@jbrowse/plugin-alignments 2.16.0 → 2.16.1

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -30,7 +30,7 @@ const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const clone_1 = __importDefault(require("clone"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 // locals
 const util_1 = require("./util");
 const tagInfo_1 = require("./tagInfo");
@@ -49,7 +49,7 @@ const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const SA = (0, util_1.getTag)('SA', feat);
     const { flags } = feat;
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { ...props, omit: omit, 
+        react_1.default.createElement(FeatureDetails_1.default, { ...props, omit: omit, 
             // @ts-expect-error
             descriptions: { ...tagInfo_1.tags, tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (react_1.default.createElement(PairLink_1.default, { model: model, locString: value })) : (react_1.default.createElement(Formatter_1.default, { value: value })) }),
         SA !== undefined ? (react_1.default.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,

package/dist/AlignmentsFeatureDetail/Flags.js

@@ -7,7 +7,7 @@ exports.default = AlignmentFlags;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
 const useStyles = (0, mui_1.makeStyles)()({
     compact: {
@@ -34,7 +34,7 @@ function AlignmentFlags(props) {
     const { classes } = useStyles();
     const { feature } = props;
     const { flags } = feature;
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Flags" },
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Flags" },
         react_1.default.createElement(SimpleField_1.default, { name: "Flag", value: flags }),
         react_1.default.createElement(material_1.FormGroup, null, flagNames.map((name, idx) => {
             const val = flags & (1 << idx);

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SuppAlignments;
 const react_1 = __importDefault(require("react"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const util_1 = require("@jbrowse/core/util");
 const LaunchPairedEndBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchPairedEndBreakpointSplitViewPanel"));
 function SuppAlignments(props) {
@@ -19,5 +19,5 @@ function SuppAlignments(props) {
     catch (e) {
         // ignore
     }
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" }, viewType ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" }, viewType ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignments;
 const react_1 = __importDefault(require("react"));
-const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const util_1 = require("@jbrowse/core/util");
+const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
 const LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
 function SupplementaryAlignments(props) {
@@ -20,7 +20,7 @@ function SupplementaryAlignments(props) {
     catch (e) {
         // ignore
     }
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" },
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" },
         react_1.default.createElement(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }),
         viewType ? (react_1.default.createElement(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
 }

package/dist/LinearPileupDisplay/model.d.ts

@@ -61,11 +61,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: React.
-            /**
+            reactElement: React.ReactElement /**
              * #action
-             */
-            ReactElement;
+             */;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -181,9 +179,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree" /**
-         * #action
-         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;

package/dist/LinearPileupDisplay/model.js

@@ -100,7 +100,7 @@ function stateModelFactory(configSchema) {
         updateModificationColorMap(uniqueModifications) {
             uniqueModifications.forEach(value => {
                 if (!self.modificationTagMap.has(value)) {
-                    self.modificationTagMap.set(value, util_2.modificationColors[value] || (0, util_2.randomColor)());
+                    self.modificationTagMap.set(value, util_2.modificationColors[value] || (0, util_2.randomColor)(value));
                 }
             });
         },

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -116,7 +116,7 @@ function stateModelFactory(pluginManager, configSchema) {
         updateModificationColorMap(uniqueModifications) {
             uniqueModifications.forEach(value => {
                 if (!self.modificationTagMap.has(value)) {
-                    self.modificationTagMap.set(value, util_2.modificationColors[value] || (0, util_3.randomColor)());
+                    self.modificationTagMap.set(value, util_2.modificationColors[value] || (0, util_3.randomColor)(value));
                 }
             });
         },

package/dist/MismatchParser/index.js

@@ -314,11 +314,17 @@ function getModificationPositions(mm, fseq, fstrand) {
                     }
                     i++;
                 } while (delta >= 0 && i < seq.length);
-                const temp = i - 1;
-                positions.push(fstrand === -1 ? seq.length - 1 - temp : temp);
-            }
-            if (fstrand === -1) {
-                positions.sort((a, b) => a - b);
+                if (fstrand === -1) {
+                    const pos = seq.length - i;
+                    if (pos >= 0) {
+                        // avoid negative-number-positions in array, seen in #4629 cause
+                        // unknown, could warrant some further investigation
+                        positions.unshift(pos);
+                    }
+                }
+                else {
+                    positions.push(i - 1);
+                }
             }
             result.push({
                 type,

package/dist/util.d.ts

@@ -23,5 +23,5 @@ type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;
 };
 export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
-export declare function randomColor(): string;
+export declare function randomColor(str: string): string;
 export {};

package/dist/util.js

@@ -113,6 +113,7 @@ exports.modificationColors = {
     g: 'rgb(255, 160, 86)',
     e: 'rgb(141, 221, 208)',
     b: 'rgb(202, 71, 47)',
+    a: 'hsl(136, 50%, 50%)',
 };
 function createAutorun(self, cb, opts) {
     (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
@@ -126,6 +127,10 @@ function createAutorun(self, cb, opts) {
         }
     }, opts));
 }
-function randomColor() {
-    return `hsl(${Math.random() * 200}, 50%, 50%)`;
+function randomColor(str) {
+    let sum = 0;
+    for (let i = 0; i < str.length; i++) {
+        sum += str.charCodeAt(i);
+    }
+    return `hsl(${sum * 10}, 20%, 50%)`;
 }

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -2,7 +2,7 @@ import React, { lazy } from 'react';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
 import clone from 'clone';
-import { FeatureDetails } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 // locals
 import { getTag } from './util';
 import { tags } from './tagInfo';

package/esm/AlignmentsFeatureDetail/Flags.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField';
 const useStyles = makeStyles()({
     compact: {

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -1,5 +1,5 @@
 import React from 'react';
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { getEnv, getSession } from '@jbrowse/core/util';
 import LaunchPairedEndBreakpointSplitViewPanel from './LaunchPairedEndBreakpointSplitViewPanel';
 export default function SuppAlignments(props) {

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -1,6 +1,6 @@
 import React from 'react';
-import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { getEnv, getSession } from '@jbrowse/core/util';
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import SupplementaryAlignmentsLocStrings from './SupplementaryAlignmentsLocStrings';
 import LaunchBreakpointSplitViewPanel from './LaunchSupplementaryAlignmentBreakpointSplitViewPanel';
 export default function SupplementaryAlignments(props) {

package/esm/LinearPileupDisplay/model.d.ts

@@ -61,11 +61,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: React.
-            /**
+            reactElement: React.ReactElement /**
              * #action
-             */
-            ReactElement;
+             */;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -181,9 +179,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree" /**
-         * #action
-         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;

package/esm/LinearPileupDisplay/model.js

@@ -72,7 +72,7 @@ function stateModelFactory(configSchema) {
         updateModificationColorMap(uniqueModifications) {
             uniqueModifications.forEach(value => {
                 if (!self.modificationTagMap.has(value)) {
-                    self.modificationTagMap.set(value, modificationColors[value] || randomColor());
+                    self.modificationTagMap.set(value, modificationColors[value] || randomColor(value));
                 }
             });
         },

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -88,7 +88,7 @@ function stateModelFactory(pluginManager, configSchema) {
         updateModificationColorMap(uniqueModifications) {
             uniqueModifications.forEach(value => {
                 if (!self.modificationTagMap.has(value)) {
-                    self.modificationTagMap.set(value, modificationColors[value] || randomColor());
+                    self.modificationTagMap.set(value, modificationColors[value] || randomColor(value));
                 }
             });
         },

package/esm/MismatchParser/index.js

@@ -295,11 +295,17 @@ export function getModificationPositions(mm, fseq, fstrand) {
                     }
                     i++;
                 } while (delta >= 0 && i < seq.length);
-                const temp = i - 1;
-                positions.push(fstrand === -1 ? seq.length - 1 - temp : temp);
-            }
-            if (fstrand === -1) {
-                positions.sort((a, b) => a - b);
+                if (fstrand === -1) {
+                    const pos = seq.length - i;
+                    if (pos >= 0) {
+                        // avoid negative-number-positions in array, seen in #4629 cause
+                        // unknown, could warrant some further investigation
+                        positions.unshift(pos);
+                    }
+                }
+                else {
+                    positions.push(i - 1);
+                }
             }
             result.push({
                 type,

package/esm/util.d.ts

@@ -23,5 +23,5 @@ type DisplayModel = IAnyStateTreeNode & {
     setError: (arg: unknown) => void;
 };
 export declare function createAutorun(self: DisplayModel, cb: () => Promise<void>, opts?: IAutorunOptions): void;
-export declare function randomColor(): string;
+export declare function randomColor(str: string): string;
 export {};

package/esm/util.js

@@ -103,6 +103,7 @@ export const modificationColors = {
     g: 'rgb(255, 160, 86)',
     e: 'rgb(141, 221, 208)',
     b: 'rgb(202, 71, 47)',
+    a: 'hsl(136, 50%, 50%)',
 };
 export function createAutorun(self, cb, opts) {
     addDisposer(self, autorun(async () => {
@@ -116,6 +117,10 @@ export function createAutorun(self, cb, opts) {
         }
     }, opts));
 }
-export function randomColor() {
-    return `hsl(${Math.random() * 200}, 50%, 50%)`;
+export function randomColor(str) {
+    let sum = 0;
+    for (let i = 0; i < str.length; i++) {
+        sum += str.charCodeAt(i);
+    }
+    return `hsl(${sum * 10}, 20%, 50%)`;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.16.0",
+  "version": "2.16.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
   "dependencies": {
     "@gmod/bam": "^2.0.0",
     "@gmod/cram": "^3.0.3",
-    "@jbrowse/sv-core": "^2.16.0",
+    "@jbrowse/sv-core": "^2.16.1",
     "@mui/icons-material": "^6.0.0",
     "canvas2svg": "^1.0.16",
     "clone": "^2.1.2",
@@ -64,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
+  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
 }