jbrowse-plugin-mafviewer 1.4.3 → 1.4.6

package/src/util/parseAssemblyName.test.ts

@@ -0,0 +1,350 @@
+import { describe, expect, test } from 'vitest'
+
+import {
+  parseAssemblyAndChr,
+  parseAssemblyAndChrSimple,
+  selectReferenceSequence,
+} from './parseAssemblyName'
+
+describe('parseAssemblyAndChr (MafTabix format)', () => {
+  test('no dot - entire string is assembly name', () => {
+    const result = parseAssemblyAndChr('hg38')
+    expect(result).toEqual({
+      assemblyName: 'hg38',
+      chr: '',
+    })
+  })
+
+  test('single dot - simple assembly.chr format', () => {
+    const result = parseAssemblyAndChr('hg38.chr1')
+    expect(result).toEqual({
+      assemblyName: 'hg38',
+      chr: 'chr1',
+    })
+  })
+
+  test('single dot - assembly.refName format with non-chr name', () => {
+    const result = parseAssemblyAndChr('mm10.scaffold_1')
+    expect(result).toEqual({
+      assemblyName: 'mm10',
+      chr: 'scaffold_1',
+    })
+  })
+
+  test('two dots with numeric version - assembly.version.chr format', () => {
+    const result = parseAssemblyAndChr('hg38.1.chr1')
+    expect(result).toEqual({
+      assemblyName: 'hg38.1',
+      chr: 'chr1',
+    })
+  })
+
+  test('two dots with multi-digit numeric version', () => {
+    const result = parseAssemblyAndChr('GRCh38.123.chrX')
+    expect(result).toEqual({
+      assemblyName: 'GRCh38.123',
+      chr: 'chrX',
+    })
+  })
+
+  test('two dots with non-numeric middle - assembly.chr.more format', () => {
+    const result = parseAssemblyAndChr('mm10.chr1.random')
+    expect(result).toEqual({
+      assemblyName: 'mm10',
+      chr: 'chr1.random',
+    })
+  })
+
+  test('two dots with non-numeric middle - chr_Un type naming', () => {
+    const result = parseAssemblyAndChr('hg38.chrUn_gl000220')
+    expect(result).toEqual({
+      assemblyName: 'hg38',
+      chr: 'chrUn_gl000220',
+    })
+  })
+
+  test('three dots with numeric version - assembly.version.chr.more format', () => {
+    const result = parseAssemblyAndChr('GRCh38.1.chr1.random')
+    expect(result).toEqual({
+      assemblyName: 'GRCh38.1',
+      chr: 'chr1.random',
+    })
+  })
+
+  test('empty string', () => {
+    const result = parseAssemblyAndChr('')
+    expect(result).toEqual({
+      assemblyName: '',
+      chr: '',
+    })
+  })
+
+  test('just a dot', () => {
+    const result = parseAssemblyAndChr('.')
+    expect(result).toEqual({
+      assemblyName: '',
+      chr: '',
+    })
+  })
+
+  test('leading dot', () => {
+    const result = parseAssemblyAndChr('.chr1')
+    expect(result).toEqual({
+      assemblyName: '',
+      chr: 'chr1',
+    })
+  })
+
+  test('trailing dot', () => {
+    const result = parseAssemblyAndChr('hg38.')
+    expect(result).toEqual({
+      assemblyName: 'hg38',
+      chr: '',
+    })
+  })
+
+  test('real world example - UCSC style', () => {
+    const result = parseAssemblyAndChr('hg19.chr6_ssto_hap7')
+    expect(result).toEqual({
+      assemblyName: 'hg19',
+      chr: 'chr6_ssto_hap7',
+    })
+  })
+
+  test('real world example - Ensembl style with numeric', () => {
+    const result = parseAssemblyAndChr('GRCh37.1.1')
+    expect(result).toEqual({
+      assemblyName: 'GRCh37.1',
+      chr: '1',
+    })
+  })
+})
+
+describe('parseAssemblyAndChrSimple (BigMaf format)', () => {
+  test('no dot - entire string is assembly name', () => {
