npm - react-msaview - Versions diffs - 5.9.0 → 5.10.0 - Mend

react-msaview 5.9.0 → 5.10.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (71) hide show

package/bundle/index.js +76 -76
package/bundle/index.js.map +3 -3
package/dist/components/ConservationTrack.js +21 -16
package/dist/components/ConservationTrack.js.map +1 -1
package/dist/components/MSAView.js +17 -23
package/dist/components/MSAView.js.map +1 -1
package/dist/components/TextTrack.js +26 -21
package/dist/components/TextTrack.js.map +1 -1
package/dist/components/header/settingsMenuItems.js +39 -72
package/dist/components/header/settingsMenuItems.js.map +1 -1
package/dist/components/msa/MSACanvasBlock.js +19 -16
package/dist/components/msa/MSACanvasBlock.js.map +1 -1
package/dist/components/msa/MSAMouseoverCanvas.js +13 -6
package/dist/components/msa/MSAMouseoverCanvas.js.map +1 -1
package/dist/components/msa/renderBoxFeatureCanvasBlock.js +9 -6
package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map +1 -1
package/dist/components/msa/renderMSAMouseover.js +31 -31
package/dist/components/msa/renderMSAMouseover.js.map +1 -1
package/dist/components/overlayColors.d.ts +2 -0
package/dist/components/overlayColors.js +5 -0
package/dist/components/overlayColors.js.map +1 -1
package/dist/components/tree/TreeCanvas.js +29 -24
package/dist/components/tree/TreeCanvas.js.map +1 -1
package/dist/components/tree/TreeCanvasBlock.js +19 -12
package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
package/dist/components/tree/renderTreeCanvas.d.ts +0 -38
package/dist/components/tree/renderTreeCanvas.js +17 -17
package/dist/components/tree/renderTreeCanvas.js.map +1 -1
package/dist/model.js +82 -113
package/dist/model.js.map +1 -1
package/dist/neighborJoining.js +12 -19
package/dist/neighborJoining.js.map +1 -1
package/dist/parseAsn1.js +32 -43
package/dist/parseAsn1.js.map +1 -1
package/dist/renderToSvg.js +3 -0
package/dist/renderToSvg.js.map +1 -1
package/dist/seqPosToGlobalCol.d.ts +6 -19
package/dist/seqPosToGlobalCol.js +6 -33
package/dist/seqPosToGlobalCol.js.map +1 -1
package/dist/useCanvasAutorun.d.ts +23 -1
package/dist/useCanvasAutorun.js +20 -8
package/dist/useCanvasAutorun.js.map +1 -1
package/dist/version.d.ts +1 -1
package/dist/version.js +1 -1
package/dist/version.js.map +1 -1
package/package.json +3 -3
package/src/components/ConservationTrack.tsx +7 -5
package/src/components/MSAView.tsx +24 -30
package/src/components/TextTrack.tsx +7 -12
package/src/components/header/settingsMenuItems.ts +40 -72
package/src/components/msa/MSACanvasBlock.tsx +16 -21
package/src/components/msa/MSAMouseoverCanvas.tsx +10 -6
package/src/components/msa/renderBoxFeatureCanvasBlock.test.ts +51 -0
package/src/components/msa/renderBoxFeatureCanvasBlock.ts +13 -8
package/src/components/msa/renderMSAMouseover.ts +37 -32
package/src/components/overlayColors.ts +6 -0
package/src/components/tree/TreeCanvas.tsx +6 -4
package/src/components/tree/TreeCanvasBlock.tsx +11 -12
package/src/components/tree/renderTreeCanvas.ts +20 -17
package/src/model.ts +97 -130
package/src/modelFilehandleLoaders.test.ts +137 -0
package/src/neighborJoining.test.ts +12 -0
package/src/neighborJoining.ts +12 -20
package/src/parseAsn1.ts +32 -40
package/src/{renderDomainLegendSvg.test.tsx → renderDomainsSvg.test.tsx} +44 -20
package/src/renderToSvg.tsx +3 -0
package/src/seqPosToGlobalCol.test.ts +39 -51
package/src/seqPosToGlobalCol.ts +6 -41
package/src/useCanvasAutorun.test.tsx +98 -0
package/src/useCanvasAutorun.ts +30 -11
package/src/version.ts +1 -1

package/dist/model.js.map CHANGED Viewed

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package/dist/neighborJoining.js CHANGED Viewed

@@ -48,37 +48,30 @@ function isGap(c) {
     return c === '-' || c === '.';
 }
 function computePairwiseDistance(seq1, seq2) {
-    if (seq1.length !== seq2.length) {
-        throw new Error('Sequences must have the same length (aligned)');
-    }
-    let matches = 0;
-    let mismatches = 0;
+    // ragged input is real -- a3m and hand-edited fasta both produce rows shorter
+    // than the alignment -- so a row that stops early counts as gapped for the
+    // remainder, the same rule the model's `blanks` getter applies. Requiring
+    // equal lengths here instead made "build tree from MSA" throw on those files.
+    const len = Math.max(seq1.length, seq2.length);
+    let compared = 0;
     let totalScore = 0;
     let maxPossibleScore = 0;
-    for (let i = 0; i < seq1.length; i++) {
-        const a = seq1[i];
-        const b = seq2[i];
+    for (let i = 0; i < len; i++) {
+        const a = seq1[i] ?? '-';
+        const b = seq2[i] ?? '-';
         const aGap = isGap(a);
         const bGap = isGap(b);
         if (aGap && bGap) {
             continue;
         }
+        compared++;
         if (aGap || bGap) {
-            mismatches++;
             continue;
         }
-        const score = getBlosum62Score(a, b);
-        totalScore += score;
+        totalScore += getBlosum62Score(a, b);
         maxPossibleScore += Math.max(getBlosum62Score(a, a), getBlosum62Score(b, b));
-        if (a.toUpperCase() === b.toUpperCase()) {
-            matches++;
-        }
-        else {
-            mismatches++;
-        }
     }
-    const total = matches + mismatches;
-    if (total === 0) {
+    if (compared === 0) {
         return 1;
     }
     // Convert similarity to distance using normalized BLOSUM62 score

package/dist/neighborJoining.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/parseAsn1.js CHANGED Viewed

