@sjcrh/proteinpaint-types 2.170.1 → 2.171.0

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Files changed (12) hide show
  1. package/dist/aiProjectAdmin.js +1 -1
  2. package/dist/{chunk-A5Z4YYMF.js → chunk-JV2F2JPK.js} +2 -2
  3. package/dist/{chunk-J2Y7RIN2.js → chunk-THQOFV2K.js} +16 -4
  4. package/dist/{chunk-YCURJJSC.js → chunk-Y2TSHHFF.js} +18 -2
  5. package/dist/grin2.js +1 -1
  6. package/dist/index.js +3 -3
  7. package/dist/termdb.boxplot.js +1 -1
  8. package/package.json +1 -1
  9. package/src/dataset.ts +3 -0
  10. package/src/routes/aiProjectAdmin.ts +1 -1
  11. package/src/routes/grin2.ts +11 -1
  12. package/src/routes/termdb.boxplot.ts +0 -2
package/dist/aiProjectAdmin.js CHANGED
@@ -2,7 +2,7 @@ import {
2
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  aiProjectAdminPayload,
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  validAIProjectAdminRequest,
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  validAIProjectAdminResponse
5
- } from "./chunk-J2Y7RIN2.js";
5
+ } from "./chunk-THQOFV2K.js";
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  import "./chunk-YNHC5SXO.js";
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  export {
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  aiProjectAdminPayload,
package/dist/{chunk-A5Z4YYMF.js → chunk-JV2F2JPK.js} RENAMED
@@ -4496,7 +4496,7 @@ var validBoxPlotResponse = (input) => {
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  return true;
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  });
4498
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  const $io3 = (input3) => "string" === typeof input3.chartId && (Array.isArray(input3.plots) && input3.plots.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && "number" === typeof input3.sampleCount && (void 0 === input3.wilcoxon || Array.isArray(input3.wilcoxon) && input3.wilcoxon.every((elem) => Array.isArray(elem) && (elem.length === 3 && ("object" === typeof elem[0] && null !== elem[0] && $io9(elem[0])) && ("object" === typeof elem[1] && null !== elem[1] && $io10(elem[1])) && ("object" === typeof elem[2] && null !== elem[2] && $io11(elem[2])))));
4499
- const $io4 = (input3) => "object" === typeof input3.boxplot && null !== input3.boxplot && $io5(input3.boxplot) && (void 0 === input3.color || "string" === typeof input3.color) && ("object" === typeof input3.descrStats && null !== input3.descrStats && false === Array.isArray(input3.descrStats) && $io7(input3.descrStats)) && (void 0 === input3.isHidden || "boolean" === typeof input3.isHidden) && "string" === typeof input3.key && true && (void 0 === input3.seriesId || "string" === typeof input3.seriesId);
4499
+ const $io4 = (input3) => "object" === typeof input3.boxplot && null !== input3.boxplot && $io5(input3.boxplot) && (void 0 === input3.color || "string" === typeof input3.color) && ("object" === typeof input3.descrStats && null !== input3.descrStats && false === Array.isArray(input3.descrStats) && $io7(input3.descrStats)) && (void 0 === input3.isHidden || "boolean" === typeof input3.isHidden) && "string" === typeof input3.key && (void 0 === input3.seriesId || "string" === typeof input3.seriesId);
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  const $io5 = (input3) => (void 0 === input3.w1 || "number" === typeof input3.w1) && (void 0 === input3.w2 || "number" === typeof input3.w2) && "number" === typeof input3.p05 && "number" === typeof input3.p25 && "number" === typeof input3.p50 && "number" === typeof input3.p75 && "number" === typeof input3.p95 && "number" === typeof input3.iqr && (Array.isArray(input3.out) && input3.out.every((elem) => "object" === typeof elem && null !== elem && $io6(elem))) && "string" === typeof input3.label;
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  const $io6 = (input3) => "number" === typeof input3.value;
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4502
  const $io7 = (input3) => Object.keys(input3).every((key) => {
@@ -4691,7 +4691,7 @@ var validBoxPlotResponse = (input) => {
4691
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  path: _path2 + ".key",
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  expected: "string",
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  value: input3.key
