@jbrowse/plugin-sequence 1.7.9 → 2.0.0

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -1,239 +1,140 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _react = _interopRequireDefault(require("react"));
-
-var _color = require("@jbrowse/core/util/color");
-
-var _ui = require("@jbrowse/core/ui");
-
-var _mobxReact = require("mobx-react");
-
-var _util = require("@jbrowse/core/util");
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-explicit-any */
+var react_1 = __importDefault(require("react"));
+var color_1 = require("@jbrowse/core/util/color");
+var ui_1 = require("@jbrowse/core/ui");
+var mobx_react_1 = require("mobx-react");
+var util_1 = require("@jbrowse/core/util");
 function Translation(props) {
-  var codonTable = props.codonTable,
-      seq = props.seq,
-      frame = props.frame,
-      bpPerPx = props.bpPerPx,
-      region = props.region,
-      height = props.height,
-      y = props.y,
-      _props$reverse = props.reverse,
-      reverse = _props$reverse === void 0 ? false : _props$reverse,
-      theme = props.theme;
-  var scale = bpPerPx; // the tilt variable normalizes the frame to where we are starting from,
-  // which increases consistency across blocks
-
-  var tilt = 3 - region.start % 3; // the effectiveFrame incorporates tilt and the frame to say what the
-  // effective frame that is plotted. The +3 is for when frame is -2 and this
-  // can otherwise result in effectiveFrame -1
-
-  var effectiveFrame = (frame + tilt + 3) % 3;
-  var seqSliced = seq.slice(effectiveFrame);
-  var translated = [];
-
-  for (var i = 0; i < seqSliced.length; i += 3) {
-    var codon = seqSliced.slice(i, i + 3);
-    var normalizedCodon = reverse ? (0, _util.revcom)(codon) : codon;
-    var aminoAcid = codonTable[normalizedCodon] || '';
-    translated.push({
-      letter: aminoAcid,
-      codon: normalizedCodon.toUpperCase()
-    });
-  }
-
-  var w = 1 / scale * 3;
-  var drop = region.start === 0 ? 0 : w;
-  var render = 1 / bpPerPx >= 12;
-  var width = (region.end - region.start) / bpPerPx;
-  var map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse();
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, translated.map(function (element, index) {
-    var x = region.reversed ? width - (w * (index + 1) + effectiveFrame / scale - drop) : w * index + effectiveFrame / scale - drop;
-    var letter = element.letter,
-        codon = element.codon;
-    return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, {
-      key: "".concat(index, "-").concat(letter)
-    }, /*#__PURE__*/_react.default.createElement("rect", {
-      x: x,
-      y: y,
-      width: render ? w : w + 0.7
-      /* small fudge factor when zoomed out*/
-      ,
-      height: height,
-      stroke: render ? '#555' : 'none',
-      fill: _util.defaultStarts.includes(codon) ? theme.palette.startCodon : _util.defaultStops.includes(codon) ? theme.palette.stopCodon : map[Math.abs(frame)]
-    }), render ? /*#__PURE__*/_react.default.createElement("text", {
-      x: x + w / 2,
-      y: y + height / 2,
-      dominantBaseline: "middle",
-      textAnchor: "middle"
-    }, letter) : null);
-  }));
+    var codonTable = props.codonTable, seq = props.seq, frame = props.frame, bpPerPx = props.bpPerPx, region = props.region, height = props.height, y = props.y, _a = props.reverse, reverse = _a === void 0 ? false : _a, theme = props.theme;
+    var scale = bpPerPx;
+    // the tilt variable normalizes the frame to where we are starting from,
+    // which increases consistency across blocks
+    var tilt = 3 - (region.start % 3);
+    // the effectiveFrame incorporates tilt and the frame to say what the
+    // effective frame that is plotted. The +3 is for when frame is -2 and this
+    // can otherwise result in effectiveFrame -1
+    var effectiveFrame = (frame + tilt + 3) % 3;
+    var seqSliced = seq.slice(effectiveFrame);
+    var translated = [];
+    for (var i = 0; i < seqSliced.length; i += 3) {
+        var codon = seqSliced.slice(i, i + 3);
+        var normalizedCodon = reverse ? (0, util_1.revcom)(codon) : codon;
+        var aminoAcid = codonTable[normalizedCodon] || '';
+        translated.push({ letter: aminoAcid, codon: normalizedCodon.toUpperCase() });
+    }
+    var w = (1 / scale) * 3;
+    var drop = region.start === 0 ? 0 : w;
+    var render = 1 / bpPerPx >= 12;
+    var width = (region.end - region.start) / bpPerPx;
+    var map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse();
+    return (react_1.default.createElement(react_1.default.Fragment, null, translated.map(function (element, index) {
+        var x = region.reversed
+            ? width - (w * (index + 1) + effectiveFrame / scale - drop)
+            : w * index + effectiveFrame / scale - drop;
+        var letter = element.letter, codon = element.codon;
+        return (react_1.default.createElement(react_1.default.Fragment, { key: "".concat(index, "-").concat(letter) },
+            react_1.default.createElement("rect", { x: x, y: y, width: render ? w : w + 0.7 /* small fudge factor when zoomed out*/, height: height, stroke: render ? '#555' : 'none', fill: util_1.defaultStarts.includes(codon)
+                    ? theme.palette.startCodon
