react-msaview 4.6.0 → 4.8.0

package/dist/rowCoordinateCalculations.js

@@ -1,67 +1,139 @@
 import { isBlank } from './util';
-export function mouseOverCoordToGlobalCoord(blanks, position) {
-    let mousePosition = 0; // Current position in mouse coordinates
-    let blankArrayIndex = 0; // Current index in the blanks array
-    let globalPosition = 0; // Position in global coordinates (return value)
+/**
+ * MSA Coordinate Systems:
+ *
+ * 1. **Global Column (globalCol)**: The column index in the full, unfiltered MSA.
+ *    Range: 0 to (MSA width - 1)
+ *    This is the "true" column position before any gap-hiding is applied.
+ *
+ * 2. **Visible Column (visibleCol)**: The column index after hiding gappy columns.
+ *    Range: 0 to (numColumns - 1) where numColumns = MSA width - blanks.length
+ *    This is what the user sees on screen when "Hide columns w/ N% gaps" is enabled.
+ *    When gap hiding is disabled, visibleCol === globalCol.
+ *
+ * 3. **Sequence Position (seqPos)**: The position within a specific row's ungapped sequence.
+ *    Range: 0 to (ungapped sequence length - 1)
+ *    This counts only non-gap characters ('-' and '.' are gaps).
+ *    Each row can have different seqPos values for the same globalCol due to gaps.
+ */
+/**
+ * Convert a visible column index to a global column index.
+ * This is used when translating mouse/screen coordinates to MSA coordinates.
+ *
+ * @param blanks - Sorted array of global column indices that are hidden
+ * @param visibleCol - The visible column index (what the user sees on screen)
+ * @returns The corresponding global column index in the full MSA
+ */
+export function visibleColToGlobalCol(blanks, visibleCol) {
+    let currentVisibleCol = 0;
+    let blankArrayIndex = 0;
+    let globalCol = 0;
     const blanksLen = blanks.length;
-    // Iterate until we reach the target mouse position
-    while (mousePosition < position) {
-        // Skip any blank positions in the sequence
-        // Check if the next position (globalPosition + 1) is blank by comparing
-        // blanks[blankArrayIndex] - 1 with current globalPosition
+    // Skip any leading blank columns (blanks at the very beginning)
+    while (blankArrayIndex < blanksLen && blanks[blankArrayIndex] === globalCol) {
+        blankArrayIndex++;
+        globalCol++;
+    }
+    while (currentVisibleCol < visibleCol) {
+        currentVisibleCol++;
+        globalCol++;
+        // Skip any blank columns after incrementing
         while (blankArrayIndex < blanksLen &&
-            blanks[blankArrayIndex] - 1 === globalPosition) {
+            blanks[blankArrayIndex] === globalCol) {
             blankArrayIndex++;
-            globalPosition++;
+            globalCol++;
         }
-        // Move to next position
-        mousePosition++;
-        globalPosition++;
     }
-    return globalPosition;
+    return globalCol;
 }
-export function globalCoordToRowSpecificCoord(seq, position) {
-    // Initialize counter for non-gap characters
-    let nonGapCount = 0;
-    // Initialize position counter
-    let currentPosition = 0;
-    const sequenceLength = seq.length;
-    // Iterate until we reach the target position or end of sequence
-    while (currentPosition < position && currentPosition < sequenceLength) {
-        // If current character is not a gap, increment the non-gap counter
-        if (!isBlank(seq[currentPosition])) {
-            nonGapCount++;
+/**
+ * Convert a global column index to a visible column index.
+ * This is the inverse of visibleColToGlobalCol.
+ *
+ * @param blanks - Sorted array of global column indices that are hidden
+ * @param globalCol - The global column index in the full MSA
+ * @returns The visible column index, or undefined if the column is hidden
+ */
+export function globalColToVisibleCol(blanks, globalCol) {
+    // Check if this column is hidden
