;
+    getChunk(buffer: Uint8Array, opts?: BaseOptions): Promise<{
+        uniqueId: string;
+        start: number;
+        end: number;
+        strand: number;
+        alignments: Record<string, OrganismRecord>;
+        seq: string;
+    } | undefined>;
     setupPre(): Promise<IndexData>;
     setup(opts?: BaseOptions): Promise<IndexData>;
     readTaiFile(): Promise<IndexData>;
@@ -11,11 +20,11 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;
-            label: string;
+            label?: string;
             color?: string;
         }[];
         tree: Record<string, any> | undefined;
     }>;
-    getLines(query: Region, byteRanges: IndexData): Promise<Uint8Array<ArrayBuffer> | undefined>;
+    getLines(query: Region, byteRanges: IndexData): Promise<unknown>;
     freeResources(): void;
 }

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js CHANGED Viewed

@@ -1,8 +1,10 @@
 import { unzip } from '@gmod/bgzf-filehandle';
 import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, updateStatus, } from '@jbrowse/core/util';
+import QuickLRU from '@jbrowse/core/util/QuickLRU';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import AbortablePromiseCache from 'abortable-promise-cache';
 import Long from 'long';
 import VirtualOffset from './virtualOffset';
 import parseNewick from '../parseNewick';
@@ -12,10 +14,116 @@ import { parseLineByLine } from './util';
 const toP = (s = 0) => +(+s).toFixed(1);
 export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     setupP;
+    cache = new AbortablePromiseCache({
+        cache: new QuickLRU({ maxSize: 50 }),
+        // @ts-expect-error
+        fill: async ({ nextEntry, firstEntry }, signal, statusCallback) => {
+            const file = openLocation(this.getConf('tafGzLocation'));
+            const response = await file.read(nextEntry.virtualOffset.blockPosition -
+                firstEntry.virtualOffset.blockPosition, firstEntry.virtualOffset.blockPosition);
+            const buffer = await unzip(response);
+            const slice = buffer.slice(firstEntry.virtualOffset.dataPosition);
+            return this.getChunk(slice, {
+                statusCallback: statusCallback,
+                signal,
+            });
+        },
+    });
     async getRefNames() {
         const data = await this.setup();
         return Object.keys(data);
     }
+    async getChunk(buffer, opts) {
+        const { statusCallback = () => { } } = opts || {};
+        const alignments = {};
+        const data = [];
+        let a0;
+        let j = 0;
+        let b = 0;
+        parseLineByLine(buffer, line => {
+            if (j++ % 100 === 0) {
+                statusCallback(`Processing ${toP(b / 1_000_000)}/${toP(buffer.length / 1_000_000)}Mb`);
+            }
+            b += line.length;
+            if (line) {
+                const [lineData, rowInstructions] = line.split(' ; ');
+                if (rowInstructions) {
+                    for (const ins of parseRowInstructions(rowInstructions)) {
+                        if (ins.type === 'i') {
+                            data.splice(ins.row, 0, ins);
+                            if (!alignments[ins.asm]) {
+                                alignments[ins.asm] = {
+                                    start: ins.start,
+                                    strand: ins.strand,
+                                    srcSize: ins.length,
+                                    chr: ins.ref,
+                                    data: '',
+                                };
+                            }
+                            const e = alignments[ins.asm];
+                            e.data += ' '.repeat(Math.max(0, j - e.data.length - 1)); // catch it up
+                        }
+                        else if (ins.type === 's') {
+                            if (!alignments[ins.asm]) {
+                                alignments[ins.asm] = {
+                                    start: ins.start,
+                                    strand: ins.strand,
+                                    srcSize: ins.length,
+                                    chr: ins.ref,
+                                    data: '',
+                                };
+                            }
+                            const e = alignments[ins.asm];
+                            e.data += ' '.repeat(Math.max(0, j - e.data.length - 1)); // catch it up
+                            data[ins.row] = ins;
+                        }
+                        else if (ins.type === 'd') {
+                            data.splice(ins.row, 1);
+                        }
+                        // no gaps for now(?)
+                        // else if (ins.type === 'g') {
+                        //   console.log('g??')
+                        // } else if (ins.type === 'G') {
+                        //   console.log('G??')
+                        // }
+                    }
+                    if (!a0) {
+                        a0 = data[0];
+                    }
+                }
+                const lineLen = lineData.length;
+                for (let i = 0; i < lineLen; i++) {
+                    const letter = lineData[i];
+                    const r = data[i];
+                    if (r) {
+                        alignments[r.asm].data += letter;
+                    }
+                    else {
+                        // not sure why but chr22_KI270731v1_random.taf.gz ends up here
+                    }
+                }
+            }
+        });
+        if (a0) {
+            const row0 = alignments[a0.asm];
+            // see
+            // https://github.com/ComparativeGenomicsToolkit/taffy/blob/f5a5354/docs/taffy_utilities.md#referenced-based-maftaf-and-indexing
+            // for the significance of row[0]:
+            //
+            // "An anchor line in TAF is a column from which all sequence
+            // coordinates can be deduced without scanning backwards to previous
+            // lines "
+            return {
+                uniqueId: `${row0.start}-${row0.data.length}`,
+                start: row0.start,
+                end: row0.start + row0.data.length,
+                strand: row0.strand,
+                alignments,
+                seq: row0.data,
+            };
+        }
+        return undefined;
+    }
     setupPre() {
         if (!this.setupP) {
             this.setupP = this.readTaiFile().catch((e) => {
@@ -72,95 +180,17 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             try {
                 const byteRanges = await this.setup();
-                const buffer = await updateStatus('Downloading alignments', statusCallback, () => this.getLines(query, byteRanges));
