jbrowse-plugin-mafviewer 1.4.0 → 1.4.1
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.
- package/dist/LinearMafRenderer/components/LinearMafRendering.js +3 -2
- package/dist/LinearMafRenderer/components/LinearMafRendering.js.map +1 -1
- package/dist/LinearMafRenderer/rendering/features.js +4 -6
- package/dist/LinearMafRenderer/rendering/features.js.map +1 -1
- package/dist/LinearMafRenderer/rendering/insertions.d.ts +1 -1
- package/dist/LinearMafRenderer/rendering/insertions.js +1 -1
- package/dist/LinearMafRenderer/rendering/insertions.js.map +1 -1
- package/dist/LinearMafRenderer/rendering/matches.d.ts +1 -1
- package/dist/LinearMafRenderer/rendering/matches.js +1 -1
- package/dist/LinearMafRenderer/rendering/matches.js.map +1 -1
- package/dist/LinearMafRenderer/rendering/mismatches.d.ts +1 -1
- package/dist/LinearMafRenderer/rendering/mismatches.js +2 -2
- package/dist/LinearMafRenderer/rendering/mismatches.js.map +1 -1
- package/dist/LinearMafRenderer/rendering/text.d.ts +1 -1
- package/dist/LinearMafRenderer/rendering/text.js +1 -1
- package/dist/LinearMafRenderer/rendering/text.js.map +1 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +5 -5
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +3 -3
- package/dist/out.js +10 -16
- package/dist/out.js.map +2 -2
- package/package.json +1 -1
- package/src/LinearMafRenderer/components/LinearMafRendering.tsx +3 -2
- package/src/LinearMafRenderer/rendering/features.ts +0 -10
- package/src/LinearMafRenderer/rendering/insertions.ts +0 -1
- package/src/LinearMafRenderer/rendering/matches.ts +0 -1
- package/src/LinearMafRenderer/rendering/mismatches.ts +1 -2
- package/src/LinearMafRenderer/rendering/text.ts +0 -2
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@@ -16,8 +16,9 @@ const LinearMafRendering = observer(function (props) {
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}
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const x = rbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
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if (x.length) {
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const elt = x.
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const r = elt !==
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const elt = x.find(idx => items[idx]?.isInsertion);
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const r = elt !== undefined ? items[elt] : items[x[0]];
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console.log({ x, r });
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const s = samples[r.sampleId];
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return {
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...r,
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@@ -1 +1 @@
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-
{"version":3,"file":"LinearMafRendering.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/components/LinearMafRendering.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAA;AACpD,OAAO,QAAQ,MAAM,UAAU,CAAA;AAC/B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAMrC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAO7C;IACC,MAAM,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAChE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAA;IAEjE,SAAS,oBAAoB,CAAC,YAAoB,EAAE,YAAoB;QACtE,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;YAChB,MAAM,CAAC,GAAG,GAAG,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAA;YAC7C,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,IAAI,CAAA;YAC/B,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,GAAG,CAAA;QAChC,CAAC;QAED,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,CAAC,CAAC,CAAA;QACnE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;YACb,MAAM,GAAG,GAAG,CAAC,CAAC,
