jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/dist/LinearMafRenderer/rendering/mismatches.d.ts

@@ -10,4 +10,4 @@ import type { RenderingContext } from './types';
  * @param alignmentStart - Start position of the alignment
  * @param chr - Chromosome/sequence name
  */
-export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number, alignmentStart: number, chr: string): void;
+export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, rowIndex: number, alignmentStart: number, chr: string): void;

package/dist/LinearMafRenderer/rendering/mismatches.js

@@ -12,7 +12,7 @@ import { GAP_STROKE_OFFSET } from './types';
  * @param alignmentStart - Start position of the alignment
  * @param chr - Chromosome/sequence name
  */
-export function renderMismatches(context, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
+export function renderMismatches(context, alignment, seq, leftPx, rowTop, rowIndex, alignmentStart, chr) {
     const { ctx, scale, h, canvasWidth, showAllLetters, mismatchRendering, colorForBase, } = context;
     for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
         const currentChar = alignment[i];
@@ -30,7 +30,7 @@ export function renderMismatches(context, alignment, seq, leftPx, rowTop, sample
                             pos: genomicOffset + alignmentStart,
                             chr,
                             base: currentChar,
-                            sampleId,
+                            rowIndex,
                         });
                     }
                 }
@@ -45,7 +45,7 @@ export function renderMismatches(context, alignment, seq, leftPx, rowTop, sample
                             pos: genomicOffset + alignmentStart,
                             chr,
                             base: currentChar,
-                            sampleId,
+                            rowIndex,
                         });
                     }
                 }

package/dist/LinearMafRenderer/rendering/types.d.ts

@@ -21,7 +21,7 @@ export interface RenderedBase {
     pos: number;
     chr: string;
     base: string;
-    sampleId: number;
+    rowIndex: number;
     isInsertion?: boolean;
     isLargeInsertion?: boolean;
 }

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
 import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
 import { getSession, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { getRoot } from '@jbrowse/mobx-state-tree';
 import { Button, FormControl, FormControlLabel, FormLabel, Paper, Radio, RadioGroup, TextField, } from '@mui/material';
-import { getRoot } from 'mobx-state-tree';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     textbox: {