+    const result = parseAssemblyAndChrSimple('hg38')
+    expect(result).toEqual({
+      assemblyName: 'hg38',
+      chr: '',
+    })
+  })
+
+  test('single dot - simple org.chr format', () => {
+    const result = parseAssemblyAndChrSimple('hg38.chr1')
+    expect(result).toEqual({
+      assemblyName: 'hg38',
+      chr: 'chr1',
+    })
+  })
+
+  test('multiple dots - only splits on first dot', () => {
+    const result = parseAssemblyAndChrSimple('mm10.chr1.random')
+    expect(result).toEqual({
+      assemblyName: 'mm10',
+      chr: 'chr1.random',
+    })
+  })
+
+  test('empty string', () => {
+    const result = parseAssemblyAndChrSimple('')
+    expect(result).toEqual({
+      assemblyName: '',
+      chr: '',
+    })
+  })
+})
+
+describe('selectReferenceSequence', () => {
+  const alignments = {
+    hg38: { seq: 'ACGTACGT' },
+    mm10: { seq: 'TGCATGCA' },
+    panTro6: { seq: 'GGGGGGGG' },
+  }
+
+  test('uses refAssemblyName when provided and exists', () => {
+    const result = selectReferenceSequence(
+      alignments,
+      'mm10',
+      'hg38',
+      'panTro6',
+    )
+    expect(result).toBe('TGCATGCA')
+  })
+
+  test('falls back to queryAssemblyName when refAssemblyName is empty', () => {
+    const result = selectReferenceSequence(alignments, '', 'hg38', 'panTro6')
+    expect(result).toBe('ACGTACGT')
+  })
+
+  test('falls back to queryAssemblyName when refAssemblyName is undefined', () => {
+    const result = selectReferenceSequence(
+      alignments,
+      undefined,
+      'hg38',
+      'panTro6',
+    )
+    expect(result).toBe('ACGTACGT')
+  })
+
+  test('falls back to firstAssemblyNameFound when queryAssemblyName does not match', () => {
+    const result = selectReferenceSequence(
+      alignments,
+      undefined,
+      'galGal6', // not in alignments
+      'hg38',
+    )
+    expect(result).toBe('ACGTACGT')
+  })
+
+  test('falls back to firstAssemblyNameFound when both config values are empty', () => {
+    const result = selectReferenceSequence(alignments, '', '', 'panTro6')
+    expect(result).toBe('GGGGGGGG')
+  })
+
+  test('returns undefined when refAssemblyName does not exist in alignments', () => {
+    const result = selectReferenceSequence(
+      alignments,
+      'nonexistent',
+      undefined,
+      undefined,
+    )
+    expect(result).toBeUndefined()
+  })
+
+  test('returns undefined when no matches and all params undefined', () => {
+    const result = selectReferenceSequence(
+      alignments,
+      undefined,
+      undefined,
+      undefined,
+    )
+    expect(result).toBeUndefined()
+  })
+
+  test('returns undefined for empty alignments object', () => {
+    const result = selectReferenceSequence({}, 'hg38', 'mm10', 'panTro6')
+    expect(result).toBeUndefined()
+  })
+
+  test('skips refAssemblyName when it does not exist and uses queryAssemblyName', () => {
+    const result = selectReferenceSequence(
+      alignments,
+      'galGal6', // not in alignments
+      'hg38',
+      'panTro6',
+    )
+    expect(result).toBe('ACGTACGT')
+  })
+
+  test('skips both refAssemblyName and queryAssemblyName when neither exists', () => {
+    const result = selectReferenceSequence(
+      alignments,
+      'galGal6', // not in alignments
+      'rn6', // not in alignments
+      'mm10',
+    )
+    expect(result).toBe('TGCATGCA')
+  })
+})
+
