@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/dist/LinearPileupDisplay/components/ColorByTag.js

@@ -22,36 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    root: {
-        width: 300,
-    },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+const ui_1 = require("@jbrowse/core/ui");
 function ColorByTagDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const [tag, setTag] = (0, react_1.useState)('');
     const 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,
-            "Color 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))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag" },
         react_1.default.createElement(material_1.DialogContent, { style: { overflowX: 'hidden' } },
             react_1.default.createElement(material_1.Typography, null, "Enter tag to color by: "),
             react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),

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

@@ -1 +1 @@
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+{"version":3,"file":"ColorByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AAEzC,SAAS,aAAa,CAAC,KAGtB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IAEnD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,cAAc;QACrD,8BAAC,wBAAa,IAAC,KAAK,EAAE,EAAE,SAAS,EAAE,QAAQ,EAAE;YAC3C,8BAAC,qBAAU,kCAAqC;YAChD,8BAAC,qBAAU,IAAC,KAAK,EAAC,eAAe,+IAGpB;YAEb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC7C,WAAW,EAAC,gBAAgB,EAC5B,UAAU,EAAE;oBACV,SAAS,EAAE,CAAC;oBACZ,aAAa,EAAE,sBAAsB;iBACtC,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,gBAAgB,GAC5B;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC;4BACnB,IAAI,EAAE,KAAK;4BACX,GAAG;yBACJ,CAAC,CAAA;wBACF,WAAW,EAAE,CAAA;oBACf,CAAC,EACD,QAAQ,EAAE,CAAC,QAAQ,aAGZ;gBACT,8BAAC,iBAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAE,WAAW,aAEzD,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,aAAa,CAAC,CAAA"}

package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts

@@ -1,8 +1,8 @@
 /// <reference types="react" />
 declare function SetFeatureHeightDlg(props: {
     model: {
-        setFeatureHeight: Function;
-        setNoSpacing: Function;
+        setFeatureHeight: (arg?: number) => void;
+        setNoSpacing: (arg?: boolean) => void;
         featureHeightSetting: number;
         noSpacing?: boolean;
     };

package/dist/LinearPileupDisplay/components/SetFeatureHeight.js

@@ -22,40 +22,21 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+const ui_1 = require("@jbrowse/core/ui");
 function SetFeatureHeightDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const { featureHeightSetting, noSpacing: noSpacingSetting } = model;
     const [height, setHeight] = (0, react_1.useState)(`${featureHeightSetting}`);
     const [noSpacing, setNoSpacing] = (0, react_1.useState)(noSpacingSetting);
     const ok = height !== '' && !Number.isNaN(+height);
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Set feature height",
-            react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: handleClose },
-                react_1.default.createElement(Close_1.default, null))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set feature height" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, null, "Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."),
-            react_1.default.createElement(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => {
-                    setHeight(event.target.value);
-                } }),
+            react_1.default.createElement(material_1.TextField, { value: height, helperText: "Feature height", onChange: event => setHeight(event.target.value) }),
             react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: !!noSpacing, onChange: () => setNoSpacing(val => !val) }), label: "Remove spacing between features in y-direction?" }),
             react_1.default.createElement(material_1.DialogActions, null,
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !ok, onClick: () => {

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

@@ -1 +1 @@
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+{"version":3,"file":"SetFeatureHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetFeatureHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAQsB;AACtB,yCAAyC;AAEzC,SAAS,mBAAmB,CAAC,KAQ5B;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,oBAAoB,EAAE,SAAS,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,oBAAoB,EAAE,CAAC,CAAA;IAC/D,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,IAAA,gBAAQ,EAAC,gBAAgB,CAAC,CAAA;IAE5D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAA;IAElD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,oBAAoB;QAC3D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,wKAIE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,MAAM,EACb,UAAU,EAAC,gBAAgB,EAC3B,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,GAChD;YACF,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,CAAC,CAAC,SAAS,EACpB,QAAQ,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GACzC,EAEJ,KAAK,EAAC,iDAAiD,GACvD;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,QAAQ,EAAE,CAAC,EAAE,EACb,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,CACpB,MAAM,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAC9D,CAAA;wBACD,KAAK,CAAC,YAAY,CAAC,SAAS,CAAC,CAAA;wBAC7B,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,mBAAmB,CAAC,CAAA"}