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- }), true, void 0 === input3.seriesId || "string" === typeof input3.seriesId || $report(_exceptionable2, {
4694
+ }), void 0 === input3.seriesId || "string" === typeof input3.seriesId || $report(_exceptionable2, {
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  path: _path2 + ".seriesId",
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  expected: "(string | undefined)",
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  value: input3.seriesId
package/dist/{chunk-J2Y7RIN2.js → chunk-THQOFV2K.js} RENAMED
@@ -99,7 +99,7 @@ var validAIProjectAdminResponse = (input) => {
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  const errors = [];
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  const __is = (input2) => {
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  const $io0 = (input3) => ("ok" === input3.status || "error" === input3.status) && (void 0 === input3.projectId || "number" === typeof input3.projectId) && (Array.isArray(input3.images) && input3.images.every((elem) => "string" === typeof elem)) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.data || Array.isArray(input3.data) && input3.data.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)));
102
- const $io1 = (input3) => Array.isArray(input3.cols) && Array.isArray(input3.rows) && (Array.isArray(input3.images) && input3.images.every((elem) => "string" === typeof elem));
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+ const $io1 = (input3) => Array.isArray(input3.cols) && Array.isArray(input3.rows) && (void 0 === input3.images || Array.isArray(input3.images) && input3.images.every((elem) => "string" === typeof elem)) && (void 0 === input3.selectedImages || Array.isArray(input3.selectedImages) && input3.selectedImages.every((elem) => "string" === typeof elem));
103
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  return "object" === typeof input2 && null !== input2 && $io0(input2);
104
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  };
105
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  if (false === __is(input)) {
@@ -154,9 +154,9 @@ var validAIProjectAdminResponse = (input) => {
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  path: _path2 + ".rows",
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  expected: "Array<any>",
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  value: input3.rows
157
- }), (Array.isArray(input3.images) || $report(_exceptionable2, {
157
+ }), void 0 === input3.images || (Array.isArray(input3.images) || $report(_exceptionable2, {
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  path: _path2 + ".images",
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- expected: "Array<string>",
159
+ expected: "(Array<string> | undefined)",
160
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  value: input3.images
161
161
  })) && input3.images.map((elem, _index3) => "string" === typeof elem || $report(_exceptionable2, {
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162
  path: _path2 + ".images[" + _index3 + "]",
@@ -164,8 +164,20 @@ var validAIProjectAdminResponse = (input) => {
164
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  value: elem
165
165
  })).every((flag) => flag) || $report(_exceptionable2, {
166
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  path: _path2 + ".images",
167
- expected: "Array<string>",
167
+ expected: "(Array<string> | undefined)",
168
168
  value: input3.images
169
+ }), void 0 === input3.selectedImages || (Array.isArray(input3.selectedImages) || $report(_exceptionable2, {
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+ path: _path2 + ".selectedImages",
171
+ expected: "(Array<string> | undefined)",
172
+ value: input3.selectedImages
173
+ })) && input3.selectedImages.map((elem, _index4) => "string" === typeof elem || $report(_exceptionable2, {
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+ path: _path2 + ".selectedImages[" + _index4 + "]",
175
+ expected: "string",
176
+ value: elem
177
+ })).every((flag) => flag) || $report(_exceptionable2, {
178
+ path: _path2 + ".selectedImages",
179
+ expected: "(Array<string> | undefined)",
180
+ value: input3.selectedImages
169
181
  })].every((flag) => flag);
170
