@jbrowse/plugin-alignments 2.14.0 → 2.15.0

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -181,9 +181,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree" /**
-             * #property
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            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>>;
         }, {
@@ -345,7 +343,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree" /**
+         * #stateModel SharedLinearPileupDisplayMixin
+         * #category display
+         * extends `BaseLinearDisplay`
+         */).IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -182,7 +182,11 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', { featureData: feature.toJSON(), view: (0, util_1.getContainingView)(self) });
+                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', {
+                    featureData: feature.toJSON(),
+                    view: (0, util_1.getContainingView)(self),
+                    track: (0, util_1.getContainingTrack)(self),
+                });
                 session.showWidget(featureWidget);
             }
             session.setSelection(feature);

package/dist/LinearPileupDisplay/components/SetMaxHeightDialog.js

@@ -38,10 +38,10 @@ const SetMaxHeightDialog = (0, mobx_react_1.observer)(function (props) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = (0, react_1.useState)(`${maxHeight}`);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         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 => {
+            react_1.default.createElement(material_1.TextField, { value: max, autoFocus: true, onChange: event => {
                     setMax(event.target.value);
                 }, placeholder: "Enter max height for layout" }),
             react_1.default.createElement(material_1.DialogActions, null,

package/dist/MismatchParser/index.js

@@ -80,7 +80,7 @@ function cigarToMismatches(ops, seq, ref, qual) {
         }
         else if (op === 'X') {
             const r = (seq === null || seq === void 0 ? void 0 : seq.slice(soffset, soffset + len)) || [];
-            const q = (qual === null || qual === void 0 ? void 0 : qual.slice(soffset, soffset + len)) || [];
+            const q = (qual === null || qual === void 0 ? void 0 : qual.subarray(soffset, soffset + len)) || [];
             for (let j = 0; j < len; j++) {
                 mismatches.push({
                     start: roffset + j,

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -181,9 +181,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree" /**
-             * #property
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            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>>;
         }, {
@@ -345,7 +343,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree" /**
+         * #stateModel SharedLinearPileupDisplayMixin
+         * #category display
+         * extends `BaseLinearDisplay`
+         */).IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -5,7 +5,7 @@ import copy from 'copy-to-clipboard';
 import { ConfigurationReference, readConfObject, getConf, } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { getEnv, getSession, isSessionModelWithWidgets, getContainingView, SimpleFeature, } from '@jbrowse/core/util';
+import { getEnv, getSession, isSessionModelWithWidgets, getContainingView, SimpleFeature, getContainingTrack, } from '@jbrowse/core/util';
 import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
 // icons
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
@@ -153,7 +153,11 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
         selectFeature(feature) {
             const session = getSession(self);
             if (isSessionModelWithWidgets(session)) {
-                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', { featureData: feature.toJSON(), view: getContainingView(self) });
+                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', {
+                    featureData: feature.toJSON(),
+                    view: getContainingView(self),
+                    track: getContainingTrack(self),
+                });
                 session.showWidget(featureWidget);
             }
             session.setSelection(feature);

package/esm/LinearPileupDisplay/components/SetMaxHeightDialog.js

@@ -13,10 +13,10 @@ const SetMaxHeightDialog = observer(function (props) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = useState(`${maxHeight}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Filter options" },
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         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 => {
+            React.createElement(TextField, { value: max, autoFocus: true, onChange: event => {
                     setMax(event.target.value);
                 }, placeholder: "Enter max height for layout" }),
             React.createElement(DialogActions, null,

package/esm/MismatchParser/index.js

@@ -61,7 +61,7 @@ export function cigarToMismatches(ops, seq, ref, qual) {
         }
         else if (op === 'X') {
             const r = (seq === null || seq === void 0 ? void 0 : seq.slice(soffset, soffset + len)) || [];
-            const q = (qual === null || qual === void 0 ? void 0 : qual.slice(soffset, soffset + len)) || [];
+            const q = (qual === null || qual === void 0 ? void 0 : qual.subarray(soffset, soffset + len)) || [];
             for (let j = 0; j < len; j++) {
                 mismatches.push({
                     start: roffset + j,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.14.0",
+  "version": "2.15.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
   "dependencies": {
     "@gmod/bam": "^2.0.0",
     "@gmod/cram": "^3.0.3",
-    "@mui/icons-material": "^5.0.1",
+    "@mui/icons-material": "^6.0.0",
     "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
     "copy-to-clipboard": "^3.3.1",
@@ -49,7 +49,7 @@
     "@jbrowse/core": "^2.0.0",
     "@jbrowse/plugin-linear-genome-view": "^2.0.0",
     "@jbrowse/plugin-wiggle": "^2.0.0",
-    "@mui/material": "^5.0.0",
+    "@mui/material": "^6.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
+  "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
 }