react-msaview 4.4.0 → 4.4.2

package/dist/rowCoordinateCalculations.js

@@ -1,26 +1,69 @@
-export function mouseOverCoordToGlobalCoord(blanks, pos) {
-    let i = 0; // 'mouse over coord'
-    let j = 0; // 'position in blanks array'
-    let k = 0; // 'global coord'/return value
-    for (; i < pos; i++, k++) {
-        // skip multiple gaps in a row
-        while (j < blanks.length && blanks[j] - 1 === k) {
-            j++;
-            k++;
+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)
+    const blanksLen = blanks.length;
+    // Iterate until we reach the target mouse position
+    while (mousePosition < position) {
+        // Skip any blank positions in the sequence
+        while (blankArrayIndex < blanksLen &&
+            blanks[blankArrayIndex] - 1 === globalPosition) {
+            blankArrayIndex++;
+            globalPosition++;
         }
+        // Move to next position
+        mousePosition++;
+        globalPosition++;
     }
-    return k;
+    return globalPosition;
 }
-export function globalCoordToRowSpecificCoord(seq, pos) {
-    let k = 0;
-    for (let i = 0; i < pos; i++) {
-        if (seq[i] !== '-') {
-            k++;
+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 (seq[currentPosition] !== '-') {
+            nonGapCount++;
         }
-        else if (k >= pos) {
+        // If we've reached the target position in non-gap coordinates, break
+        else if (nonGapCount >= position) {
             break;
         }
+        currentPosition++;
     }
-    return k;
+    return nonGapCount;
+}
+export function mouseOverCoordToGapRemovedRowCoord({ rowName, position, rowMap, blanks, }) {
+    const seq = rowMap.get(rowName);
+    return seq !== undefined
+        ? mouseOverCoordToGapRemovedCoord({
+            seq,
+            position,
+            blanks,
+        })
+        : undefined;
+}
+export function mouseOverCoordToGapRemovedCoord({ seq, blanks, position, }) {
+    // First convert the mouse position to global coordinates
+    const globalPos = mouseOverCoordToGlobalCoord(blanks, position);
+    const seqLen = seq.length;
+    // Check if the position in the sequence is a gap
+    if (globalPos < seqLen && isBlank(seq[globalPos])) {
+        return undefined;
+    }
+    // Count non-gap characters up to the global position
+    let nonGapCount = 0;
+    for (let i = 0; i < globalPos && i < seqLen; i++) {
+        if (!isBlank(seq[i])) {
+            nonGapCount++;
+        }
+    }
+    // If we're at a valid position, return the count of non-gap characters
+    return globalPos < seqLen ? nonGapCount : undefined;
 }
 //# sourceMappingURL=rowCoordinateCalculations.js.map

