@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-IUBBQPO2.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termsetting/handlers/NumericDensity.ts"],
-  "sourcesContent": ["import type { TermSetting } from '../TermSetting.ts'\nimport type { NumRegularBin, NumCustomBins, NumCont, NumSpline } from '#tw'\nimport type { NumericBin } from '#types'\nimport { violinRenderer } from '#dom'\nimport { select, pointer, type BaseType } from 'd3-selection'\nimport { scaleLinear, drag as d3drag } from 'd3'\n//import { get_bin_label, get_bin_range_equation } from '#shared/termdb.bins.js'\n\nexport type BoundaryOpts = {\n\tvalues: BoundaryValue[]\n\tcallback: (d: DraggedLineData, value: number) => void\n}\n\nexport type BoundaryValue = {\n\tx: number\n\tisDraggable: boolean\n\tmovesWithLineIndex?: number\n\tisLastVisibleLine?: boolean\n}\n\nexport type LineData = BoundaryValue & {\n\tscaledX: number\n\tindex: number\n}\n\nexport type DraggedLineData = LineData & {\n\tdraggedX?: number\n\tstart?: number\n\tend?: number\n}\n\nexport class NumericDensity {\n\ttermsetting: TermSetting\n\topts: any // TODO\n\ttw: NumRegularBin | NumCustomBins | NumCont | NumSpline\n\n\tdom: {\n\t\t[name: string]: any\n\t} = {}\n\t// WeakMap allows deletion of value when the object/DOM key is deleted,\n\t// so better for avoiding memory leak\n\tvrByDiv: WeakMap<HTMLElement, any> = new WeakMap()\n\tvr!: violinRenderer\n\tdensity_data!: any\n\tranges: NumericBin[] = []\n\tno_density_data = false\n\tbrushes: any[] = []\n\txscale!: any\n\tplot_size: {\n\t\twidth: number\n\t\theight: number\n\t\txpad: number\n\t\typad: number\n\t\tradius: number\n\t} = {\n\t\twidth: 500,\n\t\theight: 100,\n\t\txpad: 10,\n\t\typad: 20,\n\t\tradius: 8\n\t}\n\n\tconstructor(opts) {\n\t\tthis.opts = opts\n\t\tthis.termsetting = opts.termsetting\n\t\tthis.tw = opts.termsetting.tw\n\t}\n\n\tasync setData() {\n\t\t//if (this.density_data) return this.density_data\n\t\tconst self = this.termsetting\n\t\tconst d = await self.vocabApi.getViolinBox(\n\t\t\t{\n\t\t\t\tplotType: 'violin',\n\t\t\t\ttw: { type: self.tw.type, term: self.term, q: self.q },\n\t\t\t\tsvgw: this.plot_size.width,\n\t\t\t\tradius: this.plot_size.radius,\n\t\t\t\tfilter: self.filter\n\t\t\t},\n\t\t\tself.opts.getBodyParams?.()\n\t\t)\n\t\tif (d.error) throw d\n\t\tthis.density_data = d\n\t\treturn this.density_data\n\t}\n\n\tasync showViolin(div, boundaryOpts?) {\n\t\tawait this.setData()\n\n\t\tif (!this.vrByDiv.has(div)) {\n\t\t\tdiv.style('padding', '5px').selectAll('*').remove()\n\t\t\tconst loadingDiv = div\n\t\t\t\t.append('div')\n\t\t\t\t.style('padding', '10px')\n\t\t\t\t.style('text-align', 'center')\n\t\t\t\t.html('Getting distribution data ...<br/>')\n\n\t\t\tconst densityDiv = div.append('div')\n\t\t\tloadingDiv.remove()\n\t\t\tconst vr = new violinRenderer({\n\t\t\t\tholder: densityDiv,\n\t\t\t\trd: this.density_data,\n\t\t\t\twidth: this.plot_size.width,\n\t\t\t\theight: this.plot_size.height,\n\t\t\t\tradius: this.plot_size.radius\n\t\t\t})\n\t\t\tthis.vrByDiv.set(div, vr)\n\t\t}\n\n\t\tthis.vr = this.vrByDiv.get(div)\n\t\tthis.dom.svg = this.vr.svg\n\t\tthis.vr.render()\n\t\tif (boundaryOpts) await this.setBinLines(boundaryOpts)\n\n\t\treturn this.density_data\n\t}\n\n\tasync setBinLines(boundaryOpts) {\n\t\tif (this.density_data.max == this.density_data.min) {\n\t\t\tthis.handleNoDensity()\n\t\t} else {\n\t\t\t// svg for range plot\n\t\t\t// const div = self.q.mode == 'spline' ? self.dom.knots_div : self.dom.bins_div\n\t\t\t//this.vr.render()\n\n\t\t\t// add binsize_g for termsetting lines\n\t\t\tif (this.dom.binsize_g) this.dom.binsize_g.selectAll('*').remove()\n\t\t\tthis.dom.binsize_g = this.dom.svg\n\t\t\t\t.append('g')\n\t\t\t\t.attr('transform', `translate(${this.plot_size.xpad}, ${this.plot_size.ypad})`)\n\t\t\t\t.attr('class', 'binsize_g')\n\n\t\t\tconst maxvalue = this.density_data.max\n\t\t\tconst minvalue = this.density_data.min\n\n\t\t\tthis.xscale = scaleLinear()\n\t\t\t\t.domain([minvalue, maxvalue])\n\t\t\t\t.range([this.plot_size.xpad, this.plot_size.width + this.plot_size.xpad])\n\n\t\t\tthis.ranges = []\n\t\t\tthis.brushes = []\n\t\t\tthis.renderBinLines(boundaryOpts)\n\t\t}\n\t}\n\n\thandleNoDensity() {\n\t\tthis.no_density_data = true\n\t\tthis.ranges = []\n\t\tthis.brushes = []\n\t}\n\n\trenderBinLines(boundaryOpts: BoundaryOpts) {\n\t\t//this.boundaryOpts = boundaryOpts\n\t\tconst { density_data, plot_size, tw, xscale } = this\n\t\tif (!this.density_data) throw `Missing .density_data [density.ts, renderBinLines()]`\n\t\tconst scaledMinX = Math.round(this.xscale(density_data.min))\n\t\tconst scaledMaxX = Math.round(this.xscale(density_data.max))\n\t\tconst lines: DraggedLineData[] = []\n\t\tfor (const [index, v] of boundaryOpts.values.entries()) {\n\t\t\tlines.push({ ...v, index, scaledX: Math.round(this.xscale(v.x)) })\n\t\t}\n\t\tconst lastVisibleLine = lines.find(l => l.isLastVisibleLine)\n\t\tconst lastVisibleScaledX = lastVisibleLine ? lastVisibleLine.scaledX : scaledMaxX\n\t\tconst dragger = d3drag().on('drag', onDrag).on('end', onDrag)\n\n\t\tthis.dom.binsize_g.selectAll('line').remove()\n\t\tthis.dom.binsize_g\n\t\t\t.selectAll('line')\n\t\t\t.data(lines)\n\t\t\t.enter()\n\t\t\t.append('line')\n\t\t\t.style('stroke', (d: LineData) => (d.isDraggable ? '#cc0000' : '#555'))\n\t\t\t.style('stroke-width', 1)\n\t\t\t.attr('x1', (d: LineData) => d.scaledX)\n\t\t\t.attr('y1', 0)\n\t\t\t.attr('x2', (d: LineData) => d.scaledX)\n\t\t\t.attr('y2', plot_size.height)\n\t\t\t.style('cursor', (d: LineData) => (d.isDraggable ? 'ew-resize' : ''))\n\t\t\t.attr('display', (d: LineData) => (!d.isDraggable && d.scaledX > lastVisibleScaledX ? 'none' : ''))\n\t\t\t.on('mouseover', function (this: SVGLineElement, _, d: LineData) {\n\t\t\t\tif (d.isDraggable) select(this).style('stroke-width', 3)\n\t\t\t})\n\t\t\t.on('mouseout', function (this: BaseType) {\n\t\t\t\tselect(this).style('stroke-width', 1)\n\t\t\t})\n\t\t\t.each(function (this: Element, d: LineData) {\n\t\t\t\tif (d.isDraggable) select(this).call(dragger)\n\t\t\t})\n\n\t\tconst lineElems = this.dom.binsize_g.node().querySelectorAll('line')\n\n\t\tfunction onDrag(this: any, event: PointerEvent, _d: any) {\n\t\t\tconst