+describe('assembly name lookup integration scenarios', () => {
+  test('refAssemblyName config takes precedence over query.assemblyName', () => {
+    const alignments = {
+      hg38: { seq: 'REFERENCE_SEQ' },
+      mm10: { seq: 'QUERY_SEQ' },
+    }
+    const result = selectReferenceSequence(alignments, 'hg38', 'mm10', 'mm10')
+    expect(result).toBe('REFERENCE_SEQ')
+  })
+
+  test('query.assemblyName works when refAssemblyName not configured', () => {
+    const alignments = {
+      hg38: { seq: 'QUERY_SEQ' },
+      mm10: { seq: 'OTHER_SEQ' },
+    }
+    const result = selectReferenceSequence(alignments, '', 'hg38', 'mm10')
+    expect(result).toBe('QUERY_SEQ')
+  })
+
+  test('firstAssemblyNameFound is used as last resort fallback', () => {
+    const alignments = {
+      panTro6: { seq: 'FIRST_FOUND' },
+      mm10: { seq: 'OTHER_SEQ' },
+    }
+    // When query assemblyName does not match any alignment
+    const result = selectReferenceSequence(alignments, '', 'hg38', 'panTro6')
+    expect(result).toBe('FIRST_FOUND')
+  })
+})
+
+describe('real-world MAF format parsing', () => {
+  test('ce10.chrI from UCSC 7-way alignment', () => {
+    const result = parseAssemblyAndChr('ce10.chrI')
+    expect(result).toEqual({
+      assemblyName: 'ce10',
+      chr: 'chrI',
+    })
+  })
+
+  test('caePb3.Scfld02_18 scaffold format', () => {
+    const result = parseAssemblyAndChr('caePb3.Scfld02_18')
+    expect(result).toEqual({
+      assemblyName: 'caePb3',
+      chr: 'Scfld02_18',
+    })
+  })
+
+  test('caeRem4.Crem_Contig16 contig format', () => {
+    const result = parseAssemblyAndChr('caeRem4.Crem_Contig16')
+    expect(result).toEqual({
+      assemblyName: 'caeRem4',
+      chr: 'Crem_Contig16',
+    })
+  })
+
+  test('cb4.chrI C. briggsae format', () => {
+    const result = parseAssemblyAndChr('cb4.chrI')
+    expect(result).toEqual({
+      assemblyName: 'cb4',
+      chr: 'chrI',
+    })
+  })
+
+  test('multiple assemblies from same MAF block produce correct lookup', () => {
+    const alignments = {
+      ce10: { seq: 'TCTTTTAGTATTTGTAA' },
+      caePb3: { seq: 'tcTTTTCGC-TTTATAA' },
+    }
+
+    // When querying with ce10 assembly
+    expect(selectReferenceSequence(alignments, '', 'ce10', 'ce10')).toBe(
+      'TCTTTTAGTATTTGTAA',
+    )
+
+    // When refAssemblyName is configured to override
+    expect(selectReferenceSequence(alignments, 'caePb3', 'ce10', 'ce10')).toBe(
+      'tcTTTTCGC-TTTATAA',
+    )
+  })
+})
+
+describe('refName renaming compatibility', () => {
+  test('parseAssemblyAndChr extracts chr correctly for refName alias matching', () => {
+    // When a file uses "chrI" but assembly has alias "I" -> "chrI"
+    // The chr portion extracted here should match what renameRegionsIfNeeded expects
+    const { chr } = parseAssemblyAndChr('ce10.chrI')
+    expect(chr).toBe('chrI')
+  })
+
+  test('parseAssemblyAndChrSimple extracts chr correctly for refName alias matching', () => {
+    const { chr } = parseAssemblyAndChrSimple('ce10.chrI')
+    expect(chr).toBe('chrI')
+  })
+
+  test('assembly name is isolated from chr for assembly-based lookups', () => {
+    // The assembly name (e.g., "ce10") is used to look up reference sequence
+    // It should not include the chr portion
+    const { assemblyName } = parseAssemblyAndChr('ce10.chrI')
+    expect(assemblyName).toBe('ce10')
+  })
+})

