@jbrowse/plugin-alignments 2.5.0 → 2.6.0

package/dist/LinearPileupDisplay/components/ColorByModifications.js

@@ -7,27 +7,7 @@ const react_1 = __importDefault(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 useStyles = (0, mui_1.makeStyles)()(theme => ({
-    table: {
-        border: '1px solid #888',
-        margin: theme.spacing(4),
-        '& td': {
-            padding: theme.spacing(1),
-        },
-    },
-}));
-function ModificationTable({ modifications, }) {
-    const { classes } = useStyles();
-    return (react_1.default.createElement("table", { className: classes.table },
-        react_1.default.createElement("tbody", null, modifications.map(([key, value]) => (react_1.default.createElement("tr", { key: key },
-            react_1.default.createElement("td", null, key),
-            react_1.default.createElement("td", null, value),
-            react_1.default.createElement("td", { style: {
-                    width: '1em',
-                    background: value,
-                } })))))));
-}
+const ModificationsTable_1 = __importDefault(require("./ModificationsTable"));
 function ColorByTagDlg(props) {
     const { model, handleClose } = props;
     const { colorBy, modificationTagMap } = model;
@@ -39,10 +19,10 @@ function ColorByTagDlg(props) {
             react_1.default.createElement("div", { style: { margin: 20 } },
                 (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? (react_1.default.createElement("div", null, modifications.length ? (react_1.default.createElement(react_1.default.Fragment, null,
                     "Current modification-type-to-color mapping",
-                    react_1.default.createElement(ModificationTable, { modifications: [...modificationTagMap.entries()] }))) : (react_1.default.createElement("div", null,
+                    react_1.default.createElement(ModificationsTable_1.default, { modifications: [...modificationTagMap.entries()] }))) : (react_1.default.createElement(react_1.default.Fragment, null,
                     react_1.default.createElement(material_1.Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."),
                     react_1.default.createElement(material_1.CircularProgress, { size: 15 }))))) : null,
-                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? (react_1.default.createElement(ModificationTable, { modifications: [
+                (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? (react_1.default.createElement(ModificationsTable_1.default, { modifications: [
                         ['methylated', 'red'],
                         ['unmethylated', 'blue'],
                     ] })) : null),

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

@@ -1 +1 @@
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+{"version":3,"file":"ColorByModifications.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ColorByModifications.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,4CAMsB;AACtB,yCAAyC;AACzC,8EAAoD;AAEpD,SAAS,aAAa,CAAC,KAOtB;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAE7C,MAAM,aAAa,GAAG,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,CAAA;IAEvD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,wBAAwB;QAC/D,8BAAC,wBAAa;YACZ,8BAAC,qBAAU,oRAKE;YACb,8BAAC,qBAAU,yIAGE;YACb,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE;gBACvB,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,CAAC,CAAC,CAAC,CACnC,2CACG,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CACtB;;oBAEE,8BAAC,4BAAiB,IAChB,aAAa,EAAE,CAAC,GAAG,kBAAkB,CAAC,OAAO,EAAE,CAAC,GAChD,CACD,CACJ,CAAC,CAAC,CAAC,CACF;oBACE,8BAAC,qBAAU,4FAGE;oBACb,8BAAC,2BAAgB,IAAC,IAAI,EAAE,EAAE,GAAI,CAC7B,CACJ,CACG,CACP,CAAC,CAAC,CAAC,IAAI;gBACP,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,CAAC,CAAC,CAAC,CACjC,8BAAC,4BAAiB,IAChB,aAAa,EAAE;wBACb,CAAC,YAAY,EAAE,KAAK,CAAC;wBACrB,CAAC,cAAc,EAAE,MAAM,CAAC;qBACzB,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ;YACN,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,CAAA;wBAC/C,WAAW,EAAE,CAAA;oBACf,CAAC,oBAGM;gBACT,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC,CAAA;wBAC7C,WAAW,EAAE,CAAA;oBACf,CAAC,kBAGM;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,aAAa,CAAC,CAAA"}

