@jbrowse/plugin-alignments 1.7.10 → 2.0.1

package/dist/LinearPileupDisplay/components/SetMaxHeight.js

@@ -1,90 +1,87 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _react = _interopRequireWildcard(require("react"));
-
-var _mobxReact = require("mobx-react");
-
-var _core = require("@material-ui/core");
-
-var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-var useStyles = (0, _core.makeStyles)(function (theme) {
-  return {
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importStar(require("react"));
+var mobx_react_1 = require("mobx-react");
+var material_1 = require("@mui/material");
+var mui_1 = require("tss-react/mui");
+var Close_1 = __importDefault(require("@mui/icons-material/Close"));
+var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
     root: {
-      width: 500
+        width: 500,
     },
     closeButton: {
-      position: 'absolute',
-      right: theme.spacing(1),
-      top: theme.spacing(1),
-      color: theme.palette.grey[500]
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
     },
     field: {
-      margin: theme.spacing(2)
-    }
-  };
-});
-
-function SetMaxHeightDlg(props) {
-  var model = props.model,
-      handleClose = props.handleClose;
-  var classes = useStyles();
-  var _model$maxHeight = model.maxHeight,
-      maxHeight = _model$maxHeight === void 0 ? '' : _model$maxHeight;
-
-  var _useState = (0, _react.useState)("".concat(maxHeight)),
-      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
-      max = _useState2[0],
-      setMax = _useState2[1];
-
-  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
-    open: true,
-    onClose: handleClose
-  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
-    "aria-label": "close",
-    className: classes.closeButton,
-    onClick: handleClose
-  }, /*#__PURE__*/_react.default.createElement(_Close.default, null))), /*#__PURE__*/_react.default.createElement(_core.DialogContent, {
-    className: classes.root
-  }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""), /*#__PURE__*/_react.default.createElement(_core.TextField, {
-    value: max,
-    onChange: function onChange(event) {
-      setMax(event.target.value);
+        margin: theme.spacing(2),
     },
-    placeholder: "Enter max height for layout"
-  }), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
-    variant: "contained",
-    color: "primary",
-    type: "submit",
-    autoFocus: true,
-    onClick: function onClick() {
-      model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
-      handleClose();
-    }
-  }, "Submit"), /*#__PURE__*/_react.default.createElement(_core.Button, {
-    variant: "contained",
-    color: "secondary",
-    onClick: function onClick() {
-      return handleClose();
-    }
-  }, "Cancel"))));
+}); });
+function SetMaxHeightDlg(props) {
+    var model = props.model, handleClose = props.handleClose;
+    var classes = useStyles().classes;
+    var _a = model.maxHeight, maxHeight = _a === void 0 ? '' : _a;
+    var _b = __read((0, react_1.useState)("".concat(maxHeight)), 2), max = _b[0], setMax = _b[1];
+    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
+        react_1.default.createElement(material_1.DialogTitle, null,
+            "Filter options",
+            react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
+                react_1.default.createElement(Close_1.default, null))),
+        react_1.default.createElement(material_1.DialogContent, { className: classes.root },
+            react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
+            react_1.default.createElement(material_1.TextField, { value: max, onChange: function (event) {
+                    setMax(event.target.value);
+                }, placeholder: "Enter max height for layout" }),
+            react_1.default.createElement(material_1.DialogActions, null,
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: function () {
+                        model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
+                        handleClose();
+                    } }, "Submit"),
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: function () { return handleClose(); } }, "Cancel")))));
 }
-
-var _default = (0, _mobxReact.observer)(SetMaxHeightDlg);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(SetMaxHeightDlg);
+//# sourceMappingURL=SetMaxHeight.js.map

package/dist/LinearPileupDisplay/components/SetMaxHeight.js.map

@@ -0,0 +1 @@
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package/dist/LinearPileupDisplay/components/SortByTag.js

