@sjcrh/proteinpaint-types 2.98.0 → 2.98.1-0

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@@ -1500,12 +1500,12 @@ var validViolinResponse = (input) => {
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  const __is = (input2) => {
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  const $join = import_typia.createValidate.join;
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  const $io0 = (input3) => "number" === typeof input3.status && "string" === typeof input3.error;
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- const $io1 = (input3) => "number" === typeof input3.min && "number" === typeof input3.max && (Array.isArray(input3.plots) && input3.plots.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && (void 0 === input3.pvalues || Array.isArray(input3.pvalues) && input3.pvalues.every((elem) => Array.isArray(elem) && elem.every((elem2) => "object" === typeof elem2 && null !== elem2 && false === Array.isArray(elem2) && $io8(elem2)))) && (null === input3.uncomputableValueObj || Array.isArray(input3.uncomputableValueObj) && input3.uncomputableValueObj.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io9(elem)));
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- const $io2 = (input3) => "string" === typeof input3.color && ("object" === typeof input3.density && null !== input3.density && $io3(input3.density)) && true && "string" === typeof input3.label && "number" === typeof input3.plotValueCount && "string" === typeof input3.seriesId && "string" === typeof input3.src && ("object" === typeof input3.summaryStats && null !== input3.summaryStats && $io5(input3.summaryStats)) && (null === input3.uncomputableValueObj || "object" === typeof input3.uncomputableValueObj && null !== input3.uncomputableValueObj && false === Array.isArray(input3.uncomputableValueObj) && $io7(input3.uncomputableValueObj));
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+ const $io1 = (input3) => "number" === typeof input3.min && "number" === typeof input3.max && (Array.isArray(input3.plots) && input3.plots.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && (void 0 === input3.pvalues || Array.isArray(input3.pvalues) && input3.pvalues.every((elem) => Array.isArray(elem) && elem.every((elem2) => "object" === typeof elem2 && null !== elem2 && false === Array.isArray(elem2) && $io6(elem2)))) && (null === input3.uncomputableValues || Array.isArray(input3.uncomputableValues) && input3.uncomputableValues.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io7(elem)));
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+ const $io2 = (input3) => "string" === typeof input3.color && ("object" === typeof input3.density && null !== input3.density && $io3(input3.density)) && true && "string" === typeof input3.label && "number" === typeof input3.plotValueCount && "string" === typeof input3.seriesId && "string" === typeof input3.src && (Array.isArray(input3.summaryStats) && input3.summaryStats.every((elem) => "object" === typeof elem && null !== elem && $io5(elem)));
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  const $io3 = (input3) => Array.isArray(input3.bins) && input3.bins.every((elem) => "object" === typeof elem && null !== elem && $io4(elem)) && "number" === typeof input3.densityMax && "number" === typeof input3.densityMin;
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  const $io4 = (input3) => "number" === typeof input3.x0 && "number" === typeof input3.x1 && "number" === typeof input3.density;
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- const $io5 = (input3) => Array.isArray(input3.values) && input3.values.every((elem) => "object" === typeof elem && null !== elem && $io6(elem));
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- const $io6 = (input3) => "string" === typeof input3.id && "string" === typeof input3.label && "number" === typeof input3.value;
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+ const $io5 = (input3) => "string" === typeof input3.id && "string" === typeof input3.label && "number" === typeof input3.value;
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+ const $io6 = (input3) => (void 0 === input3.value || "string" === typeof input3.value) && (void 0 === input3.html || "string" === typeof input3.html);
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  const $io7 = (input3) => Object.keys(input3).every((key) => {
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  const value = input3[key];
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  if (void 0 === value)
@@ -1514,15 +1514,6 @@ var validViolinResponse = (input) => {
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  return "number" === typeof value;
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  return true;
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  });
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- const $io8 = (input3) => (void 0 === input3.value || "string" === typeof input3.value) && (void 0 === input3.html || "string" === typeof input3.html);
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- const $io9 = (input3) => Object.keys(input3).every((key) => {
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- const value = input3[key];
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- if (void 0 === value)
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- return true;
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- if (RegExp(/(.*)/).test(key))
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- return "number" === typeof value;
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- return true;
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- });
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  const $iu0 = (input3) => (() => {
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  if (void 0 !== input3.status)
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  return $io0(input3);
@@ -1581,7 +1572,7 @@ var validViolinResponse = (input) => {
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  path: _path2 + ".pvalues[" + _index2 + "][" + _index3 + "]",
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  expected: "PValueEntries",
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  value: elem2
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- })) && $vo8(elem2, _path2 + ".pvalues[" + _index2 + "][" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
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+ })) && $vo6(elem2, _path2 + ".pvalues[" + _index2 + "][" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
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  path: _path2 + ".pvalues[" + _index2 + "][" + _index3 + "]",
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  expected: "PValueEntries",
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  value: elem2
@@ -1593,22 +1584,22 @@ var validViolinResponse = (input) => {
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  path: _path2 + ".pvalues",
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  expected: "(Array<Array<PValueEntries>> | undefined)",
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  value: input3.pvalues
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- }), null === input3.uncomputableValueObj || (Array.isArray(input3.uncomputableValueObj) || $report(_exceptionable2, {
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- path: _path2 + ".uncomputableValueObj",
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+ }), null === input3.uncomputableValues || (Array.isArray(input3.uncomputableValues) || $report(_exceptionable2, {
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+ path: _path2 + ".uncomputableValues",
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  expected: "(Array<__type> | null)",
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- value: input3.uncomputableValueObj
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- })) && input3.uncomputableValueObj.map((elem, _index4) => ("object" === typeof elem && null !== elem && false === Array.isArray(elem) || $report(_exceptionable2, {
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- path: _path2 + ".uncomputableValueObj[" + _index4 + "]",
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- expected: "__type.o2",
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+ value: input3.uncomputableValues
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+ })) && input3.uncomputableValues.map((elem, _index4) => ("object" === typeof elem && null !== elem && false === Array.isArray(elem) || $report(_exceptionable2, {