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

@@ -1,8 +1,9 @@
+import React from 'react';
 declare function ColorByTagDlg(props: {
     model: {
         setColorScheme: Function;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof ColorByTagDlg;
 export default _default;

package/dist/LinearPileupDisplay/components/ColorByTag.js

@@ -37,14 +37,10 @@ function ColorByTagDlg(props) {
             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."),
             react_1.default.createElement(material_1.TextField, { value: tag, onChange: event => setTag(event.target.value), placeholder: "Enter tag name", inputProps: {
                     maxLength: 2,
-                    'data-testid': 'color-tag-name-input',
-                }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", "data-testid": "color-tag-name" }),
+                }, error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off" }),
             react_1.default.createElement(material_1.DialogActions, null,
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
-                        model.setColorScheme({
-                            type: 'tag',
-                            tag,
-                        });
+                        model.setColorScheme({ type: 'tag', tag });
                         handleClose();
                     }, disabled: !validTag }, "Submit"),
                 react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel")))));

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

@@ -1 +1 @@
-{"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"}
+{"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;iBACb,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,GAClB;YACF,8BAAC,wBAAa;gBACZ,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,CAAC,CAAA;wBAC1C,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/LinearPileupDisplayBlurb.d.ts

@@ -1,12 +1,13 @@
+import React from 'react';
 export interface LinearPileupDisplayBlurbProps {
     model: {
         sortedBy?: {
             pos: number;
             refName: number;
             type: string;
+            tag?: string;
         };
     };
 }
-declare function LinearPileupDisplayBlurb(props: LinearPileupDisplayBlurbProps): JSX.Element | null;
-declare const _default: typeof LinearPileupDisplayBlurb;
+declare const _default: (props: LinearPileupDisplayBlurbProps) => React.JSX.Element | null;
 export default _default;

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js

@@ -6,13 +6,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-function LinearPileupDisplayBlurb(props) {
+exports.default = (0, mobx_react_1.observer)(function LinearPileupDisplayBlurb(props) {
+    var _a;
     const { model } = props;
     const { sortedBy } = model;
-    return sortedBy ? (react_1.default.createElement("div", { "data-testid": `blurb-${model.sortedBy}`, style: { backgroundColor: 'white' } },
-        react_1.default.createElement(material_1.Typography, { color: "secondary", variant: "caption" }, model.sortedBy
-            ? `Sorted by ${sortedBy.type.toLowerCase()} at ${sortedBy.refName}:${sortedBy.pos}`
+    return sortedBy ? (react_1.default.createElement("div", { "data-testid": `blurb-${sortedBy}` },
+        react_1.default.createElement(material_1.Typography, { color: "secondary", variant: "caption" }, sortedBy
+            ? `Sorted by ${(_a = sortedBy.tag) !== null && _a !== void 0 ? _a : sortedBy.type} at ${sortedBy.refName}:${sortedBy.pos}`
             : null))) : null;
-}
-exports.default = (0, mobx_react_1.observer)(LinearPileupDisplayBlurb);
+});
 //# sourceMappingURL=LinearPileupDisplayBlurb.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA0C;AAY1C,SAAS,wBAAwB,CAAC,KAAoC;IACpE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,sDACe,SAAS,KAAK,CAAC,QAAQ,EAAE,EACtC,KAAK,EAAE,EAAE,eAAe,EAAE,OAAO,EAAE;QAEnC,8BAAC,qBAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,KAAK,CAAC,QAAQ;YACb,CAAC,CAAC,aAAa,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,QAAQ,CAAC,OAAO,IAC7D,QAAQ,CAAC,GACX,EAAE;YACJ,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,wBAAwB,CAAC,CAAA"}
+{"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA0C;AAa1C,kBAAe,IAAA,qBAAQ,EAAC,SAAS,wBAAwB,CACvD,KAAoC;;IAEpC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,sDAAkB,SAAS,QAAQ,EAAE;QACnC,8BAAC,qBAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,QAAQ;YACP,CAAC,CAAC,aAAa,MAAA,QAAQ,CAAC,GAAG,mCAAI,QAAQ,CAAC,IAAI,OACxC,QAAQ,CAAC,OACX,IAAI,QAAQ,CAAC,GAAG,EAAE;YACpB,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA"}

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

@@ -0,0 +1,4 @@
+import React from 'react';
+export default function ModificationTable({ modifications, }: {
+    modifications: [string, string | undefined][];
+}): React.JSX.Element;

package/dist/LinearPileupDisplay/components/ModificationsTable.js

@@ -0,0 +1,29 @@
+"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 mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    table: {
+        border: '1px solid #888',
+        margin: theme.spacing(4),
+        '& td': {
+            padding: theme.spacing(1),
+        },
+    },
+}));
+function ModificationTable({ modifications, }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement("table", { className: classes.table },
+        react_1.default.createElement("tbody", null, modifications.map(([key, value]) => (react_1.default.createElement("tr", { key: key },
+            react_1.default.createElement("td", null, key),
+            react_1.default.createElement("td", null, value),
+            react_1.default.createElement("td", { style: {
+                    width: '1em',
+                    background: value,
+                } })))))));
+}
+exports.default = ModificationTable;
+//# sourceMappingURL=ModificationsTable.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ModificationsTable.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/ModificationsTable.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,uCAA0C;AAE1C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,MAAM,EAAE,gBAAgB;QACxB,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACxB,MAAM,EAAE;YACN,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;SAC1B;KACF;CACF,CAAC,CAAC,CAAA;AAEH,SAAwB,iBAAiB,CAAC,EACxC,aAAa,GAGd;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,yCAAO,SAAS,EAAE,OAAO,CAAC,KAAK;QAC7B,6CACG,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACnC,sCAAI,GAAG,EAAE,GAAG;YACV,0CAAK,GAAG,CAAM;YACd,0CAAK,KAAK,CAAM;YAChB,sCACE,KAAK,EAAE;oBACL,KAAK,EAAE,KAAK;oBACZ,UAAU,EAAE,KAAK;iBAClB,GACD,CACC,CACN,CAAC,CACI,CACF,CACT,CAAA;AACH,CAAC;AAxBD,oCAwBC"}

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

@@ -1,3 +1,4 @@
+import React from 'react';
 declare function SetFeatureHeightDlg(props: {
     model: {
         setFeatureHeight: (arg?: number) => void;
@@ -6,6 +7,6 @@ declare function SetFeatureHeightDlg(props: {
         noSpacing?: boolean;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof SetFeatureHeightDlg;
 export default _default;

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

@@ -1,9 +1,10 @@
+import React from 'react';
 declare function SetMaxHeightDlg(props: {
     model: {
         maxHeight?: number;
         setMaxHeight: Function;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof SetMaxHeightDlg;
 export default _default;

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

@@ -1,8 +1,9 @@
+import React from 'react';
 declare function SortByTagDlg(props: {
     model: {
         setSortedBy: Function;
     };
     handleClose: () => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof SortByTagDlg;
 export default _default;

package/dist/LinearPileupDisplay/model.d.ts

@@ -14,6 +14,7 @@ export interface Filter {
 }
 /**
  * #stateModel LinearPileupDisplay
+ * #category display
  * extends `BaseLinearDisplay`
  */
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
@@ -22,6 +23,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -34,23 +39,25 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-        /**
-         * #stateModel LinearPileupDisplay
-         * extends `BaseLinearDisplay`
-         */
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined; /**
+         * #property
+         */
         features: Map<string, Feature> | undefined;
         layout: any;
-        status: string;
+        status: string; /**
+         * #property
+         */
         error: unknown;
         message: string | undefined;
-        maxHeightReached: boolean;
+        maxHeightReached: boolean; /**
+         * #property
+         */
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
@@ -60,24 +67,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void; /**
-         * #property
-         */
+        setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
-            renderProps: any; /**
-             * #property
-             */
+            renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
@@ -133,19 +134,20 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     rendererTypeName: string;
-    error: unknown;
+    error: unknown; /**
+     * #action
+     */
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
             id: string;
-            /**
-             * #action
-             */
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<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>;
@@ -153,7 +155,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        /**
+         * #action
+         */
         onHorizontalScroll?: Function | undefined;
         blockState?: Record<string, any> | undefined;
     }>;
@@ -163,10 +169,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             type: string;
             rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string;
-            error: unknown; /**
+            rendererTypeName: string; /**
              * #action
              */
+            error: unknown;
+            message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<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>;
@@ -174,6 +181,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -183,21 +191,52 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    currBpPerPx: number;
     scrollTop: number;
-    message: string;
-    featureIdUnderMouse: string | undefined;
-    contextMenuFeature: Feature | undefined;
+} & {
+    readonly height: number;
+} & {
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number; /**
+     * #action
+     * uses copy-to-clipboard and generates notification
+     */
+} & {
     featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
     featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    currStatsBpPerPx: number;
+} & {
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    afterAttach(): void;
+} & {
+    setCurrStatsBpPerPx(n: number): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+} & {
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: Feature | undefined;
 } & {
-    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -211,63 +250,45 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly featureDensityStatsReady: boolean;
-    readonly maxAllowableBytes: number;
-} & {
-    setMessage(message: string): void;
 } & {
-    afterAttach(): void;
-    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void;
-    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
-    clearFeatureDensityStats(): void;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-    setScrollTop(scrollTop: number): void;
-    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
-    reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string; /**
-     * #action
-     * uses copy-to-clipboard and generates notification
-     */
 } & {
     reload(): Promise<void>;
 } & {
-    afterAttach(): void;
-} & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
     modificationTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: Feature | undefined;
     currSortBpPerPx: number;
-    ready: boolean;
+    modificationsReady: boolean;
+    sortReady: boolean;
+    tagsReady: boolean;
+} & {
+    readonly autorunReady: boolean;
 } & {
     /**
      * #action
      */
-    setReady(flag: boolean): void;
+    setModificationsReady(flag: boolean): void;
+    /**
+     * #action
+     */
+    setTagsReady(flag: boolean): void;
+    /**
+     * #action
+     */
+    setSortReady(flag: boolean): void;
     /**
      * #action
      */
@@ -303,8 +324,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #action
      */
     setFeatureUnderMouse(feat?: Feature): void;
-} & {
-    afterAttach(): void;
     /**
      * #action
      */
@@ -366,6 +385,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #getter
      */
     readonly featureUnderMouse: Feature | undefined;
+    /**
+     * #getter
+     */
+    readonly renderReady: boolean;
 } & {
     /**
      * #getter
@@ -388,7 +411,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     /**
      * #getter
      */
-    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => JSX.Element | null;
+    readonly DisplayBlurb: (props: import("./components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
+    /**
+     * #method
+     */
+    renderPropsPre(): any;
     /**
      * #method
      */
@@ -451,6 +478,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         disabled?: undefined;
         subMenu?: undefined;
     })[];
+} & {
+    afterAttach(): void;
 }, {
     type: string;
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -459,6 +488,10 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -482,9 +515,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         layout: any;
         status: string;
         error: unknown;
-        message: string | undefined; /**
-         * #getter
-         */
+        message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
@@ -500,17 +531,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, Feature>;
             layout: any;
-            maxHeightReached: boolean; /**
-             * #method
-             */
+            maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
@@ -519,16 +546,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         };
         fetchSizeLimit: {
             type: string;
-            defaultValue: number; /**
-             * #getter
-             */
+            defaultValue: number;
             description: string;
         };
         height: {
             type: string;
-            defaultValue: number; /**
-             * #method
-             */
+            defaultValue: number;
             description: string;
         };
         mouseover: {