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map

@@ -1 +1 @@
-{"version":3,"file":"AddTrackWorkflow.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/AddTrackWorkflow.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAEL,UAAU,EACV,yBAAyB,EACzB,sBAAsB,GACvB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EACL,MAAM,EACN,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,KAAK,EACL,KAAK,EACL,UAAU,EACV,SAAS,GACV,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,KAAK,EAAE,MAAM;KACd;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,EAAE;QACvB,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE;KACzB;IACD,MAAM,EAAE;QACN,SAAS,EAAE,EAAE;QACb,YAAY,EAAE,GAAG;QACjB,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAKH,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,KAAK,EAA4B;IACxE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAClD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,WAAW,CAAC,CAAA;IACvD,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GACvC,QAAQ,CAAqB,eAAe,CAAC,CAAA;IAC/C,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GACzC,QAAQ,CAAmB,KAAK,CAAC,CAAA;IAEnC,MAAM,SAAS,GAAG,OAAO,CAAM,KAAK,CAAC,CAAA;IACrC,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,oBAAC,KAAK;YACH,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,WAAW;gBACV,oBAAC,SAAS,oBAAsB;gBAChC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,iBAAiB,CAAC,KAAK,CAAC,MAAM,CAAC,KAA2B,CAAC,CAAA;oBAC7D,CAAC,IAEA,CAAC,eAAe,EAAE,iBAAiB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAC7C,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,cAAc,KAAK,CAAC,EAC7B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;YACb,cAAc,KAAK,eAAe,CAAC,CAAC,CAAC,CACpC,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,gBAAgB,EACrB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,MAAM,CAAC,GAAG,CAAC,CAAA;gBACb,CAAC,GACD,CACH,CAAC,CAAC,CAAC,uEAAuE;gBAC3E,cAAc,KAAK,iBAAiB,CAAC,CAAC,CAAC,CACrC;oBACE,oBAAC,WAAW;wBACV,oBAAC,SAAS,qBAAuB;wBACjC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAyB,CAAC,CAAA;4BAC5D,CAAC,IAEA,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACvB,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,eAAe,KAAK,CAAC,EAC9B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;oBACd,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,mBAAmB,EACxB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,yBAAyB,EAC9B,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,+BAA+B,EACpC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,gCAAgC,EACrC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CACK;QACR;YACE,oBAAC,YAAY,IACX,QAAQ,EAAE,KAAK,EACf,IAAI,EAAC,2BAA2B,EAChC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACf,CAAC,GACD;YACF,oBAAC,SAAS,IACR,SAAS,QACT,IAAI,EAAE,EAAE,EACR,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAChC,CAAC,EACD,UAAU,EAAC,0DAA0D,EACrE,WAAW,EACT,wFAAwF,EAE1F,OAAO,EAAC,UAAU,EAClB,SAAS,SACT,CACE;QAEN,oBAAC,SAAS,IACR,KAAK,EAAE,SAAS,EAChB,UAAU,EAAC,YAAY,EACvB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC,GACD;QACF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,CAAC;oBACH,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI,WAAW,GAAG,EAAc,CAAA;oBAChC,IAAI,CAAC;wBACH,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;oBACnC,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,WAAW,GAAG,OAAO,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;oBAC3C,CAAC;oBAED,MAAM,OAAO,GAAG;wBACd,GAAG,SAAS,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,GAAG,EAAE,EAAE;wBAC/D,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,eAAe;qBACzC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBAEV,IAAI,sBAAsB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACpC,OAAO,CAAC,YAAY,CAAC;4BACnB,OAAO;4BACP,IAAI,EAAE,UAAU;4BAChB,IAAI,EAAE,SAAS;4BACf,aAAa,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC;4BAC/B,OAAO,EACL,cAAc,KAAK,eAAe;gCAChC,CAAC,CAAC;oCACE,IAAI,EAAE,cAAc;oCACpB,cAAc,EAAE,GAAG;oCACnB,OAAO,EAAE,WAAW;oCACpB,UAAU,EAAE,KAAK;iCAClB;gCACH,CAAC,CAAC,uEAAuE;oCACvE,cAAc,KAAK,iBAAiB;wCACpC,CAAC,CAAC;4CACE,IAAI,EAAE,cAAc;4CACpB,aAAa,EAAE,GAAG;4CAClB,UAAU,EAAE,KAAK;4CACjB,KAAK,EAAE;gDACL,SAAS,EAAE,eAAe;gDAC1B,QAAQ,EAAE,QAAQ;6CACnB;4CACD,OAAO,EAAE,WAAW;yCACrB;wCACH,CAAC,CAAC;4CACE,IAAI,EAAE,cAAc;4CACpB,aAAa,EAAE,GAAG;4CAClB,WAAW,EAAE,QAAQ;4CACrB,UAAU,EAAE,KAAK;4CACjB,OAAO,EAAE,WAAW;yCACrB;yBACV,CAAC,CAAA;wBAEF,KAAK,CAAC,IAAI,EAAE,SAAS,CAAC,OAAO,CAAC,CAAA;oBAChC,CAAC;oBACD,KAAK,CAAC,SAAS,EAAE,CAAA;oBACjB,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACvC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;oBAC3B,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACb,CAAC;YACH,CAAC,aAGM,CACH,CACT,CAAA;AACH,CAAC"}
+{"version":3,"file":"AddTrackWorkflow.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/AddTrackWorkflow.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC7D,OAAO,EAEL,UAAU,EACV,yBAAyB,EACzB,sBAAsB,GACvB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAA;AAClD,OAAO,EACL,MAAM,EACN,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,KAAK,EACL,KAAK,EACL,UAAU,EACV,SAAS,GACV,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,KAAK,EAAE,MAAM;KACd;IACD,KAAK,EAAE;QACL,MAAM,EAAE,KAAK,CAAC,OAAO,EAAE;QACvB,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE;KACzB;IACD,MAAM,EAAE;QACN,SAAS,EAAE,EAAE;QACb,YAAY,EAAE,GAAG;QACjB,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAKH,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,KAAK,EAA4B;IACxE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAC9C,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAgB,CAAA;IACxD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAgB,CAAA;IAClD,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAC7C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,WAAW,CAAC,CAAA;IACvD,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GACvC,QAAQ,CAAqB,eAAe,CAAC,CAAA;IAC/C,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GACzC,QAAQ,CAAmB,KAAK,CAAC,CAAA;IAEnC,MAAM,SAAS,GAAG,OAAO,CAAM,KAAK,CAAC,CAAA;IACrC,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,oBAAC,KAAK;YACH,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAC9C,oBAAC,WAAW;gBACV,oBAAC,SAAS,oBAAsB;gBAChC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,iBAAiB,CAAC,KAAK,CAAC,MAAM,CAAC,KAA2B,CAAC,CAAA;oBAC7D,CAAC,IAEA,CAAC,eAAe,EAAE,iBAAiB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAC7C,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,cAAc,KAAK,CAAC,EAC7B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;YACb,cAAc,KAAK,eAAe,CAAC,CAAC,CAAC,CACpC,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,gBAAgB,EACrB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,MAAM,CAAC,GAAG,CAAC,CAAA;gBACb,CAAC,GACD,CACH,CAAC,CAAC,CAAC,uEAAuE;gBAC3E,cAAc,KAAK,iBAAiB,CAAC,CAAC,CAAC,CACrC;oBACE,oBAAC,WAAW;wBACV,oBAAC,SAAS,qBAAuB;wBACjC,oBAAC,UAAU,IACT,KAAK,EAAE,cAAc,EACrB,QAAQ,EAAE,KAAK,CAAC,EAAE;gCAChB,kBAAkB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAyB,CAAC,CAAA;4BAC5D,CAAC,IAEA,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACvB,oBAAC,gBAAgB,IACf,GAAG,EAAE,CAAC,EACN,KAAK,EAAE,CAAC,EACR,OAAO,EAAE,oBAAC,KAAK,OAAG,EAClB,OAAO,EAAE,eAAe,KAAK,CAAC,EAC9B,KAAK,EAAE,CAAC,GACR,CACH,CAAC,CACS,CACD;oBACd,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,mBAAmB,EACxB,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,yBAAyB,EAC9B,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,oBAAC,YAAY,IACX,QAAQ,EAAE,GAAG,EACb,IAAI,EAAC,+BAA+B,EACpC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,MAAM,CAAC,GAAG,CAAC,CAAA;wBACb,CAAC,GACD;oBACF,oBAAC,YAAY,IACX,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAC,gCAAgC,EACrC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;4BACjB,WAAW,CAAC,GAAG,CAAC,CAAA;wBAClB,CAAC,GACD,CACD,CACJ,CACK;QACR;YACE,oBAAC,YAAY,IACX,QAAQ,EAAE,KAAK,EACf,IAAI,EAAC,2BAA2B,EAChC,SAAS,EAAE,SAAS,EACpB,WAAW,EAAE,GAAG,CAAC,EAAE;oBACjB,QAAQ,CAAC,GAAG,CAAC,CAAA;gBACf,CAAC,GACD;YACF,oBAAC,SAAS,IACR,SAAS,QACT,IAAI,EAAE,EAAE,EACR,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAChC,CAAC,EACD,UAAU,EAAC,0DAA0D,EACrE,WAAW,EACT,wFAAwF,EAE1F,OAAO,EAAC,UAAU,EAClB,SAAS,SACT,CACE;QAEN,oBAAC,SAAS,IACR,KAAK,EAAE,SAAS,EAChB,UAAU,EAAC,YAAY,EACvB,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAClC,CAAC,GACD;QACF,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,CAAC;oBACH,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI,WAAW,GAAG,EAAc,CAAA;oBAChC,IAAI,CAAC;wBACH,WAAW,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;oBACnC,CAAC;oBAAC,OAAO,CAAC,EAAE,CAAC;wBACX,WAAW,GAAG,OAAO,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;oBAC3C,CAAC;oBAED,MAAM,OAAO,GAAG;wBACd,GAAG,SAAS,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,IAAI,CAAC,GAAG,EAAE,EAAE;wBAC/D,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,eAAe;qBACzC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBAEV,IAAI,sBAAsB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACpC,OAAO,CAAC,YAAY,CAAC;4BACnB,OAAO;4BACP,IAAI,EAAE,UAAU;4BAChB,IAAI,EAAE,SAAS;4BACf,aAAa,EAAE,CAAC,KAAK,CAAC,QAAQ,CAAC;4BAC/B,OAAO,EACL,cAAc,KAAK,eAAe;gCAChC,CAAC,CAAC;oCACE,IAAI,EAAE,cAAc;oCACpB,cAAc,EAAE,GAAG;oCACnB,OAAO,EAAE,WAAW;oCACpB,UAAU,EAAE,KAAK;iCAClB;gCACH,CAAC,CAAC,uEAAuE;oCACvE,cAAc,KAAK,iBAAiB;wCACpC,CAAC,CAAC;4CACE,IAAI,EAAE,cAAc;4CACpB,aAAa,EAAE,GAAG;4CAClB,UAAU,EAAE,KAAK;4CACjB,KAAK,EAAE;gDACL,SAAS,EAAE,eAAe;gDAC1B,QAAQ,EAAE,QAAQ;6CACnB;4CACD,OAAO,EAAE,WAAW;yCACrB;wCACH,CAAC,CAAC;4CACE,IAAI,EAAE,cAAc;4CACpB,aAAa,EAAE,GAAG;4CAClB,WAAW,EAAE,QAAQ;4CACrB,UAAU,EAAE,KAAK;4CACjB,OAAO,EAAE,WAAW;yCACrB;yBACV,CAAC,CAAA;wBAEF,KAAK,CAAC,IAAI,EAAE,SAAS,CAAC,OAAO,CAAC,CAAA;oBAChC,CAAC;oBACD,KAAK,CAAC,SAAS,EAAE,CAAA;oBACjB,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE,CAAC;wBACvC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAC,CAAA;oBAC3B,CAAC;gBACH,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACb,CAAC;YACH,CAAC,aAGM,CACH,CACT,CAAA;AACH,CAAC"}

