@jbrowse/plugin-alignments 3.5.0 → 3.5.1

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,5 +1,4 @@
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import type { ColorBy, FilterBy } from '../shared/types';
 import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
@@ -192,6 +191,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -234,12 +234,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature): void;
     selectFeature(feature: Feature): void;
-    copyFeatureToClipboard(feature: Feature): void;
     setConfig(conf: AnyConfigurationModel): void;
     setFilterBy(filter: FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -259,17 +259,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly filters: SerializableFilterChain;
 } & {
     readonly rendererTypeName: string;
-    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;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: import("../shared/types").SortedBy;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -40,11 +40,11 @@ exports.SharedLinearPileupDisplayMixin = SharedLinearPileupDisplayMixin;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-const Icons_1 = require("@jbrowse/core/ui/Icons");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
+const ContentCopy_1 = __importDefault(require("@mui/icons-material/ContentCopy"));
 const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const mobx_1 = require("mobx");
@@ -154,12 +154,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
             }
             session.setSelection(feature);
         },
-        copyFeatureToClipboard(feature) {
-            const { uniqueId, ...rest } = feature.toJSON();
-            const session = (0, util_1.getSession)(self);
-            (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
-            session.notify('Copied to clipboard', 'success');
-        },
         setConfig(conf) {
             self.configuration = conf;
         },
@@ -176,6 +170,12 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         },
     }))
         .views(self => ({
+        copyFeatureToClipboard(feature) {
+            const { uniqueId, ...rest } = feature.toJSON();
+            const session = (0, util_1.getSession)(self);
+            (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
+            session.notify('Copied to clipboard', 'success');
+        },
         get rendererConfig() {
             const { featureHeight: height, noSpacing, hideSmallIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
             const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
@@ -230,7 +230,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                         },
                         {
                             label: 'Copy info to clipboard',
-                            icon: Icons_1.ContentCopy,
+                            icon: ContentCopy_1.default,
                             onClick: () => {
                                 self.copyFeatureToClipboard(feat);
                             },

package/dist/LinearPileupDisplay/model.d.ts

@@ -196,6 +196,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -238,12 +239,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("../shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -263,17 +264,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {
     readonly rendererTypeName: string;
-    contextMenuItems(): ({
+    contextMenuItems(): {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-    } | {
-        label: string;
-        icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
-        onClick: () => void;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: SortedBy;

package/dist/MismatchParser/index.d.ts

@@ -1,6 +1,6 @@
 import type { Mismatch } from '../shared/types';
 import type { Feature } from '@jbrowse/core/util';
-export declare function parseCigar(cigar?: string): string[];
+export declare function parseCigar(s?: string): string[];
 export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];
 export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
 export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];

package/dist/MismatchParser/index.js

@@ -13,11 +13,26 @@ exports.getTag = getTag;
 exports.featurizeSA = featurizeSA;
 const cigarToMismatches_1 = require("./cigarToMismatches");
 const mdToMismatches_1 = require("./mdToMismatches");
-const cigarRegex = new RegExp(/([MIDNSHPX=])/);
 const startClip = new RegExp(/(\d+)[SH]$/);
 const endClip = new RegExp(/^(\d+)([SH])/);
-function parseCigar(cigar = '') {
-    return cigar.split(cigarRegex).slice(0, -1);
+function parseCigar(s = '') {
+    let currLen = '';
+    let len;
+    let op;
+    const ret = [];
+    for (let i = 0, l = s.length; i < l; i++) {
+        const c = s[i];
+        if (c >= '0' && c <= '9') {
+            currLen = currLen + c;
+        }
+        else {
+            len = currLen;
+            op = c;
+            currLen = '';
+            ret.push(len, op);
+        }
+    }
+    return ret;
 }
 function getMismatches(cigar, md, seq, ref, qual) {
     let mismatches = [];

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,5 +1,4 @@
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import type { ColorBy, FilterBy } from '../shared/types';
 import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
@@ -192,6 +191,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -234,12 +234,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature): void;
     selectFeature(feature: Feature): void;
-    copyFeatureToClipboard(feature: Feature): void;
     setConfig(conf: AnyConfigurationModel): void;
     setFilterBy(filter: FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -259,17 +259,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly filters: SerializableFilterChain;
 } & {
     readonly rendererTypeName: string;
-    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;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: import("../shared/types").SortedBy;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -1,11 +1,11 @@
 import { lazy } from 'react';
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import { SimpleFeature, getContainingTrack, getContainingView, getEnv, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
 import FilterListIcon from '@mui/icons-material/ClearAll';
+import ContentCopyIcon from '@mui/icons-material/ContentCopy';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import copy from 'copy-to-clipboard';
 import { autorun, observable } from 'mobx';
@@ -115,12 +115,6 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
             }
             session.setSelection(feature);
         },
-        copyFeatureToClipboard(feature) {
-            const { uniqueId, ...rest } = feature.toJSON();
-            const session = getSession(self);
-            copy(JSON.stringify(rest, null, 4));
-            session.notify('Copied to clipboard', 'success');
-        },
         setConfig(conf) {
             self.configuration = conf;
         },
@@ -137,6 +131,12 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
         },
     }))
         .views(self => ({
+        copyFeatureToClipboard(feature) {
+            const { uniqueId, ...rest } = feature.toJSON();
+            const session = getSession(self);
+            copy(JSON.stringify(rest, null, 4));
+            session.notify('Copied to clipboard', 'success');
+        },
         get rendererConfig() {
             const { featureHeight: height, noSpacing, hideSmallIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
             const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};

package/esm/LinearPileupDisplay/model.d.ts

@@ -196,6 +196,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -238,12 +239,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("../shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -263,17 +264,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {
     readonly rendererTypeName: string;
-    contextMenuItems(): ({
+    contextMenuItems(): {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-    } | {
-        label: string;
-        icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
-        onClick: () => void;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: SortedBy;

package/esm/MismatchParser/index.d.ts

@@ -1,6 +1,6 @@
 import type { Mismatch } from '../shared/types';
 import type { Feature } from '@jbrowse/core/util';
-export declare function parseCigar(cigar?: string): string[];
+export declare function parseCigar(s?: string): string[];
 export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];
 export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
 export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];

package/esm/MismatchParser/index.js

@@ -1,10 +1,25 @@
 import { cigarToMismatches } from './cigarToMismatches';
 import { mdToMismatches } from './mdToMismatches';
-const cigarRegex = new RegExp(/([MIDNSHPX=])/);
 const startClip = new RegExp(/(\d+)[SH]$/);
 const endClip = new RegExp(/^(\d+)([SH])/);
-export function parseCigar(cigar = '') {
-    return cigar.split(cigarRegex).slice(0, -1);
+export function parseCigar(s = '') {
+    let currLen = '';
+    let len;
+    let op;
+    const ret = [];
+    for (let i = 0, l = s.length; i < l; i++) {
+        const c = s[i];
+        if (c >= '0' && c <= '9') {
+            currLen = currLen + c;
+        }
+        else {
+            len = currLen;
+            op = c;
+            currLen = '';
+            ret.push(len, op);
+        }
+    }
+    return ret;
 }
 export function getMismatches(cigar, md, seq, ref, qual) {
     let mismatches = [];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.5.0",
+  "version": "3.5.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,10 +38,10 @@
   "dependencies": {
     "@gmod/bam": "^6.0.1",
     "@gmod/cram": "^5.0.4",
-    "@jbrowse/core": "^3.5.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.5.0",
-    "@jbrowse/plugin-wiggle": "^3.5.0",
-    "@jbrowse/sv-core": "^3.5.0",
+    "@jbrowse/core": "^3.5.1",
+    "@jbrowse/plugin-linear-genome-view": "^3.5.1",
+    "@jbrowse/plugin-wiggle": "^3.5.1",
+    "@jbrowse/sv-core": "^3.5.1",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "canvas2svg": "^1.0.16",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
+  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
 }