package/dist/LinearPileupDisplay/components/SetMaxHeight.js

@@ -22,39 +22,23 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
+const ui_1 = require("@jbrowse/core/ui");
 const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     root: {
         width: 500,
     },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-    field: {
-        margin: theme.spacing(2),
-    },
 }));
 function SetMaxHeightDlg(props) {
     const { model, handleClose } = props;
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = (0, react_1.useState)(`${maxHeight}`);
-    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))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
         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: event => {

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

@@ -1 +1 @@
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+{"version":3,"file":"SetMaxHeight.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SetMaxHeight.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AACzC,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,eAAe,CAAC,KAMxB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,SAAS,GAAG,EAAE,EAAE,GAAG,KAAK,CAAA;IAChC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BAAC,wBAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,8BAAC,qBAAU,qHAGE;YACb,8BAAC,oBAAS,IACR,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,EACD,WAAW,EAAC,6BAA6B,GACzC;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,IAAI,EAAC,QAAQ,EACb,SAAS,QACT,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,YAAY,CAChB,GAAG,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,CACrD,CAAA;wBACD,WAAW,EAAE,CAAA;oBACf,CAAC,aAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,eAAe,CAAC,CAAA"}

package/dist/LinearPileupDisplay/components/SortByTag.js

@@ -22,37 +22,16 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    root: {
-        margin: 0,
-        padding: theme.spacing(2),
-    },
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+const ui_1 = require("@jbrowse/core/ui");
 function SortByTagDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const [tag, setTag] = (0, react_1.useState)('');
     const 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))),
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
         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."),

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

@@ -1 +1 @@
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+{"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,yCAAyC;AAEzC,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,aAAa;QACpD,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,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,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,GAAG,EAAE;wBACZ,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,GAAG,EAAE,CAAC,WAAW,EAAE,aAGrB,CACK,CACF,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,YAAY,CAAC,CAAA"}

package/dist/LinearPileupDisplay/configSchema.d.ts

@@ -1,6 +1,3 @@
-import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
 declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export type LinearPileupDisplayConfigModel = ReturnType<typeof configSchemaF>;
-export type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>;
 export default configSchemaF;

package/dist/LinearPileupDisplay/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAuC;AAGvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,IAAA,mCAAmB,EACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,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;;WAEG;QACH,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,cAAc,EACZ,aAAa,CAAC,eAAe,CAAC,gBAAgB,CAAC,CAAC,YAAY;SAC/D,CAAC;QACF;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,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;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,kBAAe,aAAa,CAAA"}

package/dist/LinearPileupDisplay/index.js

@@ -15,8 +15,10 @@ function register(pluginManager) {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearPileupDisplay',
+            displayName: 'Pileup display',
             configSchema,
             stateModel: (0, model_1.default)(configSchema),
+            subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
             trackType: 'AlignmentsTrack',
             viewType: 'LinearGenomeView',
             ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,

package/dist/LinearPileupDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAgD;AAwBvB,iDAxBlB,sBAAmB,CAwBqC;AAvB/D,oDAAkC;AAsBhB,+CAtBX,eAAY,CAsBmC;AArBtD,kGAAyE;AAEzE,kFAA+E;AAE/E,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,YAAY,CAAC;YACtC,UAAU,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,UAAU,EAAE,IAAI,EAAE;YACjE,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAdD,2BAcC"}