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  return ("object" === typeof input2 && null !== input2 || $report(true, {
171
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  path: _path + "",
package/dist/{chunk-YCURJJSC.js → chunk-Y2TSHHFF.js} RENAMED
@@ -20,7 +20,7 @@ var GRIN2Payload = {
20
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  var validGRIN2Request = (input) => {
21
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  const errors = [];
22
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  const __is = (input2) => {
23
- const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.devicePixelRatio || "number" === typeof input3.devicePixelRatio) && (void 0 === input3.width || "number" === typeof input3.width) && (void 0 === input3.height || "number" === typeof input3.height) && (void 0 === input3.pngDotRadius || "number" === typeof input3.pngDotRadius) && true && (void 0 === input3.qValueThreshold || "number" === typeof input3.qValueThreshold) && (void 0 === input3.logCutoff || "number" === typeof input3.logCutoff) && true && (void 0 === input3.snvindelOptions || "object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) && $io1(input3.snvindelOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && (void 0 === input3.fusionOptions || "object" === typeof input3.fusionOptions && null !== input3.fusionOptions && false === Array.isArray(input3.fusionOptions) && $io3(input3.fusionOptions)) && (void 0 === input3.svOptions || "object" === typeof input3.svOptions && null !== input3.svOptions && false === Array.isArray(input3.svOptions) && $io4(input3.svOptions)) && (void 0 === input3.maxGenesToShow || "number" === typeof input3.maxGenesToShow);
23
+ const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.devicePixelRatio || "number" === typeof input3.devicePixelRatio) && (void 0 === input3.width || "number" === typeof input3.width) && (void 0 === input3.height || "number" === typeof input3.height) && (void 0 === input3.pngDotRadius || "number" === typeof input3.pngDotRadius) && true && (void 0 === input3.qValueThreshold || "number" === typeof input3.qValueThreshold) && (void 0 === input3.logCutoff || "number" === typeof input3.logCutoff) && "number" === typeof input3.maxCappedPoints && "number" === typeof input3.hardCap && "number" === typeof input3.binSize && true && (void 0 === input3.snvindelOptions || "object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) && $io1(input3.snvindelOptions)) && (void 0 === input3.cnvOptions || "object" === typeof input3.cnvOptions && null !== input3.cnvOptions && false === Array.isArray(input3.cnvOptions) && $io2(input3.cnvOptions)) && (void 0 === input3.fusionOptions || "object" === typeof input3.fusionOptions && null !== input3.fusionOptions && false === Array.isArray(input3.fusionOptions) && $io3(input3.fusionOptions)) && (void 0 === input3.svOptions || "object" === typeof input3.svOptions && null !== input3.svOptions && false === Array.isArray(input3.svOptions) && $io4(input3.svOptions)) && (void 0 === input3.maxGenesToShow || "number" === typeof input3.maxGenesToShow);
24
24
  const $io1 = (input3) => (void 0 === input3.minTotalDepth || "number" === typeof input3.minTotalDepth) && (void 0 === input3.minAltAlleleCount || "number" === typeof input3.minAltAlleleCount) && (void 0 === input3.consequences || Array.isArray(input3.consequences) && input3.consequences.every((elem) => "string" === typeof elem)) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
25
25
  const $io2 = (input3) => (void 0 === input3.lossThreshold || "number" === typeof input3.lossThreshold) && (void 0 === input3.gainThreshold || "number" === typeof input3.gainThreshold) && (void 0 === input3.maxSegLength || "number" === typeof input3.maxSegLength) && (void 0 === input3.hyperMutator || "number" === typeof input3.hyperMutator) && (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
26
26
  const $io3 = (input3) => (void 0 === input3.fivePrimeFlankSize || "number" === typeof input3.fivePrimeFlankSize) && (void 0 === input3.threePrimeFlankSize || "number" === typeof input3.threePrimeFlankSize);
@@ -62,6 +62,18 @@ var validGRIN2Request = (input) => {
62
62
  path: _path2 + ".logCutoff",
63
63
  expected: "(number | undefined)",
64
64