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{"version":3,"file":"LinearMafRendering.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/components/LinearMafRendering.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAA;AACpD,OAAO,QAAQ,MAAM,UAAU,CAAA;AAC/B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAMrC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAO7C;IACC,MAAM,EAAE,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAChE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAA;IAEjE,SAAS,oBAAoB,CAAC,YAAoB,EAAE,YAAoB;QACtE,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;YAChB,MAAM,CAAC,GAAG,GAAG,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAA;YAC7C,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,IAAI,CAAA;YAC/B,OAAO,GAAG,YAAY,GAAG,CAAC,CAAC,GAAG,CAAA;QAChC,CAAC;QAED,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,CAAC,CAAC,CAAA;QACnE,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;YACb,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,WAAW,CAAC,CAAA;YAClD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAE,CAAE,CAAA;YACzD,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAA;YACrB,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;YAC7B,OAAO;gBACL,GAAG,CAAC;gBACJ,QAAQ,EAAE,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,EAAE,IAAI,SAAS;aACzC,CAAA;QACH,CAAC;aAAM,CAAC;YACN,OAAO,SAAS,CAAA;QAClB,CAAC;IACH,CAAC;IACD,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,CAAC,CAAC,EAAE,CACf,YAAY,CAAC,cAAc,EAAE,CAC3B,oBAAoB,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,CAC3C,EAEH,YAAY,EAAE,GAAG,EAAE;YACjB,YAAY,CAAC,cAAc,EAAE,CAAC,SAAS,CAAC,CAAA;QAC1C,CAAC,EACD,UAAU,EAAE,GAAG,EAAE;YACf,YAAY,CAAC,cAAc,EAAE,CAAC,SAAS,CAAC,CAAA;QAC1C,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,SAAS;YACnB,QAAQ,EAAE,UAAU;YACpB,MAAM;SACP;QAED,oBAAC,iBAAiB,OACZ,KAAK,EACT,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,IAAI,EAAE,CAAC;aACR,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}
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@@ -8,7 +8,6 @@ export function processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap
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const [leftPx] = featureSpanPx(feature, region, bpPerPx);
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const alignments = feature.get('alignments');
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const referenceSeq = feature.get('seq').toLowerCase();
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const featureId = feature.id() || `feature_${feature.get('start')}_${feature.get('end')}`;
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for (const [sampleId, alignmentData] of Object.entries(alignments)) {
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const row = sampleToRowMap.get(sampleId);
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if (row === undefined) {
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@@ -18,16 +17,15 @@ export function processFeatureAlignment(feature, region, bpPerPx, sampleToRowMap
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const alignment = originalAlignment.toLowerCase();
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const rowTop = renderingContext.offset + renderingContext.rowHeight * row;
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renderGaps(renderingContext, alignment, referenceSeq, leftPx, rowTop);
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renderMatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row,
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renderMismatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row,
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renderText(renderingContext, alignment, originalAlignment, referenceSeq, leftPx, rowTop
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renderMatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row, alignmentData.start, alignmentData.chr);
