react-msaview 5.0.5 → 5.0.7

package/dist/rowCoordinateCalculations.test.js

@@ -1,224 +0,0 @@
-import { expect, test } from 'vitest';
-import { globalColToSeqPos, globalColToVisibleCol, visibleColToGlobalCol, visibleColToSeqPos, } from "./rowCoordinateCalculations.js";
-// Tests for visibleColToGlobalCol (visible → global)
-test('visibleColToGlobalCol with blanks at positions [2, 5, 8]', () => {
-    const blanks = [2, 5, 8];
-    [
-        [0, 0],
-        [1, 1],
-        [2, 3],
-        [3, 4],
-        [4, 6],
-        [5, 7],
-        [6, 9],
-        [7, 10],
-    ].forEach(r => {
-        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
-    });
-});
-test('visibleColToGlobalCol with no blanks', () => {
-    const blanks = [];
-    [
-        [0, 0],
-        [1, 1],
-        [5, 5],
-        [10, 10],
-    ].forEach(r => {
-        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
-    });
-});
-test('visibleColToGlobalCol with consecutive blanks', () => {
-    const blanks = [2, 3, 4, 7, 8];
-    [
-        [0, 0],
-        [1, 1],
-        [2, 5], // After position 1, skip 3 blanks (2,3,4)
-        [3, 6], // Next position
-        [4, 9], // After position 3, skip 2 blanks (7,8)
-        [5, 10],
-    ].forEach(r => {
-        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
-    });
-});
-test('visibleColToGlobalCol with blanks at the beginning', () => {
-    const blanks = [1, 2, 5];
-    [
-        [0, 0],
-        [1, 3], // After position 0, skip 2 blanks (1,2)
-        [2, 4],
-        [3, 6], // After position 2, skip 1 blank (5)
-        [4, 7],
-    ].forEach(r => {
-        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
-    });
-});
-test('visibleColToGlobalCol with position exceeding blanks array', () => {
-    const blanks = [2, 5];
-    [
-        [0, 0],
-        [1, 1],
-        [2, 3], // After position 1, skip 1 blank (2)
-        [3, 4],
-        [4, 6], // After position 3, skip 1 blank (5)
-        [10, 12], // Far beyond blanks array
-    ].forEach(r => {
-        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
-    });
-});
-// Tests for globalColToVisibleCol (global → visible)
-test('globalColToVisibleCol with blanks at positions [2, 5, 8]', () => {
-    const blanks = [2, 5, 8];
-    // Inverse of visibleColToGlobalCol
-    expect(globalColToVisibleCol(blanks, 0)).toBe(0);
-    expect(globalColToVisibleCol(blanks, 1)).toBe(1);
-    expect(globalColToVisibleCol(blanks, 2)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 3)).toBe(2);
-    expect(globalColToVisibleCol(blanks, 4)).toBe(3);
-    expect(globalColToVisibleCol(blanks, 5)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 6)).toBe(4);
-    expect(globalColToVisibleCol(blanks, 7)).toBe(5);
-    expect(globalColToVisibleCol(blanks, 8)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 9)).toBe(6);
-    expect(globalColToVisibleCol(blanks, 10)).toBe(7);
-});
-test('globalColToVisibleCol with no blanks', () => {
-    const blanks = [];
-    expect(globalColToVisibleCol(blanks, 0)).toBe(0);
-    expect(globalColToVisibleCol(blanks, 5)).toBe(5);
-    expect(globalColToVisibleCol(blanks, 10)).toBe(10);
-});
-test('globalColToVisibleCol with consecutive blanks', () => {
-    const blanks = [2, 3, 4, 7, 8];
-    expect(globalColToVisibleCol(blanks, 0)).toBe(0);
-    expect(globalColToVisibleCol(blanks, 1)).toBe(1);
