jbrowse-plugin-mafviewer 1.2.2 → 1.2.4

package/README.md

@@ -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

@@ -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

@@ -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

@@ -1 +1 @@
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package/dist/BigMafAdapter/BigMafAdapter.d.ts

@@ -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

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"BigMafAdapter.js","sourceRoot":"","sources":["../../src/BigMafAdapter/BigMafAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAChE,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;AAanC,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IACxD,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,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,eAAe;aACtB,CAAC,CACH,CAAC,WAAqC;SACxC,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,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,EAAE,CAAA;YACtC,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;YACD,MAAM,YAAY,CAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC/D,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;oBAC/B,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAW,CAAA;oBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBAC7B,IAAI,GAAuB,CAAA;oBAC3B,MAAM,IAAI,GAAG,EAAc,CAAA;oBAC3B,MAAM,UAAU,GAAG,EAAoC,CAAA;oBACvD,MAAM,OAAO,GAAG,EAAc,CAAA;oBAC9B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;wBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;4BAC1B,IAAI,GAAG,EAAE,CAAC;gCACR,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAE,CAAC,CAAA;gCAChC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;4BACrB,CAAC;iCAAM,CAAC;gCACN,GAAG,GAAG,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;gCAC1B,IAAI,CAAC,IAAI,CAAC,GAAI,CAAC,CAAA;gCACf,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;4BACrB,CAAC;wBACH,CAAC;oBACH,CAAC;oBAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;wBACxC,MAAM,GAAG,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;wBACvB,MAAM,EAAE,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;wBAC1B,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;wBAC3B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;wBACjB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;wBAEjB,UAAU,CAAC,GAAG,CAAC,GAAG;4BAChB,GAAG,EAAE,GAAG;4BACR,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;oBACD,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,GAAG,EAAE,IAAI,CAAC,CAAC,CAAC;4BACZ,UAAU,EAAE,UAAU;yBACvB;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/LinearMafDisplay/components/ColorLegend.d.ts

@@ -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

@@ -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

@@ -1 +1 @@
-{"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAGrC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAEzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,EACL,UAAU,EACV,WAAW,GAKZ;IACC,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,OAAO,GAAG,EAAE,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IACjE,MAAM,eAAe,GAAG,SAAS,IAAI,CAAC,CAAA;IACtC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;IAEzC,OAAO,CACL;QACE,oBAAC,MAAM,IACL,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,GAAG,SAAS,EACjC,MAAM,EAAE,WAAW,GACnB;QACF,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI;QACtB,2BAAG,SAAS,EAAE,aAAa,SAAS,GAAG,CAAC,KAAK;YAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC5B,oBAAC,MAAM,IACL,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,CAAC,EAAE,GAAG,GAAG,SAAS,EAClB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,EACrB,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE,MAAM,CAAC,KAAK,GACnB,CACH,CAAC;YACD,eAAe;gBACd,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC3B,8BACE,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,gBAAgB,EAAC,QAAQ,EACzB,QAAQ,EAAE,WAAW,EACrB,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,IAEjC,MAAM,CAAC,KAAK,CACR,CACR,CAAC;gBACJ,CAAC,CAAC,IAAI,CACN,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}
+{"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAIzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EACJ,UAAU,EACV,eAAe,EACf,WAAW,EACX,SAAS,EACT,OAAO,GAAG,EAAE,EACZ,SAAS,EACT,WAAW,GACZ,GAAG,KAAK,CAAA;IACT,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;IAEzC,OAAO,CACL;QACE,oBAAC,MAAM,IACL,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,GAAG,SAAS,EACjC,MAAM,EAAE,WAAW,GACnB;QACF,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI;QACtB,2BAAG,SAAS,EAAE,aAAa,SAAS,GAAG,CAAC,KAAK;YAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC5B,oBAAC,MAAM,IACL,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,CAAC,EAAE,GAAG,GAAG,SAAS,EAClB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,EACrB,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE,MAAM,CAAC,KAAK,GACnB,CACH,CAAC;YACD,eAAe;gBACd,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC3B,8BACE,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,gBAAgB,EAAC,QAAQ,EACzB,QAAQ,EAAE,WAAW,EACrB,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,IAEjC,MAAM,CAAC,KAAK,CACR,CACR,CAAC;gBACJ,CAAC,CAAC,IAAI,CACN,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}

package/dist/LinearMafDisplay/components/{ReactComponent.d.ts → LinearMafDisplayComponent.d.ts}

@@ -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}

@@ -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

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/components/SetRowHeightDialog.js

@@ -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