-                if (buffer) {
-                    const alignments = {};
-                    const data = [];
-                    let a0;
-                    let j = 0;
-                    let b = 0;
-                    parseLineByLine(buffer, line => {
-                        if (j++ % 100 === 0) {
-                            statusCallback(`Processing ${toP(b / 1_000_000)}/${toP(buffer.length / 1_000_000)}Mb`);
-                        }
-                        b += line.length;
-                        if (line) {
-                            const [lineData, rowInstructions] = line.split(' ; ');
-                            if (rowInstructions) {
-                                for (const ins of parseRowInstructions(rowInstructions)) {
-                                    if (ins.type === 'i') {
-                                        data.splice(ins.row, 0, ins);
-                                        if (!alignments[ins.asm]) {
-                                            alignments[ins.asm] = {
-                                                start: ins.start,
-                                                strand: ins.strand,
-                                                srcSize: ins.length,
-                                                chr: ins.ref,
-                                                data: '',
-                                            };
-                                        }
-                                        const e = alignments[ins.asm];
-                                        e.data += ' '.repeat(Math.max(0, j - e.data.length)); // catch it up
-                                    }
-                                    else if (ins.type === 's') {
-                                        if (!alignments[ins.asm]) {
-                                            alignments[ins.asm] = {
-                                                start: ins.start,
-                                                strand: ins.strand,
-                                                srcSize: ins.length,
-                                                chr: ins.ref,
-                                                data: '',
-                                            };
-                                        }
-                                        const e = alignments[ins.asm];
-                                        e.data += ' '.repeat(Math.max(0, j - e.data.length)); // catch it up
-                                        data[ins.row] = ins;
-                                    }
-                                    else if (ins.type === 'd') {
-                                        data.splice(ins.row, 1);
-                                    }
-                                    // no gaps for now(?)
-                                    // else if (ins.type === 'g') {
-                                    // }
-                                    // else if (ins.type === 'G') {
-                                    // }
-                                }
-                                if (!a0) {
-                                    a0 = data[0];
-                                }
-                            }
-                            const lineLen = lineData.length;
-                            for (let i = 0; i < lineLen; i++) {
-                                const letter = lineData[i];
-                                const r = data[i];
-                                if (r) {
-                                    alignments[r.asm].data += letter;
-                                }
-                                else {
-                                    // not sure why but chr22_KI270731v1_random.taf.gz ends up here
-                                }
-                            }
-                        }
-                    });
-                    if (a0) {
-                        const row0 = alignments[a0.asm];
-                        // see
-                        // https://github.com/ComparativeGenomicsToolkit/taffy/blob/f5a5354/docs/taffy_utilities.md#referenced-based-maftaf-and-indexing
-                        // for the significance of row[0]:
-                        //
-                        // "An anchor line in TAF is a column from which all sequence
-                        // coordinates can be deduced without scanning backwards to previous
-                        // lines "
-                        observer.next(new SimpleFeature({
-                            uniqueId: `${row0.start}-${row0.data.length}`,
-                            refName: query.refName,
-                            start: row0.start,
-                            end: row0.start + row0.data.length,
-                            strand: row0.strand,
-                            alignments,
-                            seq: row0.data,
-                        }));
-                    }
+                const feat = await updateStatus('Downloading alignments', statusCallback, () => this.getLines(query, byteRanges));
+                if (feat) {
+                    observer.next(
+                    // @ts-expect-error
+                    new SimpleFeature({
+                        ...feat,
+                        refName: query.refName,
+                    }));
+                }
+                else {
+                    console.error('no feature found');
                 }
                 statusCallback('');
                 observer.complete();
@@ -184,7 +214,6 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
     }
     // TODO: cache processed large chunks
     async getLines(query, byteRanges) {
-        const file = openLocation(this.getConf('tafGzLocation'));
         const records = byteRanges[query.refName];
         if (records) {
             let firstEntry;
@@ -211,10 +240,10 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
             // file whn you request e.g. out of range region (e.g. taf in chr22:1-100
             // and you are at chr22:200-300)
             if (firstEntry && nextEntry) {
-                const response = await file.read(nextEntry.virtualOffset.blockPosition -
-                    firstEntry.virtualOffset.blockPosition, firstEntry.virtualOffset.blockPosition);
-                const buffer = await unzip(response);
-                return buffer.slice(firstEntry.virtualOffset.dataPosition);
+                return this.cache.get(`${JSON.stringify(nextEntry)}_${JSON.stringify(firstEntry)}`, {
+                    nextEntry,
+                    firstEntry,
+                });
             }
         }
         return undefined;

