@jbrowse/plugin-alignments 2.3.4 → 2.4.1
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/BamAdapter/BamAdapter.js +2 -2
- package/dist/BamAdapter/BamAdapter.js.map +1 -1
- package/dist/BamAdapter/BamSlightlyLazyFeature.js +2 -2
- package/dist/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
- package/dist/CramAdapter/CramAdapter.js +2 -2
- package/dist/CramAdapter/CramAdapter.js.map +1 -1
- package/dist/CramAdapter/CramSlightlyLazyFeature.js +2 -2
- package/dist/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
- package/dist/CramAdapter/util.js +10 -10
- package/dist/CramAdapter/util.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
- package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/models/configSchema.js +7 -0
- package/dist/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
- package/dist/LinearAlignmentsDisplay/models/model.d.ts +21 -5
- package/dist/LinearAlignmentsDisplay/models/model.js +22 -6
- package/dist/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/dist/LinearPileupDisplay/index.d.ts +2 -3
- package/dist/LinearPileupDisplay/index.js +4 -2
- package/dist/LinearPileupDisplay/index.js.map +1 -1
- package/dist/LinearPileupDisplay/model.d.ts +70 -9
- package/dist/LinearPileupDisplay/model.js +4 -4
- package/dist/LinearPileupDisplay/model.js.map +1 -1
- package/dist/LinearReadArcsDisplay/components/ReactComponent.js +14 -11
- package/dist/LinearReadArcsDisplay/components/ReactComponent.js.map +1 -1
- package/dist/LinearReadArcsDisplay/model.d.ts +77 -28
- package/dist/LinearReadArcsDisplay/model.js +16 -4
- package/dist/LinearReadArcsDisplay/model.js.map +1 -1
- package/dist/LinearReadCloudDisplay/model.d.ts +71 -19
- package/dist/LinearReadCloudDisplay/model.js +15 -3
- package/dist/LinearReadCloudDisplay/model.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/models/model.d.ts +8 -13
- package/dist/MismatchParser/index.js +4 -6
- package/dist/MismatchParser/index.js.map +1 -1
- package/dist/NestedFrequencyTable.js +3 -13
- package/dist/NestedFrequencyTable.js.map +1 -1
- package/dist/PileupRPC/rpcMethods.d.ts +3 -4
- package/dist/PileupRPC/rpcMethods.js +6 -6
- package/dist/PileupRPC/rpcMethods.js.map +1 -1
- package/dist/PileupRenderer/PileupRenderer.d.ts +6 -4
- package/dist/PileupRenderer/PileupRenderer.js +32 -38
- package/dist/PileupRenderer/PileupRenderer.js.map +1 -1
- package/dist/PileupRenderer/components/PileupRendering.js +2 -2
- package/dist/PileupRenderer/components/PileupRendering.js.map +1 -1
- package/dist/PileupRenderer/configSchema.js +1 -1
- package/dist/PileupRenderer/configSchema.js.map +1 -1
- package/dist/PileupRenderer/sortUtil.js +5 -4
- package/dist/PileupRenderer/sortUtil.js.map +1 -1
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
- package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/dist/index.d.ts +3 -5
- package/dist/index.js +6 -6
- package/dist/index.js.map +1 -1
- package/esm/BamAdapter/BamAdapter.js +2 -2
- package/esm/BamAdapter/BamAdapter.js.map +1 -1
- package/esm/BamAdapter/BamSlightlyLazyFeature.js +2 -2
- package/esm/BamAdapter/BamSlightlyLazyFeature.js.map +1 -1
- package/esm/CramAdapter/CramAdapter.js +2 -2
- package/esm/CramAdapter/CramAdapter.js.map +1 -1
- package/esm/CramAdapter/CramSlightlyLazyFeature.js +2 -2
- package/esm/CramAdapter/CramSlightlyLazyFeature.js.map +1 -1
- package/esm/CramAdapter/util.js +10 -10
- package/esm/CramAdapter/util.js.map +1 -1
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +2 -2
- package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js.map +1 -1
- package/esm/LinearAlignmentsDisplay/models/configSchema.js +7 -0
- package/esm/LinearAlignmentsDisplay/models/configSchema.js.map +1 -1
- package/esm/LinearAlignmentsDisplay/models/model.d.ts +21 -5
- package/esm/LinearAlignmentsDisplay/models/model.js +22 -6
- package/esm/LinearAlignmentsDisplay/models/model.js.map +1 -1
- package/esm/LinearPileupDisplay/index.d.ts +2 -3
- package/esm/LinearPileupDisplay/index.js +2 -1
- package/esm/LinearPileupDisplay/index.js.map +1 -1
- package/esm/LinearPileupDisplay/model.d.ts +70 -9
- package/esm/LinearPileupDisplay/model.js +4 -4
- package/esm/LinearPileupDisplay/model.js.map +1 -1
- package/esm/LinearReadArcsDisplay/components/ReactComponent.js +14 -11
- package/esm/LinearReadArcsDisplay/components/ReactComponent.js.map +1 -1
- package/esm/LinearReadArcsDisplay/model.d.ts +77 -28
- package/esm/LinearReadArcsDisplay/model.js +16 -4