package/dist/rowCoordinateCalculations.js.map

@@ -1 +1 @@
-{"version":3,"file":"rowCoordinateCalculations.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,2BAA2B,CAAC,MAAgB,EAAE,GAAW;IACvE,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,qBAAqB;IAC/B,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,6BAA6B;IACvC,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,8BAA8B;IAExC,OAAO,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACzB,8BAA8B;QAC9B,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,IAAI,MAAM,CAAC,CAAC,CAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YACjD,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,UAAU,6BAA6B,CAAC,GAAW,EAAE,GAAW;IACpE,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QAC7B,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACnB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC;YACpB,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}
+{"version":3,"file":"rowCoordinateCalculations.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC,MAAM,UAAU,2BAA2B,CACzC,MAAgB,EAChB,QAAgB;IAEhB,IAAI,aAAa,GAAG,CAAC,CAAA,CAAC,wCAAwC;IAC9D,IAAI,eAAe,GAAG,CAAC,CAAA,CAAC,oCAAoC;IAC5D,IAAI,cAAc,GAAG,CAAC,CAAA,CAAC,gDAAgD;IACvE,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAA;IAE/B,mDAAmD;IACnD,OAAO,aAAa,GAAG,QAAQ,EAAE,CAAC;QAChC,2CAA2C;QAC3C,OACE,eAAe,GAAG,SAAS;YAC3B,MAAM,CAAC,eAAe,CAAE,GAAG,CAAC,KAAK,cAAc,EAC/C,CAAC;YACD,eAAe,EAAE,CAAA;YACjB,cAAc,EAAE,CAAA;QAClB,CAAC;QAED,wBAAwB;QACxB,aAAa,EAAE,CAAA;QACf,cAAc,EAAE,CAAA;IAClB,CAAC;IAED,OAAO,cAAc,CAAA;AACvB,CAAC;AAED,MAAM,UAAU,6BAA6B,CAAC,GAAW,EAAE,QAAgB;IACzE,4CAA4C;IAC5C,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,8BAA8B;IAC9B,IAAI,eAAe,GAAG,CAAC,CAAA;IACvB,MAAM,cAAc,GAAG,GAAG,CAAC,MAAM,CAAA;IAEjC,gEAAgE;IAChE,OAAO,eAAe,GAAG,QAAQ,IAAI,eAAe,GAAG,cAAc,EAAE,CAAC;QACtE,mEAAmE;QACnE,IAAI,GAAG,CAAC,eAAe,CAAC,KAAK,GAAG,EAAE,CAAC;YACjC,WAAW,EAAE,CAAA;QACf,CAAC;QACD,qEAAqE;aAChE,IAAI,WAAW,IAAI,QAAQ,EAAE,CAAC;YACjC,MAAK;QACP,CAAC;QACD,eAAe,EAAE,CAAA;IACnB,CAAC;IAED,OAAO,WAAW,CAAA;AACpB,CAAC;AAED,MAAM,UAAU,kCAAkC,CAAC,EACjD,OAAO,EACP,QAAQ,EACR,MAAM,EACN,MAAM,GAMP;IACC,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAC/B,OAAO,GAAG,KAAK,SAAS;QACtB,CAAC,CAAC,+BAA+B,CAAC;YAC9B,GAAG;YACH,QAAQ;YACR,MAAM;SACP,CAAC;QACJ,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,MAAM,UAAU,+BAA+B,CAAC,EAC9C,GAAG,EACH,MAAM,EACN,QAAQ,GAKT;IACC,yDAAyD;IACzD,MAAM,SAAS,GAAG,2BAA2B,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IAC/D,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,CAAA;IAEzB,iDAAiD;IACjD,IAAI,SAAS,GAAG,MAAM,IAAI,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC;QAClD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,qDAAqD;IACrD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACjD,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,WAAW,EAAE,CAAA;QACf,CAAC;IACH,CAAC;IAED,uEAAuE;IACvE,OAAO,SAAS,GAAG,MAAM,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAA;AACrD,CAAC"}

package/dist/rowCoordinateCalculations.test.js

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
-import { mouseOverCoordToGlobalCoord } from './rowCoordinateCalculations';
-test('blanks3', () => {
+import { globalCoordToRowSpecificCoord, mouseOverCoordToGapRemovedCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
+test('with blanks at positions [2, 5, 8]', () => {
     const blanks = [2, 5, 8];
     [
         [0, 0],
@@ -15,4 +15,98 @@ test('blanks3', () => {
         expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
     });
 });
+test('with no blanks', () => {
+    const blanks = [];
+    [
+        [0, 0],
+        [1, 1],
+        [5, 5],
+        [10, 10],
+    ].forEach(r => {
+        expect(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+    });
+});
+test('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(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+    });
+});
+test('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(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+    });
+});
+test('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(mouseOverCoordToGlobalCoord(blanks, r[0])).toBe(r[1]);
+    });
+});
+test('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);
+    // Position 3 in global coordinates is after the gap
+    expect(globalCoordToRowSpecificCoord(sequence, 3)).toBe(2);
+    expect(globalCoordToRowSpecificCoord(sequence, 4)).toBe(3);
+    expect(globalCoordToRowSpecificCoord(sequence, 5)).toBe(4);
+    // Position 6 in global coordinates is after the gap
+    expect(globalCoordToRowSpecificCoord(sequence, 6)).toBe(4);
+});
+test('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);
+});
+test('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);
+});
+test('with position exceeding sequence length', () => {
+    const sequence = 'AC-GT';
+    expect(globalCoordToRowSpecificCoord(sequence, 10)).toBe(4);
+});
+test('mouseOverCoordToGapRemovedCoord', () => {
+    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);
+});
 //# sourceMappingURL=rowCoordinateCalculations.test.js.map