package/dist/MafAddTrackWorkflow/index.js

@@ -1,5 +1,5 @@
 import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 import MultiMAFWidget from './AddTrackWorkflow';
 export default function MafAddTrackWorkflowF(pluginManager) {
     pluginManager.addAddTrackWorkflowType(() => new AddTrackWorkflowType({

package/dist/MafAddTrackWorkflow/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,qCAAqC,CAAA;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,OAAO,cAAc,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,OAAO,UAAU,oBAAoB,CAAC,aAA4B;IACvE,aAAa,CAAC,uBAAuB,CACnC,GAAG,EAAE,CACH,IAAI,oBAAoB,CAAC;QACvB,IAAI,EAAE,WAAW;QACjB,cAAc,EAAE,cAAc;QAC9B,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;KAC5B,CAAC,CACL,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafAddTrackWorkflow/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,oBAAoB,EAAE,MAAM,qCAAqC,CAAA;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,cAAc,MAAM,oBAAoB,CAAA;AAE/C,MAAM,CAAC,OAAO,UAAU,oBAAoB,CAAC,aAA4B;IACvE,aAAa,CAAC,uBAAuB,CACnC,GAAG,EAAE,CACH,IAAI,oBAAoB,CAAC;QACvB,IAAI,EAAE,WAAW;QACjB,cAAc,EAAE,cAAc;QAC9B,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;KAC5B,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/MafGetSequences/MafGetSequences.d.ts

@@ -12,5 +12,6 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
         headers?: Record<string, string>;
         regions: Region[];
         showAllLetters: boolean;
+        includeInsertions?: boolean;
     }, rpcDriverClassName: string): Promise<string[]>;
 }

package/dist/MafGetSequences/MafGetSequences.js

@@ -6,7 +6,7 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
     name = 'MafGetSequences';
     async execute(args, rpcDriverClassName) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { samples, regions, adapterConfig, sessionId, showAllLetters } = deserializedArgs;
+        const { samples, regions, adapterConfig, sessionId, showAllLetters, includeInsertions, } = deserializedArgs;
         const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
         const features = await firstValueFrom(dataAdapter.getFeatures(regions[0], deserializedArgs).pipe(toArray()));
         return processFeaturesToFasta({
@@ -14,6 +14,7 @@ export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRe
             samples,
             regions,
             showAllLetters,
+            includeInsertions,
         });
     }
 }

package/dist/MafGetSequences/MafGetSequences.js.map

@@ -1 +1 @@
-{"version":3,"file":"MafGetSequences.js","sourceRoot":"","sources":["../../src/MafGetSequences/MafGetSequences.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,wCAAwC,MAAM,8EAA8E,CAAA;AACnI,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAO3D,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,wCAAwC;IACnF,IAAI,GAAG,iBAAiB,CAAA;IAExB,KAAK,CAAC,OAAO,CACX,IAQC,EACD,kBAA0B;QAE1B,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACtD,IAAI,EACJ,kBAAkB,CACnB,CAAA;QACD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,cAAc,EAAE,GAClE,gBAAgB,CAAA;QAClB,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,MAAM,cAAc,CACnC,WAAW,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAE,EAAE,gBAAgB,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACvE,CAAA;QACD,OAAO,sBAAsB,CAAC;YAC5B,QAAQ,EAAE,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;YACjD,OAAO;YACP,OAAO;YACP,cAAc;SACf,CAAC,CAAA;IACJ,CAAC;CACF"}
+{"version":3,"file":"MafGetSequences.js","sourceRoot":"","sources":["../../src/MafGetSequences/MafGetSequences.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,wCAAwC,MAAM,8EAA8E,CAAA;AACnI,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,EAAE,sBAAsB,EAAE,MAAM,oBAAoB,CAAA;AAO3D,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,wCAAwC;IACnF,IAAI,GAAG,iBAAiB,CAAA;IAExB,KAAK,CAAC,OAAO,CACX,IASC,EACD,kBAA0B;QAE1B,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACtD,IAAI,EACJ,kBAAkB,CACnB,CAAA;QACD,MAAM,EACJ,OAAO,EACP,OAAO,EACP,aAAa,EACb,SAAS,EACT,cAAc,EACd,iBAAiB,GAClB,GAAG,gBAAgB,CAAA;QACpB,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,MAAM,cAAc,CACnC,WAAW,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAE,EAAE,gBAAgB,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACvE,CAAA;QACD,OAAO,sBAAsB,CAAC;YAC5B,QAAQ,EAAE,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC;YACjD,OAAO;YACP,OAAO;YACP,cAAc;YACd,iBAAiB;SAClB,CAAC,CAAA;IACJ,CAAC;CACF"}

package/dist/MafSequenceWidget/LabelsCanvas.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import type { Sample } from '../LinearMafDisplay/types';
+interface LabelsCanvasProps {
+    samples: Sample[];
+    maxLabelLength: number;
+}
+export default function LabelsCanvas({ samples, maxLabelLength, }: LabelsCanvasProps): React.JSX.Element;
+export {};

package/dist/MafSequenceWidget/LabelsCanvas.js

@@ -0,0 +1,37 @@
+import React, { useEffect, useRef } from 'react';
+import { useTheme } from '@mui/material';
+import { CHAR_WIDTH, FONT, LABEL_PADDING, ROW_HEIGHT } from './constants';
+export default function LabelsCanvas({ samples, maxLabelLength, }) {
+    const theme = useTheme();
+    const canvasRef = useRef(null);
+    const labelWidth = maxLabelLength * CHAR_WIDTH + LABEL_PADDING;
+    const canvasHeight = samples.length * ROW_HEIGHT;
+    useEffect(() => {
+        const canvas = canvasRef.current;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        const dpr = window.devicePixelRatio || 1;
+        canvas.width = labelWidth * dpr;
+        canvas.height = canvasHeight * dpr;
+        canvas.style.width = `${labelWidth}px`;
+        canvas.style.height = `${canvasHeight}px`;
+        ctx.scale(dpr, dpr);
+        ctx.fillStyle = theme.palette.background.paper;
+        ctx.fillRect(0, 0, labelWidth, canvasHeight);
+        ctx.font = FONT;
+        ctx.textBaseline = 'top';
+        for (let rowIdx = 0; rowIdx < samples.length; rowIdx++) {
+            const sample = samples[rowIdx];
+            const y = rowIdx * ROW_HEIGHT;
+            ctx.fillStyle = theme.palette.text.secondary;
+            ctx.fillText(sample.label ?? sample.id, 2, y + 2);
+        }
+    }, [samples, labelWidth, canvasHeight, theme]);
+    return React.createElement("canvas", { ref: canvasRef, style: { display: 'block' } });
+}
+//# sourceMappingURL=LabelsCanvas.js.map

