@teselagen/ove 0.8.39 → 0.8.41

package/AlignmentView/AlignmentSearchBar.d.ts

@@ -0,0 +1,2 @@
+export function AlignmentSearchBar(props: any): import("react/jsx-runtime").JSX.Element;
+export default AlignmentSearchBar;

package/AlignmentView/Mismatches.d.ts

@@ -1,20 +1,2 @@
-import { default as React } from '../../../../node_modules/react';
-declare const _default: import('../../../../node_modules/react-redux').ConnectedComponent<typeof Mismatches, {
-    context?: import('../../../../node_modules/react-redux/es/components/Context').ReactReduxContextInstance | undefined;
-    store?: import('../../../../node_modules/redux').Store | undefined;
-} | {
-    store?: import('../../../../node_modules/redux').Store | undefined;
-}>;
-export default _default;
-declare class Mismatches extends React.Component<any, any, any> {
-    constructor(props: any);
-    constructor(props: any, context: any);
-    UNSAFE_componentWillMount(): void;
-    getGapMap: (sequence: any) => number[];
-    getMismatchList: (alignmentData: any, mismatches: any) => {
-        mismatches: number;
-        start: number;
-        end: number;
-    }[];
-    render(): import("react/jsx-runtime").JSX.Element;
-}
+export function FindMismatches(props: any): import("react/jsx-runtime").JSX.Element;
+export default FindMismatches;

package/AlignmentView/findAlignmentDifferences.d.ts

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+/**
+ * @typedef {"mismatch"|"insertion"|"deletion"|"gap"} DifferenceType
+ *
+ * @typedef {Object} AlignmentDifference
+ * @property {number} position - 0-based column index in the aligned sequence
+ * @property {DifferenceType} type
+ * @property {string[]} bases - bases at this column for each track (template first)
+ */
+/**
+ * Group consecutive same-type differences into regions.
+ * Mismatches are never grouped — each is its own entry.
+ * Insertions, deletions, and gaps that are side-by-side are collapsed into
+ * one entry with a `start` and `end` (both inclusive, 0-based).
+ *
+ * @param {AlignmentDifference[]} differences
+ * @returns {Array<AlignmentDifference & { start: number, end: number }>}
+ */
+export function groupConsecutiveDifferences(differences: AlignmentDifference[]): Array<AlignmentDifference & {
+    start: number;
+    end: number;
+}>;
+/**
+ * Classify alignment columns into difference types relative to the template track.
+ *
+ * Template is alignedSeqs[0]. Non-template tracks are alignedSeqs[1+].
+ *
+ * Classification rules (per column):
+ *  - "gap"       : no non-template track is in its aligned region at this position
+ *  - "insertion" : template has '-', at least one aligned non-template has a non-gap base
+ *  - "deletion"  : template has a non-gap base, at least one aligned non-template has '-'
+ *  - "mismatch"  : no gaps among aligned tracks, unique base set has more than one member
+ *
+ * Only tracks whose aligned region covers position i participate in classification.
+ * This correctly handles multi-read alignments (e.g. Sanger) where reads cover
+ * different sub-ranges of the full alignment.
+ *
+ * @param {string[]} alignedSeqs - Aligned sequence strings, all same length
+ * @returns {AlignmentDifference[]}
+ */
+export function findAlignmentDifferences(alignedSeqs: string[]): AlignmentDifference[];
+export default findAlignmentDifferences;
+export type DifferenceType = "mismatch" | "insertion" | "deletion" | "gap";
+export type AlignmentDifference = {
+    /**
+     * - 0-based column index in the aligned sequence
+     */
+    position: number;
+    type: DifferenceType;
+    /**
+     * - bases at this column for each track (template first)
+     */
+    bases: string[];
+};

package/AlignmentView/utils.d.ts

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+/**
+ * @typedef {Object} Mismatch
+ * @property {number} position
+ * @property {string[]} bases
+ */
+/**
+ * @typedef {Object} FindMismatchesProps
+ * @property {Array<{
+ *   alignmentData: {
+ *     sequence: string
+ *   }
+ * }>} alignmentJson
+ * @property {string} id
+ */
+export function scrollToAlignmentSelection(): void;
+export function updateCaretPosition({ start, end }: {
+    start: any;
+    end: any;
+}): void;
+export type Mismatch = {
+    position: number;
+    bases: string[];
+};
+export type FindMismatchesProps = {
+    alignmentJson: Array<{
+        alignmentData: {
+            sequence: string;
+        };
+    }>;
+    id: string;
+};