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renderMismatches(renderingContext, alignment, referenceSeq, leftPx, rowTop, row, alignmentData.start, alignmentData.chr);
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renderText(renderingContext, alignment, originalAlignment, referenceSeq, leftPx, rowTop);
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}
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}
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export function processFeatureInsertions(feature, region, bpPerPx, sampleToRowMap, renderingContext) {
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const [leftPx] = featureSpanPx(feature, region, bpPerPx);
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const alignments = feature.get('alignments');
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const referenceSeq = feature.get('seq').toLowerCase();
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const featureId = feature.id() || `feature_${feature.get('start')}_${feature.get('end')}`;
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for (const [sampleId, alignmentData] of Object.entries(alignments)) {
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const row = sampleToRowMap.get(sampleId);
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if (row === undefined) {
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@@ -35,7 +33,7 @@ export function processFeatureInsertions(feature, region, bpPerPx, sampleToRowMa
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}
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const alignment = alignmentData.seq.toLowerCase();
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const rowTop = renderingContext.offset + renderingContext.rowHeight * row;
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renderInsertions(renderingContext, alignment, referenceSeq, leftPx, rowTop, bpPerPx, row,
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renderInsertions(renderingContext, alignment, referenceSeq, leftPx, rowTop, bpPerPx, row, alignmentData.start, alignmentData.chr);
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}
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}
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//# sourceMappingURL=features.js.map
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@@ -1 +1 @@
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-
{"version":3,"file":"features.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/features.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAE3D,OAAO,EAAE,UAAU,EAAE,MAAM,QAAQ,CAAA;AACnC,OAAO,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AACzC,OAAO,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAA;AAC/C,OAAO,EAAE,UAAU,EAAE,MAAM,QAAQ,CAAA;AAInC,MAAM,UAAU,uBAAuB,CACrC,OAAgB,EAChB,MAAqB,EACrB,OAAe,EACf,cAAmC,EACnC,gBAAkC;IAElC,MAAM,CAAC,MAAM,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;IACxD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAG1C,CAAA;IACD,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE,CAAA;
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{"version":3,"file":"features.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/features.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAE3D,OAAO,EAAE,UAAU,EAAE,MAAM,QAAQ,CAAA;AACnC,OAAO,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AACzC,OAAO,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAA;AAC/C,OAAO,EAAE,UAAU,EAAE,MAAM,QAAQ,CAAA;AAInC,MAAM,UAAU,uBAAuB,CACrC,OAAgB,EAChB,MAAqB,EACrB,OAAe,EACf,cAAmC,EACnC,gBAAkC;IAElC,MAAM,CAAC,MAAM,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;IACxD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAG1C,CAAA;IACD,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE,CAAA;IAErD,KAAK,MAAM,CAAC,QAAQ,EAAE,aAAa,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