  value: input3.logCutoff
65
+ }), "number" === typeof input3.maxCappedPoints || $report(_exceptionable2, {
66
+ path: _path2 + ".maxCappedPoints",
67
+ expected: "number",
68
+ value: input3.maxCappedPoints
69
+ }), "number" === typeof input3.hardCap || $report(_exceptionable2, {
70
+ path: _path2 + ".hardCap",
71
+ expected: "number",
72
+ value: input3.hardCap
73
+ }), "number" === typeof input3.binSize || $report(_exceptionable2, {
74
+ path: _path2 + ".binSize",
75
+ expected: "number",
76
+ value: input3.binSize
65
77
  }), true, void 0 === input3.snvindelOptions || ("object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) || $report(_exceptionable2, {
66
78
  path: _path2 + ".snvindelOptions",
67
79
  expected: "(__type | undefined)",
@@ -198,7 +210,7 @@ var validGRIN2Response = (input) => {
198
210
  const __is = (input2) => {
199
211
  const $join = import_typia.createValidate.join;
200
212
  const $io0 = (input3) => ("error" === input3.status || "success" === input3.status) && (void 0 === input3.error || "string" === typeof input3.error) && (void 0 === input3.pngImg || "string" === typeof input3.pngImg) && (void 0 === input3.plotData || "object" === typeof input3.plotData && null !== input3.plotData && $io1(input3.plotData)) && true && (void 0 === input3.topGeneTable || "object" === typeof input3.topGeneTable && null !== input3.topGeneTable && $io5(input3.topGeneTable)) && (void 0 === input3.totalGenes || "number" === typeof input3.totalGenes) && (void 0 === input3.showingTop || "number" === typeof input3.showingTop) && (void 0 === input3.timing || "object" === typeof input3.timing && null !== input3.timing && $io8(input3.timing)) && (void 0 === input3.processingSummary || "object" === typeof input3.processingSummary && null !== input3.processingSummary && false === Array.isArray(input3.processingSummary) && $io9(input3.processingSummary)) && (void 0 === input3.cacheFileName || "string" === typeof input3.cacheFileName);
201
- const $io1 = (input3) => Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && ("object" === typeof input3.chrom_data && null !== input3.chrom_data && false === Array.isArray(input3.chrom_data) && $io3(input3.chrom_data)) && "number" === typeof input3.total_genome_length;
213
+ const $io1 = (input3) => Array.isArray(input3.points) && input3.points.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)) && ("object" === typeof input3.chrom_data && null !== input3.chrom_data && false === Array.isArray(input3.chrom_data) && $io3(input3.chrom_data)) && "number" === typeof input3.total_genome_length && "boolean" === typeof input3.has_capped_points;
202
214
  const $io2 = (input3) => "number" === typeof input3.x && "number" === typeof input3.y && "string" === typeof input3.color && "string" === typeof input3.type && "string" === typeof input3.gene && "string" === typeof input3.chrom && "number" === typeof input3.start && "number" === typeof input3.end && "number" === typeof input3.pos && "number" === typeof input3.nsubj;
203
215
  const $io3 = (input3) => Object.keys(input3).every((key) => {
204
216
  const value = input3[key];
@@ -314,6 +326,10 @@ var validGRIN2Response = (input) => {
314
326
  path: _path2 + ".total_genome_length",
315
327
  expected: "number",
316
328
  value: input3.total_genome_length
329
+ }), "boolean" === typeof input3.has_capped_points || $report(_exceptionable2, {
330
+ path: _path2 + ".has_capped_points",
331
+ expected: "boolean",
332
+ value: input3.has_capped_points
317
333
  })].every((flag) => flag);
318
334
  const $vo2 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.x || $report(_exceptionable2, {
319
335
  path: _path2 + ".x",
package/dist/grin2.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  GRIN2Payload,
3
3
  validGRIN2Request,
4
4
  validGRIN2Response
5
- } from "./chunk-YCURJJSC.js";
5
+ } from "./chunk-Y2TSHHFF.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  GRIN2Payload,
package/dist/index.js CHANGED
@@ -132,7 +132,7 @@ import {
132
132
  boxplotPayload,
133
133
  validBoxPlotRequest,
134
134
  validBoxPlotResponse
135
- } from "./chunk-A5Z4YYMF.js";
135
+ } from "./chunk-JV2F2JPK.js";
136
136
  import {
137
137
  termdbCategoriesPayload,
138
138
  validCategoriesRequest,
@@ -217,7 +217,7 @@ import {