-    expect(globalColToVisibleCol(blanks, 2)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 3)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 4)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 5)).toBe(2);
-    expect(globalColToVisibleCol(blanks, 6)).toBe(3);
-    expect(globalColToVisibleCol(blanks, 7)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 8)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 9)).toBe(4);
-    expect(globalColToVisibleCol(blanks, 10)).toBe(5);
-});
-// Tests for globalColToSeqPos (global column → sequence position)
-test('globalColToSeqPos with gaps in sequence', () => {
-    const sequence = 'AC-GT-A';
-    expect(globalColToSeqPos(sequence, 0)).toBe(0);
-    expect(globalColToSeqPos(sequence, 1)).toBe(1);
-    expect(globalColToSeqPos(sequence, 2)).toBe(2);
-    // Position 2 is a gap, so count before it is 2
-    expect(globalColToSeqPos(sequence, 3)).toBe(2);
-    expect(globalColToSeqPos(sequence, 4)).toBe(3);
-    expect(globalColToSeqPos(sequence, 5)).toBe(4);
-    // Position 5 is a gap, so count before it is 4
-    expect(globalColToSeqPos(sequence, 6)).toBe(4);
-});
-test('globalColToSeqPos with mixed gap characters (- and .)', () => {
-    const sequence = 'AC.GT-A';
-    expect(globalColToSeqPos(sequence, 0)).toBe(0);
-    expect(globalColToSeqPos(sequence, 1)).toBe(1);
-    // Position 2 is a gap (.), so count before it is 2
-    expect(globalColToSeqPos(sequence, 2)).toBe(2);
-    expect(globalColToSeqPos(sequence, 3)).toBe(2);
-    expect(globalColToSeqPos(sequence, 4)).toBe(3);
-    // Position 5 is a gap (-), so count before it is 4
-    expect(globalColToSeqPos(sequence, 5)).toBe(4);
-    expect(globalColToSeqPos(sequence, 6)).toBe(4);
-});
-test('globalColToSeqPos with no gaps in sequence', () => {
-    const sequence = 'ACGTA';
-    expect(globalColToSeqPos(sequence, 0)).toBe(0);
-    expect(globalColToSeqPos(sequence, 1)).toBe(1);
-    expect(globalColToSeqPos(sequence, 2)).toBe(2);
-    expect(globalColToSeqPos(sequence, 3)).toBe(3);
-    expect(globalColToSeqPos(sequence, 4)).toBe(4);
-});
-test('globalColToSeqPos with all gaps in sequence', () => {
-    const sequence = '-----';
-    expect(globalColToSeqPos(sequence, 0)).toBe(0);
-    expect(globalColToSeqPos(sequence, 1)).toBe(0);
-    expect(globalColToSeqPos(sequence, 2)).toBe(0);
-    expect(globalColToSeqPos(sequence, 3)).toBe(0);
-    expect(globalColToSeqPos(sequence, 4)).toBe(0);
-});
-test('globalColToSeqPos with position exceeding sequence length', () => {
-    const sequence = 'AC-GT';
-    expect(globalColToSeqPos(sequence, 10)).toBe(4);
-});
-// Tests for visibleColToSeqPos (visible column → sequence position)
-test('visibleColToSeqPos returns sequence position or undefined for gaps', () => {
-    const seq = 'AC--GT--CT';
-    expect(visibleColToSeqPos({ seq, visibleCol: 0, blanks: [] })).toBe(0);
-    expect(visibleColToSeqPos({ seq, visibleCol: 1, blanks: [] })).toBe(1);
-    expect(visibleColToSeqPos({ seq, visibleCol: 2, blanks: [] })).toBe(undefined);
-    expect(visibleColToSeqPos({ seq, visibleCol: 3, blanks: [] })).toBe(undefined);
-    expect(visibleColToSeqPos({ seq, visibleCol: 4, blanks: [] })).toBe(2);
-    expect(visibleColToSeqPos({ seq, visibleCol: 5, blanks: [] })).toBe(3);
-    expect(visibleColToSeqPos({ seq, visibleCol: 6, blanks: [] })).toBe(undefined);
-    expect(visibleColToSeqPos({ seq, visibleCol: 7, blanks: [] })).toBe(undefined);