- package/esm/LinearReadArcsDisplay/model.js.map +1 -1
- package/esm/LinearReadCloudDisplay/model.d.ts +71 -19
- package/esm/LinearReadCloudDisplay/model.js +15 -3
- package/esm/LinearReadCloudDisplay/model.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/models/model.d.ts +8 -13
- package/esm/MismatchParser/index.js +4 -6
- package/esm/MismatchParser/index.js.map +1 -1
- package/esm/NestedFrequencyTable.js +3 -13
- package/esm/NestedFrequencyTable.js.map +1 -1
- package/esm/PileupRPC/rpcMethods.d.ts +3 -4
- package/esm/PileupRPC/rpcMethods.js +3 -4
- package/esm/PileupRPC/rpcMethods.js.map +1 -1
- package/esm/PileupRenderer/PileupRenderer.d.ts +6 -4
- package/esm/PileupRenderer/PileupRenderer.js +32 -38
- package/esm/PileupRenderer/PileupRenderer.js.map +1 -1
- package/esm/PileupRenderer/components/PileupRendering.js +2 -2
- package/esm/PileupRenderer/components/PileupRendering.js.map +1 -1
- package/esm/PileupRenderer/configSchema.js +1 -1
- package/esm/PileupRenderer/configSchema.js.map +1 -1
- package/esm/PileupRenderer/sortUtil.js +5 -4
- package/esm/PileupRenderer/sortUtil.js.map +1 -1
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js +10 -7
- package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map +1 -1
- package/esm/index.d.ts +3 -5
- package/esm/index.js +3 -3
- package/esm/index.js.map +1 -1
- package/package.json +2 -2
- package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap +13 -13
- package/src/AlignmentsFeatureDetail/index.test.tsx +1 -1
- package/src/BamAdapter/BamAdapter.ts +2 -2
- package/src/BamAdapter/BamSlightlyLazyFeature.ts +2 -2
- package/src/CramAdapter/CramAdapter.ts +2 -2
- package/src/CramAdapter/CramSlightlyLazyFeature.ts +2 -2
- package/src/CramAdapter/util.ts +10 -10
- package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx +2 -2
- package/src/LinearAlignmentsDisplay/models/configSchema.test.ts +1 -1
- package/src/LinearAlignmentsDisplay/models/configSchema.ts +8 -0
- package/src/LinearAlignmentsDisplay/models/model.tsx +21 -6
- package/src/LinearPileupDisplay/index.ts +2 -4
- package/src/LinearPileupDisplay/model.ts +4 -4
- package/src/LinearReadArcsDisplay/components/ReactComponent.tsx +14 -12
- package/src/LinearReadArcsDisplay/model.tsx +23 -5
- package/src/LinearReadCloudDisplay/model.tsx +23 -7
- package/src/LinearSNPCoverageDisplay/models/configSchema.test.ts +1 -1
- package/src/MismatchParser/index.ts +6 -8
- package/src/NestedFrequencyTable.ts +3 -11
- package/src/PileupRPC/rpcMethods.ts +3 -9
- package/src/PileupRenderer/PileupRenderer.ts +49 -65
- package/src/PileupRenderer/components/PileupRendering.tsx +2 -2
- package/src/PileupRenderer/configSchema.ts +1 -1
- package/src/PileupRenderer/sortUtil.ts +5 -4
- package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts +14 -13
- package/src/index.ts +5 -10
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+
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@@ -63,9 +63,9 @@ export default class BamSlightlyLazyFeature {
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63
63
|
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
64
64
|
get(field) {
|
|
65
65
|
const methodName = `_get_${field}`;
|
|
66
|
-
// @ts-
|
|
66
|
+
// @ts-expect-error
|
|
67
67
|
if (this[methodName]) {
|
|
68
|
-
// @ts-
|
|
68
|
+
// @ts-expect-error
|
|
69
69
|
return this[methodName]();
|
|
70
70
|
}
|
|
71
71
|
return this.record.get(field);
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|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"BamSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/BamAdapter/BamSlightlyLazyFeature.ts"],"names":[],"mappings":"AAOA,SAAS;AACT,OAAO,EAAE,OAAO,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAA;AAG1D,MAAM,CAAC,OAAO,OAAO,sBAAsB;IACzC,wEAAwE;IACxE,iFAAiF;IACjF,YACU,MAAiB,EACjB,OAAmB,EACnB,GAAY;QAFZ,WAAM,GAAN,MAAM,CAAW;QACjB,YAAO,GAAP,OAAO,CAAY;QACnB,QAAG,GAAH,GAAG,CAAS;IACnB,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;YACrD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IACrE,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE;YAC3B,CAAC,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IACpD,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAC5B,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAA;IAC9B,CAAC;IAED,GAAG,KAAI,CAAC;IAER,IAAI;QACF,MAAM,UAAU,GAAG,MAAM,CAAC,mBAAmB,CAC3C,sBAAsB,CAAC,SAAS,CACjC,CAAA;QAED,OAAO;YACL,GAAG,IAAI,GAAG,CACR,UAAU;iBACP,