package/dist/LinearPileupDisplay/model.d.ts

@@ -1,14 +1,13 @@
 /// <reference types="react" />
 import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
-import { LinearPileupDisplayConfigModel } from './configSchema';
 /**
  * #stateModel LinearPileupDisplay
  * extends `BaseLinearDisplay`
  */
-declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel): import("mobx-state-tree").IModelType<{
+declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     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>>;
@@ -35,9 +34,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
          */
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
-        features: Map<string, Feature> | undefined; /**
-         * #property
-         */
+        features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
@@ -48,9 +45,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #property
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
@@ -152,10 +147,10 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
-    scrollTop: number;
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
@@ -244,11 +239,11 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
     /**
      * #action
      */
-    setFeatureHeight(n: number): void;
+    setFeatureHeight(n?: number): void;
     /**
      * #action
      */
-    setNoSpacing(flag: boolean): void;
+    setNoSpacing(flag?: boolean): void;
     /**
      * #action
      */
@@ -325,7 +320,7 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     /**
      * #getter
      */
@@ -346,11 +341,17 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
     /**
      * #method
      */
-    contextMenuItems(): {
+    contextMenuItems(): ({
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    } | {
         label: string;
         icon: typeof ContentCopyIcon;
         onClick: () => void;
-    }[];
+    })[];
     /**
      * #getter
      */
@@ -419,7 +420,9 @@ declare function stateModelFactory(configSchema: LinearPileupDisplayConfigModel)
     })[];
 }, import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
+    height: number; /**
+     * #action
+     */
     id: string;
     rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;

package/dist/LinearPileupDisplay/model.js

@@ -41,11 +41,12 @@ const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 const Sort_1 = __importDefault(require("@mui/icons-material/Sort"));
 const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
+// locals
 const LinearPileupDisplayBlurb_1 = __importDefault(require("./components/LinearPileupDisplayBlurb"));
 const shared_1 = require("../shared");
 // async
+const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/FilterByTag'))));
 const ColorByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByTag'))));
-const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/FilterByTag'))));
 const SortByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTag'))));
 const SetFeatureHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetFeatureHeight'))));
 const SetMaxHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
@@ -115,12 +116,7 @@ function stateModelFactory(configSchema) {
         /**
          * #property
          */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
-            flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
-            flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
-            readName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-            tagFilter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.model({ tag: mobx_state_tree_1.types.string, value: mobx_state_tree_1.types.string })),
-        }), {}),
+        filterBy: mobx_state_tree_1.types.optional(shared_1.FilterModel, {}),
     }))
         .volatile(() => ({
         colorTagMap: mobx_1.observable.map({}),
@@ -679,12 +675,31 @@ function stateModelFactory(configSchema) {
                     },
                     {
                         label: 'Set feature height',
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(doneCallback => [
-                                SetFeatureHeightDlg,
-                                { model: self, handleClose: doneCallback },
-                            ]);
-                        },
+                        subMenu: [
+                            {
+                                label: 'Normal',
+                                onClick: () => {
+                                    self.setFeatureHeight(7);
+                                    self.setNoSpacing(false);
+                                },
+                            },
+                            {
+                                label: 'Compact',
+                                onClick: () => {
+                                    self.setFeatureHeight(2);
+                                    self.setNoSpacing(true);
+                                },
+                            },
+                            {
+                                label: 'Manually set height',
+                                onClick: () => {
+                                    (0, util_1.getSession)(self).queueDialog(doneCallback => [
+                                        SetFeatureHeightDlg,
+                                        { model: self, handleClose: doneCallback },
+                                    ]);
+                                },
+                            },
+                        ],
                     },
                     {
                         label: 'Set max height',

package/dist/LinearPileupDisplay/model.js.map

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package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { LinearReadArcsDisplayModel } from '../model';
+declare const _default: ({ model, }: {
+    model: LinearReadArcsDisplayModel;
+}) => JSX.Element;
+export default _default;

