@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/esm/LinearPileupDisplay/components/SetMaxHeight.js

@@ -1,32 +1,19 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
 import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
 const useStyles = 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] = useState(`${maxHeight}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Filter options",
-            React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
         React.createElement(DialogContent, { className: classes.root },
             React.createElement(Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
             React.createElement(TextField, { value: max, onChange: event => {

package/esm/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,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,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,QAAQ,CAAC,GAAG,SAAS,EAAE,CAAC,CAAA;IAE9C,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;YACpC,oBAAC,UAAU,qHAGE;YACb,oBAAC,SAAS,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,oBAAC,aAAa;gBACZ,oBAAC,MAAM,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,oBAAC,MAAM,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,eAAe,QAAQ,CAAC,eAAe,CAAC,CAAA"}

package/esm/LinearPileupDisplay/components/SortByTag.js

@@ -1,30 +1,12 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Dialog, DialogActions, DialogContent, DialogTitle, IconButton, TextField, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
-const useStyles = 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],
-    },
-}));
+import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
 function SortByTagDlg(props) {
-    const { classes } = useStyles();
     const { model, handleClose } = props;
     const [tag, setTag] = useState('');
     const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Sort by tag",
-            React.createElement(IconButton, { "aria-label": "close", className: classes.closeButton, onClick: handleClose },
-                React.createElement(CloseIcon, null))),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Sort by tag" },
         React.createElement(DialogContent, null,
             React.createElement(Typography, null, "Set the tag to sort by"),
             React.createElement(Typography, { color: "textSecondary" }, "Examples: HP for haplotype, RG for read group, etc."),

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

@@ -1 +1 @@
-{"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,UAAU,EACV,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAEjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,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,CAAC,CAAA;AAEH,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAEV,oBAAC,UAAU,kBACE,OAAO,EAClB,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,WAAW;gBAEpB,oBAAC,SAAS,OAAG,CACF,CACD;QACd,oBAAC,aAAa;YACZ,oBAAC,UAAU,iCAAoC;YAC/C,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,oBAAC,SAAS,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,oBAAC,aAAa;gBACZ,oBAAC,MAAM,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,oBAAC,MAAM,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,eAAe,QAAQ,CAAC,YAAY,CAAC,CAAA"}
+{"version":3,"file":"SortByTag.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/SortByTag.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AAEzC,SAAS,YAAY,CAAC,KAGrB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IAClC,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,uBAAuB,CAAC,CAAA;IACnD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,aAAa;QACpD,oBAAC,aAAa;YACZ,oBAAC,UAAU,iCAAoC;YAC/C,oBAAC,UAAU,IAAC,KAAK,EAAC,eAAe,0DAEpB;YACb,oBAAC,SAAS,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,oBAAC,aAAa;gBACZ,oBAAC,MAAM,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,oBAAC,MAAM,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,eAAe,QAAQ,CAAC,YAAY,CAAC,CAAA"}

package/esm/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/esm/LinearPileupDisplay/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAC1F,OAAO,EAAE,KAAK,EAAY,MAAM,iBAAiB,CAAA;AAGjD;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,mBAAmB,CACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,mBAAmB,CAAC,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,KAAK,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,qCAAqC,CAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAID,eAAe,aAAa,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAC1F,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAGvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,SAAS,aAAa,CAAC,aAA4B;IACjD,yDAAyD;IACzD,OAAO,mBAAmB,CACxB,qBAAqB,EACrB;QACE;;WAEG;QACH,gBAAgB,EAAE;YAChB,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC;YACjD,YAAY,EAAE,QAAQ;SACvB;QACD;;WAEG;QACH,SAAS,EAAE,mBAAmB,CAAC,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,KAAK,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,qCAAqC,CAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,eAAe,aAAa,CAAA"}

package/esm/LinearPileupDisplay/index.js

@@ -7,8 +7,10 @@ export default function register(pluginManager) {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
             name: 'LinearPileupDisplay',
+            displayName: 'Pileup display',
             configSchema,
             stateModel: modelFactory(configSchema),
+            subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
             trackType: 'AlignmentsTrack',
             viewType: 'LinearGenomeView',
             ReactComponent: BaseLinearDisplayComponent,

package/esm/LinearPileupDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearPileupDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,mBAAmB,MAAM,gBAAgB,CAAA;AAChD,OAAO,YAAY,MAAM,SAAS,CAAA;AAClC,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,mBAAmB,CAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,gBAAgB;YAC7B,YAAY;YACZ,UAAU,EAAE,YAAY,CAAC,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,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,OAAO,EACL,YAAY,IAAI,oCAAoC,EACpD,mBAAmB,IAAI,sCAAsC,GAC9D,CAAA"}

package/esm/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/esm/LinearPileupDisplay/model.js

@@ -13,11 +13,12 @@ import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import SortIcon from '@mui/icons-material/Sort';
 import PaletteIcon from '@mui/icons-material/Palette';
 import FilterListIcon from '@mui/icons-material/ClearAll';
+// locals
 import LinearPileupDisplayBlurb from './components/LinearPileupDisplayBlurb';
-import { getUniqueTagValues, getUniqueModificationValues } from '../shared';
+import { getUniqueTagValues, getUniqueModificationValues, FilterModel, } from '../shared';
 // async
+const FilterByTagDlg = lazy(() => import('../shared/FilterByTag'));
 const ColorByTagDlg = lazy(() => import('./components/ColorByTag'));
-const FilterByTagDlg = lazy(() => import('./components/FilterByTag'));
 const SortByTagDlg = lazy(() => import('./components/SortByTag'));
 const SetFeatureHeightDlg = lazy(() => import('./components/SetFeatureHeight'));
 const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'));
@@ -87,12 +88,7 @@ function stateModelFactory(configSchema) {
         /**
          * #property
          */
-        filterBy: types.optional(types.model({
-            flagInclude: types.optional(types.number, 0),
-            flagExclude: types.optional(types.number, 1540),
-            readName: types.maybe(types.string),
-            tagFilter: types.maybe(types.model({ tag: types.string, value: types.string })),
-        }), {}),
+        filterBy: types.optional(FilterModel, {}),
     }))
         .volatile(() => ({
         colorTagMap: observable.map({}),
@@ -651,12 +647,31 @@ function stateModelFactory(configSchema) {
                     },
                     {
                         label: 'Set feature height',
-                        onClick: () => {
-                            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: () => {
+                                    getSession(self).queueDialog(doneCallback => [
+                                        SetFeatureHeightDlg,
+                                        { model: self, handleClose: doneCallback },
+                                    ]);
+                                },
+                            },
+                        ],
                     },
                     {
                         label: 'Set max height',