package/src/util/parseAssemblyName.ts

@@ -0,0 +1,106 @@
+export interface ParsedAssemblyName {
+  assemblyName: string
+  chr: string
+}
+
+/**
+ * Parses assembly name and chromosome from a combined string in MAF tabix format.
+ *
+ * Handles multiple formats:
+ * - Single string with no dots: assemblyName is the entire string, chr is empty
+ * - `assembly.chr`: Single dot separates assembly name from chromosome
+ * - `assembly.version.chr`: Two dots where middle part is numeric (version number)
+ *   - assemblyName includes the version (e.g., "hg38.1" from "hg38.1.chr1")
+ * - `assembly.chr.more`: Two dots where middle part is non-numeric
+ *   - assemblyName is first part, chr includes rest (e.g., "mm10" and "chr1.random")
+ */
+export function parseAssemblyAndChr(
+  assemblyAndChr: string,
+): ParsedAssemblyName {
+  const firstDotIndex = assemblyAndChr.indexOf('.')
+  if (firstDotIndex === -1) {
+    return {
+      assemblyName: assemblyAndChr,
+      chr: '',
+    }
+  }
+
+  const secondDotIndex = assemblyAndChr.indexOf('.', firstDotIndex + 1)
+  if (secondDotIndex === -1) {
+    return {
+      assemblyName: assemblyAndChr.slice(0, firstDotIndex),
+      chr: assemblyAndChr.slice(firstDotIndex + 1),
+    }
+  }
+
+  const secondPart = assemblyAndChr.slice(firstDotIndex + 1, secondDotIndex)
+  const isNumeric = secondPart.length > 0 && !Number.isNaN(+secondPart)
+
+  if (isNumeric) {
+    return {
+      assemblyName: assemblyAndChr.slice(0, secondDotIndex),
+      chr: assemblyAndChr.slice(secondDotIndex + 1),
+    }
+  }
+
+  return {
+    assemblyName: assemblyAndChr.slice(0, firstDotIndex),
+    chr: assemblyAndChr.slice(firstDotIndex + 1),
+  }
+}
+
+/**
+ * Parses assembly name and chromosome from a combined string in BigMaf format.
+ *
+ * Uses simple dot splitting: org.chr where org is before the first dot,
+ * chr is everything after the first dot.
+ */
+export function parseAssemblyAndChrSimple(
+  organismChr: string,
+): ParsedAssemblyName {
+  const dotIndex = organismChr.indexOf('.')
+  if (dotIndex === -1) {
+    return {
+      assemblyName: organismChr,
+      chr: '',
+    }
+  }
+  return {
+    assemblyName: organismChr.slice(0, dotIndex),
+    chr: organismChr.slice(dotIndex + 1),
+  }
+}
+
+/**
+ * Selects the appropriate sequence from alignments based on the lookup order:
+ * 1. refAssemblyName config value (if provided)
+ * 2. query.assemblyName (from the region being queried)
+ * 3. firstAssemblyNameFound (fallback to first assembly in data)
+ */
+export function selectReferenceSequence(
+  alignments: Record<string, { seq: string }>,
+  refAssemblyName: string | undefined,
+  queryAssemblyName: string | undefined,
+  firstAssemblyNameFound: string | undefined,
+): string | undefined {
+  let entry
+  if (refAssemblyName) {
+    entry = alignments[refAssemblyName]
+    if (entry) {
+      return entry.seq
+    }
+  }
+  if (queryAssemblyName) {
+    entry = alignments[queryAssemblyName]
+    if (entry) {
+      return entry.seq
+    }
+  }
+  if (firstAssemblyNameFound) {
+    entry = alignments[firstAssemblyNameFound]
+    if (entry) {
+      return entry.seq
+    }
+  }
+  return undefined
+}

package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.d.ts

@@ -1,11 +0,0 @@
-import React from 'react';
-import type { LinearMafDisplayModel } from '../../stateModel';
-declare const GetSequenceDialog: ({ onClose, model, selectionCoords, }: {
-    onClose: () => void;
-    model: LinearMafDisplayModel;
-    selectionCoords?: {
-        dragStartX: number;
-        dragEndX: number;
-    };
-}) => React.JSX.Element;
-export default GetSequenceDialog;