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

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"BgzipTaffyAdapter.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAGL,aAAa,EACb,YAAY,GACb,MAAM,oBAAoB,CAAA;AAC3B,OAAO,QAAQ,MAAM,6BAA6B,CAAA;AAClD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,IAAI,MAAM,MAAM,CAAA;AAEvB,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,oBAAoB,EAAE,MAAM,mBAAmB,CAAA;AACxD,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;AAcxC,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,iBAAkB,SAAQ,sBAAsB;IAC5D,MAAM,CAAqB;IAE1B,KAAK,GAAG,IAAI,qBAAqB,CAAC;QACxC,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QACpC,mBAAmB;QACnB,IAAI,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,UAAU,EAAE,EAAE,MAAM,EAAE,cAAc,EAAE,EAAE;YAChE,MAAM,IAAI,GAAG,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAC,CAAA;YACxD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,IAAI,CAC9B,SAAS,CAAC,aAAa,CAAC,aAAa;gBACnC,UAAU,CAAC,aAAa,CAAC,aAAa,EACxC,UAAU,CAAC,aAAa,CAAC,aAAa,CACvC,CAAA;YACD,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,QAAQ,CAAC,CAAA;YACpC,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,aAAa,CAAC,YAAY,CAAC,CAAA;YACjE,OAAO,IAAI,CAAC,QAAQ,CAAC,KAAK,EAAE;gBAC1B,cAAc,EAAE,cAAuC;gBACvD,MAAM;aACP,CAAC,CAAA;QACJ,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,CAAC,WAAW;QACf,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC/B,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,MAAkB,EAAE,IAAkB;QACnD,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,UAAU,GAAG,EAAoC,CAAA;QACvD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,IAAI,EAAO,CAAA;QACX,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE;YAC7B,IAAI,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,EAAE,CAAC;gBACpB,cAAc,CACZ,cAAc,GAAG,CAAC,CAAC,GAAG,SAAS,CAAC,IAAI,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,SAAS,CAAC,IAAI,CACvE,CAAA;YACH,CAAC;YACD,CAAC,IAAI,IAAI,CAAC,MAAM,CAAA;YAChB,IAAI,IAAI,EAAE,CAAC;gBACT,MAAM,CAAC,QAAQ,EAAE,eAAe,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACrD,IAAI,eAAe,EAAE,CAAC;oBACpB,KAAK,MAAM,GAAG,IAAI,oBAAoB,CAAC,eAAe,CAAC,EAAE,CAAC;wBACxD,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BACrB,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;4BAC5B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gCACzB,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG;oCACpB,KAAK,EAAE,GAAG,CAAC,KAAK;oCAChB,MAAM,EAAE,GAAG,CAAC,MAAM;oCAClB,OAAO,EAAE,GAAG,CAAC,MAAM;oCACnB,GAAG,EAAE,GAAG,CAAC,GAAG;oCACZ,IAAI,EAAE,EAAE;iCACT,CAAA;4BACH,CAAC;4BACD,MAAM,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAE,CAAA;4BAC9B,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA,CAAC,cAAc;wBACzE,CAAC;6BAAM,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BAC5B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gCACzB,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG;oCACpB,KAAK,EAAE,GAAG,CAAC,KAAK;oCAChB,MAAM,EAAE,GAAG,CAAC,MAAM;oCAClB,OAAO,EAAE,GAAG,CAAC,MAAM;oCACnB,GAAG,EAAE,GAAG,CAAC,GAAG;oCACZ,IAAI,EAAE,EAAE;iCACT,CAAA;4BACH,CAAC;4BACD,MAAM,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,GAAG,CAAE,CAAA;4BAC9B,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA,CAAC,cAAc;4BACvE,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;wBACrB,CAAC;6BAAM,IAAI,GAAG,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;4BAC5B,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;wBACzB,CAAC;wBAED,qBAAqB;wBACrB,+BAA+B;wBAC/B,uBAAuB;wBACvB,iCAAiC;wBACjC,uBAAuB;wBACvB,IAAI;oBACN,CAAC;oBACD,IAAI,CAAC,EAAE,EAAE,CAAC;wBACR,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBACd,CAAC;gBACH,CAAC;gBACD,MAAM,OAAO,GAAG,QAAS,CAAC,MAAM,CAAA;gBAEhC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;oBACjC,MAAM,MAAM,GAAG,QAAS,CAAC,CAAC,CAAC,CAAA;oBAC3B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;oBAEjB,IAAI,CAAC,EAAE,CAAC;wBACN,UAAU,CAAC,CAAC,CAAC,GAAG,CAAE,CAAC,IAAI,IAAI,MAAM,CAAA;oBACnC,CAAC;yBAAM,CAAC;wBACN,+DAA+D;oBACjE,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC,CAAC,CAAA;QACF,IAAI,EAAE,EAAE,CAAC;YACP,MAAM,IAAI,GAAG,UAAU,CAAC,EAAE,CAAC,GAAG,CAAE,CAAA;YAEhC,MAAM;YACN,gIAAgI;YAChI,kCAAkC;YAClC,EAAE;YACF,6DAA6D;YAC7D,oEAAoE;YACpE,UAAU;YACV,OAAO;gBACL,QAAQ,EAAE,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;gBAC7C,KAAK,EAAE,IAAI,CAAC,KAAK;gBACjB,GAAG,EAAE,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM;gBAClC,MAAM,EAAE,IAAI,CAAC,MAAM;gBACnB,UAAU;gBACV,GAAG,EAAE,IAAI,CAAC,IAAI;aACf,CAAA;QACH,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACpD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IACD,KAAK,CAAC,IAAkB;QACtB,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI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package/dist/BigMafAdapter/BigMafAdapter.d.ts CHANGED Viewed

