@teselagen/sequence-utils 0.3.38-beta.3 → 0.3.41

package/insertGapsIntoRefSeq.d.ts

@@ -1,2 +1 @@
-import { SeqRead } from './getAllInsertionsInSeqReads';
-export default function insertGapsIntoRefSeq(refSeq: string, seqReads: SeqRead[]): string;
+export default function insertGapsIntoRefSeq(refSeq: any, seqReads: any): any;

package/insertSequenceDataAtPositionOrRange.d.ts

@@ -1,10 +1 @@
-import { Range } from '../../range-utils/src/index.ts';
-import { SequenceData } from './types';
-interface InsertSequenceDataOptions {
-    maintainOriginSplit?: boolean;
-    doNotRemoveInvalidChars?: boolean;
-    topLevelSeqData?: SequenceData;
-    [key: string]: unknown;
-}
-export default function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert: SequenceData, _existingSequenceData: SequenceData, caretPositionOrRange: number | Range, options?: InsertSequenceDataOptions): SequenceData;
-export {};
+export default function insertSequenceDataAtPositionOrRange(_sequenceDataToInsert: any, _existingSequenceData: any, caretPositionOrRange: any, options?: {}): any;

package/isEnzymeType2S.d.ts

@@ -1,2 +1 @@
-import { RestrictionEnzyme } from './types';
-export default function isEnzymeType2S(e: RestrictionEnzyme): boolean;
+export default function isEnzymeType2S(e: any): boolean;

package/mapAnnotationsToRows.d.ts

@@ -1,9 +1 @@
-import { Annotation } from './types';
-export interface MappedAnnotation extends Annotation {
-    yOffset?: number;
-    enclosingRangeType?: "beginning" | "end" | "beginningAndEnd";
-    annotation?: Annotation;
-}
-export default function mapAnnotationsToRows(annotations: Annotation[], sequenceLength: number, bpsPerRow: number, { splitForwardReverse }?: {
-    splitForwardReverse?: boolean;
-}): Record<string | number, MappedAnnotation[]>;
+export default function mapAnnotationsToRows(annotations: any, sequenceLength: any, bpsPerRow: any, { splitForwardReverse }?: {}): {};

package/package.json

@@ -1,23 +1,20 @@
 {
   "name": "@teselagen/sequence-utils",
-  "version": "0.3.38-beta.3",
+  "version": "0.3.41",
+  "repository": "https://github.com/TeselaGen/tg-oss",
   "type": "module",
   "dependencies": {
-    "@teselagen/range-utils": "0.3.14-beta.3",
     "escape-string-regexp": "5.0.0",
     "jsondiffpatch": "0.7.3",
+    "string-splice": "^1.3.0",
     "lodash-es": "^4.17.21",
-    "shortid": "2.2.16"
+    "shortid": "2.2.16",
+    "@teselagen/range-utils": "0.3.18"
   },
   "exports": {
     ".": {
-      "import": "./src/index.ts",
-      "require": "./src/index.ts"
+      "import": "./index.js",
+      "require": "./index.cjs"
     }
-  },
-  "devDependencies": {
-    "@types/lodash-es": "^4.17.12",
-    "@types/shortid": "^2.2.0"
-  },
-  "license": "MIT"
-}
+  }
+}

package/prepareCircularViewData.d.ts

@@ -1,2 +1 @@
-import { SequenceData } from './types';
-export default function prepareCircularViewData(sequenceData: SequenceData): SequenceData;
+export default function prepareCircularViewData(sequenceData: any): any;

package/prepareRowData.d.ts

@@ -1,10 +1,6 @@
-import { MappedAnnotation } from './mapAnnotationsToRows';
-import { SequenceData } from './types';
-export interface RowData {
+export default function prepareRowData(sequenceData: any, bpsPerRow: any): {
     rowNumber: number;
     start: number;
     end: number;
-    sequence: string;
-    [key: string]: MappedAnnotation[] | number | string;
-}
-export default function prepareRowData(sequenceData: SequenceData, bpsPerRow: number): RowData[];
+    sequence: any;
+}[];

