jbrowse-plugin-protein3d 0.5.3 → 0.5.4

package/dist/Protein1DViewRegistry/index.js

@@ -1,7 +1,6 @@
 import { SimpleFeature } from '@jbrowse/core/util';
-import { getCodonRange } from 'g2p_mapper';
 import { action, computed, makeObservable, observable } from 'mobx';
-import { genomeToTranscriptSeqMapping } from '../mappings';
+import { codonGenomeSpan, genomeToTranscriptSeqMapping } from '../mappings';
 class Protein1DViewRegistry {
     views = observable.map();
     constructor() {
@@ -53,13 +52,9 @@ class Protein1DViewRegistry {
         if (!mapping) {
             return undefined;
         }
-        const { p2g, strand, refName } = mapping;
-        const result = getCodonRange(p2g, proteinPos, strand);
-        if (!result) {
-            return undefined;
-        }
-        const [start, end] = result;
-        return { refName, start, end };
+        const { p2gCodon, refName } = mapping;
+        const span = codonGenomeSpan(p2gCodon, proteinPos);
+        return span ? { refName, start: span[0], end: span[1] } : undefined;
     }
 }
 export const protein1DViewRegistry = new Protein1DViewRegistry();

package/dist/ProteinView/proteinToGenomeMapping.d.ts

@@ -2,7 +2,7 @@ import type { PairwiseAlignment } from '../mappings';
 import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 interface GenomeToTranscriptSeqMapping {
-    p2g: Record<number, number>;
+    p2gCodon: Record<number, number[]>;
     strand: number;
     refName: string;
 }

package/dist/ProteinView/proteinToGenomeMapping.js

@@ -1,5 +1,5 @@
 import { getSession } from '@jbrowse/core/util';
-import { getCodonRange } from 'g2p_mapper';
+import { codonGenomeSpan } from '../mappings';
 /**
  * Maps a protein structure position to genome coordinates
  * @returns [start, end] tuple of genome coordinates, or undefined if mapping fails
@@ -9,12 +9,11 @@ export function proteinToGenomeMapping({ model, structureSeqPos, }) {
     if (!genomeToTranscriptSeqMapping || !pairwiseAlignment) {
         return undefined;
     }
-    const { p2g, strand } = genomeToTranscriptSeqMapping;
+    const { p2gCodon } = genomeToTranscriptSeqMapping;
     const transcriptPos = structureSeqToTranscriptSeqPosition?.[structureSeqPos];
-    if (transcriptPos === undefined) {
-        return undefined;
-    }
-    return getCodonRange(p2g, transcriptPos, strand);
+    return transcriptPos === undefined
+        ? undefined
+        : codonGenomeSpan(p2gCodon, transcriptPos);
 }
 /**
  * Maps a protein structure range to genome coordinates
@@ -63,7 +62,11 @@ export async function navigateToProteinPosition({ model, structureSeqPos, struct
     }
     const [start, end] = result;
     if (zoomToBaseLevel) {
-        await connectedView.navToLocString(`${refName}:${start}-${end}${strand === -1 ? '[rev]' : ''}`, undefined, 0.2);
+        // start/end are 0-based half-open (from getCodonRanges). navToLocString
+        // parses a 1-based locString (parseLocString does start -= 1), so the start
+        // must be shifted to 1-based; the half-open end already equals the 1-based
+        // inclusive end. Passing the raw 0-based start landed the view 1bp 5'.
+        await connectedView.navToLocString(`${refName}:${start + 1}-${end}${strand === -1 ? '[rev]' : ''}`, undefined, 0.2);
     }
     else {
         const { assemblyManager } = session;