-    expect(visibleColToSeqPos({ seq, visibleCol: 8, blanks: [] })).toBe(4);
-    expect(visibleColToSeqPos({ seq, visibleCol: 9, blanks: [] })).toBe(5);
-});
-// Round-trip tests: visible → global → visible should be identity for valid columns
-test('round-trip: visibleColToGlobalCol and globalColToVisibleCol are inverses', () => {
-    const blanks = [2, 5, 8];
-    // For each visible column, going to global and back should return the same value
-    for (let visibleCol = 0; visibleCol < 10; visibleCol++) {
-        const globalCol = visibleColToGlobalCol(blanks, visibleCol);
-        const backToVisible = globalColToVisibleCol(blanks, globalCol);
-        expect(backToVisible).toBe(visibleCol);
-    }
-});
-test('round-trip: globalColToVisibleCol and visibleColToGlobalCol for non-hidden columns', () => {
-    const blanks = [2, 5, 8];
-    // For each global column that is NOT hidden, going to visible and back should return the same value
-    for (let globalCol = 0; globalCol < 15; globalCol++) {
-        const visibleCol = globalColToVisibleCol(blanks, globalCol);
-        if (visibleCol !== undefined) {
-            const backToGlobal = visibleColToGlobalCol(blanks, visibleCol);
-            expect(backToGlobal).toBe(globalCol);
-        }
-    }
-});
-// Edge case: blanks at position 0
-test('globalColToVisibleCol with blank at position 0', () => {
-    const blanks = [0, 1, 5];
-    expect(globalColToVisibleCol(blanks, 0)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 1)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 2)).toBe(0); // First visible column
-    expect(globalColToVisibleCol(blanks, 3)).toBe(1);
-    expect(globalColToVisibleCol(blanks, 4)).toBe(2);
-    expect(globalColToVisibleCol(blanks, 5)).toBe(undefined); // Hidden
-    expect(globalColToVisibleCol(blanks, 6)).toBe(3);
-});
-test('visibleColToGlobalCol with blank at position 0', () => {
-    const blanks = [0, 1, 5];
-    expect(visibleColToGlobalCol(blanks, 0)).toBe(2); // Skips 0, 1
-    expect(visibleColToGlobalCol(blanks, 1)).toBe(3);
-    expect(visibleColToGlobalCol(blanks, 2)).toBe(4);
-    expect(visibleColToGlobalCol(blanks, 3)).toBe(6); // Skips 5
-});
-// Edge case: all columns before a position are blanks
-test('globalColToVisibleCol with many leading blanks', () => {
-    const blanks = [0, 1, 2, 3, 4];
-    expect(globalColToVisibleCol(blanks, 0)).toBe(undefined);
-    expect(globalColToVisibleCol(blanks, 4)).toBe(undefined);
-    expect(globalColToVisibleCol(blanks, 5)).toBe(0); // First visible
-    expect(globalColToVisibleCol(blanks, 6)).toBe(1);
-    expect(globalColToVisibleCol(blanks, 10)).toBe(5);
-});
-// Test visibleColToSeqPos with blanks (combined gap hiding and row gaps)
-test('visibleColToSeqPos with both blanks and row gaps', () => {
-    // Sequence: A-C-G (global cols 0,1,2,3,4)
-    // If blanks = [1, 3], visible sequence becomes: A C G (visible cols 0,1,2)
-    const seq = 'A-C-G';
-    const blanks = [1, 3];
-    // Visible col 0 → global col 0 → 'A' → seqPos 0
-    expect(visibleColToSeqPos({ seq, visibleCol: 0, blanks })).toBe(0);
-    // Visible col 1 → global col 2 → 'C' → seqPos 1
-    expect(visibleColToSeqPos({ seq, visibleCol: 1, blanks })).toBe(1);
-    // Visible col 2 → global col 4 → 'G' → seqPos 2
-    expect(visibleColToSeqPos({ seq, visibleCol: 2, blanks })).toBe(2);
-});
-//# sourceMappingURL=rowCoordinateCalculations.test.js.map