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;gBACxB,IAAI,KAAK,iBAAiB;gBAC1B,IAAI,KAAK,WAAW,CACvB;iBACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;iBAClD,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAC/B;SACF,CAAA;IACH,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,CAAA;IACjD,CAAC;IAED,8DAA8D;IAC9D,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,mBAAmB;QACnB,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,mBAAmB;YACnB,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC/B,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,CAAA;IACvD,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,OAAO,aAAa,CAClB,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EACjB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EACd,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EACf,IAAI,CAAC,GAAG,EACR,IAAI,CAAC,OAAO,EAAE,CACf,CAAA;IACH,CAAC;IAED,YAAY;QACV,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QACrC,OAAO,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;IAC3C,CAAC;CACF"}
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@@ -77,7 +77,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
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const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart);
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|
const trimLength = trimEnd - trimStart;
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|
const chunkSeq = chunk.get('seq') || chunk.get('residues');
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-
return chunkSeq.
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+
return chunkSeq.slice(trimStart, trimStart + trimLength);
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})
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82
|
.join('');
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83
|
if (sequence.length !== end - start) {
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@@ -175,7 +175,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
|
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175
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});
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|
if (tagFilter) {
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|
filtered = filtered.filter(record => {
|
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178
|
-
// @ts-
|
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|
+
// @ts-expect-error
|
|
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|
const val = record[tagFilter.tag];
|
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|
return val === '*' ? val !== undefined : val === tagFilter.value;
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|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"CramAdapter.js","sourceRoot":"","sources":["../../src/CramAdapter/CramAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,eAAe,EAAc,MAAM,YAAY,CAAA;AACnE,OAAO,EACL,sBAAsB,GAGvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,gBAAgB,EAAmB,MAAM,oBAAoB,CAAA;AACtE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACrC,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAe/D,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,sBAAsB;IAA/D;;QACE,cAAS,GAAW,EAAE,CAAA;QAgBtB,gFAAgF;QACxE,2BAAsB,GAAa,EAAE,CAAA;IAwQ/C,CAAC;IAtQQ,KAAK,CAAC,YAAY;QACvB,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,MAAM,YAAY,GAAG,IAAI,CAAC,OAAO,CAAC,cAAc,CAAC,CAAA;QACjD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,KAAK,CAAC,+BAA+B,CAAC,CAAA;SACjD;QACD,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAE7B,MAAM,IAAI,GAAG,IAAI,eAAe,CAAC;YAC/B,cAAc,EAAE,YAAY,CAAC,YAAY,EAAE,EAAE,CAAC;YAC9C,KAAK,EAAE,IAAI,SAAS,CAAC,EAAE,UAAU,EAAE,YAAY,CAAC,YAAY,EAAE,EAAE,CAAC,EAAE,CAAC;YACpE,QAAQ,EAAE,CAAC,GAAG,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,IAAI,CAAC;YAC7C,gBAAgB,EAAE,KAAK;YACvB,cAAc,EAAE,SAAW,EAAE,kDAAkD;SAChF,CAAC,CAAA;QAEF,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;QAC/C,MAAM,UAAU,GAAG,MAAM,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAEpD,OAAO;YACL,IAAI;YACJ,eAAe,EAAE,UAAU,CAAC,WAAkC;SAC/D,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,IAAkB;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACvC,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;IAClC,CAAC;IAEO,KAAK,CAAC,QAAQ,CACpB,KAAa,EACb,KAAa,EACb,GAAW;QAEX,KAAK,IAAI,CAAC,CAAA,CAAC,2CAA2C;QAEtD,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,MAAM