217
217
  GRIN2Payload,
218
218
  validGRIN2Request,
219
219
  validGRIN2Response
220
- } from "./chunk-YCURJJSC.js";
220
+ } from "./chunk-Y2TSHHFF.js";
221
221
  import {
222
222
  healthcheckPayload,
223
223
  validHealthCheckRequest,
@@ -272,7 +272,7 @@ import {
272
272
  aiProjectAdminPayload,
273
273
  validAIProjectAdminRequest,
274
274
  validAIProjectAdminResponse
275
- } from "./chunk-J2Y7RIN2.js";
275
+ } from "./chunk-THQOFV2K.js";
276
276
  import {
277
277
  aiProjectSelectedWSImagesResponsePayload,
278
278
  validAiProjectSelectedWSImagesRequest,
package/dist/termdb.boxplot.js CHANGED
@@ -2,7 +2,7 @@ import {
2
2
  boxplotPayload,
3
3
  validBoxPlotRequest,
4
4
  validBoxPlotResponse
5
- } from "./chunk-A5Z4YYMF.js";
5
+ } from "./chunk-JV2F2JPK.js";
6
6
  import "./chunk-YNHC5SXO.js";
7
7
  export {
8
8
  boxplotPayload,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.170.1",
3
+ "version": "2.171.0",
4
4
  "type": "module",
5
5
  "description": "Shared type definitions between ProteinPaint server and client code",
6
6
  "main": "src/index.ts",
package/src/dataset.ts CHANGED
@@ -344,6 +344,7 @@ type SnvIndelQuery = {
344
344
  format4filters?: string[]
345
345
  format?: SnvIndelFormat
346
346
  variant_filter?: VariantFilter
347
+ mafFilter?: VariantFilter
347
348
  populations?: Population[]
348
349
  /** NOTE **
349
350
  this definition can appear either in queries.snvindel{} or termdb{}
@@ -1067,6 +1068,8 @@ export type WSImages = {
1067
1068
  getAnnotationClasses?: (projectId: string) => Promise<WSIClass[] | undefined>
1068
1069
  /** ds supplied */
1069
1070
  retrainModel?: (projectId: string, wsimages: string[]) => Promise<void>
1071
+ /** ds supplied */
1072
+ selectWSIImages?: () => Promise<string[]>
1070
1073
  }
1071
1074
 
1072
1075
  export type WSIClass = { id: number; key_shortcut: string; label: string; color: string }
package/src/routes/aiProjectAdmin.ts CHANGED
@@ -24,7 +24,7 @@ export type AIProjectAdminResponse = {
24
24
  projectId?: number
25
25
  images: string[]
26
26
  error?: string
27
- data?: { cols: any[]; rows: any[]; images: string[] }[]
27
+ data?: { cols: any[]; rows: any[]; images?: string[]; selectedImages?: string[] }[]
28
28
  }
29
29
 
30
30
  export const aiProjectAdminPayload: RoutePayload = {
package/src/routes/grin2.ts CHANGED
@@ -32,7 +32,7 @@ export type GRIN2Request = {
32
32
  /** Lesion type colors */
33
33
  lesionTypeColors?: any
34
34
 
35
- /** Threshold for q-values to be included as interactive dots */
35
+ /** Threshold for q-values to be included as interactive dots, have significance indicators in the table and tooltips */
36
36
  qValueThreshold?: number
37
37
 
38
38
  /** Log cutoff for Manhattan plot rendering before we scale the y-axis (default: 40).
@@ -40,6 +40,15 @@ export type GRIN2Request = {
40
40
  * Sending it with request for consistency. In future we will allow user to set scale value or disable scaling if they wish */
41
41
  logCutoff?: number
42
42
 
43
+ /** Maximum number of points to cap the dynamic y-axis in Manhattan plots */
44
+ maxCappedPoints: number
45
+
46
+ /** Absolute maximum cap for the y-axis in Manhattan plots regardless of its data distribution */
47
+ hardCap: number
48
+
49
+ /** Bin size for Manhattan plot histogram bin size. Used in the calculation of dynamic y-axis capping process (default: 10) */
50
+ binSize: number
51
+
43
52
  /** Filter from existing PP infrastructure */
44
53
  filter?: any // Filter object passed to get_samples(filter, ds)
45
54
 
@@ -117,6 +126,7 @@ interface grin2PlotData {
117
126
  }
118
127
  >
119
128
  total_genome_length: number // Gives us the full length of the genome so we can easily append x buffer space when building d3 x-axis
129
+ has_capped_points: boolean // Whether we have capped the y-axis due to q-values exceeding the cap
120
130
  }
121
131
 
122
132
  /**
package/src/routes/termdb.boxplot.ts CHANGED
@@ -69,8 +69,6 @@ export type BoxPlotEntry = {
69
69
  * whether or not the plot is hidden by default */
70
70
  isHidden?: boolean
71
71
  key: string
72
- /** Formatted bins for numeric terms */
73
- overlayTwBins?: any
74
72
  /** Usually the same as key, but determined by the tw */
75
73
  seriesId?: string
76
74
  }