jbrowse-plugin-protein3d 0.0.3 → 0.0.5

package/dist/mappings.d.ts

@@ -1,16 +1,18 @@
 import { Feature } from '@jbrowse/core/util';
-export interface Alignment {
-    alns: {
-        id: string;
-        seq: string;
-    }[];
+export interface AlignmentRow {
+    id: string;
+    seq: string;
 }
-export declare function structureSeqVsTranscriptSeqMap(alignment: Alignment): {
-    structureSeqToTranscriptSeqPosition: Record<string, number | undefined>;
-    transcriptSeqToStructureSeqPosition: Record<string, number | undefined>;
+export interface PairwiseAlignment {
+    consensus: string;
+    alns: readonly [AlignmentRow, AlignmentRow];
+}
+export declare function structureSeqVsTranscriptSeqMap(pairwiseAlignment: PairwiseAlignment): {
+    structureSeqToTranscriptSeqPosition: Record<string, number>;
+    transcriptSeqToStructureSeqPosition: Record<string, number>;
 };
-export declare function structurePositionToAlignmentMap(alignment: Alignment): Record<string, number | undefined>;
-export declare function transcriptPositionToAlignmentMap(alignment: Alignment): Record<string, number | undefined>;
+export declare function structurePositionToAlignmentMap(pairwiseAlignment: PairwiseAlignment): Record<string, number>;
+export declare function transcriptPositionToAlignmentMap(pairwiseAlignment: PairwiseAlignment): Record<string, number>;
 export declare function genomeToTranscriptSeqMapping(feature: Feature): {
     g2p: Record<number, number | undefined>;
     p2g: Record<number, number | undefined>;

package/dist/mappings.js

@@ -1,7 +1,7 @@
 import { genomeToTranscriptSeqMapping as g2p } from 'g2p_mapper';
-export function structureSeqVsTranscriptSeqMap(alignment) {
-    const structureSeq = alignment.alns[0].seq;
-    const transcriptSeq = alignment.alns[1].seq;
+export function structureSeqVsTranscriptSeqMap(pairwiseAlignment) {
+    const structureSeq = pairwiseAlignment.alns[1].seq;
+    const transcriptSeq = pairwiseAlignment.alns[0].seq;
     if (structureSeq.length !== transcriptSeq.length) {
         throw new Error('mismatched length');
     }
@@ -37,8 +37,8 @@ export function structureSeqVsTranscriptSeqMap(alignment) {
         transcriptSeqToStructureSeqPosition,
     };
 }
-export function structurePositionToAlignmentMap(alignment) {
-    const structureSeq = alignment.alns[0].seq;
+export function structurePositionToAlignmentMap(pairwiseAlignment) {
+    const structureSeq = pairwiseAlignment.alns[1].seq;
     const structurePositionToAlignment = {};
     for (let i = 0, j = 0; i < structureSeq.length; i++) {
         if (structureSeq[i] !== '-') {
@@ -48,8 +48,8 @@ export function structurePositionToAlignmentMap(alignment) {
     }
     return structurePositionToAlignment;
 }
-export function transcriptPositionToAlignmentMap(alignment) {
-    const transcriptSeq = alignment.alns[1].seq;
+export function transcriptPositionToAlignmentMap(pairwiseAlignment) {
+    const transcriptSeq = pairwiseAlignment.alns[0].seq;
     const transcriptPositionToAlignment = {};
     for (let i = 0, j = 0; i < transcriptSeq.length; i++) {
         if (transcriptSeq[i] !== '-') {