+    // Use binary search since blanks is sorted
+    let left = 0;
+    let right = blanks.length - 1;
+    while (left <= right) {
+        const mid = Math.floor((left + right) / 2);
+        if (blanks[mid] === globalCol) {
+            return undefined; // Column is hidden
+        }
+        if (blanks[mid] < globalCol) {
+            left = mid + 1;
+        }
+        else {
+            right = mid - 1;
         }
-        currentPosition++;
     }
-    return nonGapCount;
+    // Count blanks before this column (left is now the insertion point)
+    const blanksBefore = left;
+    return globalCol - blanksBefore;
 }
-export function mouseOverCoordToGapRemovedRowCoord({ rowName, position, rowMap, blanks, }) {
-    const seq = rowMap.get(rowName);
-    return seq !== undefined
-        ? mouseOverCoordToGapRemovedCoord({
-            seq,
-            position,
-            blanks,
-        })
-        : undefined;
+/**
+ * Convert a global column index to a row-specific sequence position.
+ * This counts non-gap characters up to the given global column.
+ *
+ * @param seq - The row's sequence string (including gaps)
+ * @param globalCol - The global column index
+ * @returns The sequence position (count of non-gap characters before this column)
+ */
+export function globalColToSeqPos(seq, globalCol) {
+    let seqPos = 0;
+    let currentCol = 0;
+    const seqLen = seq.length;
+    while (currentCol < globalCol && currentCol < seqLen) {
+        if (!isBlank(seq[currentCol])) {
+            seqPos++;
+        }
+        currentCol++;
+    }
+    return seqPos;
 }
-export function mouseOverCoordToGapRemovedCoord({ seq, blanks, position, }) {
-    // First convert the mouse position to global coordinates
-    const globalPos = mouseOverCoordToGlobalCoord(blanks, position);
+/**
+ * Convert a visible column to a row-specific sequence position.
+ * Returns undefined if the position is a gap in the sequence.
+ *
+ * @param seq - The row's sequence string (including gaps)
+ * @param blanks - Sorted array of global column indices that are hidden
+ * @param visibleCol - The visible column index
+ * @returns The sequence position, or undefined if it's a gap
+ */
+export function visibleColToSeqPos({ seq, blanks, visibleCol, }) {
+    // First convert the visible column to global column
+    const globalCol = visibleColToGlobalCol(blanks, visibleCol);
     const seqLen = seq.length;
     // Check if the position in the sequence is a gap
-    if (globalPos < seqLen && isBlank(seq[globalPos])) {
+    if (globalCol < seqLen && isBlank(seq[globalCol])) {
         return undefined;
     }
     // Count non-gap characters up to the global position
-    let nonGapCount = 0;
-    for (let i = 0; i < globalPos && i < seqLen; i++) {
+    let seqPos = 0;
+    for (let i = 0; i < globalCol && i < seqLen; i++) {
         if (!isBlank(seq[i])) {
-            nonGapCount++;
+            seqPos++;
         }
     }
-    // If we're at a valid position, return the count of non-gap characters
-    return globalPos < seqLen ? nonGapCount : undefined;
+    return globalCol < seqLen ? seqPos : undefined;
+}
+/**
+ * Convert a visible column to a row-specific sequence position, with row lookup.
+ *
+ * @param rowName - The name of the row
+ * @param visibleCol - The visible column index
+ * @param rowMap - Map from row name to sequence string
+ * @param blanks - Sorted array of global column indices that are hidden
+ * @returns The sequence position, or undefined if row not found or position is a gap
+ */
+export function visibleColToSeqPosForRow({ rowName, visibleCol, rowMap, blanks, }) {
+    const seq = rowMap.get(rowName);
+    return seq !== undefined
+        ? visibleColToSeqPos({ seq, visibleCol, blanks })
+        : undefined;
 }
 //# sourceMappingURL=rowCoordinateCalculations.js.map

