jbrowse-plugin-msaview 2.6.2 → 2.6.4

package/dist/MsaViewPanel/pairwiseAlignment.js

@@ -1,138 +0,0 @@
-import BLOSUM62 from './blosum62';
-function getScore(a, b) {
-    return BLOSUM62[a.toUpperCase()]?.[b.toUpperCase()] ?? -4;
-}
-const GAP_OPEN = -10;
-const GAP_EXTEND = -0.5;
-export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_EXTEND) {
-    const m = seq1.length;
-    const n = seq2.length;
-    const M = [];
-    const Ix = [];
-    const Iy = [];
-    for (let i = 0; i <= m; i++) {
-        M[i] = [];
-        Ix[i] = [];
-        Iy[i] = [];
-        for (let j = 0; j <= n; j++) {
-            M[i][j] = -Infinity;
-            Ix[i][j] = -Infinity;
-            Iy[i][j] = -Infinity;
-        }
-    }
-    M[0][0] = 0;
-    for (let i = 1; i <= m; i++) {
-        Ix[i][0] = gapOpen + (i - 1) * gapExtend;
-    }
-    for (let j = 1; j <= n; j++) {
-        Iy[0][j] = gapOpen + (j - 1) * gapExtend;
-    }
-    for (let i = 1; i <= m; i++) {
-        for (let j = 1; j <= n; j++) {
-            const matchScore = getScore(seq1[i - 1], seq2[j - 1]);
-            M[i][j] =
-                Math.max(M[i - 1][j - 1], Ix[i - 1][j - 1], Iy[i - 1][j - 1]) +
-                    matchScore;
-            Ix[i][j] = Math.max(M[i - 1][j] + gapOpen, Ix[i - 1][j] + gapExtend);
-            Iy[i][j] = Math.max(M[i][j - 1] + gapOpen, Iy[i][j - 1] + gapExtend);
-        }
-    }
-    let alignedSeq1 = '';
-    let alignedSeq2 = '';
-    let i = m;
-    let j = n;
-    const mScore = M[m][n];
-    const ixScore = Ix[m][n];
-    const iyScore = Iy[m][n];
-    const score = Math.max(mScore, ixScore, iyScore);
-    let currentMatrix = score === mScore ? 'M' : score === ixScore ? 'Ix' : 'Iy';
-    while (i > 0 || j > 0) {
-        if (currentMatrix === 'M' && i > 0 && j > 0) {
-            alignedSeq1 = seq1[i - 1] + alignedSeq1;
-            alignedSeq2 = seq2[j - 1] + alignedSeq2;
-            const matchScore = getScore(seq1[i - 1], seq2[j - 1]);
-            const prevM = M[i - 1][j - 1];
-            const prevIx = Ix[i - 1][j - 1];
-            const currentScore = M[i][j];
-            if (currentScore === prevM + matchScore) {
-                currentMatrix = 'M';
-            }
-            else if (currentScore === prevIx + matchScore) {
-                currentMatrix = 'Ix';
-            }
-            else {
-                currentMatrix = 'Iy';
-            }
-            i--;
-            j--;
-        }
-        else if (currentMatrix === 'Ix' && i > 0) {
-            alignedSeq1 = seq1[i - 1] + alignedSeq1;
-            alignedSeq2 = '-' + alignedSeq2;
-            const ixScore = Ix[i][j];
-            const mScore = M[i - 1][j] + gapOpen;
-            currentMatrix = ixScore === mScore ? 'M' : 'Ix';
-            i--;
-        }
-        else if (j > 0) {
-            alignedSeq1 = '-' + alignedSeq1;
-            alignedSeq2 = seq2[j - 1] + alignedSeq2;
-            const iyScore = Iy[i][j];
-            const mScore = M[i][j - 1] + gapOpen;
-            currentMatrix = iyScore === mScore ? 'M' : 'Iy';
-            j--;
-        }
-        else {
-            break;
-        }
-    }
-    return { alignedSeq1, alignedSeq2, score };
-}
-function buildConsensus(alignedSeq1, alignedSeq2) {
-    let consensus = '';
-    for (let i = 0; i < alignedSeq1.length; i++) {
-        const a = alignedSeq1[i];
-        const b = alignedSeq2[i];
-        const match = a !== '-' && b !== '-' && a.toUpperCase() === b.toUpperCase();
-        consensus += match ? '|' : ' ';
-    }
-    return consensus;
-}
-export function runPairwiseAlignment(seq1, seq2) {
-    const { alignedSeq1, alignedSeq2 } = needlemanWunsch(seq1, seq2);
-    return {
-        consensus: buildConsensus(alignedSeq1, alignedSeq2),
-        alns: [
-            { id: 'msa', seq: alignedSeq1 },
-            { id: 'structure', seq: alignedSeq2 },
-        ],
-    };
-}
-export function buildAlignmentMaps(pairwiseAlignment) {
-    const seq1 = pairwiseAlignment.alns[0].seq;
-    const seq2 = pairwiseAlignment.alns[1].seq;
-    if (seq1.length !== seq2.length) {
