react-msaview 4.4.0 → 4.4.1

package/dist/components/msa/renderMSABlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"renderMSABlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSABlock.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,uBAAuB,EAAE,MAAM,oBAAoB,CAAA;AAO9E,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,GAAG,EACH,KAAK,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,kBAAkB,GAWnB;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,SAAS,EACT,QAAQ,EACR,kBAAkB,EAClB,mBAAmB,EACnB,MAAM,EACN,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;IAChD,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,GAAG,QAAQ,IAAI,CAAC,CAAA;IAE9E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IAC3E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC1D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC9D,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAEhD,IAAI,CAAC,mBAAmB,EAAE,CAAC;QACzB,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,KAAK;YACL,OAAO;YACP,OAAO;YACP,MAAM;YACN,IAAI;YACJ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;IACD,QAAQ,CAAC;QACP,KAAK;QACL,GAAG;QACH,OAAO;QACP,cAAc;QACd,KAAK;QACL,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,OAAO,EACP,GAAG,EACH,aAAa,EACb,KAAK,EACL,MAAM,EACN,IAAI,GAUL;IACC,MAAM,EACJ,OAAO,EACP,eAAe,EACf,WAAW,EACX,OAAO,EACP,QAAQ,EACR,SAAS,GACV,GAAG,KAAK,CAAA;IAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAC9C,IAAI,GAAG,EAAE,CAAC;YACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;gBACtB,MAAM,EAAE,GAAG,eAAe,KAAK,0BAA0B,CAAA;gBACzD,MAAM,EAAE,GAAG,eAAe,KAAK,0BAA0B,CAAA;gBACzD,MAAM,KAAK,GAAG,EAAE;oBACd,CAAC,CAAC,gBAAgB;oBACd,8DAA8D;oBAC9D,0BAA0B;oBAC1B,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAE,EAC3B,KAAK,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,EAC/B,KAAK,EACL,IAAI,EACJ,MAAM,GAAG,CAAC,CACX;oBACH,CAAC,CAAC,EAAE;wBACF,CAAC,CAAC,uBAAuB;wBACrB,qDAAqD;wBACrD,mCAAmC;wBACnC,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAE,EAC3B,KAAK,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,EAC/B,KAAK,EACL,IAAI,EACJ,MAAM,GAAG,CAAC,CACX;wBACH,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;gBACvC,IAAI,OAAO,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;oBACxB,GAAG,CAAC,SAAS,GAAG,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAA;oBACzD,GAAG,CAAC,QAAQ,CACV,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,EAC7C,CAAC,GAAG,SAAS,EACb,QAAQ,EACR,SAAS,CACV,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,OAAO,EACP,cAAc,EACd,GAAG,EACH,aAAa,EACb,MAAM,EACN,IAAI,GAUL;IACC,MAAM,EACJ,OAAO,EACP,mBAAmB,EACnB,cAAc,EACd,WAAW,EACX,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,SAAS,GACV,GAAG,KAAK,CAAA;IACT,IAAI,cAAc,EAAE,CAAC;QACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;YAC9B,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;YACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;YACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,GAAG,EAAE,CAAC;gBACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;oBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;oBACtB,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;oBAC/C,MAAM,QAAQ,GAAG,iBAAiB;wBAChC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,OAAO;wBACjD,CAAC,CAAC,OAAO,CAAA;oBACX,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;oBAEvD,kDAAkD;oBAClD,GAAG,CAAC,SAAS,GAAG,mBAAmB;wBACjC,CAAC,CAAC,OAAO;wBACT,CAAC,CAAC,OAAO;4BACP,CAAC,CAAC,QAAQ;4BACV,CAAC,CAAC,KAAK,IAAI,OAAO,CAAA;oBACtB,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA;gBAC3D,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/model.d.ts

@@ -734,13 +734,19 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #method
      * return a row-specific letter, or undefined if gap
      */
-    mouseOverCoordToRowLetter(rowName: string, position: number): string | undefined;
+    mouseOverCoordToRowLetter(rowName: string, pos: number): string | undefined;
     /**
      * #method
      * return a row-specific sequence coordinate, skipping gaps, given a
      * global coordinate
      */
     mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
+    /**
+     * #method
+     * return a row-specific sequence coordinate, skipping gaps, given a
+     * global coordinate
+     */
+    mouseOverCoordToGapRemovedRowCoordOneBased(rowName: string, position: number): number | undefined;
     /**
      * #method
      * return a global coordinate given a row-specific sequence coordinate