QACnE,MAAM,GAAG,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;QACxC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,SAAQ;QACV,CAAC;QAED,MAAM,iBAAiB,GAAG,aAAa,CAAC,GAAG,CAAA;QAC3C,MAAM,SAAS,GAAG,iBAAiB,CAAC,WAAW,EAAE,CAAA;QACjD,MAAM,MAAM,GAAG,gBAAgB,CAAC,MAAM,GAAG,gBAAgB,CAAC,SAAS,GAAG,GAAG,CAAA;QAEzE,UAAU,CAAC,gBAAgB,EAAE,SAAS,EAAE,YAAY,EAAE,MAAM,EAAE,MAAM,CAAC,CAAA;QACrE,aAAa,CACX,gBAAgB,EAChB,SAAS,EACT,YAAY,EACZ,MAAM,EACN,MAAM,EACN,GAAG,EACH,aAAa,CAAC,KAAK,EACnB,aAAa,CAAC,GAAG,CAClB,CAAA;QACD,gBAAgB,CACd,gBAAgB,EAChB,SAAS,EACT,YAAY,EACZ,MAAM,EACN,MAAM,EACN,GAAG,EACH,aAAa,CAAC,KAAK,EACnB,aAAa,CAAC,GAAG,CAClB,CAAA;QACD,UAAU,CACR,gBAAgB,EAChB,SAAS,EACT,iBAAiB,EACjB,YAAY,EACZ,MAAM,EACN,MAAM,CACP,CAAA;IACH,CAAC;AACH,CAAC;AAED,MAAM,UAAU,wBAAwB,CACtC,OAAgB,EAChB,MAAqB,EACrB,OAAe,EACf,cAAmC,EACnC,gBAAkC;IAElC,MAAM,CAAC,MAAM,CAAC,GAAG,aAAa,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;IACxD,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,CAG1C,CAAA;IACD,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE,CAAA;IACrD,KAAK,MAAM,CAAC,QAAQ,EAAE,aAAa,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QACnE,MAAM,GAAG,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;QACxC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,SAAQ;QACV,CAAC;QAED,MAAM,SAAS,GAAG,aAAa,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;QACjD,MAAM,MAAM,GAAG,gBAAgB,CAAC,MAAM,GAAG,gBAAgB,CAAC,SAAS,GAAG,GAAG,CAAA;QAEzE,gBAAgB,CACd,gBAAgB,EAChB,SAAS,EACT,YAAY,EACZ,MAAM,EACN,MAAM,EACN,OAAO,EACP,GAAG,EACH,aAAa,CAAC,KAAK,EACnB,aAAa,CAAC,GAAG,CAClB,CAAA;IACH,CAAC;AACH,CAAC"}
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import type { RenderingContext } from './types';
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export declare function renderInsertions(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, bpPerPx: number, sampleId: number,
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export declare function renderInsertions(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, bpPerPx: number, sampleId: number, alignmentStart: number, chr: string): void;
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import { fillRect, getCharWidthHeight } from '../util';
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import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
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import { CHAR_SIZE_WIDTH, HIGH_BP_PER_PX_THRESHOLD, HIGH_ZOOM_THRESHOLD, INSERTION_BORDER_HEIGHT, INSERTION_BORDER_WIDTH, INSERTION_LINE_WIDTH, INSERTION_PADDING, LARGE_INSERTION_THRESHOLD, MIN_ROW_HEIGHT_FOR_BORDERS, } from './types';
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export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, sampleId,
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export function renderInsertions(context, alignment, seq, leftPx, rowTop, bpPerPx, sampleId, alignmentStart, chr) {
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const { ctx, scale, h, canvasWidth, rowHeight } = context;
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const { charHeight } = getCharWidthHeight();
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for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
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{"version":3,"file":"insertions.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/insertions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAEhD,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AACtD,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,gBAAgB,CAAA;AAC3E,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,mBAAmB,EACnB,uBAAuB,EACvB,sBAAsB,EACtB,oBAAoB,EACpB,iBAAiB,EACjB,yBAAyB,EACzB,0BAA0B,GAC3B,MAAM,SAAS,CAAA;AAIhB,MAAM,UAAU,gBAAgB,CAC9B,OAAyB,EACzB,SAAiB,EACjB,GAAW,EACX,MAAc,EACd,MAAc,EACd,OAAe,EACf,QAAgB,EAChB,