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package/esm/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/esm/LinearReadArcsDisplay/components/ReactComponent.js

@@ -0,0 +1,44 @@
+import React from 'react';
+import { isAlive } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { getContainingView } from '@jbrowse/core/util';
+import { LoadingEllipses } from '@jbrowse/core/ui';
+import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
+const useStyles = 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 = observer(function ({ model, }) {
+    const view = getContainingView(model);
+    return (React.createElement("canvas", { "data-testid": `Arc-display-${model.drawn}`, ref: ref => {
+            if (isAlive(model)) {
+                model.setRef(ref);
+            }
+        }, style: {
+            position: 'absolute',
+            left: -view.offsetPx + model.lastDrawnOffsetPx,
+            width: view.dynamicBlocks.totalWidthPx,
+            height: model.height,
+        }, width: view.dynamicBlocks.totalWidthPx * 2, height: model.height * 2 }));
+});
+export default observer(function ({ model, }) {
+    const view = getContainingView(model);
+    const { classes } = useStyles();
+    const err = model.error;
+    return err ? (React.createElement(BlockMsg, { message: `${err}`, severity: "error", buttonText: 'Reload', action: model.reload })) : model.loading ? (React.createElement("div", { className: classes.loading, style: {
+            width: view.dynamicBlocks.totalWidthPx,
+            height: 20,
+            position: 'absolute',
+            left: Math.max(0, -view.offsetPx),
+        } },
+        React.createElement(LoadingEllipses, { message: model.message }))) : (React.createElement(Arcs, { model: model }));
+});
+//# sourceMappingURL=ReactComponent.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearReadArcsDisplay/components/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EACL,QAAQ,GAET,MAAM,oCAAoC,CAAA;AAO3C,MAAM,SAAS,GAAG,UAAU,EAAE,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,QAAQ,CAAC,UAAU,EAC9B,KAAK,GAGN;IACC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAAQ,CAAA;IAC5C,OAAO,CACL,+CACe,eAAe,KAAK,CAAC,KAAK,EAAE,EACzC,GAAG,EAAE,GAAG,CAAC,EAAE;YACT,IAAI,OAAO,CAAC,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,eAAe,QAAQ,CAAC,UAAU,EAChC,KAAK,GAGN;IACC,MAAM,IAAI,GAAG,iBAAiB,CAAC,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,oBAAC,QAAQ,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,6BACE,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,oBAAC,eAAe,IAAC,OAAO,EAAE,KAAK,CAAC,OAAO,GAAI,CACvC,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CACvB,CAAA;AACH,CAAC,CAAC,CAAA"}

package/esm/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;

package/esm/LinearReadArcsDisplay/configSchema.js

@@ -0,0 +1,50 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
+import { types } from 'mobx-state-tree';
+/**
+ * #config LinearReadArcsDisplay
+ */
+function configSchemaF(pluginManager) {
+    return ConfigurationSchema('LinearReadArcsDisplay', {
+        /**
+         * #slot
+         */
+        maxFeatureScreenDensity: {
+            type: 'number',
+            description: 'maximum features per pixel that is displayed in the view',
+            defaultValue: 5,
+        },
+        /**
+         * #slot
+         */
+        lineWidth: {
+            type: 'number',
+            description: 'set arc line width',
+            defaultValue: 1,
+        },
+        /**
+         * #slot
+         */
+        colorScheme: {
+            type: 'stringEnum',
+            model: types.enumeration('colorScheme', [
+                'strand',
+                'normal',
+                'insertSize',
+                'insertSizeAndOrientation',
+                'mappingQuality',
+                'tag',
+            ]),
+            description: 'color scheme to use',
+            defaultValue: 'normal',
+        },
+    }, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),
+        explicitlyTyped: true,
+    });
+}
+export default configSchemaF;
+//# sourceMappingURL=configSchema.js.map

package/esm/LinearReadArcsDisplay/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAC1F,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,aAAa,CAAC,aAA4B;IACjD,OAAO,mBAAmB,CACxB,uBAAuB,EACvB;QACE;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,oBAAoB;YACjC,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,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,qCAAqC,CAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,eAAe,aAAa,CAAA"}

package/esm/LinearReadArcsDisplay/drawFeats.d.ts

@@ -0,0 +1,14 @@
+import { ChainData } from '../shared/fetchChains';
+export declare function hasPairedReads(features: ChainData): boolean;
+export default function drawFeats(self: {
+    setLastDrawnOffsetPx: (n: number) => void;
+    drawInter?: boolean;
+    drawLongRange?: boolean;
+    setError: (e: unknown) => void;
+    colorBy?: {
+        type: string;
+    };
+    height: number;
+    chainData?: ChainData;
+    lineWidthSetting: number;
+}, ctx: CanvasRenderingContext2D): Promise<void>;