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+ path: _path2 + ".uncomputableValues[" + _index4 + "]",
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+ expected: "__type",
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  value: elem
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- })) && $vo9(elem, _path2 + ".uncomputableValueObj[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".uncomputableValueObj[" + _index4 + "]",
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- expected: "__type.o2",
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+ })) && $vo7(elem, _path2 + ".uncomputableValues[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".uncomputableValues[" + _index4 + "]",
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+ expected: "__type",
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  value: elem
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  })).every((flag) => flag) || $report(_exceptionable2, {
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- path: _path2 + ".uncomputableValueObj",
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+ path: _path2 + ".uncomputableValues",
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  expected: "(Array<__type> | null)",
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- value: input3.uncomputableValueObj
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+ value: input3.uncomputableValues
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  })].every((flag) => flag);
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  const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.color || $report(_exceptionable2, {
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  path: _path2 + ".color",
@@ -1638,33 +1629,33 @@ var validViolinResponse = (input) => {
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  path: _path2 + ".src",
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  expected: "string",
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  value: input3.src
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- }), ("object" === typeof input3.summaryStats && null !== input3.summaryStats || $report(_exceptionable2, {
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+ }), (Array.isArray(input3.summaryStats) || $report(_exceptionable2, {
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  path: _path2 + ".summaryStats",
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- expected: "__type",
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+ expected: "Array<ValuesEntries>",
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  value: input3.summaryStats
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- })) && $vo5(input3.summaryStats, _path2 + ".summaryStats", _exceptionable2) || $report(_exceptionable2, {
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+ })) && input3.summaryStats.map((elem, _index5) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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+ path: _path2 + ".summaryStats[" + _index5 + "]",
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+ expected: "ValuesEntries",
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+ value: elem
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+ })) && $vo5(elem, _path2 + ".summaryStats[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".summaryStats[" + _index5 + "]",
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+ expected: "ValuesEntries",
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+ value: elem
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+ })).every((flag) => flag) || $report(_exceptionable2, {
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  path: _path2 + ".summaryStats",
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- expected: "__type",
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+ expected: "Array<ValuesEntries>",
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  value: input3.summaryStats
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- }), null === input3.uncomputableValueObj || ("object" === typeof input3.uncomputableValueObj && null !== input3.uncomputableValueObj && false === Array.isArray(input3.uncomputableValueObj) || $report(_exceptionable2, {
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- path: _path2 + ".uncomputableValueObj",
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- expected: "(__type.o1 | null)",
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- value: input3.uncomputableValueObj
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- })) && $vo7(input3.uncomputableValueObj, _path2 + ".uncomputableValueObj", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".uncomputableValueObj",
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- expected: "(__type.o1 | null)",
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- value: input3.uncomputableValueObj
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  })].every((flag) => flag);
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  const $vo3 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.bins) || $report(_exceptionable2, {
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  path: _path2 + ".bins",
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  expected: "Array<BinsEntries>",
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  value: input3.bins
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- })) && input3.bins.map((elem, _index5) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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- path: _path2 + ".bins[" + _index5 + "]",
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+ })) && input3.bins.map((elem, _index6) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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+ path: _path2 + ".bins[" + _index6 + "]",
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  expected: "BinsEntries",
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  value: elem
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- })) && $vo4(elem, _path2 + ".bins[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".bins[" + _index5 + "]",
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+ })) && $vo4(elem, _path2 + ".bins[" + _index6 + "]", _exceptionable2) || $report(_exceptionable2, {
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+ path: _path2 + ".bins[" + _index6 + "]",
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  expected: "BinsEntries",
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  value: elem
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  })).every((flag) => flag) || $report(_exceptionable2, {
@@ -1693,24 +1684,7 @@ var validViolinResponse = (input) => {
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  expected: "number",
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  value: input3.density
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  })].every((flag) => flag);
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- const $vo5 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.values) || $report(_exceptionable2, {
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- path: _path2 + ".values",
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- expected: "Array<ValuesEntries>",
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- value: input3.values
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- })) && input3.values.map((elem, _index6) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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- path: _path2 + ".values[" + _index6 + "]",
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- expected: "ValuesEntries",
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- value: elem
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- })) && $vo6(elem, _path2 + ".values[" + _index6 + "]", _exceptionable2) || $report(_exceptionable2, {
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- path: _path2 + ".values[" + _index6 + "]",
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- expected: "ValuesEntries",
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- value: elem
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- })).every((flag) => flag) || $report(_exceptionable2, {
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- path: _path2 + ".values",
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- expected: "Array<ValuesEntries>",