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package/dist/rowCoordinateCalculations.test.js

@@ -1,6 +1,7 @@
 import { expect, test } from 'vitest';
-import { globalCoordToRowSpecificCoord, mouseOverCoordToGapRemovedCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
-test('with blanks at positions [2, 5, 8]', () => {
+import { globalColToSeqPos, globalColToVisibleCol, visibleColToGlobalCol, visibleColToSeqPos, } from './rowCoordinateCalculations';
+// Tests for visibleColToGlobalCol (visible → global)
+test('visibleColToGlobalCol with blanks at positions [2, 5, 8]', () => {
     const blanks = [2, 5, 8];
     [
         [0, 0],
@@ -12,10 +13,10 @@ test('with blanks at positions [2, 5, 8]', () => {
         [6, 9],
         [7, 10],
     ].forEach(r => {
-        expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
     });
 });
-test('with no blanks', () => {
+test('visibleColToGlobalCol with no blanks', () => {
     const blanks = [];
     [
         [0, 0],
@@ -23,10 +24,10 @@ test('with no blanks', () => {
         [5, 5],
         [10, 10],
     ].forEach(r => {
-        expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
     });
 });
-test('with consecutive blanks', () => {
+test('visibleColToGlobalCol with consecutive blanks', () => {
     const blanks = [2, 3, 4, 7, 8];
     [
         [0, 0],
@@ -36,10 +37,10 @@ test('with consecutive blanks', () => {
         [4, 9], // After position 3, skip 2 blanks (7,8)
         [5, 10],
     ].forEach(r => {
-        expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
     });
 });
-test('with blanks at the beginning', () => {
+test('visibleColToGlobalCol with blanks at the beginning', () => {
     const blanks = [1, 2, 5];
     [
         [0, 0],
@@ -48,10 +49,10 @@ test('with blanks at the beginning', () => {
         [3, 6], // After position 2, skip 1 blank (5)
         [4, 7],
     ].forEach(r => {
-        expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
     });
 });
-test('with position exceeding blanks array', () => {
+test('visibleColToGlobalCol with position exceeding blanks array', () => {
     const blanks = [2, 5];
     [
         [0, 0],
@@ -61,64 +62,163 @@ test('with position exceeding blanks array', () => {
         [4, 6], // After position 3, skip 1 blank (5)
         [10, 12], // Far beyond blanks array
     ].forEach(r => {
-        expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+        expect(visibleColToGlobalCol(blanks, r[0])).toBe(r[1]);
     });
 });
-test('with gaps in sequence', () => {
+// 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(globalCoordToRowSpecificCoord(sequence, 0)).toBe(0);
-    expect(globalCoordToRowSpecificCoord(sequence, 1)).toBe(1);
-    expect(globalCoordToRowSpecificCoord(sequence, 2)).toBe(2);
+    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(globalCoordToRowSpecificCoord(sequence, 3)).toBe(2);
-    expect(globalCoordToRowSpecificCoord(sequence, 4)).toBe(3);
-    expect(globalCoordToRowSpecificCoord(sequence, 5)).toBe(4);
+    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(globalCoordToRowSpecificCoord(sequence, 6)).toBe(4);
+    expect(globalColToSeqPos(sequence, 6)).toBe(4);
 });
-test('with mixed gap characters (- and .)', () => {
+test('globalColToSeqPos with mixed gap characters (- and .)', () => {
     const sequence = 'AC.GT-A';
-    expect(globalCoordToRowSpecificCoord(sequence, 0)).toBe(0);
-    expect(globalCoordToRowSpecificCoord(sequence, 1)).toBe(1);
+    expect(globalColToSeqPos(sequence, 0)).toBe(0);
+    expect(globalColToSeqPos(sequence, 1)).toBe(1);
     // Position 2 is a gap (.), so count before it is 2
-    expect(globalCoordToRowSpecificCoord(sequence, 2)).toBe(2);
-    expect(globalCoordToRowSpecificCoord(sequence, 3)).toBe(2);
-    expect(globalCoordToRowSpecificCoord(sequence, 4)).toBe(3);
+    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(globalCoordToRowSpecificCoord(sequence, 5)).toBe(4);
-    expect(globalCoordToRowSpecificCoord(sequence, 6)).toBe(4);
+    expect(globalColToSeqPos(sequence, 5)).toBe(4);
+    expect(globalColToSeqPos(sequence, 6)).toBe(4);
 });
-test('with no gaps in sequence', () => {
+test('globalColToSeqPos with no gaps in sequence', () => {
     const sequence = 'ACGTA';
-    expect(globalCoordToRowSpecificCoord(sequence, 0)).toBe(0);
-    expect(globalCoordToRowSpecificCoord(sequence, 1)).toBe(1);
-    expect(globalCoordToRowSpecificCoord(sequence, 2)).toBe(2);
-    expect(globalCoordToRowSpecificCoord(sequence, 3)).toBe(3);
-    expect(globalCoordToRowSpecificCoord(sequence, 4)).toBe(4);
+    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('with all gaps in sequence', () => {
+test('globalColToSeqPos with all gaps in sequence', () => {
     const sequence = '-----';
-    expect(globalCoordToRowSpecificCoord(sequence, 0)).toBe(0);
-    expect(globalCoordToRowSpecificCoord(sequence, 1)).toBe(0);
-    expect(globalCoordToRowSpecificCoord(sequence, 2)).toBe(0);
-    expect(globalCoordToRowSpecificCoord(sequence, 3)).toBe(0);
-    expect(globalCoordToRowSpecificCoord(sequence, 4)).toBe(0);
+    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('with position exceeding sequence length', () => {
+test('globalColToSeqPos with position exceeding sequence length', () => {
     const sequence = 'AC-GT';
-    expect(globalCoordToRowSpecificCoord(sequence, 10)).toBe(4);
+    expect(globalColToSeqPos(sequence, 10)).toBe(4);
 });
-test('mouseOverCoordToGapRemovedCoord', () => {
+// Tests for visibleColToSeqPos (visible column → sequence position)
+test('visibleColToSeqPos returns sequence position or undefined for gaps', () => {
     const seq = 'AC--GT--CT';
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 0, blanks: [] })).toBe(0);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 1, blanks: [] })).toBe(1);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 2, blanks: [] })).toBe(undefined);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 3, blanks: [] })).toBe(undefined);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 4, blanks: [] })).toBe(2);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 5, blanks: [] })).toBe(3);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 6, blanks: [] })).toBe(undefined);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 7, blanks: [] })).toBe(undefined);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 8, blanks: [] })).toBe(4);
-    expect(mouseOverCoordToGapRemovedCoord({ seq, position: 9, blanks: [] })).toBe(5);
+    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