package/dist/mappings.js.map

@@ -1 +1 @@
-{"version":3,"file":"mappings.js","sourceRoot":"","sources":["../src/mappings.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,4BAA4B,IAAI,GAAG,EAAE,MAAM,YAAY,CAAA;AAShE,MAAM,UAAU,8BAA8B,CAAC,SAAoB;IACjE,MAAM,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC1C,MAAM,aAAa,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3C,IAAI,YAAY,CAAC,MAAM,KAAK,aAAa,CAAC,MAAM,EAAE,CAAC;QACjD,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;IACtC,CAAC;IAED,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,MAAM,mCAAmC,GAAG,EAG3C,CAAA;IACD,MAAM,mCAAmC,GAAG,EAG3C,CAAA;IAED,+CAA+C;IAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC7C,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;QAC1B,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;QAE3B,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;YACd,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YACtB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YACtB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAE1C,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IACD,OAAO;QACL,mCAAmC;QACnC,mCAAmC;KACpC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,+BAA+B,CAAC,SAAoB;IAClE,MAAM,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC1C,MAAM,4BAA4B,GAAG,EAAwC,CAAA;IAE7E,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpD,IAAI,YAAY,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YAC5B,4BAA4B,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACnC,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO,4BAA4B,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,gCAAgC,CAAC,SAAoB;IACnE,MAAM,aAAa,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAC3C,MAAM,6BAA6B,GAAG,EAAwC,CAAA;IAE9E,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrD,IAAI,aAAa,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YAC7B,6BAA6B,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACpC,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO,6BAA6B,CAAA;AACtC,CAAC;AAED,yCAAyC;AACzC,MAAM,UAAU,4BAA4B,CAAC,OAAgB;IAC3D,mBAAmB;IACnB,OAAO,GAAG,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAA;AAC9B,CAAC"}
+{"version":3,"file":"mappings.js","sourceRoot":"","sources":["../src/mappings.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,4BAA4B,IAAI,GAAG,EAAE,MAAM,YAAY,CAAA;AAUhE,MAAM,UAAU,8BAA8B,CAC5C,iBAAoC;IAEpC,MAAM,YAAY,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAClD,MAAM,aAAa,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IACnD,IAAI,YAAY,CAAC,MAAM,KAAK,aAAa,CAAC,MAAM,EAAE,CAAC;QACjD,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;IACtC,CAAC;IAED,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,MAAM,mCAAmC,GAAG,EAA4B,CAAA;IACxE,MAAM,mCAAmC,GAAG,EAA4B,CAAA;IAExE,+CAA+C;IAC/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC7C,MAAM,EAAE,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;QAC1B,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,CAAA;QAE3B,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;YACd,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YACtB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,IAAI,EAAE,KAAK,GAAG,EAAE,CAAC;YACtB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,mCAAmC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAE1C,CAAC,EAAE,CAAA;YACH,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO;QACL,mCAAmC;QACnC,mCAAmC;KACpC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,+BAA+B,CAC7C,iBAAoC;IAEpC,MAAM,YAAY,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAClD,MAAM,4BAA4B,GAAG,EAA4B,CAAA;IAEjE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpD,IAAI,YAAY,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YAC5B,4BAA4B,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACnC,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO,4BAA4B,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,gCAAgC,CAC9C,iBAAoC;IAEpC,MAAM,aAAa,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IACnD,MAAM,6BAA6B,GAAG,EAA4B,CAAA;IAElE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACrD,IAAI,aAAa,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;YAC7B,6BAA6B,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACpC,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO,6BAA6B,CAAA;AACtC,CAAC;AAED,yCAAyC;AACzC,MAAM,UAAU,4BAA4B,CAAC,OAAgB;IAC3D,mBAAmB;IACnB,OAAO,GAAG,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAA;AAC9B,CAAC"}

