From 062e3e055ab4bc67d9040eac6ed6f7cbf347c4c9 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 3 Oct 2019 10:05:31 -0700
Subject: [PATCH] show full compId for modified residues in sequence widget
---
src/mol-model/sequence/sequence.ts | 50 +++++++++++++++++++-----------
1 file changed, 32 insertions(+), 18 deletions(-)
diff --git a/src/mol-model/sequence/sequence.ts b/src/mol-model/sequence/sequence.ts
index 72a8c13e6..946e953b3 100644
--- a/src/mol-model/sequence/sequence.ts
+++ b/src/mol-model/sequence/sequence.ts
@@ -54,30 +54,37 @@ namespace Sequence {
function determineKind(names: Column<string>) {
for (let i = 0, _i = Math.min(names.rowCount, 10); i < _i; i++) {
const name = names.value(i) || '';
- if (getProteinOneLetterCode(name) !== 'X') return { kind: Kind.Protein, code: getProteinOneLetterCode };
- if (getRnaOneLetterCode(name) !== 'X') return { kind: Kind.RNA, code: getRnaOneLetterCode };
- if (getDnaOneLetterCode(name) !== 'X') return { kind: Kind.DNA, code: getDnaOneLetterCode };
+ if (getProteinOneLetterCode(name) !== 'X') return Kind.Protein;
+ if (getRnaOneLetterCode(name) !== 'X') return Kind.RNA;
+ if (getDnaOneLetterCode(name) !== 'X') return Kind.DNA;
}
- return { kind: Kind.Generic, code: (v: string) => 'X' };
+ return Kind.Generic;
}
- function modCode(code: (name: string) => string, map: ReadonlyMap<string, string>): (name: string) => string {
- return n => {
- const ret = code(n);
- if (ret !== 'X' || !map.has(n)) return ret;
- return code(map.get(n)!);
+ function codeProvider(kind: Kind, map?: ReadonlyMap<string, string>) {
+ let code: (name: string) => string
+ switch (kind) {
+ case Kind.Protein: code = getProteinOneLetterCode; break;
+ case Kind.DNA: code = getDnaOneLetterCode; break;
+ case Kind.RNA: code = getRnaOneLetterCode; break;
+ case Kind.Generic: code = () => 'X'; break;
+ default: throw new Error(`unknown kind '${kind}'`)
}
+ if (map && map.size > 0) {
+ return (name: string) => {
+ const ret = code(name);
+ if (ret !== 'X' || !map.has(name)) return ret;
+ return code(map.get(name)!);
+ }
+ }
+ return code
}
export function ofResidueNames(compId: Column<string>, seqId: Column<number>, modifiedMap?: ReadonlyMap<string, string>): Sequence {
if (seqId.rowCount === 0) throw new Error('cannot be empty');
- const { kind, code } = determineKind(compId);
-
- if (!modifiedMap || modifiedMap.size === 0) {
- return new ResidueNamesImpl(kind, compId, seqId, code) as Sequence;
- }
- return new ResidueNamesImpl(kind, compId, seqId, modCode(code, modifiedMap)) as Sequence;
+ const kind = determineKind(compId);
+ return new ResidueNamesImpl(kind, compId, seqId, modifiedMap) as Sequence;
}
class ResidueNamesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
@@ -87,6 +94,8 @@ namespace Sequence {
private _code: Column<Alphabet> | undefined = undefined
private _label: Column<string> | undefined = undefined
+ private codeFromName: (name: string) => string
+
get code(): Column<Alphabet> {
if (this._code !== void 0) return this._code;
this.create();
@@ -142,10 +151,14 @@ namespace Sequence {
const seqId = this.seqId.value(i)
const idx = seqId - minSeqId;
const name = this.compId.value(i);
- const code = this.getCode(name);
+ const code = this.codeFromName(name);
// in case of MICROHETEROGENEITY `sequenceArray[idx]` may already be set
if (!sequenceArray[idx] || sequenceArray[idx] === '-') {
- sequenceArray[idx] = code;
+ if (code === 'X' && this.modifiedMap && this.modifiedMap.has(name)) {
+ sequenceArray[idx] = this.modifiedMap.get(name)!
+ } else {
+ sequenceArray[idx] = code;
+ }
}
labels[idx].push(code === 'X' ? name : code);
compIds[seqId].push(name);
@@ -170,8 +183,9 @@ namespace Sequence {
this._length = count
}
- constructor(public kind: K, public compId: Column<string>, public seqId: Column<number>, private getCode: (name: string) => string) {
+ constructor(public kind: K, public compId: Column<string>, public seqId: Column<number>, private modifiedMap?: ReadonlyMap<string, string>) {
+ this.codeFromName = codeProvider(kind)
}
}
--
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