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- value: input3.values
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- })].every((flag) => flag);
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- const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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+ const $vo5 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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  path: _path2 + ".id",
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  expected: "string",
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  value: input3.id
@@ -1723,19 +1697,7 @@ var validViolinResponse = (input) => {
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  expected: "number",
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  value: input3.value
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  })].every((flag) => flag);
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- const $vo7 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
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- const value = input3[key];
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- if (void 0 === value)
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- return true;
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- if (RegExp(/(.*)/).test(key))
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- return "number" === typeof value || $report(_exceptionable2, {
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- path: _path2 + $join(key),
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- expected: "number",
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- value
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- });
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- return true;
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- }).every((flag) => flag)].every((flag) => flag);
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- const $vo8 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.value || "string" === typeof input3.value || $report(_exceptionable2, {
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+ const $vo6 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.value || "string" === typeof input3.value || $report(_exceptionable2, {
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  path: _path2 + ".value",
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  expected: "(string | undefined)",
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  value: input3.value
@@ -1744,7 +1706,7 @@ var validViolinResponse = (input) => {
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  expected: "(string | undefined)",
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  value: input3.html
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  })].every((flag) => flag);
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- const $vo9 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
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+ const $vo7 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
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  const value = input3[key];
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  if (void 0 === value)
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  return true;
@@ -24,7 +24,7 @@ var validTermdbTopVariablyExpressedGenesRequest = (input) => {
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  const $join = import_typia.createValidate.join;
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  const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "number" === typeof input3.maxGenes && (void 0 === input3.geneSet || "object" === typeof input3.geneSet && null !== input3.geneSet && $io1(input3.geneSet)) && (void 0 === input3.min_median_log2_uqfpkm || "number" === typeof input3.min_median_log2_uqfpkm) && (void 0 === input3.filter_extreme_values || "number" === typeof input3.filter_extreme_values) && (void 0 === input3.min_count || "number" === typeof input3.min_count) && (void 0 === input3.min_total_count || "number" === typeof input3.min_total_count) && (void 0 === input3.rank_type || "object" === typeof input3.rank_type && null !== input3.rank_type && $io2(input3.rank_type)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io3(input3.filter)) && true;
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  const $io1 = (input3) => ("all" === input3.type || "custom" === input3.type || "msigdb" === input3.type) && (null === input3.geneList || Array.isArray(input3.geneList) && input3.geneList.every((elem) => "string" === typeof elem));
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- const $io2 = (input3) => "var" === input3.type || "iqr" === input3.type;
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+ const $io2 = (input3) => "iqr" === input3.type || "var" === input3.type;
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  const $io3 = (input3) => "lst" === input3.type && (void 0 === input3["in"] || "boolean" === typeof input3["in"]) && ("and" === input3.join || "or" === input3.join) && (void 0 === input3.tag || "string" === typeof input3.tag) && (Array.isArray(input3.lst) && input3.lst.every((elem) => "object" === typeof elem && null !== elem && $iu0(elem)));
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  const $io4 = (input3) => (void 0 === input3.join || "string" === typeof input3.join) && (void 0 === input3.isnot || "boolean" === typeof input3.isnot) && ("object" === typeof input3.term && null !== input3.term && $io5(input3.term)) && (void 0 === input3.groupset_label || "string" === typeof input3.groupset_label) && (Array.isArray(input3.values) && input3.values.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io7(elem)));
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  const $io5 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "categorical" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io6(input3.values)) && ("object" === typeof input3.groupsetting && null !== input3.groupsetting && $iu4(input3.groupsetting));
@@ -221,7 +221,7 @@ var validTermdbTopVariablyExpressedGenesRequest = (input) => {
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  expected: "(Array<string> | null)",
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  value: input3.geneList
223
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  })].every((flag) => flag);
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- const $vo2 = (input3, _path2, _exceptionable2 = true) => ["var" === input3.type || "iqr" === input3.type || $report(_exceptionable2, {
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+ const $vo2 = (input3, _path2, _exceptionable2 = true) => ["iqr" === input3.type || "var" === input3.type || $report(_exceptionable2, {
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  path: _path2 + ".type",
226
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  expected: '("iqr" | "var")',
227
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  value: input3.type
package/dist/index.js CHANGED
@@ -2,12 +2,12 @@ import {
2
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  termdbTopVariablyExpressedGenesPayload,
3
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  validTermdbTopVariablyExpressedGenesRequest,
4
4
  validTermdbTopVariablyExpressedGenesResponse
5
- } from "./chunk-WCMW6A75.js";
5
+ } from "./chunk-Y4KYTIK6.js";
6
6
  import {
7
7
  validViolinRequest,
8
8
  validViolinResponse,
9
9
  violinPayload
10
- } from "./chunk-SRDMLS6D.js";
10
+ } from "./chunk-GQVW2DPA.js";
11
11
  import {
12
12
  tilePayload,
13
13
  validTileRequest,
@@ -2,7 +2,7 @@ import {
2
2
  termdbTopVariablyExpressedGenesPayload,
3
3
  validTermdbTopVariablyExpressedGenesRequest,
4
4
  validTermdbTopVariablyExpressedGenesResponse
5
- } from "./chunk-WCMW6A75.js";
5
+ } from "./chunk-Y4KYTIK6.js";
6
6
  import "./chunk-Z6B6IQIY.js";
7
7
  export {
8
8
  termdbTopVariablyExpressedGenesPayload,
@@ -2,7 +2,7 @@ import {
2
2
  validViolinRequest,
3
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  validViolinResponse,
4
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  violinPayload
5
- } from "./chunk-SRDMLS6D.js";
5
+ } from "./chunk-GQVW2DPA.js";
6
6
  import "./chunk-Z6B6IQIY.js";
7
7
  export {
8
8
  validViolinRequest,
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@sjcrh/proteinpaint-types",
3
- "version": "2.98.0",
3
+ "version": "2.98.1-0",
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
@@ -951,6 +951,15 @@ type SurvivalSettings = {
951
951
  xTickValues?: number[]
952
952
  }
953
953
 