package/dist/mappings.test.js

@@ -1,16 +1,18 @@
+import { expect, test } from 'vitest';
 import { genomeToTranscriptSeqMapping, structureSeqVsTranscriptSeqMap, } from './mappings';
 import { SimpleFeature } from '@jbrowse/core/util';
-import { feature, alignment } from './test_data/gene';
+import { feature, pairwiseAlignment } from './test_data/gene';
 test('test', () => {
-    const ret = structureSeqVsTranscriptSeqMap(alignment);
+    const ret = structureSeqVsTranscriptSeqMap(pairwiseAlignment);
     expect(ret).toMatchSnapshot();
 });
 test('mapping', () => {
+    // @ts-expect-error
     const res = genomeToTranscriptSeqMapping(new SimpleFeature(feature));
     const { p2g } = res;
-    const aln = structureSeqVsTranscriptSeqMap(alignment);
+    const aln = structureSeqVsTranscriptSeqMap(pairwiseAlignment);
     // expected position in sequence
-    const s2 = alignment.alns[1].seq;
+    const s2 = pairwiseAlignment.alns[1].seq;
     expect(s2[392]).toBe('M');
     expect(s2[393]).toBe('K');
     expect(s2[394]).toBe('A');
@@ -18,7 +20,7 @@ test('mapping', () => {
     // maps the 392 position in the "pdb version of the protein" to the 0th
     // position in the genome version of the protein, and then maps that back to
     // the genome
-    const p0 = aln.structureSeqToTranscriptSeqPosition[392];
+    const p0 = aln.transcriptSeqToStructureSeqPosition[392];
     const g0 = p2g[p0];
     expect(p0).toBe(0);
     expect(g0).toBe(51_296_155);

package/dist/mappings.test.js.map

@@ -1 +1 @@
-{"version":3,"file":"mappings.test.js","sourceRoot":"","sources":["../src/mappings.test.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,4BAA4B,EAC5B,8BAA8B,GAC/B,MAAM,YAAY,CAAA;AACnB,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAClD,OAAO,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAA;AAErD,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE;IAChB,MAAM,GAAG,GAAG,8BAA8B,CAAC,SAAS,CAAC,CAAA;IACrD,MAAM,CAAC,GAAG,CAAC,CAAC,eAAe,EAAE,CAAA;AAC/B,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;IACnB,MAAM,GAAG,GAAG,4BAA4B,CAAC,IAAI,aAAa,CAAC,OAAO,CAAC,CAAC,CAAA;IACpE,MAAM,EAAE,GAAG,EAAE,GAAG,GAAG,CAAA;IACnB,MAAM,GAAG,GAAG,8BAA8B,CAAC,SAAS,CAAC,CAAA;IAErD,gCAAgC;IAChC,MAAM,EAAE,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IAChC,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,uEAAuE;IACvE,4EAA4E;IAC5E,aAAa;IACb,MAAM,EAAE,GAAG,GAAG,CAAC,mCAAmC,CAAC,GAAG,CAAE,CAAA;IACxD,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAClB,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAClB,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;IAC3B,MAAM,CAAC,GAAG,CAAC,CAAC,eAAe,EAAE,CAAA;AAC/B,CAAC,CAAC,CAAA"}
+{"version":3,"file":"mappings.test.js","sourceRoot":"","sources":["../src/mappings.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AACrC,OAAO,EACL,4BAA4B,EAC5B,8BAA8B,GAC/B,MAAM,YAAY,CAAA;AACnB,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAClD,OAAO,EAAE,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAA;AAE7D,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE;IAChB,MAAM,GAAG,GAAG,8BAA8B,CAAC,iBAAiB,CAAC,CAAA;IAC7D,MAAM,CAAC,GAAG,CAAC,CAAC,eAAe,EAAE,CAAA;AAC/B,CAAC,CAAC,CAAA;AAEF,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;IACnB,mBAAmB;IACnB,MAAM,GAAG,GAAG,4BAA4B,CAAC,IAAI,aAAa,CAAC,OAAO,CAAC,CAAC,CAAA;IACpE,MAAM,EAAE,GAAG,EAAE,GAAG,GAAG,CAAA;IACnB,MAAM,GAAG,GAAG,8BAA8B,CAAC,iBAAiB,CAAC,CAAA;IAE7D,gCAAgC;IAChC,MAAM,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;IACxC,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;IACzB,uEAAuE;IACvE,4EAA4E;IAC5E,aAAa;IACb,MAAM,EAAE,GAAG,GAAG,CAAC,mCAAmC,CAAC,GAAG,CAAE,CAAA;IACxD,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAClB,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAClB,MAAM,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;IAC3B,MAAM,CAAC,GAAG,CAAC,CAAC,eAAe,EAAE,CAAA;AAC/B,CAAC,CAAC,CAAA"}