package/dist/model.js

@@ -1,4 +1,4 @@
-import { groupBy, notEmpty, sum } from '@jbrowse/core/util';
+import { clamp, fetchAndMaybeUnzipText, groupBy, localStorageGetBoolean, localStorageSetBoolean, notEmpty, sum, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
 import { colord } from 'colord';
@@ -8,7 +8,6 @@ import { parseEmfTree } from 'emf-js';
 import { saveAs } from 'file-saver';
 import { autorun, transaction } from 'mobx';
 import { addDisposer, cast, types } from 'mobx-state-tree';
-import { ungzip } from 'pako';
 import Stockholm from 'stockholm-js';
 import { blocksX, blocksY } from './calculateBlocks';
 import colorSchemes from './colorSchemes';
@@ -27,8 +26,9 @@ import EmfMSA from './parsers/EmfMSA';
 import FastaMSA from './parsers/FastaMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import { reparseTree } from './reparseTree';
-import { globalCoordToRowSpecificCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
-import { clamp, collapse, generateNodeIds, isGzip, len, localStorageGetBoolean, localStorageSetBoolean, maxLength, setBrLength, skipBlanks, } from './util';
+import { mouseOverCoordToGapRemovedRowCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
+import { seqCoordToRowSpecificGlobalCoord } from './seqCoordToRowSpecificGlobalCoord';
+import { collapse, generateNodeIds, isBlank, len, maxLength, setBrLength, skipBlanks, } from './util';
 const defaultRowHeight = 16;
 const defaultColWidth = 12;
 const showZoomStarKey = 'msa-showZoomStar';
@@ -547,11 +547,11 @@ function stateModelFactory() {
          */
         get tree() {
             const text = self.data.tree;
-            return text
-                ? reparseTree(generateNodeIds(text.startsWith('BioTreeContainer')
+            return reparseTree(text
+                ? generateNodeIds(text.startsWith('BioTreeContainer')
                     ? flatToTree(parseAsn1(text))
-                    : parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text)))
-                : reparseTree(this.MSA?.getTree() || {
+                    : parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text))
+                : this.MSA?.getTree() || {
                     noTree: true,
                     children: [],
                     id: 'empty',
@@ -617,16 +617,18 @@ function stateModelFactory() {
             if (hideGaps) {
                 const strs = this.leaves
                     .map(leaf => this.MSA?.getRow(leaf.data.name))
-                    .filter((item) => !!item);
+                    .filter(notEmpty);
                 if (strs.length) {
-                    for (let i = 0; i < strs[0].length; i++) {
+                    const s0len = strs[0].length;
+                    for (let i = 0; i < s0len; i++) {
                         let counter = 0;
-                        for (const str of strs) {
-                            if (str[i] === '-') {
+                        const l = strs.length;
+                        for (let j = 0; j < l; j++) {
+                            if (isBlank(strs[j][i])) {
                                 counter++;
                             }
                         }
-                        if (counter / strs.length >= realAllowedGappyness / 100) {
+                        if (counter / l >= realAllowedGappyness / 100) {
                             blanks.push(i);
                         }
                     }
@@ -838,14 +840,14 @@ function stateModelFactory() {
          */
         zoomOutHorizontal() {
             self.colWidth = Math.max(1, Math.floor(self.colWidth * 0.75));
-            self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
+            self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
         },
         /**
          * #action
          */
         zoomInHorizontal() {
             self.colWidth = Math.ceil(self.colWidth * 1.5);
-            self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
+            self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
         },
         /**
          * #action
@@ -866,7 +868,7 @@ function stateModelFactory() {
             transaction(() => {
                 self.colWidth = Math.ceil(self.colWidth * 1.5);
                 self.rowHeight = Math.ceil(self.rowHeight * 1.5);
-                self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
+                self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
             });
         },
         /**
@@ -876,7 +878,7 @@ function stateModelFactory() {
             transaction(() => {
                 self.colWidth = Math.max(1, Math.floor(self.colWidth * 0.75));
                 self.rowHeight = Math.max(1.5, Math.floor(self.rowHeight * 0.75));
-                self.scrollX = clamp(self.maxScrollX, self.scrollX, 0);
+                self.scrollX = clamp(self.scrollX, self.maxScrollX, 0);
             });
         },
         /**
@@ -889,19 +891,19 @@ function stateModelFactory() {
          * #action
          */
         doScrollY(deltaY) {
-            self.scrollY = clamp(-self.totalHeight + 10, self.scrollY + deltaY, 0);
+            self.scrollY = clamp(self.scrollY + deltaY, -self.totalHeight + 10, 0);
         },
         /**
          * #action
          */
         doScrollX(deltaX) {
-            self.scrollX = clamp(self.maxScrollX, self.scrollX + deltaX, 0);
+            self.scrollX = clamp(self.scrollX + deltaX, self.maxScrollX, 0);
         },
         /**
          * #action
          */
         setScrollX(n) {
-            self.scrollX = clamp(self.maxScrollX, n, 0);
+            self.scrollX = clamp(n, self.maxScrollX, 0);
         },
         /**
          * #action
@@ -1007,9 +1009,9 @@ function stateModelFactory() {
          * #method
          * return a row-specific letter, or undefined if gap
          */