draggedX: number = pointer(event, this)[0]\n\t\t\tif (draggedX <= scaledMinX || draggedX >= scaledMaxX) return\n\n\t\t\tconst d = _d as DraggedLineData\n\t\t\td.draggedX = draggedX\n\t\t\tselect(this).attr('x1', d.draggedX).attr('y1', 0).attr('x2', d.draggedX).attr('y2', plot_size.height)\n\n\t\t\tconst lastVisibleScaledX = lastVisibleLine?.draggedX ?? lastVisibleLine?.scaledX ?? scaledMaxX\n\n\t\t\tconst xOffset = d.draggedX - d.scaledX\n\t\t\tif (xOffset) {\n\t\t\t\tfor (const elem of lineElems) {\n\t\t\t\t\tconst c = elem.__data__\n\t\t\t\t\tif (c.movesWithLineIndex !== d.index) continue\n\t\t\t\t\tc.draggedX = c.scaledX + xOffset\n\t\t\t\t\tselect(elem)\n\t\t\t\t\t\t.attr('x1', c.draggedX)\n\t\t\t\t\t\t.attr('x2', c.draggedX)\n\t\t\t\t\t\t.style('display', c.draggedX >= lastVisibleScaledX ? 'none' : '')\n\t\t\t\t}\n\t\t\t\tconst inverted = xscale.invert(d.draggedX)\n\t\t\t\tconst value = tw.term.type == 'integer' ? Math.round(inverted) : inverted.toFixed(3)\n\t\t\t\tboundaryOpts.callback(d, Number(value))\n\t\t\t}\n\t\t}\n\t}\n\n\tdestroy() {\n\t\tfor (const [k, v] of Object.entries(this.dom)) {\n\t\t\tdelete this.dom[k]\n\t\t\tif (typeof v.remove == 'function') v.remove()\n\t\t}\n\t}\n}\n"],
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-  "names": ["lastVisibleScaledX"]
-}

package/dist/chunk-J4USU73L.js

@@ -1,26 +0,0 @@
-import {
-  plotColor
-} from "./chunk-6PNPHACF.js";
-
-// plots/boxplot/defaults.ts
-function getDefaultBoxplotSettings(app, overrides = {}) {
-  const defaults = {
-    plotLength: 550,
-    color: plotColor,
-    displayMode: "default",
-    labelPad: 10,
-    isLogScale: false,
-    isVertical: false,
-    orderByMedian: false,
-    rowHeight: 50,
-    rowSpace: 15,
-    removeOutliers: false,
-    showAssocTests: true
-  };
-  return Object.assign(defaults, overrides);
-}
-
-export {
-  getDefaultBoxplotSettings
-};
-//# sourceMappingURL=chunk-J4USU73L.js.map

package/dist/chunk-JNITUVXP.js

@@ -1,41 +0,0 @@
-// ../shared/utils/dist/src/helpers.js
-function isNumeric(n) {
-  const v = typeof n != "string" || n === "" ? n : Number(n);
-  const f = parseFloat(n);
-  return !isNaN(f) && Number.isFinite(v) && v === f;
-}
-function isStrictNumeric(n) {
-  return typeof n === "number" && Number.isFinite(n);
-}
-function convertUnits(v, fromUnit, toUnit, scaleFactor, compact) {
-  if (scaleFactor >= 1) {
-    const toUnitV2 = Math.floor(v * scaleFactor);
-    if (compact) return `${toUnitV2}${toUnit.charAt(0)}`;
-    return `${toUnitV2} ${toUnitV2 > 1 ? toUnit + "s" : ""}`;
-  }
-  const toUnitV = Math.floor(v * scaleFactor);
-  const fromUnitV = Math.ceil(v % (1 / scaleFactor));
-  if (fromUnitV == 0) {
-    if (compact) return `${toUnitV}${toUnit.charAt(0)}`;
-    return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : ""}`;
-  }
-  if (compact) return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`;
-  return `${toUnitV} ${toUnitV > 1 ? toUnit + "s" : toUnit} ${fromUnitV} ${fromUnitV > 1 ? fromUnit + "s" : fromUnit}`;
-}
-var CustomError = class extends Error {
-  constructor(message, opts = {}) {
-    super(message);