package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js

@@ -1,97 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, TextField, ToggleButton, ToggleButtonGroup, } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import { useSequences } from '../../../util/useSequences';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
-    textAreaInput: {
-        fontFamily: 'monospace',
-        whiteSpace: 'pre',
-        overflowX: 'auto',
-    },
-    ml: {
-        marginLeft: 10,
-    },
-});
-const GetSequenceDialog = observer(function ({ onClose, model, selectionCoords, }) {
-    const [showAllLetters, setShowAllLetters] = useState(true);
-    const { classes } = useStyles();
-    const { sequence, loading, error } = useSequences({
-        model,
-        selectionCoords,
-        showAllLetters,
-    });
-    const sequenceTooLarge = sequence ? sequence.length > 1_000_000 : false;
-    return (React.createElement(Dialog, { open: true, onClose: onClose, title: "Subsequence Data", maxWidth: "xl" },
-        React.createElement(DialogContent, null,
-            React.createElement("div", { style: {
-                    display: 'flex',
-                    alignItems: 'center',
-                    marginBottom: '16px',
-                } },
-                React.createElement(ToggleButtonGroup, { value: showAllLetters, exclusive: true, size: "small", onChange: (_event, newDisplayMode) => {
-                        if (newDisplayMode !== null) {
-                            setShowAllLetters(newDisplayMode);
-                        }
-                    } },
-                    React.createElement(ToggleButton, { value: true }, "Show All Letters"),
-                    React.createElement(ToggleButton, { value: false }, "Show Only Differences")),
-                React.createElement("div", { style: { flexGrow: 1 } }),
-                React.createElement(Button, { variant: "contained", color: "primary", disabled: loading || !sequence, onClick: () => {
-                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                        ;
-                        (async () => {
-                            try {
-                                await navigator.clipboard.writeText(sequence);
-                                getSession(model).notify('Sequence copied to clipboard', 'info');
-                            }
-                            catch (e) {
-                                console.error(e);
-                                getSession(model).notifyError(`${e}`, e);
-                            }
-                        })();
-                    } }, "Copy to Clipboard"),
-                React.createElement(Button, { variant: "contained", color: "secondary", disabled: loading || !sequence, onClick: () => {
-                        try {
-                            const url = URL.createObjectURL(new Blob([sequence], { type: 'text/plain' }));
-                            // Create a temporary anchor element
-                            const a = document.createElement('a');
-                            a.href = url;
-                            a.download = 'sequence.fasta';
-                            // Trigger the download
-                            document.body.append(a);
-                            a.click();
-                            // Clean up
-                            a.remove();
-                            URL.revokeObjectURL(url);
-                            getSession(model).notify('Sequence downloaded', 'info');
-                        }
-                        catch (e) {
-                            console.error(e);
-                            getSession(model).notifyError(`${e}`, e);
-                        }
-                    } }, "Download")),
-            error ? (React.createElement(ErrorMessage, { error: error })) : (React.createElement(React.Fragment, null,
-                loading ? React.createElement(LoadingEllipses, null) : null,
-                React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: loading
-                        ? 'Loading...'
-                        : sequenceTooLarge
-                            ? 'Reference sequence too large to display, use the download FASTA button'
-                            : sequence, slotProps: {
-                        input: {
-                            readOnly: true,
-                            classes: {
-                                input: classes.textAreaInput,
-                            },
-                        },
-                    } })))),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "outlined", onClick: onClose }, "Close"))));
-});
-export default GetSequenceDialog;
-//# sourceMappingURL=GetSequenceDialog.js.map