+                    : util_1.defaultStops.includes(codon)
+                        ? theme.palette.stopCodon
+                        : map[Math.abs(frame)] }),
+            render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle" }, letter)) : null));
+    })));
 }
-
 function DNA(props) {
-  var bpPerPx = props.bpPerPx,
-      region = props.region,
-      feature = props.feature,
-      theme = props.theme,
-      height = props.height,
-      seq = props.seq,
-      y = props.y;
-  var render = 1 / bpPerPx >= 12;
-
-  var _bpSpanPx = (0, _util.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx),
-      _bpSpanPx2 = (0, _slicedToArray2.default)(_bpSpanPx, 2),
-      leftPx = _bpSpanPx2[0],
-      rightPx = _bpSpanPx2[1];
-
-  var reverse = region.reversed;
-  var len = feature.get('end') - feature.get('start');
-  var w = Math.max((rightPx - leftPx) / len, 0.8);
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, seq.split('').map(function (letter, index) {
-    var color = theme.palette.bases[letter.toUpperCase()];
-    var x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
-    return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, {
-      key: index
-    }, /*#__PURE__*/_react.default.createElement("rect", {
-      x: x,
-      y: y,
-      width: w,
-      height: height,
-      fill: color ? color.main : '#aaa',
-      stroke: render ? '#555' : 'none'
-    }), render ? /*#__PURE__*/_react.default.createElement("text", {
-      x: x + w / 2,
-      y: y + height / 2,
-      dominantBaseline: "middle",
-      textAnchor: "middle",
-      fill: color ? (0, _color.contrastingTextColor)(color.main) : 'black'
-    }, letter) : null);
-  }));
+    var bpPerPx = props.bpPerPx, region = props.region, feature = props.feature, theme = props.theme, height = props.height, seq = props.seq, y = props.y;
+    var render = 1 / bpPerPx >= 12;
+    var _a = __read((0, util_1.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx), 2), leftPx = _a[0], rightPx = _a[1];
+    var reverse = region.reversed;
+    var len = feature.get('end') - feature.get('start');
+    var w = Math.max((rightPx - leftPx) / len, 0.8);
+    return (react_1.default.createElement(react_1.default.Fragment, null, seq.split('').map(function (letter, index) {
+        var color = theme.palette.bases[letter.toUpperCase()];
+        var x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
+        return (react_1.default.createElement(react_1.default.Fragment, { key: index },
+            react_1.default.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
+            render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? (0, color_1.contrastingTextColor)(color.main) : 'black' }, letter)) : null));
+    })));
 }
-
-var SequenceSVG = function SequenceSVG(_ref) {
-  var regions = _ref.regions,
-      configTheme = _ref.theme,
-      _ref$features = _ref.features,
-      features = _ref$features === void 0 ? new Map() : _ref$features,
-      showReverse = _ref.showReverse,
-      showForward = _ref.showForward,
-      showTranslation = _ref.showTranslation,
-      bpPerPx = _ref.bpPerPx;
-
-  var _regions = (0, _slicedToArray2.default)(regions, 1),
-      region = _regions[0];
-
-  var theme = (0, _ui.createJBrowseTheme)(configTheme);
-  var codonTable = (0, _util.generateCodonTable)(_util.defaultCodonTable);
-  var height = 20;
-
-  var _ref2 = (0, _toConsumableArray2.default)(features.values()),
-      feature = _ref2[0];
-
-  if (!feature) {
-    return null;
-  }
-
-  var seq = feature.get('seq');
-
-  if (!seq) {
-    return null;
-  } // incrementer for the y-position of the current sequence being rendered
-  // (applies to both translation rows and dna rows)
-
-
-  var currY = -20;
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, showTranslation && (region.reversed ? showReverse : showForward) ? [2, 1, 0].map(function (index) {
-    return /*#__PURE__*/_react.default.createElement(Translation, {
-      key: "translation-".concat(index),
-      seq: seq,
-      y: currY += 20,
-      codonTable: codonTable,
-      frame: index,
-      bpPerPx: bpPerPx,
-      region: region,
-      theme: theme,
-      height: height,
-      reverse: region.reversed
-    });
-  }) : null, showForward ? /*#__PURE__*/_react.default.createElement(DNA, {
-    height: height,
-    y: currY += 20,
-    feature: feature,
-    region: region,
-    seq: region.reversed ? (0, _util.complement)(seq) : seq,
-    bpPerPx: bpPerPx,
-    theme: theme
-  }) : null, showReverse ? /*#__PURE__*/_react.default.createElement(DNA, {
-    height: height,
-    y: currY += 20,
-    feature: feature,
-    region: region,
-    seq: region.reversed ? seq : (0, _util.complement)(seq),
-    bpPerPx: bpPerPx,
-    theme: theme
-  }) : null, showTranslation && (region.reversed ? showForward : showReverse) ? [0, -1, -2].map(function (index) {
-    return /*#__PURE__*/_react.default.createElement(Translation, {
-      key: "rev-translation-".concat(index),
-      seq: seq,
-      y: currY += 20,
-      codonTable: codonTable,
-      frame: index,
-      bpPerPx: bpPerPx,
-      region: region,
-      theme: theme,
-      height: height,
-      reverse: !region.reversed