@@ -17,7 +17,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
     getSamples(_query: Region): Promise<{
         samples: {
             id: string;
-            label: string;
+            label?: string;
             color?: string;
         }[];
         tree: Record<string, any> | undefined;

package/dist/BigMafAdapter/BigMafAdapter.js CHANGED Viewed

@@ -12,12 +12,11 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
         if (!this.getSubAdapter) {
             throw new Error('no getSubAdapter available');
         }
-        const adapter = await this.getSubAdapter({
-            ...getSnapshot(this.config),
-            type: 'BigBedAdapter',
-        });
         return {
-            adapter: adapter.dataAdapter,
+            adapter: (await this.getSubAdapter({
+                ...getSnapshot(this.config),
+                type: 'BigBedAdapter',
+            })).dataAdapter,
         };
     }
     async setupPre() {
@@ -41,53 +40,55 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
         const { statusCallback = () => { } } = opts || {};
         return ObservableCreate(async (observer) => {
             const { adapter } = await this.setup();
-            const features = await updateStatus('Downloading alignment', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
-            for (const feature of features) {
-                const maf = feature.get('mafBlock');
-                const blocks = maf.split(';');
-                let aln;
-                const alns = [];
-                const alignments = {};
-                const blocks2 = [];
-                for (const block of blocks) {
-                    if (block.startsWith('s')) {
-                        if (aln) {
-                            alns.push(block.split(/ +/)[6]);
-                            blocks2.push(block);
-                        }
-                        else {
-                            aln = block.split(/ +/)[6];
-                            alns.push(aln);
-                            blocks2.push(block);
+            const features = await updateStatus('Downloading alignments', statusCallback, () => firstValueFrom(adapter.getFeatures(query).pipe(toArray())));
+            await updateStatus('Processing alignments', statusCallback, () => {
+                for (const feature of features) {
+                    const maf = feature.get('mafBlock');
+                    const blocks = maf.split(';');
+                    let aln;
+                    const alns = [];
+                    const alignments = {};
+                    const blocks2 = [];
+                    for (const block of blocks) {
+                        if (block.startsWith('s')) {
+                            if (aln) {
+                                alns.push(block.split(/ +/)[6]);
+                                blocks2.push(block);
+                            }
+                            else {
+                                aln = block.split(/ +/)[6];
+                                alns.push(aln);
+                                blocks2.push(block);
+                            }
                         }
                     }
+                    for (let i = 0; i < blocks2.length; i++) {
+                        const elt = blocks2[i];
+                        const ad = elt.split(/ +/);
+                        const y = ad[1].split('.');
+                        const org = y[0];
+                        const chr = y[1];
+                        alignments[org] = {
+                            chr: chr,
+                            start: +ad[1],
+                            srcSize: +ad[2],
+                            strand: ad[3] === '+' ? 1 : -1,