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{"version":3,"file":"insertions.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/insertions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAEhD,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AACtD,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,gBAAgB,CAAA;AAC3E,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,mBAAmB,EACnB,uBAAuB,EACvB,sBAAsB,EACtB,oBAAoB,EACpB,iBAAiB,EACjB,yBAAyB,EACzB,0BAA0B,GAC3B,MAAM,SAAS,CAAA;AAIhB,MAAM,UAAU,gBAAgB,CAC9B,OAAyB,EACzB,SAAiB,EACjB,GAAW,EACX,MAAc,EACd,MAAc,EACd,OAAe,EACf,QAAgB,EAChB,cAAsB,EACtB,GAAW;IAEX,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,OAAO,CAAA;IACzD,MAAM,EAAE,UAAU,EAAE,GAAG,kBAAkB,EAAE,CAAA;IAE3C,KACE,IAAI,CAAC,GAAG,CAAC,EAAE,aAAa,GAAG,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC,MAAM,EAC1D,CAAC,GAAG,SAAS,EACb,CAAC,EAAE,EACH,CAAC;QACD,IAAI,iBAAiB,GAAG,EAAE,CAAA;QAC1B,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACtB,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;gBACjD,iBAAiB,IAAI,SAAS,CAAC,CAAC,CAAC,CAAA;YACnC,CAAC;YACD,CAAC,EAAE,CAAA;QACL,CAAC;QACD,IAAI,iBAAiB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACjC,qBAAqB;YACrB,MAAM,IAAI,GAAG,MAAM,GAAG,KAAK,GAAG,aAAa,GAAG,oBAAoB,CAAA;YAElE,iEAAiE;YACjE,IAAI,UAAkB,CAAA;YACtB,IAAI,WAAmB,CAAA;YAEvB,2DAA2D;YAC3D,IAAI,iBAAiB,CAAC,MAAM,GAAG,yBAAyB,EAAE,CAAC;gBACzD,MAAM,UAAU,GAAG,GAAG,iBAAiB,CAAC,MAAM,EAAE,CAAA;gBAChD,IAAI,OAAO,GAAG,wBAAwB,EAAE,CAAC;oBACvC,+BAA+B;oBAC/B,UAAU,GAAG,IAAI,GAAG,oBAAoB,CAAA;oBACxC,WAAW,GAAG,sBAAsB,CAAA;oBACpC,QAAQ,CACN,GAAG,EACH,UAAU,EACV,MAAM,EACN,WAAW,EACX,CAAC,EACD,WAAW,EACX,QAAQ,CACT,CAAA;gBACH,CAAC;qBAAM,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;oBAC1B,yCAAyC;oBACzC,MAAM,SAAS,GAAG,WAAW,CAAC,UAAU,EAAE,eAAe,CAAC,CAAA;oBAC1D,MAAM,OAAO,GAAG,iBAAiB,CAAA;oBACjC,UAAU,GAAG,IAAI,GAAG,SAAS,GAAG,CAAC,GAAG,OAAO,CAAA;oBAC3C,WAAW,GAAG,SAAS,GAAG,CAAC,GAAG,OAAO,CAAA;oBACrC,QAAQ,CACN,GAAG,EACH,UAAU,EACV,MAAM,EACN,WAAW,EACX,CAAC,EACD,WAAW,EACX,QAAQ,CACT,CAAA;oBACD,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;oBACvB,GAAG,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,GAAG,SAAS,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACtE,CAAC;qBAAM,CAAC;oBACN,MAAM,OAAO,GAAG,iBAAiB,CAAA;oBACjC,UAAU,GAAG,IAAI,GAAG,OAAO,CAAA;oBAC3B,WAAW,GAAG,CAAC,GAAG,OAAO,CAAA;oBACzB,QAAQ,CACN,GAAG,EACH,UAAU,EACV,MAAM,EACN,WAAW,EACX,CAAC,EACD,WAAW,EACX,QAAQ,CACT,CAAA;gBACH,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,oEAAoE;gBACpE,UAAU,GAAG,IAAI,CAAA;gBACjB,WAAW,GAAG,oBAAoB,CAAA;gBAClC,QAAQ,CAAC,GAAG,EAAE,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAA;gBACxE,IACE,OAAO,GAAG,mBAAmB;oBAC7B,SAAS,GAAG,0BAA0B,EACtC,CAAC;oBACD,qDAAqD;oBACrD,oDAAoD;oBACpD,UAAU,GAAG,IAAI,GAAG,sBAAsB,CAAA;oBAC1C,WAAW,GAAG,uBAAuB,CAAA;oBACrC,QAAQ,CACN,GAAG,EACH,IAAI,GAAG,sBAAsB,EAC7B,MAAM,EACN,uBAAuB,EACvB,oBAAoB,EACpB,WAAW,CACZ,CAAA;oBACD,QAAQ,CACN,GAAG,EACH,IAAI,GAAG,sBAAsB,EAC7B,MAAM,GAAG,CAAC,GAAG,oBAAoB,EACjC,uBAAuB,EACvB,oBAAoB,EACpB,WAAW,CACZ,CAAA;gBACH,CAAC;YACH,CAAC;YAED,iEAAiE;YACjE,2CAA2C;YAC3C,IAAI,uBAAuB,CAAC,UAAU,EAAE,OAAO,EAAE,IAAI,CAAC,EAAE,CAAC;gBACvD,iBAAiB,CACf,OAAO,EACP,UAAU,EACV,MAAM,EACN,UAAU,GAAG,WAAW,EACxB,MAAM,GAAG,OAAO,CAAC,CAAC,EAClB;oBACE,GAAG,EAAE,aAAa,GAAG,cAAc;oBACnC,GAAG;oBACH,IAAI,EAAE,iBAAiB;oBACvB,QAAQ;oBACR,WAAW,EAAE,IAAI;iBAClB,CACF,CAAA;YACH,CAAC;QACH,CAAC;QACD,aAAa,EAAE,CAAA;IACjB,CAAC;AACH,CAAC"}
|
|
@@ -1,2 +1,2 @@
|
|
|
1
1
|
import type { RenderingContext } from './types';
|
|
2
|
-
export declare function renderMatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number,
|
|
2
|
+
export declare function renderMatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number, alignmentStart: number, chr: string): void;
|
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { fillRect } from '../util';
|
|
2
2
|