package/dist/rowCoordinateCalculations.test.js.map

@@ -1 +1 @@
-{"version":3,"file":"rowCoordinateCalculations.test.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAErC,OAAO,EAAE,2BAA2B,EAAE,MAAM,6BAA6B,CAAA;AACzE,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;IACnB,MAAM,MAAM,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CACvB;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,EAAE,CAAC;KAEV,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
+{"version":3,"file":"rowCoordinateCalculations.test.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAErC,OAAO,EACL,6BAA6B,EAC7B,+BAA+B,EAC/B,2BAA2B,GAC5B,MAAM,6BAA6B,CAAA;AAEpC,IAAI,CAAC,oCAAoC,EAAE,GAAG,EAAE;IAC9C,MAAM,MAAM,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CACvB;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,EAAE,CAAC;KAEV,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,gBAAgB,EAAE,GAAG,EAAE;IAC1B,MAAM,MAAM,GAAa,EAAE,CAC1B;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,EAAE,EAAE,EAAE,CAAC;KAEX,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,yBAAyB,EAAE,GAAG,EAAE;IACnC,MAAM,MAAM,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAC7B;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,0CAA0C;QAClD,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,gBAAgB;QACxB,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,wCAAwC;QAChD,CAAC,CAAC,EAAE,EAAE,CAAC;KAEV,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;IACxC,MAAM,MAAM,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CACvB;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,wCAAwC;QAChD,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,qCAAqC;QAC7C,CAAC,CAAC,EAAE,CAAC,CAAC;KAET,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,sCAAsC,EAAE,GAAG,EAAE;IAChD,MAAM,MAAM,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CACpB;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,qCAAqC;QAC7C,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,qCAAqC;QAC7C,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,0BAA0B;KAEvC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,uBAAuB,EAAE,GAAG,EAAE;IACjC,MAAM,QAAQ,GAAG,SAAS,CAAA;IAC1B,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,oDAAoD;IACpD,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,oDAAoD;IACpD,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;AAC5D,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,0BAA0B,EAAE,GAAG,EAAE;IACpC,MAAM,QAAQ,GAAG,OAAO,CAAA;IACxB,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;AAC5D,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,2BAA2B,EAAE,GAAG,EAAE;IACrC,MAAM,QAAQ,GAAG,OAAO,CAAA;IACxB,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC1D,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;AAC5D,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,yCAAyC,EAAE,GAAG,EAAE;IACnD,MAAM,QAAQ,GAAG,OAAO,CAAA;IACxB,MAAM,CAAC,6BAA6B,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;AAC7D,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,iCAAiC,EAAE,GAAG,EAAE;IAC3C,MAAM,GAAG,GAAG,YAAY,CAAA;IACxB,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACT,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACT,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;IACjB,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;IACjB,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACT,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACT,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;IACjB,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;IACjB,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACT,MAAM,CACJ,+BAA+B,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAClE,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;AACX,CAAC,CAAC,CAAA"}

package/dist/seqCoordToRowSpecificGlobalCoord.d.ts

@@ -0,0 +1,4 @@
+export declare function seqCoordToRowSpecificGlobalCoord({ row, position, }: {
+    row: string;
+    position: number;
+}): number;

package/dist/seqCoordToRowSpecificGlobalCoord.js

@@ -0,0 +1,15 @@
+import { isBlank } from './util';
+export function seqCoordToRowSpecificGlobalCoord({ row, position, }) {
+    let k = 0;
+    let i = 0;
+    for (; k < position; i++) {
+        if (!isBlank(row[i])) {
+            k++;
+        }
+        else if (k >= position) {
+            break;
+        }
+    }
+    return i;
+}
+//# sourceMappingURL=seqCoordToRowSpecificGlobalCoord.js.map

package/dist/seqCoordToRowSpecificGlobalCoord.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seqCoordToRowSpecificGlobalCoord.js","sourceRoot":"","sources":["../src/seqCoordToRowSpecificGlobalCoord.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA;AAEhC,MAAM,UAAU,gCAAgC,CAAC,EAC/C,GAAG,EACH,QAAQ,GAIT;IACC,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,OAAO,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;QACzB,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACrB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,CAAC,IAAI,QAAQ,EAAE,CAAC;YACzB,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC"}