package/dist/MafSequenceWidget/LabelsCanvas.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"LabelsCanvas.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/LabelsCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAEhD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AASzE,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,EACnC,OAAO,EACP,cAAc,GACI;IAClB,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,SAAS,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAEjD,MAAM,UAAU,GAAG,cAAc,GAAG,UAAU,GAAG,aAAa,CAAA;IAC9D,MAAM,YAAY,GAAG,OAAO,CAAC,MAAM,GAAG,UAAU,CAAA;IAEhD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAA;QAChC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAM;QACR,CAAC;QAED,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,MAAM,GAAG,GAAG,MAAM,CAAC,gBAAgB,IAAI,CAAC,CAAA;QACxC,MAAM,CAAC,KAAK,GAAG,UAAU,GAAG,GAAG,CAAA;QAC/B,MAAM,CAAC,MAAM,GAAG,YAAY,GAAG,GAAG,CAAA;QAClC,MAAM,CAAC,KAAK,CAAC,KAAK,GAAG,GAAG,UAAU,IAAI,CAAA;QACtC,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,GAAG,YAAY,IAAI,CAAA;QACzC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAEnB,GAAG,CAAC,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAA;QAC9C,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,UAAU,EAAE,YAAY,CAAC,CAAA;QAE5C,GAAG,CAAC,IAAI,GAAG,IAAI,CAAA;QACf,GAAG,CAAC,YAAY,GAAG,KAAK,CAAA;QAExB,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC;YACvD,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,CAAE,CAAA;YAC/B,MAAM,CAAC,GAAG,MAAM,GAAG,UAAU,CAAA;YAE7B,GAAG,CAAC,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAA;YAC5C,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,EAAE,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;QACnD,CAAC;IACH,CAAC,EAAE,CAAC,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,KAAK,CAAC,CAAC,CAAA;IAE9C,OAAO,gCAAQ,GAAG,EAAE,SAAS,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,EAAE,GAAI,CAAA;AAChE,CAAC"}

package/dist/MafSequenceWidget/MafSequenceHoverHighlight.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const MafSequenceHoverHighlight: ({ model, }: {
+    model: LinearGenomeViewModel;
+}) => React.JSX.Element | null;
+export default MafSequenceHoverHighlight;

package/dist/MafSequenceWidget/MafSequenceHoverHighlight.js

@@ -0,0 +1,52 @@
+import React from 'react';
+import { getSession } from '@jbrowse/core/util';
+import { colord } from '@jbrowse/core/util/colord';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    highlight: {
+        height: '100%',
+        position: 'absolute',
+        background: colord(theme.palette.primary.main).alpha(0.4).toRgbString(),
+        borderLeft: `2px solid ${theme.palette.primary.main}`,
+        borderRight: `2px solid ${theme.palette.primary.main}`,
+        pointerEvents: 'none',
+        zIndex: 10,
+    },
+}));
+const MafSequenceHoverHighlight = observer(function MafSequenceHoverHighlight({ model, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { assemblyManager } = session;
+    // Find MafSequenceWidget instances that are connected to this view
+    const widgets = 'widgets' in session ? session.widgets : undefined;
+    if (!widgets) {
+        return null;
+    }
+    const highlights = [];
+    for (const [, widget] of widgets) {
+        const w = widget;
+        if (w.type === 'MafSequenceWidget' && w.connectedViewId === model.id) {
+            const mafWidget = widget;
+            const { hoverHighlight } = mafWidget;
+            if (hoverHighlight) {
+                const { refName, start, end, assemblyName } = hoverHighlight;
+                const assembly = assemblyManager.get(assemblyName);
+                const canonicalRefName = assembly?.getCanonicalRefName(refName) ?? refName;
+                const startPx = model.bpToPx({
+                    refName: canonicalRefName,
+                    coord: start,
+                });
+                const endPx = model.bpToPx({ refName: canonicalRefName, coord: end });
+                if (startPx && endPx) {
+                    const left = Math.min(startPx.offsetPx, endPx.offsetPx) - model.offsetPx;
+                    const width = Math.max(Math.abs(endPx.offsetPx - startPx.offsetPx), 3);
+                    highlights.push(React.createElement("div", { key: `maf-hover-${mafWidget.id}`, className: classes.highlight, style: { left, width } }));
+                }
+            }
+        }
+    }
+    return React.createElement(React.Fragment, null, highlights);
+});
+export default MafSequenceHoverHighlight;
+//# sourceMappingURL=MafSequenceHoverHighlight.js.map

package/dist/MafSequenceWidget/MafSequenceHoverHighlight.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MafSequenceHoverHighlight.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/MafSequenceHoverHighlight.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,MAAM,EAAE,MAAM,2BAA2B,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAK1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,SAAS,EAAE;QACT,MAAM,EAAE,MAAM;QACd,QAAQ,EAAE,UAAU;QACpB,UAAU,EAAE,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE;QACvE,UAAU,EAAE,aAAa,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE;QACrD,WAAW,EAAE,aAAa,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE;QACtD,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,EAAE;KACX;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,yBAAyB,GAAG,QAAQ,CAAC,SAAS,yBAAyB,CAAC,EAC5E,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IAEnC,mEAAmE;IACnE,MAAM,OAAO,GACX,SAAS,IAAI,OAAO,CAAC,CAAC,CAAE,OAAO,CAAC,OAAgC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,OAAO,IAAI,CAAA;IACb,CAAC;IAED,MAAM,UAAU,GAAsB,EAAE,CAAA;IAExC,KAAK,MAAM,CAAC,EAAE,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;QACjC,MAAM,CAAC,GAAG,MAIT,CAAA;QACD,IAAI,CAAC,CAAC,IAAI,KAAK,mBAAmB,IAAI,CAAC,CAAC,eAAe,KAAK,KAAK,CAAC,EAAE,EAAE,CAAC;YACrE,MAAM,SAAS,GAAG,MAAgC,CAAA;YAClD,MAAM,EAAE,cAAc,EAAE,GAAG,SAAS,CAAA;YAEpC,IAAI,cAAc,EAAE,CAAC;gBACnB,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,YAAY,EAAE,GAAG,cAAc,CAAA;gBAC5D,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBAClD,MAAM,gBAAgB,GACpB,QAAQ,EAAE,mBAAmB,CAAC,OAAO,CAAC,IAAI,OAAO,CAAA;gBAEnD,MAAM,OAAO,GAAG,KAAK,CAAC,MAAM,CAAC;oBAC3B,OAAO,EAAE,gBAAgB;oBACzB,KAAK,EAAE,KAAK;iBACb,CAAC,CAAA;gBACF,MAAM,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,gBAAgB,EAAE,KAAK,EAAE,GAAG,EAAE,CAAC,CAAA;gBAErE,IAAI,OAAO,IAAI,KAAK,EAAE,CAAC;oBACrB,MAAM,IAAI,GACR,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,QAAQ,EAAE,KAAK,CAAC,QAAQ,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAA;oBAC7D,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,QAAQ,GAAG,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAA;oBAEtE,UAAU,CAAC,IAAI,CACb,6BACE,GAAG,EAAE,aAAa,SAAS,CAAC,EAAE,EAAE,EAChC,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAE,EAAE,IAAI,EAAE,KAAK,EAAE,GACtB,CACH,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,0CAAG,UAAU,CAAI,CAAA;AAC1B,CAAC,CAAC,CAAA;AAEF,eAAe,yBAAyB,CAAA"}