@@ -1,95 +1,87 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _react = _interopRequireWildcard(require("react"));
-
-var _mobxReact = require("mobx-react");
-
-var _core = require("@material-ui/core");
-
-var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-var useStyles = (0, _core.makeStyles)(function (theme) {
-  return {
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importStar(require("react"));
+var mobx_react_1 = require("mobx-react");
+var material_1 = require("@mui/material");
+var mui_1 = require("tss-react/mui");
+var Close_1 = __importDefault(require("@mui/icons-material/Close"));
+var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
     root: {
-      margin: 0,
-      padding: theme.spacing(2)
+        margin: 0,
+        padding: theme.spacing(2),
     },
     closeButton: {
-      position: 'absolute',
-      right: theme.spacing(1),
-      top: theme.spacing(1),
-      color: theme.palette.grey[500]
-    }
-  };
-});
-
-function SortByTagDlg(props) {
-  var classes = useStyles();
-  var model = props.model,
-      handleClose = props.handleClose;
-
-  var _useState = (0, _react.useState)(''),
-      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
-      tag = _useState2[0],
-      setTag = _useState2[1];
-
-  var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
-  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
-    open: true,
-    onClose: handleClose
-  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Sort by tag", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
-    "aria-label": "close",
-    className: classes.closeButton,
-    onClick: handleClose
-  }, /*#__PURE__*/_react.default.createElement(_Close.default, null))), /*#__PURE__*/_react.default.createElement(_core.DialogContent, null, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Set the tag to sort by"), /*#__PURE__*/_react.default.createElement(_core.Typography, {
-    color: "textSecondary"
-  }, "Examples: HP for haplotype, RG for read group, etc."), /*#__PURE__*/_react.default.createElement(_core.TextField, {
-    value: tag,
-    onChange: function onChange(event) {
-      return setTag(event.target.value);
-    },
-    placeholder: "Enter tag name",
-    inputProps: {
-      maxLength: 2,
-      'data-testid': 'sort-tag-name-input'
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
     },
-    error: tag.length === 2 && !validTag,
-    helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
-    autoComplete: "off",
-    "data-testid": "sort-tag-name"
-  }), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
-    variant: "contained",
-    color: "primary",
-    type: "submit",
-    autoFocus: true,
-    onClick: function onClick() {
-      model.setSortedBy('tag', tag);
-      handleClose();
-    }
-  }, "Submit"), /*#__PURE__*/_react.default.createElement(_core.Button, {
-    variant: "contained",
-    color: "secondary",
-    onClick: function onClick() {
-      return handleClose();
-    }
-  }, "Cancel"))));
+}); });
+function SortByTagDlg(props) {
+    var classes = useStyles().classes;
+    var model = props.model, handleClose = props.handleClose;
+    var _a = __read((0, react_1.useState)(''), 2), tag = _a[0], setTag = _a[1];
+    var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
+    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
+        react_1.default.createElement(material_1.DialogTitle, null,
+            "Sort by tag",
+            react_1.default.createElement(material_1.IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
+                react_1.default.createElement(Close_1.default, null))),
+        react_1.default.createElement(material_1.DialogContent, null,
+            react_1.default.createElement(material_1.Typography, null, "Set the tag to sort by"),
+            react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),
+            react_1.default.createElement(material_1.TextField, { value: tag, onChange: function (event) { return setTag(event.target.value); }, placeholder: "Enter tag name", inputProps: {
+                    maxLength: 2,
+                    'data-testid': 'sort-tag-name-input',
+                }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "sort-tag-name" }),
+            react_1.default.createElement(material_1.DialogActions, null,
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: function () {
+                        model.setSortedBy('tag', tag);
+                        handleClose();
+                    } }, "Submit"),
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: function () { return handleClose(); } }, "Cancel")))));
 }
-
-var _default = (0, _mobxReact.observer)(SortByTagDlg);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(SortByTagDlg);
+//# sourceMappingURL=SortByTag.js.map

package/dist/LinearPileupDisplay/components/SortByTag.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,6CAAuC;AACvC,yCAAqC;AACrC,0CASsB;AACtB,qCAA0C;AAE1C,oEAAiD;AAEjD,IAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,UAAA,KAAK,IAAI,OAAA,CAAC;IACvC,IAAI,EAAE;QACJ,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;IACD,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;CACF,CAAC,EAXsC,CAWtC,CAAC,CAAA;AAEH,SAAS,YAAY,CAAC,KAGrB;IACS,IAAA,OAAO,GAAK,SAAS,EAAE,QAAhB,CAAgB;IACvB,IAAA,KAAK,GAAkB,KAAK,MAAvB,EAAE,WAAW,GAAK,KAAK,YAAV,CAAU;IAC9B,IAAA,KAAA,OAAgB,IAAA,gBAAQ,EAAC,EAAE,CAAC,IAAA,EAA3B,GAAG,QAAA,EAAE,MAAM,QAAgB,CAAA;IAClC,IAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,8BAAC,iBAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,8BAAC,sBAAW;;YAEV,8BAAC,qBAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,8BAAC,eAAS,OAAG,CACF,CACD;QACd,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,iCAAoC;YAC/C,8BAAC,qBAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,UAAA,KAAK,IAAI,OAAA,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAA1B,CAA0B,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,qBAAqB;iBACrC,EACD,KAAK,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,EACpC,UAAU,EAAE,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,CAAC,EAAE,EAClE,YAAY,EAAC,KAAK,iBACN,eAAe,GAC3B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE;wBACP,KAAK,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,cAAM,OAAA,WAAW,EAAE,EAAb,CAAa,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,YAAY,CAAC,CAAA"}