-    this.level = "";
-    if (opts.name) this.name = opts.name;
-    if (opts.code) this.code = opts.code;
-    if (opts.level) this.level = opts.level;
-  }
-};
-
-export {
-  isNumeric,
-  isStrictNumeric,
-  convertUnits,
-  CustomError
-};
-//# sourceMappingURL=chunk-JNITUVXP.js.map

package/dist/chunk-JNITUVXP.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/helpers.ts"],
-  "sourcesContent": ["/*\nthis is a helper file with a collection of functions to be used in backend and client side code. Here is a list.\n\n1. isNumeric(n)\n2. strictNumeric(n) \n2. convertUnits\n3. TODO - move computepercentile, roundValue, etc here?\n*/\n\n// checks whether given argument n is Numeric, with option to cast from string\nexport function isNumeric(n) {\n\tconst v = typeof n != 'string' || n === '' ? n : Number(n)\n\tconst f = parseFloat(n)\n\treturn !isNaN(f) && Number.isFinite(v) && v === f\n}\n\n// like isNumeric but does not cast from string\nexport function isStrictNumeric(n) {\n\treturn typeof n === 'number' && Number.isFinite(n)\n}\n\n// converts a value from a unit to another unit\nexport function convertUnits(v, fromUnit, toUnit, scaleFactor, compact?: boolean) {\n\t// do floor() on toUnit\n\t// do ceil() on fromUnit, in case v is decimal (from violin range selection) and to keep showing integer fromUnit\n\tif (scaleFactor >= 1) {\n\t\tconst toUnitV = Math.floor(v * scaleFactor)\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : ''}`\n\t}\n\tconst toUnitV = Math.floor(v * scaleFactor)\n\tconst fromUnitV = Math.ceil(v % (1 / scaleFactor))\n\n\tif (fromUnitV == 0) {\n\t\tif (compact) return `${toUnitV}${toUnit.charAt(0)}`\n\t\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : ''}`\n\t}\n\n\tif (compact) return `${toUnitV}${toUnit.charAt(0)}${fromUnitV}${fromUnit.charAt(0)}`\n\treturn `${toUnitV} ${toUnitV > 1 ? toUnit + 's' : toUnit} ${fromUnitV} ${fromUnitV > 1 ? fromUnit + 's' : fromUnit}`\n}\n\nexport function deepEqual(x, y) {\n\tif (x === y) {\n\t\treturn true\n\t} else if (typeof x == 'object' && x != null && typeof y == 'object' && y != null) {\n\t\tif (Object.keys(x).length != Object.keys(y).length) {\n\t\t\treturn false\n\t\t}\n\n\t\tfor (const prop of Object.keys(x)) {\n\t\t\tif (Object.prototype.hasOwnProperty.call(y, prop)) {\n\t\t\t\tif (!deepEqual(x[prop], y[prop])) return false\n\t\t\t} else {\n\t\t\t\treturn false\n\t\t\t}\n\t\t}\n\t\treturn true\n\t} else return false\n}\n\nexport function deepFreeze(obj) {\n\tObject.freeze(obj)\n\t// not using for..in loop, in order to not descend into inherited props/methods\n\tfor (const value of Object.values(obj)) {\n\t\tif (value !== null && typeof value == 'object') deepFreeze(value)\n\t}\n\treturn obj\n}\n\nexport class CustomError extends Error {\n\tlevel = '' // '' | 'warn'\n\tcode?: string\n\n\tconstructor(message, opts: { name?: string; code?: string; level?: string } = {}) {\n\t\tsuper(message)\n\t\tif (opts.name) this.name = opts.name\n\t\tif (opts.code) this.code = opts.code\n\t\tif (opts.level) this.level = opts.level\n\t}\n}\n"],
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