package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"GetSequenceDialog.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,YAAY,EACZ,iBAAiB,GAClB,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,EAAE,YAAY,EAAE,MAAM,4BAA4B,CAAA;AAIzD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,aAAa,EAAE;QACb,UAAU,EAAE,WAAW;QACvB,UAAU,EAAE,KAAK;QACjB,SAAS,EAAE,MAAM;KAClB;IACD,EAAE,EAAE;QACF,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,OAAO,EACP,KAAK,EACL,eAAe,GAQhB;IACC,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC1D,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,YAAY,CAAC;QAChD,KAAK;QACL,eAAe;QACf,cAAc;KACf,CAAC,CAAA;IACF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,SAAS,CAAC,CAAC,CAAC,KAAK,CAAA;IAEvE,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,OAAO,EAAE,KAAK,EAAC,kBAAkB,EAAC,QAAQ,EAAC,IAAI;QACnE,oBAAC,aAAa;YACZ,6BACE,KAAK,EAAE;oBACL,OAAO,EAAE,MAAM;oBACf,UAAU,EAAE,QAAQ;oBACpB,YAAY,EAAE,MAAM;iBACrB;gBAED,oBAAC,iBAAiB,IAChB,KAAK,EAAE,cAAc,EACrB,SAAS,QACT,IAAI,EAAC,OAAO,EACZ,QAAQ,EAAE,CAAC,MAAM,EAAE,cAAc,EAAE,EAAE;wBACnC,IAAI,cAAc,KAAK,IAAI,EAAE,CAAC;4BAC5B,iBAAiB,CAAC,cAAc,CAAC,CAAA;wBACnC,CAAC;oBACH,CAAC;oBAED,oBAAC,YAAY,IAAC,KAAK,EAAE,IAAI,uBAAiC;oBAC1D,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,4BAAsC,CAC9C;gBACpB,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,GAAI;gBAC/B,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,QAAQ,EAAE,OAAO,IAAI,CAAC,QAAQ,EAC9B,OAAO,EAAE,GAAG,EAAE;wBACZ,mEAAmE;wBACnE,CAAC;wBAAA,CAAC,KAAK,IAAI,EAAE;4BACX,IAAI,CAAC;gCACH,MAAM,SAAS,CAAC,SAAS,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;gCAC7C,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CACtB,8BAA8B,EAC9B,MAAM,CACP,CAAA;4BACH,CAAC;4BAAC,OAAO,CAAC,EAAE,CAAC;gCACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gCAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;4BAC1C,CAAC;wBACH,CAAC,CAAC,EAAE,CAAA;oBACN,CAAC,wBAGM;gBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,QAAQ,EAAE,OAAO,IAAI,CAAC,QAAQ,EAC9B,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,CAAC;4BACH,MAAM,GAAG,GAAG,GAAG,CAAC,eAAe,CAC7B,IAAI,IAAI,CAAC,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAC7C,CAAA;4BAED,oCAAoC;4BACpC,MAAM,CAAC,GAAG,QAAQ,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;4BACrC,CAAC,CAAC,IAAI,GAAG,GAAG,CAAA;4BACZ,CAAC,CAAC,QAAQ,GAAG,gBAAgB,CAAA;4BAE7B,uBAAuB;4BACvB,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;4BACvB,CAAC,CAAC,KAAK,EAAE,CAAA;4BAET,WAAW;4BACX,CAAC,CAAC,MAAM,EAAE,CAAA;4BACV,GAAG,CAAC,eAAe,CAAC,GAAG,CAAC,CAAA;4BACxB,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,qBAAqB,EAAE,MAAM,CAAC,CAAA;wBACzD,CAAC;wBAAC,OAAO,CAAC,EAAE,CAAC;4BACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;4BAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;wBAC1C,CAAC;oBACH,CAAC,eAGM,CACL;YAEL,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAC/B,CAAC,CAAC,CAAC,CACF;gBACG,OAAO,CAAC,CAAC,CAAC,oBAAC,eAAe,OAAG,CAAC,CAAC,CAAC,IAAI;gBACrC,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,QAAQ,EAAE,gBAAgB,EAC1B,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,SAAS,QACT,KAAK,EACH,OAAO;wBACL,CAAC,CAAC,YAAY;wBACd,CAAC,CAAC,gBAAgB;4BAChB,CAAC,CAAC,wEAAwE;4BAC1E,CAAC,CAAC,QAAQ,EAEhB,SAAS,EAAE;wBACT,KAAK,EAAE;4BACL,QAAQ,EAAE,IAAI;4BACd,OAAO,EAAE;gCACP,KAAK,EAAE,OAAO,CAAC,aAAa;6BAC7B;yBACF;qBACF,GACD,CACD,CACJ,CACa;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IAAC,KAAK,EAAC,SAAS,EAAC,OAAO,EAAC,UAAU,EAAC,OAAO,EAAE,OAAO,YAElD,CACK,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/LinearMafDisplay/components/util.d.ts

@@ -1 +0,0 @@
-export declare function max(arr: number[], init?: number): number;

package/dist/LinearMafDisplay/components/util.js

@@ -1,8 +0,0 @@
-export function max(arr, init = Number.NEGATIVE_INFINITY) {
-    let max = init;
-    for (const entry of arr) {
-        max = Math.max(entry, max);
-    }
-    return max;
-}
-//# sourceMappingURL=util.js.map

package/dist/LinearMafDisplay/components/util.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,GAAG,CAAC,GAAa,EAAE,IAAI,GAAG,MAAM,CAAC,iBAAiB;IAChE,IAAI,GAAG,GAAG,IAAI,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,GAAG,EAAE,CAAC;QACxB,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAC5B,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/dist/LinearMafRenderer/components/util.d.ts