package/dist/MafSequenceWidget/MafSequenceHoverHighlightExtension.d.ts

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

package/dist/MafSequenceWidget/MafSequenceHoverHighlightExtension.js

@@ -0,0 +1,12 @@
+import React from 'react';
+import MafSequenceHoverHighlight from './MafSequenceHoverHighlight';
+export default function MafSequenceHoverHighlightExtensionF(pluginManager) {
+    pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent', (rest, props) => {
+        const model = props.model;
+        return [
+            ...rest,
+            React.createElement(MafSequenceHoverHighlight, { key: "maf-sequence-hover-highlight", model: model }),
+        ];
+    });
+}
+//# sourceMappingURL=MafSequenceHoverHighlightExtension.js.map

package/dist/MafSequenceWidget/MafSequenceHoverHighlightExtension.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MafSequenceHoverHighlightExtension.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/MafSequenceHoverHighlightExtension.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,yBAAyB,MAAM,6BAA6B,CAAA;AAKnE,MAAM,CAAC,OAAO,UAAU,mCAAmC,CACzD,aAA4B;IAE5B,aAAa,CAAC,mBAAmB,CAC/B,2CAA2C,EAC3C,CAAC,IAAuB,EAAE,KAA8B,EAAE,EAAE;QAC1D,MAAM,KAAK,GAAG,KAAK,CAAC,KAA8B,CAAA;QAClD,OAAO;YACL,GAAG,IAAI;YACP,oBAAC,yBAAyB,IACxB,GAAG,EAAC,8BAA8B,EAClC,KAAK,EAAE,KAAK,GACZ;SACH,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC"}

package/dist/MafSequenceWidget/MafSequenceWidget.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MafSequenceWidgetModel } from './stateModelFactory';
+declare const MafSequenceWidget: ({ model, }: {
+    model: MafSequenceWidgetModel;
+}) => React.JSX.Element;
+export default MafSequenceWidget;

package/dist/MafSequenceWidget/MafSequenceWidget.js

@@ -0,0 +1,189 @@
+import React, { useEffect, useState } from 'react';
+import { CascadingMenuButton, ErrorMessage, LoadingEllipses, } from '@jbrowse/core/ui';
+import { getSession, useLocalStorage } from '@jbrowse/core/util';
+import { Button, Paper } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { ContentCopy as CopyIcon, Difference as DifferenceIcon, Download as DownloadIcon, FormatColorFill as ColorBackgroundIcon, KeyboardArrowDown, Label as LabelIcon, PlaylistAdd as InsertionsIcon, Subject as AllLettersIcon, TableRows as TableRowsIcon, } from '@mui/icons-material';
+import SequenceDisplay from './SequenceDisplay';
+import { copyToClipboard, downloadAsFile } from '../util/clipboard';
+const useStyles = makeStyles()(theme => ({
+    root: {
+        padding: theme.spacing(2),
+    },
+    controls: {
+        display: 'flex',
+        alignItems: 'center',
+        flexWrap: 'wrap',
+        gap: theme.spacing(1),
+        marginBottom: theme.spacing(2),
+    },
+}));
+const MafSequenceWidget = observer(function MafSequenceWidget({ model, }) {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const { adapterConfig, samples, regions } = model;
+    const [showAllLetters, setShowAllLetters] = useLocalStorage('mafSequenceWidget-showAllLetters', true);
+    const [includeInsertions, setIncludeInsertions] = useLocalStorage('mafSequenceWidget-includeInsertions', false);
+    const [singleLineFormat, setSingleLineFormat] = useLocalStorage('mafSequenceWidget-singleLineFormat', false);
+    const [colorBackground, setColorBackground] = useLocalStorage('mafSequenceWidget-colorBackground', true);
+    const [showSampleNames, setShowSampleNames] = useLocalStorage('mafSequenceWidget-showSampleNames', true);
+    const [rawSequences, setRawSequences] = useState([]);
+    const [formattedSequence, setFormattedSequence] = useState('');
+    const [loading, setLoading] = useState(true);
+    const [error, setError] = useState();
+    useEffect(() => {
+        if (!adapterConfig || !samples || !regions) {
+            return;
+        }
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                setLoading(true);
+                setError(undefined);
+                const { rpcManager } = session;
+                const fastaSequence = (await rpcManager.call('MafSequenceWidget', 'MafGetSequences', {
+                    sessionId: 'MafSequenceWidget',
+                    adapterConfig,
+                    samples,
+                    showAllLetters,
+                    includeInsertions,
+                    regions,
+                }));
+                setRawSequences(fastaSequence);
+                let formatted;
+                if (singleLineFormat) {
+                    const maxLabelLength = Math.max(...samples.map(s => (s.label ?? s.id).length));
+                    formatted = fastaSequence
+                        .map((r, idx) => {
+                        const sample = samples[idx];
+                        const label = sample.label ?? sample.id;
+                        const padding = ' '.repeat(maxLabelLength - label.length + 2);
+                        return `>${label}${padding}${r}`;
+                    })
+                        .join('\n');
+                }
+                else {
+                    formatted = fastaSequence
+                        .map((r, idx) => {
+                        const sample = samples[idx];
+                        return `>${sample.label ?? sample.id}\n${r}`;
+                    })
+                        .join('\n');
+                }
+                setFormattedSequence(formatted);
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+            finally {
+                setLoading(false);
+            }
+        })();
+    }, [
+        adapterConfig,
+        samples,
+        regions,
+        showAllLetters,
+        includeInsertions,
+        singleLineFormat,
+        session,
+    ]);
+    const sequenceTooLarge = formattedSequence
+        ? formattedSequence.length > 5_000_000
+        : false;
+    if (!adapterConfig || !samples || !regions) {
+        return (React.createElement(Paper, { className: classes.root },
+            React.createElement("div", null, "No sequence data available")));
+    }
+    return (React.createElement(Paper, { className: classes.root },
+        React.createElement("div", { className: classes.controls },
+            React.createElement(CascadingMenuButton, { menuItems: [
+                    {
+                        label: 'Show all letters',
+                        icon: AllLettersIcon,
+                        type: 'radio',
+                        checked: showAllLetters,
+                        onClick: () => {
+                            setShowAllLetters(true);
+                        },
+                    },
+                    {
+                        label: 'Show only differences',
+                        icon: DifferenceIcon,
+                        type: 'radio',
+                        checked: !showAllLetters,
+                        onClick: () => {
+                            setShowAllLetters(false);
+                        },
+                    },
+                    {
+                        label: 'Include insertions',
+                        icon: InsertionsIcon,
+                        type: 'checkbox',
+                        checked: includeInsertions,
+                        onClick: () => {
+                            setIncludeInsertions(!includeInsertions);
+                        },
+                    },
+                    {
+                        label: 'Single line format',
+                        icon: TableRowsIcon,
+                        type: 'checkbox',
+                        checked: singleLineFormat,
+                        onClick: () => {
+                            setSingleLineFormat(!singleLineFormat);
+                        },
+                    },
+                    {
+                        label: 'Color background',
+                        icon: ColorBackgroundIcon,
+                        type: 'checkbox',
+                        checked: colorBackground,
+                        onClick: () => {
+                            setColorBackground(!colorBackground);
+                        },
+                    },
+                    {
+                        label: 'Show sample names',
+                        icon: LabelIcon,
+                        type: 'checkbox',
+                        checked: showSampleNames,
+                        onClick: () => {
+                            setShowSampleNames(!showSampleNames);
+                        },
+                    },
+                    { type: 'divider' },
+                    {
+                        label: 'Copy to clipboard',
+                        icon: CopyIcon,
+                        disabled: loading || !formattedSequence,
+                        onClick: () => {
+                            copyToClipboard(formattedSequence, () => {
+                                session.notify('Sequence copied to clipboard', 'info');
+                            }, e => {
+                                session.notifyError(`${e}`, e);
+                            }).catch((e) => {
+                                console.error(e);
+                            });
+                        },
+                    },
+                    {
+                        label: 'Download as FASTA',
+                        icon: DownloadIcon,
+                        disabled: loading || !formattedSequence,
+                        onClick: () => {
+                            downloadAsFile(formattedSequence, 'sequence.fasta', () => {
+                                session.notify('Sequence downloaded', 'info');
+                            }, e => {
+                                session.notifyError(`${e}`, e);
+                            });
+                        },
+                    },
+                ], ButtonComponent: props => (React.createElement(Button, { ...props, variant: "contained", size: "small", endIcon: React.createElement(KeyboardArrowDown, null) }, "Actions")) })),
+        error ? (React.createElement(ErrorMessage, { error: error })) : (React.createElement(React.Fragment, null, loading ? (React.createElement(LoadingEllipses, null)) : sequenceTooLarge ? (React.createElement("div", null, "Reference sequence too large to display, use the Download button")) : (React.createElement(SequenceDisplay, { model: model, sequences: rawSequences, singleLineFormat: singleLineFormat, includeInsertions: includeInsertions, colorBackground: colorBackground, showSampleNames: showSampleNames }))))));
+});
+export default MafSequenceWidget;
+//# sourceMappingURL=MafSequenceWidget.js.map