-        throw new Error('Aligned sequences must have same length');
-    }
-    let pos1 = 0;
-    let pos2 = 0;
-    const seq1ToSeq2 = new Map();
-    const seq2ToSeq1 = new Map();
-    for (let i = 0; i < seq1.length; i++) {
-        const c1 = seq1[i];
-        const c2 = seq2[i];
-        if (c1 !== '-' && c2 !== '-') {
-            seq1ToSeq2.set(pos1, pos2);
-            seq2ToSeq1.set(pos2, pos1);
-            pos1++;
-            pos2++;
-        }
-        else if (c1 === '-') {
-            pos2++;
-        }
-        else {
-            pos1++;
-        }
-    }
-    return { seq1ToSeq2, seq2ToSeq1 };
-}

package/dist/MsaViewPanel/pairwiseAlignment.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/MsaViewPanel/pairwiseAlignment.test.js

@@ -1,111 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { buildAlignmentMaps, needlemanWunsch, runPairwiseAlignment, } from './pairwiseAlignment';
-describe('needlemanWunsch', () => {
-    test('identical sequences align perfectly', () => {
-        const result = needlemanWunsch('MKAA', 'MKAA');
-        expect(result.alignedSeq1).toBe('MKAA');
-        expect(result.alignedSeq2).toBe('MKAA');
-        expect(result.score).toBeGreaterThan(0);
-    });
-    test('aligned sequences have same length', () => {
-        const result = needlemanWunsch('MKAAYLSMFG', 'MKAYLSMFG');
-        expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length);
-    });
-    test('aligned sequences preserve original characters', () => {
-        const seq1 = 'MKAAYLSMFG';
-        const seq2 = 'MKAYLSMFG';
-        const result = needlemanWunsch(seq1, seq2);
-        expect(result.alignedSeq1.replaceAll('-', '')).toBe(seq1);
-        expect(result.alignedSeq2.replaceAll('-', '')).toBe(seq2);
-    });
-    test('handles empty sequences', () => {
-        const result = needlemanWunsch('', '');
-        expect(result.alignedSeq1).toBe('');
-        expect(result.alignedSeq2).toBe('');
-    });
-    test('handles one empty sequence', () => {
-        const result = needlemanWunsch('MKA', '');
-        expect(result.alignedSeq1.replaceAll('-', '')).toBe('MKA');
-        expect(result.alignedSeq2.replaceAll('-', '')).toBe('');
-        expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length);
-    });
-});
-describe('runPairwiseAlignment', () => {
-    test('returns PairwiseAlignment format', () => {
-        const result = runPairwiseAlignment('MKAA', 'MKAA');
-        expect(result.consensus).toBeDefined();
-        expect(result.alns).toHaveLength(2);
-        expect(result.alns[0].id).toBe('msa');
-        expect(result.alns[1].id).toBe('structure');
-    });
-    test('consensus marks matches with pipe', () => {
-        const result = runPairwiseAlignment('MKAA', 'MKAA');
-        expect(result.consensus).toBe('||||');
-    });
-    test('consensus marks gaps with space', () => {
-        const result = runPairwiseAlignment('MKAA', 'MKA');
-        expect(result.consensus).toContain(' ');
-    });
-    test('consensus marks mismatches with space', () => {
-        const result = runPairwiseAlignment('MKAA', 'MKBA');
-        // A vs B should be a space in consensus
-        expect(result.consensus).toContain(' ');
-    });
-});
-describe('buildAlignmentMaps', () => {
-    test('builds bidirectional maps for identical sequences', () => {
-        const alignment = runPairwiseAlignment('MKAA', 'MKAA');
-        const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment);
-        expect(seq1ToSeq2.get(0)).toBe(0);
-        expect(seq1ToSeq2.get(1)).toBe(1);
-        expect(seq1ToSeq2.get(2)).toBe(2);
-        expect(seq1ToSeq2.get(3)).toBe(3);
-        expect(seq2ToSeq1.get(0)).toBe(0);
-        expect(seq2ToSeq1.get(1)).toBe(1);
-        expect(seq2ToSeq1.get(2)).toBe(2);
-        expect(seq2ToSeq1.get(3)).toBe(3);
-    });
-    test('maps are inverses of each other for matched positions', () => {
-        const alignment = runPairwiseAlignment('MKAAYLSMFG', 'MKAYLSMFG');
-        const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment);
-        // For every mapped position, the inverse should return the original