954
+ type RegressionSettings = {
955
+ /** disable interactions */
956
+ disableInteractions?: boolean
957
+ /** hide type III statistics table in results */
958
+ hideType3?: boolean
959
+ /** hide statistical tests table in results */
960
+ hideTests?: boolean
961
+ }
962
+
954
963
  type MatrixSettings = {
955
964
  maxSample?: number
956
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  svgCanvasSwitch?: number
@@ -1021,6 +1030,11 @@ type Survival = {
1021
1030
  settings?: SurvivalSettings
1022
1031
  }
1023
1032
 
1033
+ type Regression = {
1034
+ /** default settings for regression */
1035
+ settings?: RegressionSettings
1036
+ }
1037
+
1024
1038
  type MatrixPlotsEntry = {
1025
1039
  name: string
1026
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  file: string
@@ -1132,17 +1146,13 @@ keep this setting here for reason of:
1132
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  matrix?: Matrix
1133
1147
  numericDictTermCluster?: NumericDictTermCluster
1134
1148
  survival?: Survival
1149
+ regression?: Regression
1135
1150
  logscaleBase2?: boolean
1136
1151
  plotConfigByCohort?: PlotConfigByCohort
1137
1152
  /** Functionality */
1138
1153
  dataDownloadCatch?: DataDownloadCatch
1139
1154
  helpPages?: URLEntry[]
1140
1155
  multipleTestingCorrection?: MultipleTestingCorrection
1141
- /** regression settings for neuro-oncology portals:
1142
- - no interaction terms
1143
- - report event counts of cox coefficients
1144
- - hide type III stats and miscellaneous statistical tests */
1145
- neuroOncRegression?: boolean
1146
1156
  urlTemplates?: {
1147
1157
  /** gene link definition */
1148
1158
  gene?: UrlTemplateBase
@@ -1676,15 +1686,10 @@ export type PreInit = {
1676
1686
  }
1677
1687
  }
1678
1688
 
