@sjcrh/proteinpaint-types 2.170.1 → 2.171.0-0

package/dist/{chunk-A5Z4YYMF.js → chunk-JV2F2JPK.js}

@@ -4496,7 +4496,7 @@ var validBoxPlotResponse = (input) => {
       return true;
     });
     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])))));
-    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);
+    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);
     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;
     const $io6 = (input3) => "number" === typeof input3.value;
     const $io7 = (input3) => Object.keys(input3).every((key) => {
@@ -4691,7 +4691,7 @@ var validBoxPlotResponse = (input) => {
         path: _path2 + ".key",
         expected: "string",
         value: input3.key
-      }), true, void 0 === input3.seriesId || "string" === typeof input3.seriesId || $report(_exceptionable2, {
+      }), void 0 === input3.seriesId || "string" === typeof input3.seriesId || $report(_exceptionable2, {
         path: _path2 + ".seriesId",
         expected: "(string | undefined)",
         value: input3.seriesId

package/dist/{chunk-YCURJJSC.js → chunk-Y2TSHHFF.js}

@@ -20,7 +20,7 @@ var GRIN2Payload = {
 var validGRIN2Request = (input) => {
   const errors = [];
   const __is = (input2) => {
-    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);
+    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);
     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);
     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);
     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) => {
         path: _path2 + ".logCutoff",
         expected: "(number | undefined)",
         value: input3.logCutoff
+      }), "number" === typeof input3.maxCappedPoints || $report(_exceptionable2, {
+        path: _path2 + ".maxCappedPoints",
+        expected: "number",
+        value: input3.maxCappedPoints
+      }), "number" === typeof input3.hardCap || $report(_exceptionable2, {
+        path: _path2 + ".hardCap",
+        expected: "number",
+        value: input3.hardCap
+      }), "number" === typeof input3.binSize || $report(_exceptionable2, {
+        path: _path2 + ".binSize",
+        expected: "number",
+        value: input3.binSize
       }), true, void 0 === input3.snvindelOptions || ("object" === typeof input3.snvindelOptions && null !== input3.snvindelOptions && false === Array.isArray(input3.snvindelOptions) || $report(_exceptionable2, {
         path: _path2 + ".snvindelOptions",
         expected: "(__type | undefined)",
@@ -198,7 +210,7 @@ var validGRIN2Response = (input) => {
   const __is = (input2) => {
     const $join = import_typia.createValidate.join;
     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);
-    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;
+    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;
     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;
     const $io3 = (input3) => Object.keys(input3).every((key) => {
       const value = input3[key];
@@ -314,6 +326,10 @@ var validGRIN2Response = (input) => {
         path: _path2 + ".total_genome_length",
         expected: "number",
         value: input3.total_genome_length
+      }), "boolean" === typeof input3.has_capped_points || $report(_exceptionable2, {
+        path: _path2 + ".has_capped_points",
+        expected: "boolean",
+        value: input3.has_capped_points
       })].every((flag) => flag);
       const $vo2 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.x || $report(_exceptionable2, {
         path: _path2 + ".x",

package/dist/grin2.js

@@ -2,7 +2,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-YCURJJSC.js";
+} from "./chunk-Y2TSHHFF.js";
 import "./chunk-YNHC5SXO.js";
 export {
   GRIN2Payload,

package/dist/index.js

@@ -132,7 +132,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-A5Z4YYMF.js";
+} from "./chunk-JV2F2JPK.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
@@ -217,7 +217,7 @@ import {
   GRIN2Payload,
   validGRIN2Request,
   validGRIN2Response
-} from "./chunk-YCURJJSC.js";
+} from "./chunk-Y2TSHHFF.js";
 import {
   healthcheckPayload,
   validHealthCheckRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-A5Z4YYMF.js";
+} from "./chunk-JV2F2JPK.js";
 import "./chunk-YNHC5SXO.js";
 export {
   boxplotPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.170.1",
+  "version": "2.171.0-0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/routes/grin2.ts

@@ -32,7 +32,7 @@ export type GRIN2Request = {
 	/** Lesion type colors */
 	lesionTypeColors?: any
 
-	/** Threshold for q-values to be included as interactive dots */
+	/** Threshold for q-values to be included as interactive dots, have significance indicators in the table and tooltips */
 	qValueThreshold?: number
 
 	/** Log cutoff for Manhattan plot rendering before we scale the y-axis (default: 40).
@@ -40,6 +40,15 @@ export type GRIN2Request = {
 	 * Sending it with request for consistency. In future we will allow user to set scale value or disable scaling if they wish */
 	logCutoff?: number
 
+	/** Maximum number of points to cap the dynamic y-axis in Manhattan plots */
+	maxCappedPoints: number
+
+	/** Absolute maximum cap for the y-axis in Manhattan plots regardless of its data distribution */
+	hardCap: number
+
+	/** Bin size for Manhattan plot histogram bin size. Used in the calculation of dynamic y-axis capping process (default: 10) */
+	binSize: number
+
 	/** Filter from existing PP infrastructure */
 	filter?: any // Filter object passed to get_samples(filter, ds)
 
@@ -117,6 +126,7 @@ interface grin2PlotData {
 		}
 	>
 	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
+	has_capped_points: boolean // Whether we have capped the y-axis due to q-values exceeding the cap
 }
 
 /**

package/src/routes/termdb.boxplot.ts

@@ -69,8 +69,6 @@ export type BoxPlotEntry = {
 	 * whether or not the plot is hidden by default */
 	isHidden?: boolean
 	key: string
-	/** Formatted bins for numeric terms */
-	overlayTwBins?: any
 	/** Usually the same as key, but determined by the tw */
 	seriesId?: string
 }