package/dist/MafSequenceWidget/MafSequenceWidget.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"MafSequenceWidget.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/MafSequenceWidget.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EACL,mBAAmB,EACnB,YAAY,EACZ,eAAe,GAChB,MAAM,kBAAkB,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EACL,WAAW,IAAI,QAAQ,EACvB,UAAU,IAAI,cAAc,EAC5B,QAAQ,IAAI,YAAY,EACxB,eAAe,IAAI,mBAAmB,EACtC,iBAAiB,EACjB,KAAK,IAAI,SAAS,EAClB,WAAW,IAAI,cAAc,EAC7B,OAAO,IAAI,cAAc,EACzB,SAAS,IAAI,aAAa,GAC3B,MAAM,qBAAqB,CAAA;AAE5B,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,cAAc,EAAE,MAAM,mBAAmB,CAAA;AAKnE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;IACD,QAAQ,EAAE;QACR,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,QAAQ,EAAE,MAAM;QAChB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,iBAAiB,GAAG,QAAQ,CAAC,SAAS,iBAAiB,CAAC,EAC5D,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAEjD,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,eAAe,CACzD,kCAAkC,EAClC,IAAI,CACL,CAAA;IACD,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,eAAe,CAC/D,qCAAqC,EACrC,KAAK,CACN,CAAA;IACD,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,eAAe,CAC7D,oCAAoC,EACpC,KAAK,CACN,CAAA;IACD,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,eAAe,CAC3D,mCAAmC,EACnC,IAAI,CACL,CAAA;IACD,MAAM,CAAC,eAAe,EAAE,kBAAkB,CAAC,GAAG,eAAe,CAC3D,mCAAmC,EACnC,IAAI,CACL,CAAA;IACD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAW,EAAE,CAAC,CAAA;IAC9D,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CAAS,EAAE,CAAC,CAAA;IACtE,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAAW,CAAA;IAE7C,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC,aAAa,IAAI,CAAC,OAAO,IAAI,CAAC,OAAO,EAAE,CAAC;YAC3C,OAAM;QACR,CAAC;QACD,mEAAmE;QACnE,CAAC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI,CAAC;gBACH,UAAU,CAAC,IAAI,CAAC,CAAA;gBAChB,QAAQ,CAAC,SAAS,CAAC,CAAA;gBAEnB,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAE9B,MAAM,aAAa,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAC1C,mBAAmB,EACnB,iBAAiB,EACjB;oBACE,SAAS,EAAE,mBAAmB;oBAC9B,aAAa;oBACb,OAAO;oBACP,cAAc;oBACd,iBAAiB;oBACjB,OAAO;iBACR,CACF,CAAa,CAAA;gBAEd,eAAe,CAAC,aAAa,CAAC,CAAA;gBAE9B,IAAI,SAAiB,CAAA;gBACrB,IAAI,gBAAgB,EAAE,CAAC;oBACrB,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,CAC7B,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,EAAE,CAAC,CAAC,MAAM,CAAC,CAC9C,CAAA;oBACD,SAAS,GAAG,aAAa;yBACtB,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;wBACd,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAE,CAAA;wBAC5B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,EAAE,CAAA;wBACvC,MAAM,OAAO,GAAG,GAAG,CAAC,MAAM,CAAC,cAAc,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;wBAC7D,OAAO,IAAI,KAAK,GAAG,OAAO,GAAG,CAAC,EAAE,CAAA;oBAClC,CAAC,CAAC;yBACD,IAAI,CAAC,IAAI,CAAC,CAAA;gBACf,CAAC;qBAAM,CAAC;oBACN,SAAS,GAAG,aAAa;yBACtB,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;wBACd,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAE,CAAA;wBAC5B,OAAO,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,EAAE,KAAK,CAAC,EAAE,CAAA;oBAC9C,CAAC,CAAC;yBACD,IAAI,CAAC,IAAI,CAAC,CAAA;gBACf,CAAC;gBAED,oBAAoB,CAAC,SAAS,CAAC,CAAA;YACjC,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,QAAQ,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;oBAAS,CAAC;gBACT,UAAU,CAAC,KAAK,CAAC,CAAA;YACnB,CAAC;QACH,CAAC,CAAC,EAAE,CAAA;IACN,CAAC,EAAE;QACD,aAAa;QACb,OAAO;QACP,OAAO;QACP,cAAc;QACd,iBAAiB;QACjB,gBAAgB;QAChB,OAAO;KACR,CAAC,CAAA;IAEF,MAAM,gBAAgB,GAAG,iBAAiB;QACxC,CAAC,CAAC,iBAAiB,CAAC,MAAM,GAAG,SAAS;QACtC,CAAC,CAAC,KAAK,CAAA;IAET,IAAI,CAAC,aAAa,IAAI,CAAC,OAAO,IAAI,CAAC,OAAO,EAAE,CAAC;QAC3C,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YAC5B,8DAAqC,CAC/B,CACT,CAAA;IACH,CAAC;IAED,OAAO,CACL,oBAAC,KAAK,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;QAC5B,6BAAK,SAAS,EAAE,OAAO,CAAC,QAAQ;YAC9B,oBAAC,mBAAmB,IAClB,SAAS,EACP;oBACE;wBACE,KAAK,EAAE,kBAAkB;wBACzB,IAAI,EAAE,cAAc;wBACpB,IAAI,EAAE,OAAO;wBACb,OAAO,EAAE,cAAc;wBACvB,OAAO,EAAE,GAAG,EAAE;4BACZ,iBAAiB,CAAC,IAAI,CAAC,CAAA;wBACzB,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,uBAAuB;wBAC9B,IAAI,EAAE,cAAc;wBACpB,IAAI,EAAE,OAAO;wBACb,OAAO,EAAE,CAAC,cAAc;wBACxB,OAAO,EAAE,GAAG,EAAE;4BACZ,iBAAiB,CAAC,KAAK,CAAC,CAAA;wBAC1B,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,oBAAoB;wBAC3B,IAAI,EAAE,cAAc;wBACpB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,iBAAiB;wBAC1B,OAAO,EAAE,GAAG,EAAE;4BACZ,oBAAoB,CAAC,CAAC,iBAAiB,CAAC,CAAA;wBAC1C,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,oBAAoB;wBAC3B,IAAI,EAAE,aAAa;wBACnB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,gBAAgB;wBACzB,OAAO,EAAE,GAAG,EAAE;4BACZ,mBAAmB,CAAC,CAAC,gBAAgB,CAAC,CAAA;wBACxC,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,kBAAkB;wBACzB,IAAI,EAAE,mBAAmB;wBACzB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,eAAe;wBACxB,OAAO,EAAE,GAAG,EAAE;4BACZ,kBAAkB,CAAC,CAAC,eAAe,CAAC,CAAA;wBACtC,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,mBAAmB;wBAC1B,IAAI,EAAE,SAAS;wBACf,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,eAAe;wBACxB,OAAO,EAAE,GAAG,EAAE;4BACZ,kBAAkB,CAAC,CAAC,eAAe,CAAC,CAAA;wBACtC,CAAC;qBACF;oBACD,EAAE,IAAI,EAAE,SAAS,EAAE;oBACnB;wBACE,KAAK,EAAE,mBAAmB;wBAC1B,IAAI,EAAE,QAAQ;wBACd,QAAQ,EAAE,OAAO,IAAI,CAAC,iBAAiB;wBACvC,OAAO,EAAE,GAAG,EAAE;4BACZ,eAAe,CACb,iBAAiB,EACjB,GAAG,EAAE;gCACH,OAAO,CAAC,MAAM,CAAC,8BAA8B,EAAE,MAAM,CAAC,CAAA;4BACxD,CAAC,EACD,CAAC,CAAC,EAAE;gCACF,OAAO,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;4BAChC,CAAC,CACF,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gCACrB,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAClB,CAAC,CAAC,CAAA;wBACJ,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,mBAAmB;wBAC1B,IAAI,EAAE,YAAY;wBAClB,QAAQ,EAAE,OAAO,IAAI,CAAC,iBAAiB;wBACvC,OAAO,EAAE,GAAG,EAAE;4BACZ,cAAc,CACZ,iBAAiB,EACjB,gBAAgB,EAChB,GAAG,EAAE;gCACH,OAAO,CAAC,MAAM,CAAC,qBAAqB,EAAE,MAAM,CAAC,CAAA;4BAC/C,CAAC,EACD,CAAC,CAAC,EAAE;gCACF,OAAO,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;4BAChC,CAAC,CACF,CAAA;wBACH,CAAC;qBACF;iBACY,EAEjB,eAAe,EAAE,KAAK,CAAC,EAAE,CAAC,CACxB,oBAAC,MAAM,OACD,KAAK,EACT,OAAO,EAAC,WAAW,EACnB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,oBAAC,iBAAiB,OAAG,cAGvB,CACV,GACD,CACE;QAEL,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,CACF,0CACG,OAAO,CAAC,CAAC,CAAC,CACT,oBAAC,eAAe,OAAG,CACpB,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,CACrB,oGAEM,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,eAAe,IACd,KAAK,EAAE,KAAK,EACZ,SAAS,EAAE,YAAY,EACvB,gBAAgB,EAAE,gBAAgB,EAClC,iBAAiB,EAAE,iBAAiB,EACpC,eAAe,EAAE,eAAe,EAChC,eAAe,EAAE,eAAe,GAChC,CACH,CACA,CACJ,CACK,CACT,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/MafSequenceWidget/SequenceCanvas.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import type { Sample } from '../LinearMafDisplay/types';
+interface SequenceCanvasProps {
+    samples: Sample[];
+    sequences: string[];
+    colorBackground: boolean;
+    hoveredCol?: number;
+    onHover: (col: number | undefined, row: number | undefined, clientX: number, clientY: number) => void;
+    onLeave: () => void;
+}
+export default function SequenceCanvas({ samples, sequences, colorBackground, hoveredCol, onHover, onLeave, }: SequenceCanvasProps): React.JSX.Element;
+export {};