-    });
-  }) : null);
-};
-
-var Wrapper = function Wrapper(_ref3) {
-  var exportSVG = _ref3.exportSVG,
-      width = _ref3.width,
-      totalHeight = _ref3.totalHeight,
-      children = _ref3.children;
-  return exportSVG ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, children) : /*#__PURE__*/_react.default.createElement("svg", {
-    "data-testid": "sequence_track",
-    width: width,
-    height: totalHeight,
-    style: {
-      width: width,
-      height: totalHeight
+var SequenceSVG = function (_a) {
+    var regions = _a.regions, configTheme = _a.theme, _b = _a.features, features = _b === void 0 ? new Map() : _b, showReverse = _a.showReverse, showForward = _a.showForward, showTranslation = _a.showTranslation, bpPerPx = _a.bpPerPx;
+    var _c = __read(regions, 1), region = _c[0];
+    var theme = (0, ui_1.createJBrowseTheme)(configTheme);
+    var codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
+    var height = 20;
+    var _d = __read(__spreadArray([], __read(features.values()), false), 1), feature = _d[0];
+    if (!feature) {
+        return null;
     }
-  }, children);
+    var seq = feature.get('seq');
+    if (!seq) {
+        return null;
+    }
+    // incrementer for the y-position of the current sequence being rendered
+    // (applies to both translation rows and dna rows)
+    var currY = -20;
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        showTranslation && (region.reversed ? showReverse : showForward)
+            ? [2, 1, 0].map(function (index) { return (react_1.default.createElement(Translation, { key: "translation-".concat(index), seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: region.reversed })); })
+            : null,
+        showForward ? (react_1.default.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
+        showReverse ? (react_1.default.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null,
+        showTranslation && (region.reversed ? showForward : showReverse)
+            ? [0, -1, -2].map(function (index) { return (react_1.default.createElement(Translation, { key: "rev-translation-".concat(index), seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })); })
+            : null));
+};
+var Wrapper = function (_a) {
+    var exportSVG = _a.exportSVG, width = _a.width, totalHeight = _a.totalHeight, children = _a.children;
+    return exportSVG ? (react_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width: width, height: totalHeight } }, children));
 };
-
 function Sequence(props) {
-  var regions = props.regions,
-      bpPerPx = props.bpPerPx;
-
-  var _regions2 = (0, _slicedToArray2.default)(regions, 1),
-      region = _regions2[0];
-
-  var width = (region.end - region.start) / bpPerPx;
-  var totalHeight = 200;
-  return /*#__PURE__*/_react.default.createElement(Wrapper, (0, _extends2.default)({}, props, {
-    totalHeight: totalHeight,
-    width: width
-  }), /*#__PURE__*/_react.default.createElement(SequenceSVG, props));
+    var regions = props.regions, bpPerPx = props.bpPerPx;
+    var _a = __read(regions, 1), region = _a[0];
+    var width = (region.end - region.start) / bpPerPx;
+    var totalHeight = 200;
+    return (react_1.default.createElement(Wrapper, __assign({}, props, { totalHeight: totalHeight, width: width }),
+        react_1.default.createElement(SequenceSVG, __assign({}, props))));
 }
-
-var _default = (0, _mobxReact.observer)(Sequence);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(Sequence);
+//# sourceMappingURL=DivSequenceRendering.js.map

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js.map

@@ -0,0 +1 @@
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package/dist/DivSequenceRenderer/configSchema.js

@@ -1,20 +1,11 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('DivSequenceRenderer', {
-  height: {
-    type: 'number',
-    description: 'height in pixels of each line of sequence',
-    defaultValue: 16
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('DivSequenceRenderer', {
+    height: {
+        type: 'number',
+        description: 'height in pixels of each line of sequence',
+        defaultValue: 16,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/DivSequenceRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,2CAA2C;QACxD,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/DivSequenceRenderer/index.js

@@ -1,23 +1,11 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "ReactComponent", {
-  enumerable: true,
-  get: function get() {
-    return _DivSequenceRendering.default;
-  }
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _DivSequenceRendering = _interopRequireDefault(require("./components/DivSequenceRendering"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = exports.ReactComponent = void 0;
+var DivSequenceRendering_1 = require("./components/DivSequenceRendering");
+Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(DivSequenceRendering_1).default; } });
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/DivSequenceRenderer/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/index.ts"],"names":[],"mappings":";;;;;;AAAA,0EAA6E;AAApE,uIAAA,OAAO,OAAkB;AAClC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}