,OAAO,GAAG,IAAI,CAAC,mBAAmB,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QAC1E,IAAI,CAAC,OAAO,EAAE;YACZ,MAAM,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;SAC3B;QAED,MAAM,SAAS,GAAG,MAAM,cAAc,CACpC,eAAe;aACZ,WAAW,CAAC;YACX,OAAO;YACP,KAAK;YACL,GAAG;YACH,YAAY,EAAE,EAAE;SACjB,CAAC;aACD,IAAI,CAAC,OAAO,EAAE,CAAC,CACnB,CAAA;QAED,MAAM,QAAQ,GAAG,SAAS;aACvB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;aAC/C,GAAG,CAAC,KAAK,CAAC,EAAE;YACX,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;YACrC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,UAAU,EAAE,CAAC,CAAC,CAAA;YACjD,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,UAAU,EAAE,QAAQ,GAAG,UAAU,CAAC,CAAA;YACjE,MAAM,UAAU,GAAG,OAAO,GAAG,SAAS,CAAA;YACtC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;YAC1D,OAAO,QAAQ,CAAC,KAAK,CAAC,SAAS,EAAE,SAAS,GAAG,UAAU,CAAC,CAAA;QAC1D,CAAC,CAAC;aACD,IAAI,CAAC,EAAE,CAAC,CAAA;QAEX,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,GAAG,KAAK,EAAE;YACnC,MAAM,IAAI,KAAK,CACb,mCAAmC,OAAO,IAAI,CAC5C,KAAK,GAAG,CAAC,CACV,CAAC,cAAc,EAAE,IAAI,GAAG,CAAC,cAAc,EAAE,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CACzH,GAAG,GAAG,KAAK,CACZ,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;SACF;QACD,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,QAAQ,CAAC,IAAkB;QACvC,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACnC,cAAc,CAAC,mBAAmB,CAAC,CAAA;QACnC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;QACrB,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,CAAA;QAEhD,oDAAoD;QACpD,2CAA2C;QAC3C,MAAM,QAAQ,GAAa,EAAE,CAAA;QAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,SAAS;aACN,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,OAAO,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;YACzB,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;gBACzB,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;oBACrB,uBAAuB;oBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;oBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;iBAC1B;YACH,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QAEJ,MAAM,UAAU,GAAG,SAAS;aACzB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC;aAC3B,GAAG,CAAC,MAAM,CAAC,EAAE,WAAC,OAAA,MAAA,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,KAAK,IAAI,CAAC,0CAAE,KAAK,CAAA,EAAA,CAAC,CAAA;QAEpE,MAAM,IAAI,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAA;QAC/C,cAAc,CAAC,EAAE,CAAC,CAAA;QAClB,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;QACrB,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,IAAI,EAAE,CAAA;IACrC,CAAC;IAEO,KAAK,CAAC,KAAK,CAAC,IAAkB;QACpC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC1C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,IAAkB;QAClC,MAAM,EAAE,SAAS,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC5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@@ -92,9 +92,9 @@ export default class CramSlightlyLazyFeature {
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92
92
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}
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93
93
|
get(field) {
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|
94
94
|
const methodName = `_get_${field}`;
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|
95
|
-
// @ts-
|
|
95
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+
// @ts-expect-error
|
|
96
96
|
if (this[methodName]) {
|
|
97
|
-
// @ts-
|
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97
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+
// @ts-expect-error
|
|
98
98
|
return this[methodName]();
|
|
99
99
|
}
|
|
100
100
|
return undefined;
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":"AASA,OAAO,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAEtE,MAAM,CAAC,OAAO,OAAO,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;;QACX,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,IAAI,0CAAE,cAAc,CAAA;IACzC,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,mBAAmB,CACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,
|
|
1
|
+