package/dist/MafSequenceWidget/SequenceCanvas.js

@@ -0,0 +1,86 @@
+import React, { useCallback, useEffect, useRef } from 'react';
+import { alpha, useTheme } from '@mui/material';
+import { getBaseColor, getContrastText } from './baseColors';
+import { CHAR_WIDTH, FONT, ROW_HEIGHT } from './constants';
+export default function SequenceCanvas({ samples, sequences, colorBackground, hoveredCol, onHover, onLeave, }) {
+    const theme = useTheme();
+    const canvasRef = useRef(null);
+    const seqLength = sequences[0]?.length || 0;
+    const canvasWidth = seqLength * CHAR_WIDTH;
+    const canvasHeight = samples.length * ROW_HEIGHT;
+    useEffect(() => {
+        const canvas = canvasRef.current;
+        if (!canvas) {
+            return;
+        }
+        const ctx = canvas.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        const dpr = window.devicePixelRatio || 1;
+        canvas.width = canvasWidth * dpr;
+        canvas.height = canvasHeight * dpr;
+        canvas.style.width = `${canvasWidth}px`;
+        canvas.style.height = `${canvasHeight}px`;
+        ctx.scale(dpr, dpr);
+        ctx.fillStyle = theme.palette.background.paper;
+        ctx.fillRect(0, 0, canvasWidth, canvasHeight);
+        ctx.font = FONT;
+        ctx.textBaseline = 'top';
+        for (let rowIdx = 0; rowIdx < samples.length; rowIdx++) {
+            const seq = sequences[rowIdx] || '';
+            const y = rowIdx * ROW_HEIGHT;
+            for (let colIdx = 0; colIdx < seq.length; colIdx++) {
+                const char = seq[colIdx];
+                const x = colIdx * CHAR_WIDTH;
+                if (colorBackground && char !== '-' && char !== '.') {
+                    ctx.fillStyle = getBaseColor(char, theme);
+                    ctx.fillRect(x, y, CHAR_WIDTH, ROW_HEIGHT);
+                }
+                if (colIdx === hoveredCol) {
+                    const highlight = theme.palette.highlight;
+                    const highlightColor = highlight?.main ?? '#FFB11D';
+                    ctx.fillStyle = alpha(highlightColor, 0.5);
+                    ctx.fillRect(x, y, CHAR_WIDTH, ROW_HEIGHT);
+                }
+                if (char === '-') {
+                    ctx.fillStyle = theme.palette.grey[400];
+                }
+                else if (char === '.') {
+                    ctx.fillStyle = theme.palette.grey[500];
+                }
+                else if (colorBackground) {
+                    ctx.fillStyle = getContrastText(char, theme);
+                }
+                else {
+                    ctx.fillStyle = getBaseColor(char, theme);
+                }
+                ctx.fillText(char, x + 2, y + 2);
+            }
+        }
+    }, [
+        samples,
+        sequences,
+        canvasWidth,
+        canvasHeight,
+        hoveredCol,
+        colorBackground,
+        theme,
+    ]);
+    const handleMouseMove = useCallback((e) => {
+        const canvas = canvasRef.current;
+        if (!canvas) {
+            return;
+        }
+        const rect = canvas.getBoundingClientRect();
+        const x = e.clientX - rect.left;
+        const y = e.clientY - rect.top;
+        const col = Math.floor(x / CHAR_WIDTH);
+        const row = Math.floor(y / ROW_HEIGHT);
+        const validCol = col >= 0 && col < seqLength ? col : undefined;
+        const validRow = row >= 0 && row < samples.length ? row : undefined;
+        onHover(validCol, validRow, e.clientX, e.clientY);
+    }, [seqLength, samples.length, onHover]);
+    return (React.createElement("canvas", { ref: canvasRef, style: { display: 'block' }, onMouseMove: handleMouseMove, onMouseLeave: onLeave }));
+}
+//# sourceMappingURL=SequenceCanvas.js.map