+                            unknown: +ad[4],
+                            data: alns[i],
+                        };
+                    }
+                    observer.next(new SimpleFeature({
+                        id: feature.id(),
+                        data: {
+                            start: feature.get('start'),
+                            end: feature.get('end'),
+                            refName: feature.get('refName'),
+                            seq: alns[0],
+                            alignments: alignments,
+                        },
+                    }));
                 }
-                for (let i = 0; i < blocks2.length; i++) {
-                    const elt = blocks2[i];
-                    const ad = elt.split(/ +/);
-                    const y = ad[1].split('.');
-                    const org = y[0];
-                    const chr = y[1];
-                    alignments[org] = {
-                        chr: chr,
-                        start: +ad[1],
-                        srcSize: +ad[2],
-                        strand: ad[3] === '+' ? 1 : -1,
-                        unknown: +ad[4],
-                        data: alns[i],
-                    };
-                }
-                observer.next(new SimpleFeature({
-                    id: feature.id(),
-                    data: {
-                        start: feature.get('start'),
-                        end: feature.get('end'),
-                        refName: feature.get('refName'),
-                        seq: alns[0],
-                        alignments: alignments,
-                    },
-                }));
-            }
+            });
             observer.complete();
         });
     }

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

	@@ -1 +1 @@
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package/dist/LinearMafDisplay/components/ColorLegend.d.ts CHANGED Viewed

@@ -1,8 +1,6 @@
 import React from 'react';
-import { LinearMafDisplayModel } from '../stateModel';
-declare const ColorLegend: ({ model, labelWidth, svgFontSize, }: {
+import type { LinearMafDisplayModel } from '../stateModel';
+declare const ColorLegend: ({ model, }: {
     model: LinearMafDisplayModel;
-    svgFontSize: number;
-    labelWidth: number;
 }) => React.JSX.Element;
 export default ColorLegend;

package/dist/LinearMafDisplay/components/ColorLegend.js CHANGED Viewed

@@ -2,9 +2,8 @@ import React from 'react';
 import { observer } from 'mobx-react';
 import RectBg from './RectBg';
 import Tree from './Tree';
-const ColorLegend = observer(function ({ model, labelWidth, svgFontSize, }) {
-    const { totalHeight, treeWidth, samples = [], rowHeight } = model;
-    const canDisplayLabel = rowHeight >= 8;
+const ColorLegend = observer(function ({ model, }) {
+    const { labelWidth, canDisplayLabel, totalHeight, treeWidth, samples = [], rowHeight, svgFontSize, } = model;
     const boxHeight = Math.min(20, rowHeight);
     return (React.createElement(React.Fragment, null,
         React.createElement(RectBg, { y: 0, x: 0, width: labelWidth + 5 + treeWidth, height: totalHeight }),

package/dist/LinearMafDisplay/components/ColorLegend.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearMafDisplay/components/{ReactComponent.d.ts → LinearMafDisplayComponent.d.ts} RENAMED Viewed

@@ -1,5 +1,5 @@
 import React from 'react';
-import { LinearMafDisplayModel } from '../stateModel';
+import type { LinearMafDisplayModel } from '../stateModel';
 declare const LinearMafDisplay: (props: {
     model: LinearMafDisplayModel;
 }) => React.JSX.Element;

package/dist/LinearMafDisplay/components/{ReactComponent.js → LinearMafDisplayComponent.js} RENAMED Viewed