{"version":3,"file":"CramSlightlyLazyFeature.js","sourceRoot":"","sources":["../../src/CramAdapter/CramSlightlyLazyFeature.ts"],"names":[],"mappings":"AASA,OAAO,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,QAAQ,CAAA;AAEtE,MAAM,CAAC,OAAO,OAAO,uBAAuB;IAC1C,wEAAwE;IACxE,iFAAiF;IACjF,YAAoB,MAAkB,EAAU,MAAmB;QAA/C,WAAM,GAAN,MAAM,CAAY;QAAU,WAAM,GAAN,MAAM,CAAa;IAAG,CAAC;IAEvE,SAAS;QACP,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAA;IAC7B,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,QAAQ;;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,GAAG,CAAC,MAAA,IAAI,CAAC,MAAM,CAAC,WAAW,mCAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACxE,CAAC;IAED,uBAAuB;QACrB,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IACjC,CAAC;IAED,SAAS;QACP,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,CAAA;IACnC,CAAC;IAED,UAAU;QACR,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAA;IAC1B,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,MAAM,CAAC,qBAAqB,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,CAAC;IAED,cAAc;QACZ,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,UAAU,CAAA;QAC3C,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACrD,CAAC;IAED,SAAS;QACP,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,aAAa,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACpD,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,MAAM,CAAC,aAAa,CAAA;IAClC,CAAC;IAED,YAAY;QACV,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IACxD,CAAC;IAED,cAAc;QACZ,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAA;IAC3B,CAAC;IAED,qBAAqB;QACnB,OAAO,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,SAAS,CAAA;IAC9E,CAAC;IAED,oBAAoB;QAClB,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,IAAI,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;IAC/D,CAAC;IAED,aAAa;QACX,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC;YACtD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,0BAA0B;QACxB,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI;YACrB,CAAC,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,IACrD,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,cACnB,EAAE;YACJ,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,aAAa;;QACX,OAAO,MAAA,IAAI,CAAC,MAAM,CAAC,IAAI,0CAAE,cAAc,CAAA;IACzC,CAAC;IAED,SAAS;QACP,MAAM,EAAE,GAAG,IAAI,CAAC,cAAc,EAAE,CAAA;QAChC,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAA;QAC5B,4DAA4D;QAC5D,OAAO,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;IAClD,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,CAAA;IACnC,CAAC;IAED,kDAAkD;IAClD,UAAU;QACR,OAAO,mBAAmB,CACxB,IAAI,CAAC,MAAM,CAAC,YAAY,EACxB,IAAI,CAAC,MAAM,CAAC,cAAc,EAC1B,IAAI,CAAC,MAAM,CAAC,UAAU,EACtB,IAAI,CAAC,MAAM,CAAC,UAAU,CACvB,CAAA;IACH,CAAC;IAED,IAAI;QACF,OAAO,MAAM,CAAC,mBAAmB,CAAC,uBAAuB,CAAC,SAAS,CAAC;aACjE,MAAM,CACL,IAAI,CAAC,EAAE,CACL,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC;YACxB,IAAI,KAAK,iBAAiB;YAC1B,IAAI,KAAK,yBAAyB,CACrC;aACA,GAAG,CAAC,UAAU,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;IACvD,CAAC;IAED,EAAE;QACA,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,IAAI,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;IACpD,CAAC;IAED,GAAG,CAAC,KAAa;QACf,MAAM,UAAU,GAAG,QAAQ,KAAK,EAAE,CAAA;QAClC,mBAAmB;QACnB,IAAI,IAAI,CAAC,UAAU,CAAC,EAAE;YACpB,mBAAmB;YACnB,OAAO,IAAI,CAAC,UAAU,CAAC,EAAE,CAAA;SAC1B;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM;QACJ,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,QAAQ;QACN,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,GAAG,KAAI,CAAC;IAER,aAAa;QACX,OAAO,KAAK,CAAA;IACd,CAAC;IAED,YAAY;QACV,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;QACzC,IAAI,UAAU,CAAC,MAAM,EAAE;YACrB,MAAM,MAAM,GACV,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC;gBACvB,CAAC,CAAC,UAAU,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC,CAAC;gBACnC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YAChC,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,EAAE;gBAC9C,OAAO,OAAO,CAAA;aACf;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,OAAO;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI,CAAC,IAAI,EAAE;iBACR,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;iBAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CACvC;YACD,QAAQ,EAAE,IAAI,CAAC,EAAE,EAAE;SACpB,CAAA;IACH,CAAC;IAED,eAAe;QACb,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,CAAC,YAAY,CAAA;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,EAAE,CAAA;QAC3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QAC/B,OAAO,wBAAwB,CAAC,YAAY,EAAE,KAAK,EAAE,IAAI,CAAC,CAAA;IAC5D,CAAC;CACF"}
|
package/esm/CramAdapter/util.js
CHANGED
|
@@ -133,14 +133,14 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
|
|
|
133
133
|
for (let i = 0; i < readFeatures.length; i++) {
|
|
134
134
|
const { code, refPos, sub, data } = readFeatures[i];
|
|
135
135
|
sublen = refPos - lastPos;
|
|
136
|
-
seq += ref.