package/dist/MafSequenceWidget/SequenceCanvas.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SequenceCanvas.js","sourceRoot":"","sources":["../../src/MafSequenceWidget/SequenceCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAE7D,OAAO,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAE/C,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,cAAc,CAAA;AAC5D,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAkB1D,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EACrC,OAAO,EACP,SAAS,EACT,eAAe,EACf,UAAU,EACV,OAAO,EACP,OAAO,GACa;IACpB,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,SAAS,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAEjD,MAAM,SAAS,GAAG,SAAS,CAAC,CAAC,CAAC,EAAE,MAAM,IAAI,CAAC,CAAA;IAC3C,MAAM,WAAW,GAAG,SAAS,GAAG,UAAU,CAAA;IAC1C,MAAM,YAAY,GAAG,OAAO,CAAC,MAAM,GAAG,UAAU,CAAA;IAEhD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAA;QAChC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAM;QACR,CAAC;QAED,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACnC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,MAAM,GAAG,GAAG,MAAM,CAAC,gBAAgB,IAAI,CAAC,CAAA;QACxC,MAAM,CAAC,KAAK,GAAG,WAAW,GAAG,GAAG,CAAA;QAChC,MAAM,CAAC,MAAM,GAAG,YAAY,GAAG,GAAG,CAAA;QAClC,MAAM,CAAC,KAAK,CAAC,KAAK,GAAG,GAAG,WAAW,IAAI,CAAA;QACvC,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,GAAG,YAAY,IAAI,CAAA;QACzC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAEnB,GAAG,CAAC,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,CAAA;QAC9C,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,YAAY,CAAC,CAAA;QAE7C,GAAG,CAAC,IAAI,GAAG,IAAI,CAAA;QACf,GAAG,CAAC,YAAY,GAAG,KAAK,CAAA;QAExB,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC;YACvD,MAAM,GAAG,GAAG,SAAS,CAAC,MAAM,CAAC,IAAI,EAAE,CAAA;YACnC,MAAM,CAAC,GAAG,MAAM,GAAG,UAAU,CAAA;YAE7B,KAAK,IAAI,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC;gBACnD,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAE,CAAA;gBACzB,MAAM,CAAC,GAAG,MAAM,GAAG,UAAU,CAAA;gBAE7B,IAAI,eAAe,IAAI,IAAI,KAAK,GAAG,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;oBACpD,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;oBACzC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,UAAU,EAAE,UAAU,CAAC,CAAA;gBAC5C,CAAC;gBAED,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;oBAC1B,MAAM,SAAS,GAAI,KAAK,CAAC,OAAe,CAAC,SAE5B,CAAA;oBACb,MAAM,cAAc,GAAG,SAAS,EAAE,IAAI,IAAI,SAAS,CAAA;oBACnD,GAAG,CAAC,SAAS,GAAG,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC,CAAA;oBAC1C,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,UAAU,EAAE,UAAU,CAAC,CAAA;gBAC5C,CAAC;gBAED,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;oBACjB,GAAG,CAAC,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACzC,CAAC;qBAAM,IAAI,IAAI,KAAK,GAAG,EAAE,CAAC;oBACxB,GAAG,CAAC,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACzC,CAAC;qBAAM,IAAI,eAAe,EAAE,CAAC;oBAC3B,GAAG,CAAC,SAAS,GAAG,eAAe,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;gBAC9C,CAAC;qBAAM,CAAC;oBACN,GAAG,CAAC,SAAS,GAAG,YAAY,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;gBAC3C,CAAC;gBACD,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC,EAAE;QACD,OAAO;QACP,SAAS;QACT,WAAW;QACX,YAAY;QACZ,UAAU;QACV,eAAe;QACf,KAAK;KACN,CAAC,CAAA;IAEF,MAAM,eAAe,GAAG,WAAW,CACjC,CAAC,CAAsC,EAAE,EAAE;QACzC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAA;QAChC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAM;QACR,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,CAAC,qBAAqB,EAAE,CAAA;QAC3C,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,IAAI,CAAA;QAC/B,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,GAAG,CAAA;QAC9B,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,UAAU,CAAC,CAAA;QACtC,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,UAAU,CAAC,CAAA;QAEtC,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,IAAI,GAAG,GAAG,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAA;QAC9D,MAAM,QAAQ,GAAG,GAAG,IAAI,CAAC,IAAI,GAAG,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CAAA;QAEnE,OAAO,CAAC,QAAQ,EAAE,QAAQ,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,CAAA;IACnD,CAAC,EACD,CAAC,SAAS,EAAE,OAAO,CAAC,MAAM,EAAE,OAAO,CAAC,CACrC,CAAA;IAED,OAAO,CACL,gCACE,GAAG,EAAE,SAAS,EACd,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,EAAE,EAC3B,WAAW,EAAE,eAAe,EAC5B,YAAY,EAAE,OAAO,GACrB,CACH,CAAA;AACH,CAAC"}

package/dist/MafSequenceWidget/SequenceDisplay.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import type { MafSequenceWidgetModel } from './stateModelFactory';
+interface SequenceDisplayProps {
+    model: MafSequenceWidgetModel;
+    sequences: string[];
+    singleLineFormat: boolean;
+    includeInsertions: boolean;
+    colorBackground: boolean;
+    showSampleNames: boolean;
+}
+declare const SequenceDisplay: ({ model, sequences, colorBackground, showSampleNames, }: SequenceDisplayProps) => React.JSX.Element;
+export default SequenceDisplay;