-        for (const [pos1, pos2] of seq1ToSeq2) {
-            expect(seq2ToSeq1.get(pos2)).toBe(pos1);
-        }
-    });
-    test('handles gaps correctly - positions without counterpart are not in map', () => {
-        // Aligning 'MKAAA' with 'MKA' should result in gaps
-        const alignment = runPairwiseAlignment('MKAAA', 'MKA');
-        const { seq1ToSeq2 } = buildAlignmentMaps(alignment);
-        // seq1 has 5 positions, seq2 has 3
-        // Only matched positions should be in the map
-        expect(seq1ToSeq2.size).toBeLessThanOrEqual(3);
-    });
-    test('handles real protein sequence alignment', () => {
-        const msaSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG';
-        const structureSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG';
-        const alignment = runPairwiseAlignment(msaSeq, structureSeq);
-        const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment);
-        // Identical sequences should have 1:1 mapping
-        expect(seq1ToSeq2.size).toBe(msaSeq.length);
-        expect(seq2ToSeq1.size).toBe(structureSeq.length);
-        // Check a few positions
-        expect(seq1ToSeq2.get(0)).toBe(0);
-        expect(seq1ToSeq2.get(10)).toBe(10);
-        expect(seq2ToSeq1.get(20)).toBe(20);
-    });
-    test('handles sequences with insertions/deletions', () => {
-        // MSA sequence has an extra 'X' in the middle
-        const msaSeq = 'MKAXYLSMFG';
-        const structureSeq = 'MKAYLSMFG';
-        const alignment = runPairwiseAlignment(msaSeq, structureSeq);
-        const { seq1ToSeq2 } = buildAlignmentMaps(alignment);
-        // Positions before the insertion should map correctly
-        expect(seq1ToSeq2.get(0)).toBe(0); // M
-        expect(seq1ToSeq2.get(1)).toBe(1); // K
-        expect(seq1ToSeq2.get(2)).toBe(2); // A
-        // The mapping should handle the offset after insertion
-        // (exact behavior depends on alignment algorithm)
-        expect(seq1ToSeq2.size).toBeLessThanOrEqual(structureSeq.length);
-    });
-});

package/src/MsaViewPanel/components/ConnectStructureDialog.tsx

@@ -1,154 +0,0 @@
-import React, { useState } from 'react'
-
-import { Dialog, ErrorMessage } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  FormControl,
-  InputLabel,
-  MenuItem,
-  Select,
-  Typography,
-} from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-import { getProteinViews } from '../structureConnection'
-
-import type { JBrowsePluginMsaViewModel } from '../model'
-
-const useStyles = makeStyles()(theme => ({
-  formControl: {
-    marginBottom: theme.spacing(2),
-  },
-}))
-
-const ConnectStructureDialog = observer(function ConnectStructureDialog({
-  model,
-  handleClose,
-}: {
-  model: JBrowsePluginMsaViewModel
-  handleClose: () => void
-}) {
-  const { classes } = useStyles()
-  const session = getSession(model)
-  const [selectedViewId, setSelectedViewId] = useState('')
-  const [selectedStructureIdx, setSelectedStructureIdx] = useState(0)
-  const [selectedMsaRow, setSelectedMsaRow] = useState(model.querySeqName)
-  const [error, setError] = useState<string>()
-
-  const proteinViews = getProteinViews(session.views)
-
-  const selectedView = proteinViews.find(v => v.id === selectedViewId)
-  const structures = selectedView?.structures ?? []
-
-  const msaRowNames = model.rows.map(r => r[0])
-
-  const handleConnect = () => {
-    if (!selectedViewId) {
-      setError('Please select a protein view')
-      return
-    }
-
-    try {
-      model.connectToStructure(
-        selectedViewId,
-        selectedStructureIdx,
-        selectedMsaRow,
-      )
-      handleClose()
-    } catch (e) {
-      setError(e instanceof Error ? e.message : String(e))
-    }
-  }
-
-  return (
-    <Dialog
-      maxWidth="sm"
-      title="Connect to Protein Structure"
-      open
-      onClose={handleClose}
-    >
-      <DialogContent>
-        {proteinViews.length === 0 ? (
-          <Typography color="textSecondary">
-            No protein views are currently open. Please open a protein structure
-            view first.
-          </Typography>
-        ) : (
-          <>
-            <FormControl fullWidth className={classes.formControl}>
-              <InputLabel>Protein View</InputLabel>
-              <Select
-                value={selectedViewId}
-                label="Protein View"
-                onChange={e => {
-                  setSelectedViewId(e.target.value)
-                  setSelectedStructureIdx(0)
-                }}
-              >
-                {proteinViews.map(view => (
-                  <MenuItem key={view.id} value={view.id}>
-                    {view.displayName ?? `ProteinView ${view.id}`}
-                  </MenuItem>
-                ))}
-              </Select>
-            </FormControl>
-
-            {structures.length > 1 ? (
-              <FormControl fullWidth className={classes.formControl}>
-                <InputLabel>Structure</InputLabel>
-                <Select
-                  value={selectedStructureIdx}
-                  label="Structure"
-                  onChange={e => {
-                    setSelectedStructureIdx(e.target.value)
-                  }}
-                >
-                  {structures.map((structure, idx) => (
-                    <MenuItem key={idx} value={idx}>
-                      {structure.url ?? `Structure ${idx + 1}`}
-                    </MenuItem>
-                  ))}
-                </Select>
-              </FormControl>
-            ) : null}
-
-            <FormControl fullWidth className={classes.formControl}>
-              <InputLabel>MSA Row</InputLabel>
-              <Select
-                value={selectedMsaRow}
-                label="MSA Row"
-                onChange={e => {
-                  setSelectedMsaRow(e.target.value)
-                }}
-              >
-                {msaRowNames.map(name => (
-                  <MenuItem key={name} value={name}>
-                    {name}
-                  </MenuItem>
-                ))}
-              </Select>
-            </FormControl>
-
-            {error ? <ErrorMessage error={error} /> : null}
-          </>
-        )}
-      </DialogContent>
-      <DialogActions>
-        <Button onClick={handleClose}>Cancel</Button>
-        <Button
-          onClick={handleConnect}
-          variant="contained"
-          disabled={proteinViews.length === 0 || !selectedViewId}
-        >
-          Connect
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-})
-
-export default ConnectStructureDialog

package/src/MsaViewPanel/pairwiseAlignment.test.ts

@@ -1,140 +0,0 @@
-import { describe, expect, test } from 'vitest'
-
-import {
-  buildAlignmentMaps,
-  needlemanWunsch,
-  runPairwiseAlignment,
-} from './pairwiseAlignment'
-
-describe('needlemanWunsch', () => {
-  test('identical sequences align perfectly', () => {
-    const result = needlemanWunsch('MKAA', 'MKAA')
-    expect(result.alignedSeq1).toBe('MKAA')
-    expect(result.alignedSeq2).toBe('MKAA')
-    expect(result.score).toBeGreaterThan(0)
-  })
-
-  test('aligned sequences have same length', () => {
-    const result = needlemanWunsch('MKAAYLSMFG', 'MKAYLSMFG')
-    expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length)
-  })
-
-  test('aligned sequences preserve original characters', () => {
-    const seq1 = 'MKAAYLSMFG'
-    const seq2 = 'MKAYLSMFG'
-    const result = needlemanWunsch(seq1, seq2)
-    expect(result.alignedSeq1.replaceAll('-', '')).toBe(seq1)
-    expect(result.alignedSeq2.replaceAll('-', '')).toBe(seq2)
-  })
-
-  test('handles empty sequences', () => {
-    const result = needlemanWunsch('', '')
-    expect(result.alignedSeq1).toBe('')
-    expect(result.alignedSeq2).toBe('')
-  })
-
-  test('handles one empty sequence', () => {
-    const result = needlemanWunsch('MKA', '')
-    expect(result.alignedSeq1.replaceAll('-', '')).toBe('MKA')
-    expect(result.alignedSeq2.replaceAll('-', '')).toBe('')
-    expect(result.alignedSeq1.length).toBe(result.alignedSeq2.length)
-  })
-})
-
-describe('runPairwiseAlignment', () => {
-  test('returns PairwiseAlignment format', () => {
-    const result = runPairwiseAlignment('MKAA', 'MKAA')
-    expect(result.consensus).toBeDefined()
-    expect(result.alns).toHaveLength(2)
-    expect(result.alns[0].id).toBe('msa')
-    expect(result.alns[1].id).toBe('structure')
-  })
-
-  test('consensus marks matches with pipe', () => {
-    const result = runPairwiseAlignment('MKAA', 'MKAA')
-    expect(result.consensus).toBe('||||')
-  })
-
-  test('consensus marks gaps with space', () => {
-    const result = runPairwiseAlignment('MKAA', 'MKA')
-    expect(result.consensus).toContain(' ')
-  })
-
-  test('consensus marks mismatches with space', () => {
-    const result = runPairwiseAlignment('MKAA', 'MKBA')
-    // A vs B should be a space in consensus
-    expect(result.consensus).toContain(' ')
-  })
-})
-
-describe('buildAlignmentMaps', () => {
-  test('builds bidirectional maps for identical sequences', () => {
-    const alignment = runPairwiseAlignment('MKAA', 'MKAA')
-    const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment)
-
-    expect(seq1ToSeq2.get(0)).toBe(0)
-    expect(seq1ToSeq2.get(1)).toBe(1)
-    expect(seq1ToSeq2.get(2)).toBe(2)
-    expect(seq1ToSeq2.get(3)).toBe(3)
-
-    expect(seq2ToSeq1.get(0)).toBe(0)
-    expect(seq2ToSeq1.get(1)).toBe(1)
-    expect(seq2ToSeq1.get(2)).toBe(2)
-    expect(seq2ToSeq1.get(3)).toBe(3)
-  })
-
-  test('maps are inverses of each other for matched positions', () => {
-    const alignment = runPairwiseAlignment('MKAAYLSMFG', 'MKAYLSMFG')
-    const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment)
-
-    // For every mapped position, the inverse should return the original
-    for (const [pos1, pos2] of seq1ToSeq2) {
-      expect(seq2ToSeq1.get(pos2)).toBe(pos1)
-    }
-  })
-
-  test('handles gaps correctly - positions without counterpart are not in map', () => {
-    // Aligning 'MKAAA' with 'MKA' should result in gaps
-    const alignment = runPairwiseAlignment('MKAAA', 'MKA')
-    const { seq1ToSeq2 } = buildAlignmentMaps(alignment)
-
-    // seq1 has 5 positions, seq2 has 3
-    // Only matched positions should be in the map
-    expect(seq1ToSeq2.size).toBeLessThanOrEqual(3)
-  })
-
-  test('handles real protein sequence alignment', () => {
-    const msaSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG'
-    const structureSeq = 'MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG'
-
-    const alignment = runPairwiseAlignment(msaSeq, structureSeq)
-    const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment)
-
-    // Identical sequences should have 1:1 mapping
-    expect(seq1ToSeq2.size).toBe(msaSeq.length)
-    expect(seq2ToSeq1.size).toBe(structureSeq.length)
-
-    // Check a few positions
-    expect(seq1ToSeq2.get(0)).toBe(0)
-    expect(seq1ToSeq2.get(10)).toBe(10)
-    expect(seq2ToSeq1.get(20)).toBe(20)
-  })
-
-  test('handles sequences with insertions/deletions', () => {
-    // MSA sequence has an extra 'X' in the middle
-    const msaSeq = 'MKAXYLSMFG'
-    const structureSeq = 'MKAYLSMFG'
-
-    const alignment = runPairwiseAlignment(msaSeq, structureSeq)
-    const { seq1ToSeq2 } = buildAlignmentMaps(alignment)
-
-    // Positions before the insertion should map correctly
-    expect(seq1ToSeq2.get(0)).toBe(0) // M
-    expect(seq1ToSeq2.get(1)).toBe(1) // K
-    expect(seq1ToSeq2.get(2)).toBe(2) // A
-
-    // The mapping should handle the offset after insertion
-    // (exact behavior depends on alignment algorithm)
-    expect(seq1ToSeq2.size).toBeLessThanOrEqual(structureSeq.length)
-  })
-})