@jbrowse/plugin-gccontent 3.6.4 → 3.6.5

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Files changed (3) hide show
  1. package/dist/GCContentAdapter/GCContentAdapter.js +54 -15
  2. package/esm/GCContentAdapter/GCContentAdapter.js +54 -15
  3. package/package.json +6 -6
package/dist/GCContentAdapter/GCContentAdapter.js CHANGED
@@ -46,28 +46,67 @@ class GCContentAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  }, opts)
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  .pipe((0, operators_1.toArray)()));
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  const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
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- let start = performance.now();
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  await (0, util_1.updateStatus)('Calculating GC', statusCallback, () => {
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+ let nc = 0;
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+ let ng = 0;
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+ let len = 0;
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+ let start = performance.now();
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+ const startIdx = halfWindowSize;
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+ for (let j = startIdx - halfWindowSize; j < startIdx + halfWindowSize; j++) {
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+ const letter = residues[j];
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+ if (letter === 'c' || letter === 'C') {
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+ nc++;
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+ }
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+ else if (letter === 'g' || letter === 'G') {
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+ ng++;
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+ }
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+ if (letter !== 'N') {
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+ len++;
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+ }
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+ }
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  for (let i = halfWindowSize; i < residues.length - halfWindowSize; i += windowDelta) {
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  if (performance.now() - start > 400) {
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  (0, stopToken_1.checkStopToken)(stopToken);
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  start = performance.now();
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  }
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- const r = isWindowSizeOneBp
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- ? residues[i]
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- : residues.slice(i - halfWindowSize, i + halfWindowSize);
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- let nc = 0;
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- let ng = 0;
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- let len = 0;
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- for (const letter of r) {
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- if (letter === 'c' || letter === 'C') {
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- nc++;
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- }
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- else if (letter === 'g' || letter === 'G') {
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- ng++;
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+ if (isWindowSizeOneBp) {
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+ const letter = residues[i];
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+ nc = letter === 'c' || letter === 'C' ? 1 : 0;
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+ ng = letter === 'g' || letter === 'G' ? 1 : 0;
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+ len = letter !== 'N' ? 1 : 0;
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+ }
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+ else if (i > halfWindowSize) {
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+ const prevStart = i - windowDelta - halfWindowSize;
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+ const prevEnd = i - windowDelta + halfWindowSize;
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+ const currStart = i - halfWindowSize;
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+ const currEnd = i + halfWindowSize;
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+ for (let j = prevStart; j < Math.min(prevEnd, currStart); j++) {
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+ if (j >= 0 && j < residues.length) {
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+ const letter = residues[j];
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+ if (letter === 'c' || letter === 'C') {
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+ nc--;
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+ }
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+ else if (letter === 'g' || letter === 'G') {
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+ ng--;
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+ }
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+ if (letter !== 'N') {
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+ len--;
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+ }
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+ }
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  }
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- if (letter !== 'N') {
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- len++;
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+ for (let j = Math.max(prevEnd, currStart); j < currEnd; j++) {
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+ if (j >= 0 && j < residues.length) {
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+ const letter = residues[j];
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+ if (letter === 'c' || letter === 'C') {
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+ nc++;
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+ }
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+ else if (letter === 'g' || letter === 'G') {
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+ ng++;
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+ }
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+ if (letter !== 'N') {
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+ len++;
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+ }
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+ }
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  }
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  }
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  const pos = qs;
package/esm/GCContentAdapter/GCContentAdapter.js CHANGED
@@ -44,28 +44,67 @@ class GCContentAdapter extends BaseFeatureDataAdapter {
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  }, opts)
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  .pipe(toArray()));
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  const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
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- let start = performance.now();
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  await updateStatus('Calculating GC', statusCallback, () => {
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+ let nc = 0;
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+ let ng = 0;
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+ let len = 0;
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+ let start = performance.now();
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+ const startIdx = halfWindowSize;
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+ for (let j = startIdx - halfWindowSize; j < startIdx + halfWindowSize; j++) {
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+ const letter = residues[j];
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+ if (letter === 'c' || letter === 'C') {
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+ nc++;
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+ }
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+ else if (letter === 'g' || letter === 'G') {
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+ ng++;
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+ }
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+ if (letter !== 'N') {
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+ len++;
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+ }
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+ }
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  for (let i = halfWindowSize; i < residues.length - halfWindowSize; i += windowDelta) {
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  if (performance.now() - start > 400) {
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  checkStopToken(stopToken);
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  start = performance.now();
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  }
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- const r = isWindowSizeOneBp
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- ? residues[i]
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- : residues.slice(i - halfWindowSize, i + halfWindowSize);
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- let nc = 0;
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- let ng = 0;
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- let len = 0;
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- for (const letter of r) {
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- if (letter === 'c' || letter === 'C') {
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- nc++;
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- }
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- else if (letter === 'g' || letter === 'G') {
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- ng++;
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+ if (isWindowSizeOneBp) {
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+ const letter = residues[i];
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+ nc = letter === 'c' || letter === 'C' ? 1 : 0;
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+ ng = letter === 'g' || letter === 'G' ? 1 : 0;
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+ len = letter !== 'N' ? 1 : 0;
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+ }
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+ else if (i > halfWindowSize) {
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+ const prevStart = i - windowDelta - halfWindowSize;
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+ const prevEnd = i - windowDelta + halfWindowSize;
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+ const currStart = i - halfWindowSize;
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+ const currEnd = i + halfWindowSize;
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+ for (let j = prevStart; j < Math.min(prevEnd, currStart); j++) {
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+ if (j >= 0 && j < residues.length) {
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+ const letter = residues[j];
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+ if (letter === 'c' || letter === 'C') {
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+ nc--;
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+ }
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+ else if (letter === 'g' || letter === 'G') {
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+ ng--;
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+ }
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+ if (letter !== 'N') {
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+ len--;
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+ }
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+ }
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  }
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- if (letter !== 'N') {
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- len++;
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+ for (let j = Math.max(prevEnd, currStart); j < currEnd; j++) {
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+ if (j >= 0 && j < residues.length) {
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+ const letter = residues[j];
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+ if (letter === 'c' || letter === 'C') {
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+ nc++;
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+ }
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+ else if (letter === 'g' || letter === 'G') {
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+ ng++;
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+ }
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+ if (letter !== 'N') {
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+ len++;
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+ }
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+ }
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  }
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  }
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  const pos = qs;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-gccontent",
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- "version": "3.6.4",
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+ "version": "3.6.5",
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  "description": "JBrowse 2 gccontent concepts",
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  "keywords": [
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  "jbrowse",
@@ -36,10 +36,10 @@
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  "clean": "rimraf dist esm *.tsbuildinfo"
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  },
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  "dependencies": {
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- "@jbrowse/core": "^3.6.4",
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- "@jbrowse/plugin-linear-genome-view": "^3.6.4",
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- "@jbrowse/plugin-sequence": "^3.6.4",
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- "@jbrowse/plugin-wiggle": "^3.6.4",
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+ "@jbrowse/core": "^3.6.5",
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+ "@jbrowse/plugin-linear-genome-view": "^3.6.5",
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+ "@jbrowse/plugin-sequence": "^3.6.5",
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+ "@jbrowse/plugin-wiggle": "^3.6.5",
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  "@mui/material": "^7.0.0",
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  "mobx": "^6.0.0",
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  "mobx-react": "^9.0.0",
@@ -55,5 +55,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "3db8e50ce2bd9c081efbf6c2e7ae5f342380a25a"
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+ "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
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  }