@@ -1,6 +1,6 @@
 import React, { useRef, useState } from 'react';
+import { SanitizedHTML } from '@jbrowse/core/ui';
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
-import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
 import { getContainingView, getEnv } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
@@ -47,4 +47,4 @@ const LinearMafDisplay = observer(function (props) {
                         .join('\n') })))) : null));
 });
 export default LinearMafDisplay;
-//# sourceMappingURL=ReactComponent.js.map
+//# sourceMappingURL=LinearMafDisplayComponent.js.map

package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"LinearMafDisplayComponent.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/LinearMafDisplayComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE/C,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,iBAAiB,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAC9D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,cAAc,CAAA;AAKrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,aAAa,EAAE,MAAM;KACtB;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,KAE3C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAChE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IAExC,MAAM,kBAAkB,GAAG,aAAa,CAAC,SAAS,CAChD,wBAAwB,CAC+B,CAAA;IACzD,MAAM,EAAE,0BAA0B,EAAE,GAAG,kBAAkB,CAAC,OAAO,CAAA;IAEjE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAU,CAAA;IAC9C,MAAM,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAEnE,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,EAAE,qBAAqB,EAAE,CAAA;YACjD,MAAM,GAAG,GAAG,IAAI,EAAE,GAAG,IAAI,CAAC,CAAA;YAC1B,MAAM,IAAI,GAAG,IAAI,EAAE,IAAI,IAAI,CAAC,CAAA;YAC5B,SAAS,CAAC,KAAK,CAAC,OAAO,GAAG,GAAG,CAAC,CAAA;YAC9B,SAAS,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAA;QACjC,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,SAAS,CAAC,SAAS,CAAC,CAAA;YACpB,SAAS,CAAC,SAAS,CAAC,CAAA;QACtB,CAAC;QAED,oBAAC,0BAA0B,OAAK,KAAK,GAAI;QACzC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,MAAM,IAAI,OAAO,CAAC,CAAC,CAAC,CACnB,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;YAClC,6BACE,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;oBACL,QAAQ,EAAE,UAAU;oBACpB,GAAG,EAAE,SAAS;iBACf;gBAED,8BACE,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,KAAK,EACT,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,MAAM,EAAC,OAAO,GACd;gBACF,8BAAM,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAC,OAAO,GAAG,CAC9D;YACN,oBAAC,WAAW;gBACV,oBAAC,aAAa,IACZ,IAAI,EAAE,MAAM,CAAC,OAAO,CAClB,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,SAAS,CAAC,CAAC,IAAI,EAAE,CAC9C;yBACE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,GAAG,KAAK,OAAO,IAAI,GAAG,KAAK,IAAI,CAAC;yBAClD,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,IAAI,KAAK,EAAE,CAAC;yBACxC,IAAI,CAAC,IAAI,CAAC,GACb,CACU,CACV,CACP,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/LinearMafDisplay/components/SetRowHeightDialog.js ADDED Viewed

@@ -0,0 +1,38 @@
+import React, { useState } from 'react';
+import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    root: {
+        width: 500,
+    },
+});
+const SetRowHeightDialog = observer(function (props) {
+    const { model, handleClose } = props;
+    const { classes } = useStyles();
+    const [rowHeight, setRowHeight] = useState(`${model.rowHeight}`);
+    const [rowProportion, setRowProportion] = useState(`${model.rowProportion}`);
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set row height" },
+        React.createElement("form", { onSubmit: event => {
+                event.preventDefault();
+                model.setRowProportion(+rowProportion);
+                model.setRowHeight(+rowHeight);
+                handleClose();
+            } },
+            React.createElement(DialogContent, { className: classes.root },
+                React.createElement(Typography, null, "Set row height and the proportion of the row height to use for drawing each row"),
+                React.createElement(TextField, { value: rowHeight, helperText: "Enter row height", autoFocus: true, onChange: event => {
+                        setRowHeight(event.target.value);
+                    } }),
+                React.createElement(TextField, { value: rowProportion, helperText: "Enter row proportion", onChange: event => {
+                        setRowProportion(event.target.value);
+                    } }),
+                React.createElement(DialogActions, null,
+                    React.createElement(Button, { variant: "contained", color: "primary", type: "submit" }, "Submit"),
+                    React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        } }, "Cancel"))))));
+});
+export default SetRowHeightDialog;
+//# sourceMappingURL=SetRowHeightDialog.js.map