package/dist/seqCoordToRowSpecificGlobalCoord.test.d.ts

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

package/dist/seqCoordToRowSpecificGlobalCoord.test.js

@@ -0,0 +1,42 @@
+import { describe, expect, test } from 'vitest';
+import { seqCoordToRowSpecificGlobalCoord } from './seqCoordToRowSpecificGlobalCoord';
+describe('seqCoordToRowSpecificGlobalCoord', () => {
+    test('converts sequence coordinate to global coordinate with no gaps', () => {
+        const row = 'ATGCATGC';
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(3);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 8 })).toBe(8);
+    });
+    test('converts sequence coordinate to global coordinate with gaps', () => {
+        const row = 'A-TG-CA-TGC';
+        // A(0) -(1) T(2) G(3) -(4) C(5) A(6) -(7) T(8) G(9) C(10)
+        // Sequence positions: A(0) T(1) G(2) C(3) A(4) T(5) G(6) C(7)
+        // Position 0 (first A) -> Global index 0
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+        // Position 1 (T after first gap) -> Global index 2
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(1);
+        // Position 3 (C after second gap) -> Global index 5
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(4);
+        // Position 5 (T after third gap) -> Global index 8
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 5 })).toBe(7);
+        // Position 8 (end of sequence) -> Global index 11
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 8 })).toBe(11);
+    });
+    test('handles empty row', () => {
+        expect(seqCoordToRowSpecificGlobalCoord({ row: '', position: 0 })).toBe(0);
+    });
+    test('handles row with only gaps', () => {
+        const row = '---..--';
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+    });
+    test('handles mixed gap characters', () => {
+        const row = 'A-.G-C.';
+        // A(0) -(1) .(2) G(3) -(4) C(5) .(6)
+        // Sequence positions: A(0) G(1) C(2)
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 0 })).toBe(0);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 1 })).toBe(1);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 2 })).toBe(4);
+        expect(seqCoordToRowSpecificGlobalCoord({ row, position: 3 })).toBe(6);
+    });
+});
+//# sourceMappingURL=seqCoordToRowSpecificGlobalCoord.test.js.map

package/dist/seqCoordToRowSpecificGlobalCoord.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"seqCoordToRowSpecificGlobalCoord.test.js","sourceRoot":"","sources":["../src/seqCoordToRowSpecificGlobalCoord.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE/C,OAAO,EAAE,gCAAgC,EAAE,MAAM,oCAAoC,CAAA;AAErF,QAAQ,CAAC,kCAAkC,EAAE,GAAG,EAAE;IAChD,IAAI,CAAC,gEAAgE,EAAE,GAAG,EAAE;QAC1E,MAAM,GAAG,GAAG,UAAU,CAAA;QACtB,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACxE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,6DAA6D,EAAE,GAAG,EAAE;QACvE,MAAM,GAAG,GAAG,aAAa,CAAA;QACzB,0DAA0D;QAC1D,8DAA8D;QAE9D,yCAAyC;QACzC,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,mDAAmD;QACnD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,oDAAoD;QACpD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,mDAAmD;QACnD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QAEtE,kDAAkD;QAClD,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACzE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,mBAAmB,EAAE,GAAG,EAAE;QAC7B,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC5E,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,4BAA4B,EAAE,GAAG,EAAE;QACtC,MAAM,GAAG,GAAG,SAAS,CAAA;QACrB,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACxE,CAAC,CAAC,CAAA;IAEF,IAAI,CAAC,8BAA8B,EAAE,GAAG,EAAE;QACxC,MAAM,GAAG,GAAG,SAAS,CAAA;QACrB,qCAAqC;QACrC,qCAAqC;QAErC,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACtE,MAAM,CAAC,gCAAgC,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IACxE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