|
|
136
|
+
seq += ref.slice(lastPos - refStart, refPos - refStart);
|
|
137
137
|
lastPos = refPos;
|
|
138
138
|
if (insLen > 0 && sublen) {
|
|
139
139
|
cigar += `${insLen}I`;
|
|
140
140
|
insLen = 0;
|
|
141
141
|
}
|
|
142
142
|
if (oplen && op !== 'M') {
|
|
143
|
-
cigar += oplen
|
|
143
|
+
cigar += `${oplen}${op}`;
|
|
144
144
|
oplen = 0;
|
|
145
145
|
}
|
|
146
146
|
if (sublen) {
|
|
@@ -171,7 +171,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
|
|
|
171
171
|
// Deletion or Ref Skip
|
|
172
172
|
lastPos += data;
|
|
173
173
|
if (oplen) {
|
|
174
|
-
cigar += oplen
|
|
174
|
+
cigar += `${oplen}${op}`;
|
|
175
175
|
}
|
|
176
176
|
cigar += data + code;
|
|
177
177
|
oplen = 0;
|
|
@@ -180,7 +180,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
|
|
|
180
180
|
// Insertion or soft-clip
|
|
181
181
|
seq += data;
|
|
182
182
|
if (oplen) {
|
|
183
|
-
cigar += oplen
|
|
183
|
+
cigar += `${oplen}${op}`;
|
|
184
184
|
}
|
|
185
185
|
cigar += data.length + code;
|
|
186
186
|
oplen = 0;
|
|
@@ -189,7 +189,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
|
|
|
189
189
|
// Single base insertion
|
|
190
190
|
// seq += data
|
|
191
191
|
if (oplen) {
|
|
192
|
-
cigar += oplen
|
|
192
|
+
cigar += `${oplen}${op}`;
|
|
193
193
|
}
|
|
194
194
|
insLen++;
|
|
195
195
|
seq += data;
|
|
@@ -198,14 +198,14 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
|
|
|
198
198
|
else if (code === 'P') {
|
|
199
199
|
// Padding
|
|
200
200
|
if (oplen) {
|
|
201
|
-
cigar += oplen
|
|
201
|
+
cigar += `${oplen}${op}`;
|
|
202
202
|
}
|
|
203
203
|
cigar += `${data}P`;
|
|
204
204
|
}
|
|
205
205
|
else if (code === 'H') {
|
|
206
206
|
// Hard clip
|
|
207
207
|
if (oplen) {
|
|
208
|
-
cigar += oplen
|
|
208
|
+
cigar += `${oplen}${op}`;
|
|
209
209
|
}
|
|
210
210
|
cigar += `${data}H`;
|
|
211
211
|
oplen = 0;
|
|
@@ -217,9 +217,9 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
|
|
|
217
217
|
}
|
|
218
218
|
if (seq.length !== readLen) {
|
|
219
219
|
sublen = readLen - seq.length;
|
|
220
|
-
seq += ref.