import { addToSpatialIndex, shouldAddToSpatialIndex } from './spatialIndex';
|
|
3
3
|
import { GAP_STROKE_OFFSET } from './types';
|
|
4
|
-
export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId,
|
|
4
|
+
export function renderMatches(context, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
|
|
5
5
|
if (context.showAllLetters) {
|
|
6
6
|
return;
|
|
7
7
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"matches.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/matches.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,gBAAgB,CAAA;AAC3E,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAI3C,MAAM,UAAU,aAAa,CAC3B,OAAyB,EACzB,SAAiB,EACjB,GAAW,EACX,MAAc,EACd,MAAc,EACd,QAAgB,EAChB,
|
|
1
|
+
{"version":3,"file":"matches.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/matches.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,gBAAgB,CAAA;AAC3E,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAI3C,MAAM,UAAU,aAAa,CAC3B,OAAyB,EACzB,SAAiB,EACjB,GAAW,EACX,MAAc,EACd,MAAc,EACd,QAAgB,EAChB,cAAsB,EACtB,GAAW;IAEX,IAAI,OAAO,CAAC,cAAc,EAAE,CAAC;QAC3B,OAAM;IACR,CAAC;IAED,MAAM,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;IAC9C,GAAG,CAAC,SAAS,GAAG,WAAW,CAAA;IAE3B,sDAAsD;IACtD,KACE,IAAI,CAAC,GAAG,CAAC,EAAE,aAAa,GAAG,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC,MAAM,EAC1D,CAAC,GAAG,SAAS,EACb,CAAC,EAAE,EACH,CAAC;QACD,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACnB,8CAA8C;YAC9C,MAAM,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;YAChC,MAAM,IAAI,GAAG,MAAM,GAAG,KAAK,GAAG,aAAa,CAAA;YAC3C,IACE,GAAG,CAAC,CAAC,CAAC,KAAK,WAAW;gBACtB,WAAW,KAAK,GAAG;gBACnB,WAAW,KAAK,GAAG,EACnB,CAAC;gBACD,QAAQ,CAAC,GAAG,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,GAAG,iBAAiB,EAAE,CAAC,EAAE,WAAW,CAAC,CAAA;gBAEtE,iDAAiD;gBACjD,IAAI,uBAAuB,CAAC,IAAI,EAAE,OAAO,CAAC,EAAE,CAAC;oBAC3C,iBAAiB,CACf,OAAO,EACP,IAAI,EACJ,MAAM,EACN,IAAI,GAAG,OAAO,CAAC,KAAK,GAAG,iBAAiB,EACxC,MAAM,GAAG,OAAO,CAAC,CAAC,EAClB;wBACE,GAAG,EAAE,aAAa,GAAG,cAAc;wBACnC,GAAG;wBACH,IAAI,EAAE,WAAW,IAAI,EAAE;wBACvB,QAAQ;qBACT,CACF,CAAA;gBACH,CAAC;YACH,CAAC;YACD,aAAa,EAAE,CAAA;QACjB,CAAC;IACH,CAAC;AACH,CAAC"}
|
|
@@ -10,4 +10,4 @@ import type { RenderingContext } from './types';
|
|
|
10
10
|
* @param alignmentStart - Start position of the alignment
|
|
11
11
|
* @param chr - Chromosome/sequence name
|
|
12
12
|
*/
|
|
13
|
-
export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number,
|
|
13
|
+
export declare function renderMismatches(context: RenderingContext, alignment: string, seq: string, leftPx: number, rowTop: number, sampleId: number, alignmentStart: number, chr: string): void;
|
|
@@ -12,7 +12,7 @@ import { GAP_STROKE_OFFSET } from './types';
|
|
|
12
12
|
* @param alignmentStart - Start position of the alignment
|
|
13
13
|
* @param chr - Chromosome/sequence name
|
|
14
14
|
*/
|
|
15
|
-
export function renderMismatches(context, alignment, seq, leftPx, rowTop, sampleId,
|
|
15
|
+
export function renderMismatches(context, alignment, seq, leftPx, rowTop, sampleId, alignmentStart, chr) {
|
|
16
16
|
const { ctx, scale, h, canvasWidth, showAllLetters, mismatchRendering, colorForBase, } = context;
|
|
17
17
|
for (let i = 0, genomicOffset = 0, seqLength = alignment.length; i < seqLength; i++) {
|
|
18
18
|
const currentChar = alignment[i];
|
|
@@ -30,7 +30,7 @@ export function renderMismatches(context, alignment, seq, leftPx, rowTop, sample
|
|
|
30
30
|
pos: genomicOffset + alignmentStart,
|
|
31
31
|
chr,
|
|
32
32
|
base: currentChar,
|
|
33
|
-
sampleId
|
|
33
|
+
sampleId,
|
|
34
34
|
});
|
|
35
35
|
}
|
|
36
36
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"mismatches.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/mismatches.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,gBAAgB,CAAA;AAC3E,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAI3C;;;;;;;;;;GAUG;AACH,MAAM,UAAU,gBAAgB,CAC9B,OAAyB,EACzB,SAAiB,EACjB,GAAW,EACX,MAAc,EACd,MAAc,EACd,QAAgB,EAChB,