package/dist/rowCoordinateCalculations.test.js.map

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package/dist/seqPosToGlobalCol.test.d.ts

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

package/dist/seqPosToGlobalCol.test.js

@@ -1,60 +0,0 @@
-import { describe, expect, test } from 'vitest';
-import { seqPosToGlobalCol } from "./seqPosToGlobalCol.js";
-describe('seqPosToGlobalCol', () => {
-    test('converts sequence position to global column with no gaps', () => {
-        const row = 'ATGCATGC';
-        expect(seqPosToGlobalCol({ row, seqPos: 0 })).toBe(0);
-        expect(seqPosToGlobalCol({ row, seqPos: 3 })).toBe(3);
-        expect(seqPosToGlobalCol({ row, seqPos: 7 })).toBe(7);
-        expect(seqPosToGlobalCol({ row, seqPos: 8 })).toBe(8); // Past end
-    });
-    test('converts sequence position to global column with gaps', () => {
-        const row = 'A-TG-CA-TGC';
-        // Global: A(0) -(1) T(2) G(3) -(4) C(5) A(6) -(7) T(8) G(9) C(10)
-        // SeqPos: A(0)      T(1) G(2)      C(3) A(4)      T(5) G(6) C(7)
-        expect(seqPosToGlobalCol({ row, seqPos: 0 })).toBe(0); // A
-        expect(seqPosToGlobalCol({ row, seqPos: 1 })).toBe(2); // T
-        expect(seqPosToGlobalCol({ row, seqPos: 2 })).toBe(3); // G
-        expect(seqPosToGlobalCol({ row, seqPos: 3 })).toBe(5); // C
-        expect(seqPosToGlobalCol({ row, seqPos: 4 })).toBe(6); // A
-        expect(seqPosToGlobalCol({ row, seqPos: 5 })).toBe(8); // T
-        expect(seqPosToGlobalCol({ row, seqPos: 6 })).toBe(9); // G
-        expect(seqPosToGlobalCol({ row, seqPos: 7 })).toBe(10); // C
-        expect(seqPosToGlobalCol({ row, seqPos: 8 })).toBe(11); // Past end
-    });
-    test('handles empty row', () => {
-        expect(seqPosToGlobalCol({ row: '', seqPos: 0 })).toBe(0);
-    });
-    test('handles row with only gaps', () => {
-        const row = '---..--';
-        expect(seqPosToGlobalCol({ row, seqPos: 0 })).toBe(0);
-        expect(seqPosToGlobalCol({ row, seqPos: 1 })).toBe(7); // Past end
-    });
-    test('handles mixed gap characters (- and .)', () => {
-        const row = 'A-.G-C.';
-        // Global: A(0) -(1) .(2) G(3) -(4) C(5) .(6)
-        // SeqPos: A(0)           G(1)      C(2)
-        expect(seqPosToGlobalCol({ row, seqPos: 0 })).toBe(0); // A
-        expect(seqPosToGlobalCol({ row, seqPos: 1 })).toBe(3); // G
-        expect(seqPosToGlobalCol({ row, seqPos: 2 })).toBe(5); // C
-        expect(seqPosToGlobalCol({ row, seqPos: 3 })).toBe(7); // Past end
-    });
-    test('handles leading gaps', () => {
-        const row = '--ACG';
-        // Global: -(0) -(1) A(2) C(3) G(4)
-        // SeqPos:           A(0) C(1) G(2)
-        expect(seqPosToGlobalCol({ row, seqPos: 0 })).toBe(2); // A
-        expect(seqPosToGlobalCol({ row, seqPos: 1 })).toBe(3); // C
-        expect(seqPosToGlobalCol({ row, seqPos: 2 })).toBe(4); // G
-    });
-    test('handles trailing gaps', () => {
-        const row = 'ACG--';
-        // Global: A(0) C(1) G(2) -(3) -(4)
-        // SeqPos: A(0) C(1) G(2)
-        expect(seqPosToGlobalCol({ row, seqPos: 0 })).toBe(0); // A
-        expect(seqPosToGlobalCol({ row, seqPos: 1 })).toBe(1); // C
-        expect(seqPosToGlobalCol({ row, seqPos: 2 })).toBe(2); // G
-        expect(seqPosToGlobalCol({ row, seqPos: 3 })).toBe(5); // Past end
-    });
-});
-//# sourceMappingURL=seqPosToGlobalCol.test.js.map

package/dist/seqPosToGlobalCol.test.js.map

@@ -1 +0,0 @@
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