package/dist/util.d.ts

@@ -12,13 +12,8 @@ export declare function skipBlanks(blanks: number[], arg: string | string[]): st
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function collapse(d: HierarchyNode<NodeWithIds>): void;
-export declare function clamp(min: number, num: number, max: number): number;
 export declare function len(a: {
     end: number;
     start: number;
 }): number;
-export declare function localStorageGetItem(item: string): string | null | undefined;
-export declare function localStorageGetBoolean(key: string, defaultVal: boolean): boolean;
-export declare function localStorageSetItem(str: string, item: string): void;
-export declare function localStorageSetBoolean(key: string, value: boolean): void;
-export declare function isGzip(buf: Uint8Array): boolean;
+export declare function isBlank(s?: string): s is "-" | ".";

package/dist/util.js

@@ -23,7 +23,7 @@ export function colorContrast(colorScheme, theme) {
 export function skipBlanks(blanks, arg) {
     let s = '';
     let b = 0;
-    for (let j = 0; j < arg.length; j++) {
+    for (let j = 0, l = arg.length; j < l; j++) {
         if (j === blanks[b]) {
             b++;
         }
@@ -57,29 +57,12 @@ export function collapse(d) {
         d.children = null;
     }
 }
-export function clamp(min, num, max) {
-    return Math.min(Math.max(num, min), max);
-}
 export function len(a) {
     return a.end - a.start;
 }
-export function localStorageGetItem(item) {
-    return typeof localStorage !== 'undefined'
-        ? localStorage.getItem(item)
-        : undefined;
-}
-export function localStorageGetBoolean(key, defaultVal) {
-    return Boolean(JSON.parse(localStorageGetItem(key) || JSON.stringify(defaultVal)));
-}
-export function localStorageSetItem(str, item) {
-    if (typeof localStorage !== 'undefined') {
-        localStorage.setItem(str, item);
-    }
-}
-export function localStorageSetBoolean(key, value) {
-    localStorageSetItem(key, JSON.stringify(value));
-}
-export function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+// https://sonnhammer.sbc.su.se/Stockholm.html
+// gaps can be a . or - in stockholm
+export function isBlank(s) {
+    return s === '-' || s === '.';
 }
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAM9B,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,MAAM,UAAU,SAAS,CACvB,GAAsB,EACtB,EAAsC;IAEtC,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,QAAQ,EACN,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC1B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,WAAmC,EACnC,KAAY;IAEZ,OAAO,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QACjD,MAAM;QACN,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;KACrD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,MAAgB,EAAE,GAAsB;IACjE,IAAI,CAAC,GAAG,EAAE,CAAA;IACV,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpC,IAAI,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,CAA6B;IACpD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,mBAAmB;QACnB,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,QAAQ,CAAA;QACxB,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,GAAW,EAAE,GAAW,EAAE,GAAW;IACzD,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;AAC1C,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,IAAY;IAC9C,OAAO,OAAO,YAAY,KAAK,WAAW;QACxC,CAAC,CAAC,YAAY,CAAC,OAAO,CAAC,IAAI,CAAC;QAC5B,CAAC,CAAC,SAAS,CAAA;AACf,CAAC;AAED,MAAM,UAAU,sBAAsB,CAAC,GAAW,EAAE,UAAmB;IACrE,OAAO,OAAO,CACZ,IAAI,CAAC,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CACnE,CAAA;AACH,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,GAAW,EAAE,IAAY;IAC3D,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;QACxC,YAAY,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACjC,CAAC;AACH,CAAC;AACD,MAAM,UAAU,sBAAsB,CAAC,GAAW,EAAE,KAAc;IAChE,mBAAmB,CAAC,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAA;AACjD,CAAC;AAED,MAAM,UAAU,MAAM,CAAC,GAAe;IACpC,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAC9C,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAM9B,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,MAAM,UAAU,SAAS,CACvB,GAAsB,EACtB,EAAsC;IAEtC,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,QAAQ,EACN,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC1B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,WAAmC,EACnC,KAAY;IAEZ,OAAO,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QACjD,MAAM;QACN,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;KACrD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,MAAgB,EAAE,GAAsB;IACjE,IAAI,CAAC,GAAG,EAAE,CAAA;IACV,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,IAAI,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,CAA6B;IACpD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,mBAAmB;QACnB,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,QAAQ,CAAA;QACxB,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,GAAG,CAAC,CAAiC;IACnD,OAAO,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;AACxB,CAAC;AAED,8CAA8C;AAC9C,oCAAoC;AACpC,MAAM,UAAU,OAAO,CAAC,CAAU;IAChC,OAAO,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAA;AAC/B,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.4.0";
+export declare const version = "4.4.2";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '4.4.0';
+export const version = '4.4.2';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "4.4.0",
+  "version": "4.4.2",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",

package/src/colorSchemes.ts

@@ -2,7 +2,7 @@ import { blue, green, orange, red } from '@mui/material/colors'
 import { colord, extend } from 'colord'
 import namesPlugin from 'colord/plugins/names'
 