|
|
1
|
+
{"version":3,"file":"mismatches.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/mismatches.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAA;AAClC,OAAO,EAAE,iBAAiB,EAAE,uBAAuB,EAAE,MAAM,gBAAgB,CAAA;AAC3E,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAI3C;;;;;;;;;;GAUG;AACH,MAAM,UAAU,gBAAgB,CAC9B,OAAyB,EACzB,SAAiB,EACjB,GAAW,EACX,MAAc,EACd,MAAc,EACd,QAAgB,EAChB,cAAsB,EACtB,GAAW;IAEX,MAAM,EACJ,GAAG,EACH,KAAK,EACL,CAAC,EACD,WAAW,EACX,cAAc,EACd,iBAAiB,EACjB,YAAY,GACb,GAAG,OAAO,CAAA;IAEX,KACE,IAAI,CAAC,GAAG,CAAC,EAAE,aAAa,GAAG,CAAC,EAAE,SAAS,GAAG,SAAS,CAAC,MAAM,EAC1D,CAAC,GAAG,SAAS,EACb,CAAC,EAAE,EACH,CAAC;QACD,MAAM,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;QAChC,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YACnB,IAAI,WAAW,KAAK,GAAG,EAAE,CAAC;gBACxB,MAAM,IAAI,GAAG,MAAM,GAAG,KAAK,GAAG,aAAa,CAAA;gBAC3C,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,WAAW,IAAI,WAAW,KAAK,GAAG,EAAE,CAAC;oBAClD,8CAA8C;oBAC9C,QAAQ,CACN,GAAG,EACH,IAAI,EACJ,MAAM,EACN,KAAK,GAAG,iBAAiB,EACzB,CAAC,EACD,WAAW,EACX,iBAAiB;wBACf,CAAC,CAAC,CAAC,YAAY,CAAC,WAAY,CAAC,IAAI,OAAO,CAAC;wBACzC,CAAC,CAAC,QAAQ,CACb,CAAA;oBAED,iDAAiD;oBACjD,IAAI,uBAAuB,CAAC,IAAI,EAAE,OAAO,CAAC,EAAE,CAAC;wBAC3C,iBAAiB,CACf,OAAO,EACP,IAAI,EACJ,MAAM,EACN,IAAI,GAAG,OAAO,CAAC,KAAK,GAAG,iBAAiB,EACxC,MAAM,GAAG,OAAO,CAAC,CAAC,EAClB;4BACE,GAAG,EAAE,aAAa,GAAG,cAAc;4BACnC,GAAG;4BACH,IAAI,EAAE,WAAY;4BAClB,QAAQ;yBACT,CACF,CAAA;oBACH,CAAC;gBACH,CAAC;qBAAM,IAAI,cAAc,EAAE,CAAC;oBAC1B,0EAA0E;oBAC1E,QAAQ,CACN,GAAG,EACH,IAAI,EACJ,MAAM,EACN,KAAK,GAAG,iBAAiB,EACzB,CAAC,EACD,WAAW,EACX,iBAAiB;wBACf,CAAC,CAAC,CAAC,YAAY,CAAC,WAAY,CAAC,IAAI,OAAO,CAAC;wBACzC,CAAC,CAAC,WAAW,CAChB,CAAA;oBAED,iDAAiD;oBACjD,IAAI,uBAAuB,CAAC,IAAI,EAAE,OAAO,CAAC,EAAE,CAAC;wBAC3C,iBAAiB,CACf,OAAO,EACP,IAAI,EACJ,MAAM,EACN,IAAI,GAAG,OAAO,CAAC,KAAK,GAAG,iBAAiB,EACxC,MAAM,GAAG,OAAO,CAAC,CAAC,EAClB;4BACE,GAAG,EAAE,aAAa,GAAG,cAAc;4BACnC,GAAG;4BACH,IAAI,EAAE,WAAY;4BAClB,QAAQ;yBACT,CACF,CAAA;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;YACD,aAAa,EAAE,CAAA;QACjB,CAAC;IACH,CAAC;AACH,CAAC"}
|
|
@@ -9,4 +9,4 @@ import type { RenderingContext } from './types';
|
|
|
9
9
|
* @param leftPx - Left pixel position of the feature
|
|
10
10
|
* @param rowTop - Top pixel position of the row
|
|
11
11
|
*/
|
|
12
|
-
export declare function renderText(context: RenderingContext, alignment: string, origAlignment: string, seq: string, leftPx: number, rowTop: number
|
|
12
|
+
export declare function renderText(context: RenderingContext, alignment: string, origAlignment: string, seq: string, leftPx: number, rowTop: number): void;
|
|
@@ -13,7 +13,7 @@ function getLetter(a, showAsUpperCase) {
|
|
|
13
13
|
* @param leftPx - Left pixel position of the feature
|
|
14
14
|
* @param rowTop - Top pixel position of the row
|
|
15
15
|
*/
|
|
16
|
-
export function renderText(context, alignment, origAlignment, seq, leftPx, rowTop
|
|
16
|
+
export function renderText(context, alignment, origAlignment, seq, leftPx, rowTop) {
|
|
17
17
|
const { ctx, scale, hp2, rowHeight, showAllLetters, mismatchRendering, contrastForBase, showAsUpperCase, } = context;
|
|
18
18
|
const { charHeight } = getCharWidthHeight();
|
|
19
19
|
// Render text labels when zoomed in enough and row is tall enough
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"text.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/rendering/text.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,eAAe,EAAE,oBAAoB,EAAE,MAAM,SAAS,CAAA;AAI/D,SAAS,SAAS,CAAC,CAAS,EAAE,eAAwB;IACpD,OAAO,eAAe,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,UAAU,CACxB,OAAyB,EACzB,SAAiB,EACjB,aAAqB,EACrB,GAAW,EACX,MAAc,EACd,MAAc
|
|
1
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+
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