package/dist/LinearPileupDisplay/configSchema.js

@@ -1,45 +1,43 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
-
-var _mobxStateTree = require("mobx-state-tree");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+var mobx_state_tree_1 = require("mobx-state-tree");
 function PileupConfigFactory(pluginManager) {
-  var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema; // modify config schema to take in a sub coverage display
-
-  return (0, _configuration.ConfigurationSchema)('LinearPileupDisplay', {
-    defaultRendering: {
-      type: 'stringEnum',
-      model: _mobxStateTree.types.enumeration('Rendering', ['pileup']),
-      defaultValue: 'pileup'
-    },
-    renderers: (0, _configuration.ConfigurationSchema)('RenderersConfiguration', {
-      PileupRenderer: PileupRendererConfigSchema
-    }),
-    renderer: '',
-    maxFeatureScreenDensity: {
-      type: 'number',
-      description: 'maximum features per pixel that is displayed in the view',
-      defaultValue: 5
-    },
-    colorScheme: {
-      type: 'stringEnum',
-      model: _mobxStateTree.types.enumeration('colorScheme', ['strand', 'normal', 'insertSize', 'insertSizeAndOrientation', 'mappingQuality', 'tag']),
-      description: 'color scheme to use',
-      defaultValue: 'normal'
-    }
-  }, {
-    baseConfiguration: (0, _pluginLinearGenomeView.linearBasicDisplayConfigSchemaFactory)(pluginManager),
-    explicitlyTyped: true
-  });
+    var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
+    // modify config schema to take in a sub coverage display
+    return (0, configuration_1.ConfigurationSchema)('LinearPileupDisplay', {
+        defaultRendering: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('Rendering', ['pileup']),
+            defaultValue: 'pileup',
+        },
+        renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
+            PileupRenderer: PileupRendererConfigSchema,
+        }),
+        renderer: '',
+        maxFeatureScreenDensity: {
+            type: 'number',
+            description: 'maximum features per pixel that is displayed in the view',
+            defaultValue: 5,
+        },
+        colorScheme: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('colorScheme', [
+                'strand',
+                'normal',
+                'insertSize',
+                'insertSizeAndOrientation',
+                'mappingQuality',
+                'tag',
+            ]),
+            description: 'color scheme to use',
+            defaultValue: 'normal',
+        },
+    }, {
+        baseConfiguration: (0, plugin_linear_genome_view_1.linearBasicDisplayConfigSchemaFactory)(pluginManager),
+        explicitlyTyped: true,
+    });
 }
-
-var _default = PileupConfigFactory;
-exports.default = _default;
+exports.default = PileupConfigFactory;
+//# sourceMappingURL=configSchema.js.map

package/dist/LinearPileupDisplay/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AACjE,gFAA0F;AAC1F,mDAAiD;AAGjD,SAAS,mBAAmB,CAAC,aAA4B;IACvD,IAAM,0BAA0B,GAC9B,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY,CAAA;IAE9D,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EAAE,0BAA0B;SAC3C,CAAC;QACF,QAAQ,EAAE,EAAE;QACZ,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QACD,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAMD,kBAAe,mBAAmB,CAAA"}

package/dist/LinearPileupDisplay/index.js

@@ -1,30 +1,24 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = register;
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-var _model = _interopRequireDefault(require("./model"));
-
-var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-
-var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var configSchema_1 = __importDefault(require("./configSchema"));
+var model_1 = __importDefault(require("./model"));
+var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 function register(pluginManager) {
-  pluginManager.addDisplayType(function () {
-    var configSchema = (0, _configSchema.default)(pluginManager);
-    return new _DisplayType.default({
-      name: 'LinearPileupDisplay',
-      configSchema: configSchema,
-      stateModel: (0, _model.default)(configSchema),
-      trackType: 'AlignmentsTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: _pluginLinearGenomeView.BaseLinearDisplayComponent
+    pluginManager.addDisplayType(function () {
+        var configSchema = (0, configSchema_1.default)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'LinearPileupDisplay',
+            configSchema: configSchema,
+            stateModel: (0, model_1.default)(configSchema),
+            trackType: 'AlignmentsTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
+        });
     });
-  });
-}
+}
+exports.default = register;
+//# sourceMappingURL=index.js.map

package/dist/LinearPileupDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;AAAA,gEAAgD;AAChD,kDAAkC;AAClC,gGAAyE;AAEzE,gFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC;QAC3B,IAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY,cAAA;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}

package/dist/LinearPileupDisplay/model.d.ts

@@ -93,11 +93,11 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     error: unknown;
 } & {
     readonly RenderingComponent: import("react").FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -112,11 +112,11 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         blockState?: Record<string, any> | undefined;
     }>;
     readonly DisplayBlurb: import("react").FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -149,7 +149,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -202,7 +202,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
         label: string;
-        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         onClick: () => void;
     }[];
     renderProps(): any;
@@ -264,7 +266,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
     renderProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
-        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         type: string;
         checked: boolean;
         onClick: () => void;
@@ -272,7 +276,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         subMenu?: undefined;
     } | {
         label: string;
-        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         disabled: boolean;
         subMenu: {
             label: string;
@@ -283,7 +289,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         onClick?: undefined;
     } | {
         label: string;
-        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         subMenu: {
             label: string;
             onClick: () => void;
@@ -294,7 +302,9 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         disabled?: undefined;
     } | {
         label: string;
-        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         onClick: () => void;
         type?: undefined;
         checked?: undefined;
@@ -310,10 +320,10 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         subMenu?: undefined;
     })[];
 }, import("mobx-state-tree")._NotCustomized, {
-    id: string;
     type: string;
-    rpcDriverName: string | undefined;
     height: number;
+    id: string;
+    rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;