-import { transform } from './util'
+import { isBlank, transform } from './util'
 
 extend([namesPlugin])
 
@@ -518,7 +518,7 @@ export function getPercentIdentityColor(
   let ent = 0
   let letter = ''
   for (const entry of entries) {
-    if (entry[1] > ent && entry[0] !== '-') {
+    if (entry[1] > ent && !isBlank(entry[0])) {
       letter = entry[0]
       ent = entry[1]
     }

package/src/components/VerticalScrollbar.tsx

@@ -1,9 +1,8 @@
 import React, { useEffect, useRef, useState } from 'react'
 
+import { clamp } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
-import { clamp } from '../util'
-
 import type { MsaViewModel } from '../model'
 
 const VerticalScrollbar = observer(({ model }: { model: MsaViewModel }) => {
@@ -28,8 +27,8 @@ const VerticalScrollbar = observer(({ model }: { model: MsaViewModel }) => {
           window.requestAnimationFrame(() => {
             model.setScrollY(
               clamp(
-                -totalHeight,
                 mouseDown.scrollY - (event.clientY - mouseDown.clientY) / unit,
+                -totalHeight,
                 0,
               ),
             )

package/src/components/dialogs/SettingsDialog.tsx

@@ -30,6 +30,8 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
+const toP = (s = 0) => +(+s).toFixed(1)
+
 const SettingsContent = observer(function ({ model }: { model: MsaViewModel }) {
   return (
     <>
@@ -189,7 +191,7 @@ const MSASettings = observer(function MSASettings({
         </div>
       ) : null}
       <div className={classes.flex}>
-        <Typography>Column width ({colWidth}px)</Typography>
+        <Typography>Column width ({toP(colWidth)}px)</Typography>
         <Slider
           className={classes.field}
           min={1}
@@ -201,7 +203,7 @@ const MSASettings = observer(function MSASettings({
         />
       </div>
       <div className={classes.flex}>
-        <Typography>Row height ({rowHeight}px)</Typography>
+        <Typography>Row height ({toP(rowHeight)}px)</Typography>
         <Slider
           className={classes.field}
           min={1}

package/src/components/header/Header.tsx

@@ -5,11 +5,11 @@ import Help from '@mui/icons-material/Help'
 import { IconButton } from '@mui/material'
 import { observer } from 'mobx-react'
 
+import SettingsMenu from './SettingsMenu'
 import HeaderInfoArea from './HeaderInfoArea'
 import HeaderMenu from './HeaderMenu'
 import HeaderStatusArea from './HeaderStatusArea'
 import MultiAlignmentSelector from './MultiAlignmentSelector'
-import SettingsMenu from './SettingsMenu'
 import ZoomControls from './ZoomControls'
 import ZoomMenu from './ZoomMenu'
 import ZoomStar from './ZoomStar'

package/src/components/header/HeaderInfoArea.tsx

@@ -19,8 +19,11 @@ const HeaderInfoArea = observer(function ({ model }: { model: MsaViewModel }) {
   return mouseOverRowName && mouseCol !== undefined ? (
     <Typography className={classes.margin}>
       {mouseOverRowName}:
-      {model.mouseOverCoordToGapRemovedRowCoord(mouseOverRowName, mouseCol)} (
-      {model.mouseOverCoordToRowLetter(mouseOverRowName, mouseCol)})
+      {model.mouseOverCoordToGapRemovedRowCoordOneBased(
+        mouseOverRowName,
+        mouseCol,
+      )}{' '}
+      ({model.mouseOverCoordToRowLetter(mouseOverRowName, mouseCol)})
     </Typography>
   ) : null
 })