-        mouseOverCoordToRowLetter(rowName, position) {
+        mouseOverCoordToRowLetter(rowName, pos) {
             const { rowMap, blanks } = self;
-            return rowMap.get(rowName)?.[mouseOverCoordToGlobalCoord(blanks, position)];
+            return rowMap.get(rowName)?.[mouseOverCoordToGlobalCoord(blanks, pos)];
         },
         /**
          * #method
@@ -1017,16 +1019,21 @@ function stateModelFactory() {
          * global coordinate
          */
         mouseOverCoordToGapRemovedRowCoord(rowName, position) {
-            const { rowMap, blanks } = self;
-            const seq = rowMap.get(rowName);
-            if (seq !== undefined) {
-                const pos2 = mouseOverCoordToGlobalCoord(blanks, position);
-                const pos1 = globalCoordToRowSpecificCoord(seq, pos2);
-                return seq[pos1] === '-' || !seq[pos1] ? undefined : pos1;
-            }
-            else {
-                return undefined;
-            }
+            return mouseOverCoordToGapRemovedRowCoord({
+                rowName,
+                position,
+                rowMap: self.rowMap,
+                blanks: self.blanks,
+            });
+        },
+        /**
+         * #method
+         * return a row-specific sequence coordinate, skipping gaps, given a
+         * global coordinate
+         */
+        mouseOverCoordToGapRemovedRowCoordOneBased(rowName, position) {
+            const val = this.mouseOverCoordToGapRemovedRowCoord(rowName, position);
+            return val !== undefined ? val + 1 : undefined;
         },
         /**
          * #method
@@ -1036,21 +1043,12 @@ function stateModelFactory() {
         seqCoordToRowSpecificGlobalCoord(rowName, position) {
             const { rowNames, rows } = self;
             const index = rowNames.indexOf(rowName);
-            if (index !== -1 && rows[index]) {
-                const row = rows[index][1];
-                let k = 0;
-                let i = 0;
-                for (; k < position; i++) {
-                    if (row[i] !== '-') {
-                        k++;
-                    }
-                    else if (k >= position) {
-                        break;
-                    }
-                }
-                return i;
-            }
-            return 0;
+            return index !== -1 && rows[index]
+                ? seqCoordToRowSpecificGlobalCoord({
+                    row: rows[index][1],
+                    position,
+                })
+                : 0;
         },
     }))
         .views(self => ({
@@ -1180,7 +1178,11 @@ function stateModelFactory() {
          * #action
          */
         reset() {
-            self.setData({ tree: '', msa: '' });
+            self.setData({
+                tree: '',
+                msa: '',
+            });
+            self.resetZoom();
             self.setError(undefined);
             self.setScrollY(0);
             self.setScrollX(0);
@@ -1244,7 +1246,7 @@ function stateModelFactory() {
                 if (treeFilehandle) {
                     try {
                         self.setLoadingTree(true);
-                        self.setTree(await openLocation(treeFilehandle).readFile('utf8'));
+                        self.setTree(await fetchAndMaybeUnzipText(openLocation(treeFilehandle)));
                         if (treeFilehandle.locationType === 'BlobLocation') {
                             // clear filehandle after loading if from a local file
                             self.setTreeFilehandle(undefined);
@@ -1264,7 +1266,7 @@ function stateModelFactory() {
                 const { treeMetadataFilehandle } = self;
                 if (treeMetadataFilehandle) {
                     try {
-                        self.setTreeMetadata(await openLocation(treeMetadataFilehandle).readFile('utf8'));
+                        self.setTreeMetadata(await fetchAndMaybeUnzipText(openLocation(treeMetadataFilehandle)));
                     }
                     catch (e) {
                         console.error(e);
@@ -1278,9 +1280,8 @@ function stateModelFactory() {
                 if (msaFilehandle) {
                     try {
                         self.setLoadingMSA(true);
-                        const res = await openLocation(msaFilehandle).readFile();
-                        const buf = isGzip(res) ? ungzip(res) : res;
-                        const txt = new TextDecoder('utf8').decode(buf);
+                        self.setError(undefined);
+                        const txt = await fetchAndMaybeUnzipText(openLocation(msaFilehandle));
                         transaction(() => {
                             self.setMSA(txt);
                             if (msaFilehandle.locationType === 'BlobLocation') {

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package/dist/rowCoordinateCalculations.d.ts

@@ -1,2 +1,13 @@
-export declare function mouseOverCoordToGlobalCoord(blanks: number[], pos: number): number;
-export declare function globalCoordToRowSpecificCoord(seq: string, pos: number): number;
+export declare function mouseOverCoordToGlobalCoord(blanks: number[], position: number): number;
+export declare function globalCoordToRowSpecificCoord(seq: string, position: number): number;
+export declare function mouseOverCoordToGapRemovedRowCoord({ rowName, position, rowMap, blanks, }: {
+    rowName: string;
+    position: number;
+    rowMap: Map<string, string>;
+    blanks: number[];
+}): number | undefined;
+export declare function mouseOverCoordToGapRemovedCoord({ seq, blanks, position, }: {
+    seq: string;
+    blanks: number[];
+    position: number;
+}): number | undefined;

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

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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