1679
- /** supply "isSupported()" kind of callback per chart type,
1680
- that will overwrite default logic in getSupportedChartTypes()
1681
- - the callback can have arbitrary logic based on requirements from this ds
1682
- - can supply ()=>false to hide charts that will otherwise shown
1683
- - can define arbitrary chart type names for purpose-specific charts
1684
- */
1685
-
1689
+ /** see details in termdb.server.init.ts
1690
+ */
1686
1691
  export type isSupportedChartCallbacks = {
1687
- [chartType: string]: (f: any, auth: any) => boolean | undefined
1692
+ [chartType: string]: (f: any) => boolean | undefined
1688
1693
  }
1689
1694
 
1690
1695
  export type Mds3 = BaseMds & {
@@ -62,11 +62,11 @@ export type BoxPlotData = {
62
62
  }
63
63
 
64
64
  export type BoxPlotDescrStatsEntry = {
65
- /** Use lower case for sanity check
66
- * 'total' | 'min' | 'p25' | 'median' | 'mean' | 'p75' | 'max' | 'sd' | 'variance' | 'iqr'
67
- */
68
- id: string
65
+ /** Short hand for summary stat. Use lower case for sanity check */
66
+ id: 'total' | 'min' | 'p25' | 'median' | 'mean' | 'p75' | 'max' | 'sd' | 'variance' | 'iqr' | string
67
+ /** Full label displayed to the user */
69
68
  label: string
69
+ /** Calculated value. */
70
70
  value: number
71
71
  }
72
72
 
@@ -89,11 +89,8 @@ export type ViolinPlotEntry = {
89
89
  seriesId: string
90
90
  /** Plot image to display */
91
91
  src: string
92
- summaryStats: {
93
- /** Descriptive stats (i.e. min, max, sd, etc.) */
94
- values: ValuesEntries[]
95
- }
96
- uncomputableValueObj: { [index: string]: number } | null
92
+ /** Descriptive stats (i.e. min, max, sd, etc.) */
93
+ summaryStats: ValuesEntries[]
97
94
  }
98
95
 
99
96
  export type ViolinResponse = ValidResponse | ErrorResponse
@@ -105,7 +102,7 @@ type ValidResponse = {
105
102
  max: number
106
103
  plots: ViolinPlotEntry[]
107
104
  pvalues?: PValueEntries[][]
108
- uncomputableValueObj: { [index: string]: number }[] | null
105
+ uncomputableValues: { [index: string]: number }[] | null
109
106
  }
110
107
 
111
108
  export const violinPayload: RoutePayload = {
@@ -6,20 +6,21 @@
6
6
  * Use this type for that purpose.
7
7
  */
8
8
 
9
+ type SampleEntry = {
10
+ /** stringified integer sample id */
11
+ sample: string | number
12
+ } & {
13
+ /** key and values for terms, separated by tw.$id */
14
+ [index: string]: {
15
+ key: number
16
+ value: number
17
+ }
18
+ }
19
+
9
20
  export type ValidGetDataResponse = {
10
- samples: Record<
11
- string,
12
- {
13
- /** stringified integer sample id */
14
- key: number
15
- /** value: {
16
- sample: integerId,
17
- <tw.$id>: {key, value},
18
- <more terms...>
19
- } */
20
- value: number
21
- }
22
- >
21
+ samples: {
22
+ [index: string | number]: SampleEntry
23
+ }
23
24
  /** Metadata */
24
25
  refs: {
25
26
  /** metadata about terms