|
|
220
|
+
seq += ref.slice(lastPos - refStart, lastPos - refStart + sublen);
|
|
221
221
|
if (oplen && op !== 'M') {
|
|
222
|
-
cigar += oplen
|
|
222
|
+
cigar += `${oplen}${op}`;
|
|
223
223
|
oplen = 0;
|
|
224
224
|
}
|
|
225
225
|
op = 'M';
|
|
@@ -229,7 +229,7 @@ export function readFeaturesToCIGAR(readFeatures, alignmentStart, readLen, refRe
|
|
|
229
229
|
cigar += `${insLen}I`;
|
|
230
230
|
}
|
|
231
231
|
if (oplen) {
|
|
232
|
-
cigar += oplen
|
|
232
|
+
cigar += `${oplen}${op}`;
|
|
233
233
|
}
|
|
234
234
|
return cigar;
|
|
235
235
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -3,13 +3,13 @@ import { observer } from 'mobx-react';
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3
3
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import { makeStyles } from 'tss-react/mui';
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4
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import { getConf } from '@jbrowse/core/configuration';
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5
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import { ResizeHandle } from '@jbrowse/core/ui';
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-
const useStyles = makeStyles()(
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6
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+
const useStyles = makeStyles()({
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resizeHandle: {
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height: 2,
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position: 'absolute',
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zIndex: 2,
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11
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},
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12
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-
})
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12
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});
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13
13
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function AlignmentsDisplay({ model }) {
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14
14
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const { PileupDisplay, SNPCoverageDisplay } = model;
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15
15
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const { classes } = useStyles();
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAK/C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC
|
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1
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+
{"version":3,"file":"AlignmentsDisplay.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,OAAO,EAAE,MAAM,6BAA6B,CAAA;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAK/C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAA;AAEF,SAAS,iBAAiB,CAAC,EAAE,KAAK,EAAqC;IACrE,MAAM,EAAE,aAAa,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnD,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,kBAAkB,CAAC,MAAM,CAAA;IACrC,OAAO,CACL,4CACe,WAAW,OAAO,CAAC,KAAK,EAAE,WAAW,CAAC,EAAE,EACrD,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAE/B,4CAAiB,sBAAsB;YACrC,oBAAC,kBAAkB,CAAC,kBAAkB,IAAC,KAAK,EAAE,kBAAkB,GAAI,CAChE;QACN,oBAAC,YAAY,IACX,MAAM,EAAE,KAAK,CAAC,EAAE;gBACd,kBAAkB,CAAC,SAAS,CAAC,kBAAkB,CAAC,MAAM,GAAG,KAAK,CAAC,CAAA;gBAC/D,OAAO,KAAK,CAAA;YACd,CAAC,EACD,SAAS,EAAE,OAAO,CAAC,YAAY,EAC/B,KAAK,EAAE,EAAE,GAAG,EAAE,GACd;QAEF,4CACc,iBAAiB,EAC7B,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG;aACJ;YAED,oBAAC,aAAa,CAAC,kBAAkB,IAAC,KAAK,EAAE,aAAa,GAAI,CACtD,CACF,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,iBAAiB,CAAC,CAAA"}
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@@ -16,6 +16,13 @@ export default function configModelFactory(pm) {
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*/
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snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
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.configSchema,
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/**
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* #slot
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*/
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height: {
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type: 'number',
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defaultValue: 250,
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},
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}, {
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/**
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* #baseConfiguration
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAGlF;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EAAiB;IAC1D,OAAO,mBAAmB,CACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QAEpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;
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1
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+
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAGlF;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EAAiB;IAC1D,OAAO,mBAAmB,CACxB,yBAAyB,EACzB;QACE;;WAEG;QACH,aAAa,EAAE,EAAE,CAAC,cAAc,CAAC,qBAAqB,CAAC,CAAC,YAAY;QAEpE;;WAEG;QACH,kBAAkB,EAAE,EAAE,CAAC,cAAc,CAAC,0BAA0B,CAAC;aAC9D,YAAY;QAEf;;WAEG;QACH,MAAM,EAAE;YACN,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,GAAG;SAClB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,6BAA6B;QAChD,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC"}
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@@ -17,7 +17,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
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type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
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configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
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heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
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}, {
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@@ -58,9 +58,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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}, {
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rendererTypeName: string;
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error: unknown;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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*/
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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}> | null;
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readonly adapterConfig: any;
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readonly parentTrack: any;
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*/
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setSNPCoverageHeight(n: number): void;
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} & {
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*/
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readonly height: any;
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@@ -152,7 +155,20 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
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trackMenuItems(): MenuItem[];
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}, import("mobx-state-tree").