@@ -1 +0,0 @@
-export declare function minElt<T>(arr: Iterable<T>, cb: (arg: T) => number): T | undefined;

package/dist/LinearMafRenderer/components/util.js

@@ -1,13 +0,0 @@
-export function minElt(arr, cb) {
-    let min = Infinity;
-    let minElement;
-    for (const entry of arr) {
-        const val = cb(entry);
-        if (val < min) {
-            min = val;
-            minElement = entry;
-        }
-    }
-    return minElement;
-}
-//# sourceMappingURL=util.js.map

package/dist/LinearMafRenderer/components/util.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/components/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,MAAM,CAAI,GAAgB,EAAE,EAAsB;IAChE,IAAI,GAAG,GAAG,QAAQ,CAAA;IAClB,IAAI,UAAyB,CAAA;IAC7B,KAAK,MAAM,KAAK,IAAI,GAAG,EAAE,CAAC;QACxB,MAAM,GAAG,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;QAErB,IAAI,GAAG,GAAG,GAAG,EAAE,CAAC;YACd,GAAG,GAAG,GAAG,CAAA;YACT,UAAU,GAAG,KAAK,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,UAAU,CAAA;AACnB,CAAC"}

package/dist/util/fetchSequences.d.ts

@@ -1,18 +0,0 @@
-import type { LinearMafDisplayModel } from '../LinearMafDisplay/stateModel';
-interface SelectionCoords {
-    dragStartX: number;
-    dragEndX: number;
-}
-/**
- * Fetch sequences for the given selection coordinates
- * @param model - The LinearMafDisplayModel
- * @param selectionCoords - The selection coordinates (dragStartX and dragEndX)
- * @param showAllLetters - Whether to show all letters or just the differences
- * @returns Promise that resolves to the FASTA sequence
- */
-export declare function fetchSequences({ model, selectionCoords, showAllLetters, }: {
-    model: LinearMafDisplayModel;
-    selectionCoords: SelectionCoords;
-    showAllLetters: boolean;
-}): Promise<string>;
-export {};

package/dist/util/fetchSequences.js

@@ -1,39 +0,0 @@
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-/**
- * Fetch sequences for the given selection coordinates
- * @param model - The LinearMafDisplayModel
- * @param selectionCoords - The selection coordinates (dragStartX and dragEndX)
- * @param showAllLetters - Whether to show all letters or just the differences
- * @returns Promise that resolves to the FASTA sequence
- */
-export async function fetchSequences({ model, selectionCoords, showAllLetters, }) {
-    const { samples, adapterConfig } = model;
-    const { rpcManager } = getSession(model);
-    const sessionId = getRpcSessionId(model);
-    const view = getContainingView(model);
-    const { refName, assemblyName } = view.displayedRegions[0];
-    const { dragStartX, dragEndX } = selectionCoords;
-    const [s, e] = [
-        Math.min(dragStartX, dragEndX),
-        Math.max(dragStartX, dragEndX),
-    ];
-    const fastaSequence = (await rpcManager.call(sessionId, 'MafGetSequences', {
-        sessionId,
-        adapterConfig,
-        samples,
-        showAllLetters,
-        regions: [
-            {
-                refName,
-                start: view.pxToBp(s).coord - 1,
-                end: view.pxToBp(e).coord,
-                assemblyName,
-            },
-        ],
-    }));
-    return fastaSequence
-        .map((r, idx) => `>${samples[idx].label}\n${r}`)
-        .join('\n');
-}
-//# sourceMappingURL=fetchSequences.js.map

package/dist/util/fetchSequences.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"fetchSequences.js","sourceRoot":"","sources":["../../src/util/fetchSequences.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAClE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAU3D;;;;;;GAMG;AACH,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,EACnC,KAAK,EACL,eAAe,EACf,cAAc,GAKf;IACC,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IACxC,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,eAAe,CAAC,KAAK,CAAC,CAAA;IACxC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAE,CAAA;IAC3D,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,eAAe,CAAA;IAChD,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG;QACb,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,QAAQ,CAAC;QAC9B,IAAI,CAAC,GAAG,CAAC,UAAU,EAAE,QAAQ,CAAC;KAC/B,CAAA;IAED,MAAM,aAAa,GAAG,CAAC,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QACzE,SAAS;QACT,aAAa;QACb,OAAO;QACP,cAAc;QACd,OAAO,EAAE;YACP;gBACE,OAAO;gBACP,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC;gBAC/B,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK;gBACzB,YAAY;aACb;SACF;KACF,CAAC,CAAa,CAAA;IAEf,OAAO,aAAa;SACjB,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CAAC,IAAI,OAAQ,CAAC,GAAG,CAAE,CAAC,KAAK,KAAK,CAAC,EAAE,CAAC;SACjD,IAAI,CAAC,IAAI,CAAC,CAAA;AACf,CAAC"}