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package/dist/seqPosToGlobalCol.d.ts

@@ -0,0 +1,19 @@
+/**
+ * Convert a sequence position (ungapped, 0-based) to a global column index.
+ * This finds the global column that contains the Nth non-gap character.
+ *
+ * @param row - The row's sequence string (including gaps)
+ * @param seqPos - The sequence position (0-based count of non-gap characters)
+ * @returns The global column index containing the seqPos-th non-gap character
+ *
+ * @example
+ * // Row: "A-TG-C" (A at 0, T at 2, G at 3, C at 5)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 0 }) // → 0 (A)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 1 }) // → 2 (T)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 2 }) // → 3 (G)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 3 }) // → 5 (C)
+ */
+export declare function seqPosToGlobalCol({ row, seqPos, }: {
+    row: string;
+    seqPos: number;
+}): number;

package/dist/seqPosToGlobalCol.js

@@ -0,0 +1,34 @@
+import { isBlank } from './util';
+/**
+ * Convert a sequence position (ungapped, 0-based) to a global column index.
+ * This finds the global column that contains the Nth non-gap character.
+ *
+ * @param row - The row's sequence string (including gaps)
+ * @param seqPos - The sequence position (0-based count of non-gap characters)
+ * @returns The global column index containing the seqPos-th non-gap character
+ *
+ * @example
+ * // Row: "A-TG-C" (A at 0, T at 2, G at 3, C at 5)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 0 }) // → 0 (A)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 1 }) // → 2 (T)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 2 }) // → 3 (G)
+ * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 3 }) // → 5 (C)
+ */
+export function seqPosToGlobalCol({ row, seqPos, }) {
+    let nonGapCount = 0;
+    let globalCol = 0;
+    // Find the seqPos-th non-gap character
+    while (globalCol < row.length) {
+        if (!isBlank(row[globalCol])) {
+            if (nonGapCount === seqPos) {
+                return globalCol;
+            }
+            nonGapCount++;
+        }
+        globalCol++;
+    }
+    // If seqPos is 0 and we didn't find any non-gap character, return 0
+    // Otherwise return globalCol (which is row.length at this point)
+    return seqPos === 0 ? 0 : globalCol;
+}
+//# sourceMappingURL=seqPosToGlobalCol.js.map

package/dist/seqPosToGlobalCol.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seqPosToGlobalCol.js","sourceRoot":"","sources":["../src/seqPosToGlobalCol.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,iBAAiB,CAAC,EAChC,GAAG,EACH,MAAM,GAIP;IACC,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,uCAAuC;IACvC,OAAO,SAAS,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;QAC9B,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC;YAC7B,IAAI,WAAW,KAAK,MAAM,EAAE,CAAC;gBAC3B,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,WAAW,EAAE,CAAA;QACf,CAAC;QACD,SAAS,EAAE,CAAA;IACb,CAAC;IACD,oEAAoE;IACpE,iEAAiE;IACjE,OAAO,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACrC,CAAC"}

package/dist/seqPosToGlobalCol.test.js

@@ -0,0 +1,60 @@
+import { describe, expect, test } from 'vitest';
+import { seqPosToGlobalCol } from './seqPosToGlobalCol';
+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