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+
}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
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id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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type: import("mobx-state-tree").ISimpleType<string>;
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rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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} & {
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PileupDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyType>;
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SNPCoverageDisplay: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IAnyModelType>;
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snpCovHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
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type: import("mobx-state-tree").ISimpleType<"LinearAlignmentsDisplay">;
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configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
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heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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userFeatureScreenDensity: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
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lowerPanelType: import("mobx-state-tree").IType<string | undefined, string, string>;
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}>>, import("mobx-state-tree")._NotCustomized>;
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export default stateModelFactory;
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export type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>;
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export type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>;
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@@ -9,9 +9,9 @@ const minDisplayHeight = 20;
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9
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function getLowerPanelDisplays(pluginManager) {
|
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10
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|
return (pluginManager
|
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11
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.getDisplayElements()
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|
-
// @ts-
|
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12
|
+
// @ts-expect-error
|
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13
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|
.filter(f => { var _a; return ((_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.type) === 'LinearAlignmentsDisplay'; })
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// @ts-
|
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+
// @ts-expect-error
|
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|
.filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; }));
|
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}
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function deepSnap(x1, x2) {
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@@ -49,7 +49,6 @@ function AlignmentsModel(pluginManager, configSchema) {
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* #property
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50
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|
* refers to LinearPileupDisplay sub-display model
|
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*/
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|
-
// @ts-ignore
|
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53
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|
PileupDisplay: types.maybe(types.union(...lowerPanelDisplays)),
|
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/**
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55
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* #property
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@@ -71,7 +70,7 @@ function AlignmentsModel(pluginManager, configSchema) {
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/**
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* #property
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*/
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-
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+
heightPreConfig: types.maybe(types.number),
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/**
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* #property
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*/
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@@ -105,6 +104,15 @@ function stateModelFactory(pluginManager, configSchema) {
|
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105
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|
setSNPCoverageHeight(n) {
|
|
106
105
|
self.snpCovHeight = n;
|
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107
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|
},
|
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107
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+
}))
|
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108
|
+
.views(self => ({
|
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|
+
/**
|
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110
|
+
* #getter
|
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111
|
+
*/
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|
+
get height() {
|
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|
+
var _a;
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|
+
return (_a = self.heightPreConfig) !== null && _a !== void 0 ? _a : getConf(self, 'height');
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|
+
},
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}))
|
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|
.views(self => ({
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/**
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@@ -191,8 +199,8 @@ function stateModelFactory(pluginManager, configSchema) {
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|
* #action
|
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|
*/
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|
setHeight(n) {
|
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|
-
self.
|
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|
-
return self.
|
|
202
|
+
self.heightPreConfig = Math.max(n, minDisplayHeight);
|
|
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|
+
return self.heightPreConfig;
|
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|
},
|
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|
/**
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|
* #action
|
|
@@ -283,6 +291,14 @@ function stateModelFactory(pluginManager, configSchema) {
|
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283
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|
];
|
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|
},
|
|
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|
};
|
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|
+
})
|
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|
+
.preProcessSnapshot(snap => {
|
|
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|
+
if (!snap) {
|
|
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|
+
return snap;
|
|
298
|
+
}
|
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299
|
+
// @ts-expect-error
|
|
300
|
+
const { height, ...rest } = snap;
|
|
301
|
+
return { heightPreConfig: height, ...rest };
|
|
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|
});
|
|
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|
}
|
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|
export default stateModelFactory;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../../src/LinearAlignmentsDisplay/models/model.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AACpC,OAAO,EACL,WAAW,EACX,WAAW,EACX,OAAO,EACP,KAAK,GAGN,MAAM,iBAAiB,CAAA;AACxB,OAAO,SAAS,MAAM,iBAAiB,CAAA;AAEvC,UAAU;AACV,OAAO,EACL,sBAAsB,EAGtB,OAAO,GACR,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,WAAW,EAAE,MAAM,4CAA4C,CAAA;AAIxE,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAE3B,SAAS,qBAAqB,CAAC,aAA4B;IACzD,OAAO,CACL,aAAa;SACV,kBAAkB,EAAE;QACrB,
|
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1
|
+
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@@ -1,5 +1,4 @@
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1
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-
import configSchemaFactory from './configSchema';
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2
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-
import modelFactory from './model';
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3
1
|
import PluginManager from '@jbrowse/core/PluginManager';
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4
2
|
export default function register(pluginManager: PluginManager): void;
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5
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-
export {
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3
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+
export { default as linearPileupDisplayStateModelFactory } from './model';
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4
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+
export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';
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@@ -17,5 +17,6 @@ export default function register(pluginManager) {
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|
17
17
|
});
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18
18
|
});
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19
19
|
}
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20
|
-
export {
|
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20
|
+
export { default as linearPileupDisplayStateModelFactory } from './model';
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21
|
+
export { default as linearPileupDisplayConfigSchemaFactory } from './configSchema';
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21
22
|
//# sourceMappingURL=index.js.map
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@@ -1 +1 @@
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1
|
-
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|
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1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,YAAY,MAAM,SAAS,CAAA;AAClC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,YAAY,CAAC;YACtC,UAAU,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,UAAU,EAAE,IAAI,EAAE;YACjE,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,OAAO,EAAE,OAAO,IAAI,oCAAoC,EAAE,MAAM,SAAS,CAAA;AACzE,OAAO,EAAE,OAAO,IAAI,sCAAsC,EAAE,MAAM,gBAAgB,CAAA"}
|