package/dist/LinearReadArcsDisplay/components/ReactComponent.js

@@ -0,0 +1,49 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const ui_1 = require("@jbrowse/core/ui");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    loading: {
+        paddingLeft: '0.6em',
+        backgroundColor: theme.palette.action.disabledBackground,
+        backgroundImage: 'repeating-linear-gradient(45deg, transparent, transparent 5px, rgba(255,255,255,.5) 5px, rgba(255,255,255,.5) 10px)',
+        height: '100%',
+        width: '100%',
+        pointerEvents: 'none',
+        textAlign: 'center',
+    },
+}));
+const Arcs = (0, mobx_react_1.observer)(function ({ model, }) {
+    const view = (0, util_1.getContainingView)(model);
+    return (react_1.default.createElement("canvas", { "data-testid": `Arc-display-${model.drawn}`, ref: ref => {
+            if ((0, mobx_state_tree_1.isAlive)(model)) {
+                model.setRef(ref);
+            }
+        }, style: {
+            position: 'absolute',
+            left: -view.offsetPx + model.lastDrawnOffsetPx,
+            width: view.dynamicBlocks.totalWidthPx,
+            height: model.height,
+        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+});
+exports.default = (0, mobx_react_1.observer)(function ({ model, }) {
+    const view = (0, util_1.getContainingView)(model);
+    const { classes } = useStyles();
+    const err = model.error;
+    return err ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${err}`, severity: "error", buttonText: 'Reload', action: model.reload })) : model.loading ? (react_1.default.createElement("div", { className: classes.loading, style: {
+            width: view.dynamicBlocks.totalWidthPx,
+            height: 20,
+            position: 'absolute',
+            left: Math.max(0, -view.offsetPx),
+        } },
+        react_1.default.createElement(ui_1.LoadingEllipses, { message: model.message }))) : (react_1.default.createElement(Arcs, { model: model }));
+});
+//# sourceMappingURL=ReactComponent.js.map

package/dist/LinearReadArcsDisplay/components/ReactComponent.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearReadArcsDisplay/components/ReactComponent.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,qDAAyC;AACzC,uCAA0C;AAC1C,2CAAqC;AACrC,6CAAsD;AACtD,yCAAkD;AAClD,kFAG2C;AAO3C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,WAAW,EAAE,OAAO;QACpB,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,kBAAkB;QACxD,eAAe,EACb,qHAAqH;QACvH,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,MAAM;QACb,aAAa,EAAE,MAAM;QACrB,SAAS,EAAE,QAAQ;KACpB;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,IAAI,GAAG,IAAA,qBAAQ,EAAC,UAAU,EAC9B,KAAK,GAGN;IACC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,KAAK,CAAQ,CAAA;IAC5C,OAAO,CACL,yDACe,eAAe,KAAK,CAAC,KAAK,EAAE,EACzC,GAAG,EAAE,GAAG,CAAC,EAAE;YACT,IAAI,IAAA,yBAAO,EAAC,KAAK,CAAC,EAAE;gBAClB,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;aAClB;QACH,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,CAAC,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,iBAAiB;YAC9C,KAAK,EAAE,IAAI,CAAC,aAAa,CAAC,YAAY;YACtC,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,EACD,KAAK,EAAE,IAAI,CAAC,aAAa,CAAC,YAAY,GAAG,CAAC,EAC1C,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,CAAC,GACxB,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,kBAAe,IAAA,qBAAQ,EAAC,UAAU,EAChC,KAAK,GAGN;IACC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,KAAK,CAAC,CAAA;IACrC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,GAAG,GAAG,KAAK,CAAC,KAAK,CAAA;IACvB,OAAO,GAAG,CAAC,CAAC,CAAC,CACX,8BAAC,oCAAQ,IACP,OAAO,EAAE,GAAG,GAAG,EAAE,EACjB,QAAQ,EAAC,OAAO,EAChB,UAAU,EAAE,QAAQ,EACpB,MAAM,EAAE,KAAK,CAAC,MAAM,GACpB,CACH,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAClB,uCACE,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,KAAK,EAAE;YACL,KAAK,EAAE,IAAI,CAAC,aAAa,CAAC,YAAY;YACtC,MAAM,EAAE,EAAE;YACV,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC;SAClC;QAED,8BAAC,oBAAe,IAAC,OAAO,EAAE,KAAK,CAAC,OAAO,GAAI,CACvC,CACP,CAAC,CAAC,CAAC,CACF,8BAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CACvB,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/LinearReadArcsDisplay/configSchema.d.ts

@@ -0,0 +1,6 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config LinearReadArcsDisplay
+ */
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchemaF;