@complat/react-spectra-editor 1.7.1 → 1.8.0

package/dist/features/lc-ms/submit/index.js

@@ -0,0 +1,24 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "formatLcmsIntegralsForBackend", {
+  enumerable: true,
+  get: function get() {
+    return _peaks.formatLcmsIntegralsForBackend;
+  }
+});
+Object.defineProperty(exports, "formatLcmsPeaksForBackend", {
+  enumerable: true,
+  get: function get() {
+    return _peaks.formatLcmsPeaksForBackend;
+  }
+});
+Object.defineProperty(exports, "getLcmsMzPageData", {
+  enumerable: true,
+  get: function get() {
+    return _peaks.getLcmsMzPageData;
+  }
+});
+var _peaks = require("./peaks");

package/dist/features/lc-ms/submit/peaks.js

@@ -0,0 +1,66 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.formatLcmsIntegralsForBackend = formatLcmsIntegralsForBackend;
+exports.formatLcmsPeaksForBackend = formatLcmsPeaksForBackend;
+exports.getLcmsMzPageData = getLcmsMzPageData;
+function formatLcmsPeaksForBackend(hplcMsSt) {
+  const allPeaks = [];
+  if (hplcMsSt && hplcMsSt.uvvis && hplcMsSt.uvvis.spectraList) {
+    hplcMsSt.uvvis.spectraList.forEach(spectrum => {
+      if (spectrum.peaks && spectrum.peaks.length > 0) {
+        const {
+          pageValue
+        } = spectrum;
+        spectrum.peaks.forEach(peak => {
+          allPeaks.push({
+            ...peak,
+            wavelength: pageValue
+          });
+        });
+      }
+    });
+  }
+  return allPeaks;
+}
+function formatLcmsIntegralsForBackend(hplcMsSt) {
+  const allIntegrals = [];
+  if (hplcMsSt && hplcMsSt.uvvis && hplcMsSt.uvvis.spectraList) {
+    hplcMsSt.uvvis.spectraList.forEach(spectrum => {
+      if (spectrum.integrations && spectrum.integrations.length > 0) {
+        const {
+          pageValue
+        } = spectrum;
+        spectrum.integrations.forEach(integral => {
+          allIntegrals.push({
+            from: integral.xL,
+            to: integral.xU,
+            value: integral.area,
+            integral: integral.absoluteArea,
+            wavelength: pageValue
+          });
+        });
+      }
+    });
+  }
+  return allIntegrals;
+}
+function getLcmsMzPageData(hplcMsSt) {
+  const tic = hplcMsSt?.tic;
+  const ms = hplcMsSt?.ms;
+  if (!tic || !ms) return null;
+  const polarity = tic.polarity || 'positive';
+  let polarityKey = 'neutral';
+  if (polarity === 'negative') polarityKey = 'negative';else if (polarity === 'positive') polarityKey = 'positive';
+  const ticDataX = tic[polarityKey]?.data?.x;
+  if (!Array.isArray(ticDataX) || !Number.isFinite(tic.currentPageValue)) return null;
+  let currentIndex = ms[polarityKey]?.pageValues?.findIndex(value => Number.isFinite(value) && Math.abs(value - tic.currentPageValue) < 1e-6);
+  if (!Number.isFinite(currentIndex) || currentIndex < 0) {
+    currentIndex = ticDataX.findIndex(x => Math.abs(x - tic.currentPageValue) < 1e-6);
+  }
+  if (currentIndex < 0) return null;
+  const peaks = ms[polarityKey]?.peaks?.[currentIndex];
+  return Array.isArray(peaks) ? peaks : null;
+}

package/dist/features/lc-ms/ui/wavelengthSelect.js

@@ -0,0 +1,54 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = void 0;
+var _react = _interopRequireDefault(require("react"));
+var _classnames = _interopRequireDefault(require("classnames"));
+var _material = require("@mui/material");
+var _jsxRuntime = require("react/jsx-runtime");
+/* eslint-disable react/function-component-definition */
+
+const renderWavelengthSelect = (classes, hplcMsSt, updateWavelengthAct, options = {}) => {
+  const {
+    labelId = 'select-decimal-label',
+    label = 'Decimal',
+    width = '140px'
+  } = options;
+  const uvvis = hplcMsSt && hplcMsSt.uvvis || {};
+  const {
+    listWaveLength = null,
+    selectedWaveLength
+  } = uvvis;
+  const items = listWaveLength ? listWaveLength.map(d => /*#__PURE__*/(0, _jsxRuntime.jsx)(_material.MenuItem, {
+    value: d,
+    children: /*#__PURE__*/(0, _jsxRuntime.jsx)("span", {
+      className: (0, _classnames.default)(classes.txtOpt, 'option-sv-bar-decimal'),
+      children: d
+    })
+  }, d)) : [];
+  const hasSelectedWaveLength = listWaveLength && listWaveLength.includes(selectedWaveLength);
+  const resolvedSelectedWaveLength = hasSelectedWaveLength ? selectedWaveLength : listWaveLength && listWaveLength[0];
+  return /*#__PURE__*/(0, _jsxRuntime.jsxs)(_material.FormControl, {
+    className: (0, _classnames.default)(classes.fieldDecimal),
+    variant: "outlined",
+    style: {
+      width
+    },
+    children: [/*#__PURE__*/(0, _jsxRuntime.jsx)(_material.InputLabel, {
+      id: labelId,
+      className: (0, _classnames.default)(classes.selectLabel, 'select-sv-bar-label'),
+      children: "Wavelength (nm)"
+    }), /*#__PURE__*/(0, _jsxRuntime.jsx)(_material.Select, {
+      labelId: labelId,
+      label: label,
+      value: resolvedSelectedWaveLength,
+      onChange: updateWavelengthAct,
+      className: (0, _classnames.default)(classes.selectInput, 'input-sv-bar-decimal'),
+      children: items
+    })]
+  });
+};
+var _default = exports.default = renderWavelengthSelect;

package/dist/fn.js

@@ -10,14 +10,17 @@ var _chem = require("./helpers/chem");
 var _converter = require("./helpers/converter");
 var _multiplicity_calc = require("./helpers/multiplicity_calc");
 var _carbonFeatures = require("./helpers/carbonFeatures");
+var _integration_jcamp = require("./helpers/integration_jcamp");
 var _list_layout = require("./constants/list_layout");
 /* eslint-disable prefer-object-spread */
 
 const FN = Object.assign({}, _format.default, {
   ExtractJcamp: _chem.ExtractJcamp,
+  buildLcmsMsPageJcamp: _chem.buildLcmsMsPageJcamp,
   ToXY: _converter.ToXY,
   LIST_LAYOUT: _list_layout.LIST_LAYOUT,
   CalcMpyCenter: _multiplicity_calc.calcMpyCenter,
-  CarbonFeatures: _carbonFeatures.carbonFeatures
+  CarbonFeatures: _carbonFeatures.carbonFeatures,
+  serializeIntegrationRecords: _integration_jcamp.serializeIntegrationRecords
 });
 var _default = exports.default = FN;

package/dist/helpers/brush.js

@@ -1,31 +1,43 @@
 "use strict";
 
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.default = void 0;
 var _compass = require("./compass");
+var _integration_draft = require("./integration_draft.js");
+var _sweep = require("./sweep.js");
+var _list_ui = require("../constants/list_ui");
+var _cfg = _interopRequireDefault(require("./cfg"));
 /* eslint-disable prefer-object-spread */
 
+// eslint-disable-line import/extensions
+// eslint-disable-line import/extensions
+
 const d3 = require('d3');
 const wheeled = (focus, event) => {
   const {
     currentExtent,
-    scrollUiWheelAct
+    scrollUiWheelAct,
+    brushClass
   } = focus;
   // WORKAROUND: firefox wheel compatibilty
   const wheelEvent = focus.isFirefox ? -event.deltaY : event.wheelDelta; // eslint-disable-line
   const direction = wheelEvent > 0;
   scrollUiWheelAct(Object.assign({}, currentExtent, {
-    direction
+    direction,
+    brushClass
   }));
 };
-const brushed = (focus, isUiAddIntgSt, event) => {
+const usesTwoClickIntegAdd = (focus, isUiAddIntgSt) => isUiAddIntgSt && _cfg.default.showIntegSplitTools(focus.layout);
+const brushed = (focus, xOnly, event, brushedClass = '.d3Svg') => {
   const {
     selectUiSweepAct,
     data,
     dataPks,
     brush,
+    brushX,
     w,
     h,
     scales
@@ -42,7 +54,15 @@ const brushed = (focus, isUiAddIntgSt, event) => {
     yL: yes[0],
     yU: yes[1]
   };
-  if (isUiAddIntgSt) {
+  if (xOnly) {
+    if (focus.isUiAddIntgSt) {
+      const payload = (0, _sweep.buildSweepPayloadFromXBounds)(focus, scales.x.invert(selection[0]), scales.x.invert(selection[1]));
+      selectUiSweepAct(payload);
+      if (brushX) {
+        focus.svg.selectAll('.brushX').call(brushX.move, null);
+      }
+      return;
+    }
     xes = selection.map(scales.x.invert).sort((a, b) => a - b);
     xExtent = {
       xL: xes[0],
@@ -67,34 +87,69 @@ const brushed = (focus, isUiAddIntgSt, event) => {
     data,
     dataPks
   });
-  d3.select('.d3Svg').selectAll('.brush').call(brush.move, null);
+  let svgSel = null;
+  if (focus?.svg && typeof focus.svg.selectAll === 'function') {
+    svgSel = focus.svg;
+  } else if (typeof brushedClass === 'string') {
+    svgSel = d3.select(brushedClass);
+  }
+  if (svgSel && typeof svgSel.selectAll === 'function' && !svgSel.empty()) {
+    const brushSelection = xOnly ? svgSel.selectAll('.brushX') : svgSel.selectAll('.brush');
+    if (!brushSelection.empty()) {
+      if (xOnly && brushX) {
+        brushSelection.call(brushX.move, null);
+      } else if (brush) {
+        brushSelection.call(brush.move, null);
+      }
+    }
+  }
 };
-const MountBrush = (focus, isUiAddIntgSt, isUiNoBrushSt) => {
+const MountBrush = (focus, isUiAddIntgSt, isUiNoBrushSt, brushedClass = '.d3Svg') => {
   const {
     root,
     svg,
     brush,
     brushX,
     w,
-    h
+    h,
+    uiSt,
+    graphIndex
   } = focus;
-  svg.selectAll('.brush').remove();
-  svg.selectAll('.brushX').remove();
-  const brushedCb = event => brushed(focus, isUiAddIntgSt, event);
+  Object.assign(focus, {
+    isUiAddIntgSt
+  });
+  const twoClickIntegAdd = usesTwoClickIntegAdd(focus, isUiAddIntgSt);
+  const {
+    firstIntegrationPoint,
+    data,
+    jcampIdx
+  } = focus;
+  const isSameIntegrationDraft = firstIntegrationPoint && firstIntegrationPoint.jcampIdx === jcampIdx && firstIntegrationPoint.dataLength === data.length;
+  if (!isUiAddIntgSt || firstIntegrationPoint && !isSameIntegrationDraft) {
+    (0, _integration_draft.clearPendingIntegrationDraft)();
+    Object.assign(focus, {
+      firstIntegrationPoint: null
+    });
+    (0, _compass.clearIntegrationPreview)(focus);
+  }
+  if (!root || !svg || typeof svg.selectAll !== 'function') return;
+  svg.selectAll('.brush, .brushX').remove();
+  const isZoomInSubview = uiSt?.zoom?.sweepTypes?.[graphIndex] === _list_ui.LIST_UI_SWEEP_TYPE.ZOOMIN;
+  const isZoomInGlobal = uiSt?.sweepType === _list_ui.LIST_UI_SWEEP_TYPE.ZOOMIN;
+  const isIntegrationAdd = uiSt?.sweepType === _list_ui.LIST_UI_SWEEP_TYPE.INTEGRATION_ADD;
+  const isMultiplicitySweepAdd = uiSt?.sweepType === _list_ui.LIST_UI_SWEEP_TYPE.MULTIPLICITY_SWEEP_ADD;
+  const isZoomIn = isZoomInSubview || isZoomInGlobal;
+  if (graphIndex !== undefined && !(graphIndex === 0 && isIntegrationAdd) && !isZoomIn && !isMultiplicitySweepAdd) return;
+  const isXAxisOnly = focus?.xOnlyBrush === true;
+  const xOnly = isUiAddIntgSt || isXAxisOnly && !isZoomIn;
+  const brushedCb = event => brushed(focus, xOnly, event, brushedClass);
   const wheeledCb = event => wheeled(focus, event);
-  if (isUiNoBrushSt) {
+  if (isUiNoBrushSt && !twoClickIntegAdd) {
     const target = isUiAddIntgSt ? brushX : brush;
     target.handleSize(10).extent([[0, 0], [w, h]]).on('end', brushedCb);
-
-    // append brush components
     const klass = isUiAddIntgSt ? 'brushX' : 'brush';
     root.append('g').attr('class', klass).on('mousemove', event => (0, _compass.MouseMove)(event, focus)).call(target);
   }
   svg.on('wheel', wheeledCb);
 };
-var _default = exports.default = MountBrush; // const resetedCb = () => reseted(main);
-// main.svg.on('dblclick', resetedCb);
-// const reseted = (main) => {
-//   const { selectUiSweepAct } = main;
-//   selectUiSweepAct({ xExtent: false, yExtent: false });
-// };
+var _default = exports.default = MountBrush;

package/dist/helpers/calc.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.calcSlope = exports.almostEqual = void 0;
+exports.findClosest = exports.calcSlope = exports.almostEqual = void 0;
 const almostEqual = (a, b) => Math.abs(a - b) < 0.00000001 * Math.abs(a + b);
 exports.almostEqual = almostEqual;
 const calcSlope = (x1, y1, x2, y2) => {
@@ -12,4 +12,6 @@ const calcSlope = (x1, y1, x2, y2) => {
   }
   return (y2 - y1) / (x2 - x1);
 };
-exports.calcSlope = calcSlope;
+exports.calcSlope = calcSlope;
+const findClosest = (arr, target) => arr.reduce((prev, curr) => Math.abs(curr - target) < Math.abs(prev - target) ? curr : prev); // eslint-disable-line
+exports.findClosest = findClosest;

package/dist/helpers/cfg.js

@@ -6,14 +6,14 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 var _format = _interopRequireDefault(require("./format"));
-const btnCmdAnaViewer = layoutSt => _format.default.isMsLayout(layoutSt) || _format.default.isRamanLayout(layoutSt) || _format.default.is19FLayout(layoutSt) || _format.default.isUvVisLayout(layoutSt) || _format.default.isHplcUvVisLayout(layoutSt) || _format.default.isTGALayout(layoutSt) || _format.default.isDSCLayout(layoutSt) || _format.default.isXRDLayout(layoutSt) || _format.default.is31PLayout(layoutSt) || _format.default.is15NLayout(layoutSt) || _format.default.is29SiLayout(layoutSt) || _format.default.isCyclicVoltaLayout(layoutSt) || _format.default.isCDSLayout(layoutSt) || _format.default.isSECLayout(layoutSt) || _format.default.isGCLayout(layoutSt);
+const btnCmdAnaViewer = layoutSt => _format.default.isMsLayout(layoutSt) || _format.default.isLCMsLayout(layoutSt) || _format.default.isRamanLayout(layoutSt) || _format.default.is19FLayout(layoutSt) || _format.default.isUvVisLayout(layoutSt) || _format.default.isHplcUvVisLayout(layoutSt) || _format.default.isTGALayout(layoutSt) || _format.default.isDSCLayout(layoutSt) || _format.default.isXRDLayout(layoutSt) || _format.default.is31PLayout(layoutSt) || _format.default.is15NLayout(layoutSt) || _format.default.is29SiLayout(layoutSt) || _format.default.isCyclicVoltaLayout(layoutSt) || _format.default.isCDSLayout(layoutSt) || _format.default.isSECLayout(layoutSt) || _format.default.isGCLayout(layoutSt);
 const hideCmdAnaViewer = () => false;
 const btnCmdAddPeak = layoutSt => _format.default.isMsLayout(layoutSt);
 const btnCmdRmPeak = layoutSt => _format.default.isMsLayout(layoutSt);
-const btnCmdSetRef = layoutSt => !_format.default.isNmrLayout(layoutSt); // eslint-disable-line
-
-const btnCmdIntg = layoutSt => !(_format.default.isNmrLayout(layoutSt) || _format.default.isHplcUvVisLayout(layoutSt)); // eslint-disable-line
+const btnCmdSetRef = layoutSt => !_format.default.isNmrLayout(layoutSt);
+const btnCmdIntg = layoutSt => !(_format.default.isNmrLayout(layoutSt) || _format.default.isHplcUvVisLayout(layoutSt) || _format.default.isLCMsLayout(layoutSt)); // eslint-disable-line
 
+const showIntegSplitTools = layoutSt => _format.default.isHplcUvVisLayout(layoutSt);
 const btnCmdMpy = layoutSt => !_format.default.isNmrLayout(layoutSt);
 const btnCmdMpyPeak = (layoutSt, mpySt, curveIdx = 0) => {
   const {
@@ -50,6 +50,7 @@ const Config = {
   btnCmdRmPeak,
   btnCmdSetRef,
   btnCmdIntg,
+  showIntegSplitTools,
   btnCmdMpy,
   btnCmdMpyPeak,
   hideCmdThres,