@@ -10,29 +10,38 @@ const remap = {
     'common-name': 'commonName',
     'leaf-count': 'leafCount',
 };
+// index just past the '}' closing the '{' at openIdx, or -1 when it never
+// closes. Braces nest (a node holds features, which hold values), so finding the
+// end of a block means counting depth rather than taking the next '}'.
+function afterMatchingBrace(str, openIdx) {
+    let depth = 1;
+    let pos = openIdx + 1;
+    while (pos < str.length && depth > 0) {
+        if (str[pos] === '{') {
+            depth++;
+        }
+        else if (str[pos] === '}') {
+            depth--;
+        }
+        pos++;
+    }
+    return depth === 0 ? pos : -1;
+}
+// the contents of each top-level {...} block in str, siblings only
 function extractBracedBlocks(str) {
     const blocks = [];
     let pos = 0;
     while (pos < str.length) {
-        pos = str.indexOf('{', pos);
-        if (pos === -1) {
+        const openIdx = str.indexOf('{', pos);
+        if (openIdx === -1) {
             break;
         }
-        let depth = 1;
-        const start = pos + 1;
-        pos++;
-        while (pos < str.length && depth > 0) {
-            if (str[pos] === '{') {
-                depth++;
-            }
-            else if (str[pos] === '}') {
-                depth--;
-            }
-            pos++;
-        }
-        if (depth === 0) {
-            blocks.push(str.slice(start, pos - 1).trim());
+        const end = afterMatchingBrace(str, openIdx);
+        if (end === -1) {
+            break;
         }
+        blocks.push(str.slice(openIdx + 1, end - 1).trim());
+        pos = end;
     }
     return blocks;
 }
@@ -41,18 +50,8 @@ function findBracedContent(str, after) {
     if (openIdx === -1) {
         return undefined;
     }
-    let depth = 1;
-    let pos = openIdx + 1;
-    while (pos < str.length && depth > 0) {
-        if (str[pos] === '{') {
-            depth++;
-        }
-        else if (str[pos] === '}') {
-            depth--;
-        }
-        pos++;
-    }
-    return depth === 0 ? str.slice(openIdx + 1, pos - 1).trim() : undefined;
+    const end = afterMatchingBrace(str, openIdx);
+    return end === -1 ? undefined : str.slice(openIdx + 1, end - 1).trim();
 }
 export function parseAsn1(asnString) {
     const normalized = asnString
@@ -120,22 +119,12 @@ function extractSections(asnString) {
             pos = pos === -1 ? content.length : pos + 1;
             continue;
         }
-        let depth = 1;
-        const start = pos + 1;
-        pos++;
-        while (pos < content.length && depth > 0) {
-            if (content[pos] === '{') {
-                depth++;
-            }
-            else if (content[pos] === '}') {
-                depth--;
-            }
-            pos++;
-        }
-        if (depth === 0) {
-            sections[name] = content.slice(start, pos - 1).trim();
+        const end = afterMatchingBrace(content, pos);
+        if (end === -1) {
+            break;
         }
-        pos = content.indexOf(',', pos);
+        sections[name] = content.slice(pos + 1, end - 1).trim();
+        pos = content.indexOf(',', end);
         pos = pos === -1 ? content.length : pos + 1;
     }
     return sections;

package/dist/parseAsn1.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/renderToSvg.js CHANGED Viewed

@@ -111,6 +111,9 @@ function CoreRendering({ model, theme, layout, Context, }) {
         ctx: msaCtx,
         offsetX,
         offsetY,
+        // the overlay culls bands to this width; without it the export falls back
+        // to the on-screen 500px block size and drops every band past it
+        blockSizeXOverride: msaAreaWidth,
         blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });

package/dist/renderToSvg.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/seqPosToGlobalCol.d.ts CHANGED Viewed

@@ -1,26 +1,13 @@
 /**
- * Convert a sequence position (ungapped, 0-based) to a global column index.
- * This finds the global column that contains the Nth non-gap character.
+ * The global column of every ungapped sequence position in a row, i.e.
+ * index[seqPos] is the column holding the seqPos-th 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
+ * A row is indexed once and then answers seqPos -> column by lookup, which is
+ * what makes the domain overlay affordable: it resolves one position per feature
+ * per row on every redraw, and scanning the row for each would be quadratic.
  *
  * @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)
- */
-/**
- * The global column of every ungapped sequence position in a row, i.e.
- * index[seqPos] is the column holding the seqPos-th non-gap character. Amortizes
- * repeated seqPosToGlobalCol lookups (the domain overlay does one per feature
- * per row) into a single pass per row.
+ * buildSeqPosIndex('A-TG-C') // → [0, 2, 3, 5]
  */
 export declare function buildSeqPosIndex(row: string): Int32Array<ArrayBuffer>;
-export declare function seqPosToGlobalCol({ row, seqPos, }: {
-    row: string;
-    seqPos: number;
-}): number;