package/proteinAlphabet.d.ts

@@ -1,3 +1,4 @@
+export default proteinAlphabet;
 declare const proteinAlphabet: {
     A: {
         value: string;
@@ -260,4 +261,3 @@ declare const proteinAlphabet: {
         mass: number;
     };
 };
-export default proteinAlphabet;

package/rotateBpsToPosition.d.ts

@@ -1 +1 @@
-export default function rotateBpsToPosition(bps: string, caretPosition: number): string;
+export default function rotateBpsToPosition(bps: any, caretPosition: any): any;

package/rotateSequenceDataToPosition.d.ts

@@ -1,3 +1 @@
-import { TidyUpSequenceDataOptions } from './tidyUpSequenceData';
-import { SequenceData } from './types';
-export default function rotateSequenceDataToPosition(sequenceData: SequenceData, caretPosition: number, options?: TidyUpSequenceDataOptions): SequenceData;
+export default function rotateSequenceDataToPosition(sequenceData: any, caretPosition: any, options: any): any;

package/shiftAnnotationsByLen.d.ts

@@ -1,6 +1,5 @@
-import { SequenceData } from './types';
 export default function shiftAnnotationsByLen({ seqData, caretPosition, insertLength }: {
-    seqData: SequenceData;
-    caretPosition: number;
-    insertLength: number;
+    seqData: any;
+    caretPosition: any;
+    insertLength: any;
 }): void;

package/src/autoAnnotate.test.js

@@ -1,3 +1,4 @@
+/* eslint-disable no-unused-expressions */
 import {
   autoAnnotate,
   convertApELikeRegexToRegex,

package/src/getSequenceDataBetweenRange.js

@@ -1,5 +1,5 @@
 import { flatMap, extend, forEach, startCase } from "lodash-es";
-import { getRangeLength } from "@teselagen/range-utils";
+import { getRangeLength, isRangeWithinRange } from "@teselagen/range-utils";
 import convertDnaCaretPositionOrRangeToAa from "./convertDnaCaretPositionOrRangeToAA";
 import insertSequenceDataAtPosition from "./insertSequenceDataAtPosition";
 import {
@@ -112,7 +112,16 @@ function getAnnotationsBetweenRange(
     const overlaps = getZeroedRangeOverlaps(annotation, range, maxLength).map(
       overlap => {
         //we get back 1 or more overlaps here
-
+        const allLocations = annotation.locations;
+        if (allLocations && allLocations.length) {
+          // Filter the 'allLocations' that in this overlap
+          const newLocations = allLocations.filter(loc => {
+            return isRangeWithinRange(loc, overlap, maxLength);
+          })
+          return extend({}, annotation, overlap, {
+            locations: newLocations
+          });
+        }
         return extend({}, annotation, overlap);
       }
     );

package/src/getSequenceDataBetweenRange.test.js

@@ -462,4 +462,46 @@ describe("getSequenceDataBetweenRange", () => {
       ]
     });
   });
+  it("feature with locations, circular sequence, non-fully enclosing range range that cross the origin", () =>{
+    const res = getSequenceDataBetweenRange(
+      {
+        circular: true,
+        sequence: "gggatgcatgca",
+        features: [
+          {
+            start: 5,
+            end: 3,
+            locations: [
+              { start: 5, end: 6 },
+              { start: 7, end: 8 },
+              { start: 9, end: 1 },
+              { start: 2, end: 3 }
+            ],
+            name: "testing"
+          }
+        ]
+      },
+      {
+        start: 2,
+        end: 7
+      }
+    );
+    res.should.containSubset({
+      sequence: "gatgca",
+      features: [
+        {
+          start: 0,
+          end: 1,
+          name: "testing",
+          locations: undefined
+        },
+        {
+          start: 3,
+          end: 5,
+          name: "testing",
+          locations: [{start:3, end:4}, {start:5, end:5}]
+        }
+      ]
+    });
+  })
 });

package/src/prepareRowData_output1.json

@@ -138,7 +138,6 @@
         },
         "start": 1,
         "end": 3,
-        "forward": true,
         "yOffset": 0,
         "enclosingRangeType": "beginningAndEnd"
       }