@rcsb/rcsb-saguaro-app
Version:
RCSB 1D Saguaro Web App
296 lines (295 loc) • 14.6 kB
JavaScript
"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.PairwiseAlignmentBuilder = void 0;
const RcsbAnnotationConstants_1 = require("../../RcsbAnnotationConfig/RcsbAnnotationConstants");
const GqlTypes_1 = require("@rcsb/rcsb-api-tools/lib/RcsbGraphQL/Types/Borrego/GqlTypes");
const FeatureTools_1 = require("../../RcsbCollectTools/FeatureTools/FeatureTools");
const TrackUtils_1 = require("../../RcsbFvWeb/RcsbFvFactories/RcsbFvTrackFactory/TrackFactoryImpl/Helper/TrackUtils");
const gradient = (color1, color2, weight) => {
const w1 = weight;
const w2 = 1 - w1;
return [Math.round(color1[0] * w1 + color2[0] * w2),
Math.round(color1[1] * w1 + color2[1] * w2),
Math.round(color1[2] * w1 + color2[2] * w2)];
};
//TODO This class is not using factories to build PFV row configurations
class PairwiseAlignmentBuilder {
constructor(paI) {
this.querySequence = paI.querySequence;
this.targetSequence = paI.targetSequence;
this.queryAlignment = paI.queryAlignment;
this.targetAlignment = paI.targetAlignment;
this.queryBegin = paI.queryBegin;
this.targetBegin = paI.targetBegin;
this.targetId = paI.targetId;
this.queryId = paI.queryId;
this.sequenceId = paI.sequenceId;
this.isQueryExternal = paI.isQueryExternal;
this.isTargetExternal = paI.isTargetExternal;
this.pairwiseView = paI.pairwiseView;
if (this.queryAlignment.length != this.targetAlignment.length)
throw "Sequence alignments length mismatch";
if (this.pairwiseView)
this.alignmentLength = this.queryAlignment.length;
else
this.alignmentLength = this.querySequence.length;
}
getLength() {
return this.alignmentLength;
}
buildReferenceAlignment() {
const qA = this.queryAlignment.split('');
const tA = this.targetAlignment.split('');
const alignedBlocks = [];
const mismatchData = [];
const targetSequence = [];
let currentQueryIndex = this.queryBegin;
let currentTargetIndex = this.targetBegin;
let blockQueryStart = this.queryBegin;
let blockTargetStart = this.targetBegin;
qA.forEach((q, i) => {
const t = tA[i];
if ((t === "-" || q === "-") && blockQueryStart > 0) {
alignedBlocks.push({
begin: blockQueryStart,
end: (currentQueryIndex - 1),
oriBegin: blockTargetStart,
oriEnd: (currentTargetIndex - 1),
source: this.isTargetExternal ? RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.userInput : TrackUtils_1.TrackUtils.transformSourceFromTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity),
sourceId: this.targetId,
provenanceName: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.mmseqs,
provenanceColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
type: "ALIGNED_BLOCK",
title: "ALIGNED REGION"
});
blockQueryStart = 0;
}
if (q != "-" && t != "-") {
targetSequence.push({
begin: currentQueryIndex,
oriBegin: currentTargetIndex,
source: this.isTargetExternal ? RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.userInput : TrackUtils_1.TrackUtils.transformSourceFromTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity),
sourceId: this.targetId,
provenanceName: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.targetId, this.targetId).name,
provenanceColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.targetId, this.targetId).color,
label: t,
type: "RESIDUE",
title: "RESIDUE"
});
if (q != t) {
mismatchData.push({
begin: currentQueryIndex,
oriBegin: currentTargetIndex,
source: this.isTargetExternal ? RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.userInput : TrackUtils_1.TrackUtils.transformSourceFromTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity),
sourceId: this.targetId,
provenanceName: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.mmseqs,
provenanceColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
type: "MISMATCH",
title: "MISMATCH"
});
}
}
if (t != "-" && q != "-" && blockQueryStart == 0) {
blockQueryStart = currentQueryIndex;
blockTargetStart = currentTargetIndex;
}
if (q != "-") {
currentQueryIndex++;
}
if (t != "-") {
currentTargetIndex++;
}
});
if (blockQueryStart > 0) {
alignedBlocks.push({
begin: blockQueryStart,
end: (currentQueryIndex - 1),
oriBegin: blockTargetStart,
oriEnd: (currentTargetIndex - 1),
source: this.isTargetExternal ? RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.userInput : TrackUtils_1.TrackUtils.transformSourceFromTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity),
sourceId: this.targetId,
provenanceName: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.mmseqs,
provenanceColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
type: "ALIGNED_BLOCK",
title: "ALIGNED REGION"
});
}
this.addBlockTerminalTags(alignedBlocks);
const queryTrack = {
trackId: "query_sequence",
displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
trackColor: "#F9F9F9",
displayColor: "#000000",
titleFlagColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.queryId, GqlTypes_1.SequenceReference.PdbEntity).color,
rowTitle: this.queryId,
nonEmptyDisplay: true,
trackData: this.querySequence.split('').map((s, n) => ({
source: this.isQueryExternal ? RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.userInput : TrackUtils_1.TrackUtils.transformSourceFromTarget(this.queryId, GqlTypes_1.SequenceReference.PdbEntity),
sourceId: this.queryId,
provenanceName: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.queryId, this.queryId).name,
provenanceColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.queryId, this.queryId).color,
label: s,
begin: n + 1
}))
};
const targetSequenceDisplay = {
displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
displayColor: "#333333",
displayData: targetSequence
};
const mismatchDisplay = {
displayType: "pin" /* RcsbFvDisplayTypes.PIN */,
displayColor: "#FF9999",
displayData: mismatchData,
minRatio: 5
};
const blockColor = "rgb(" + gradient([153, 153, 255], [50, 50, 50], this.sequenceId).join(",") + ")";
const alignmentDisplay = {
displayType: "block" /* RcsbFvDisplayTypes.BLOCK */,
displayColor: blockColor,
displayData: alignedBlocks
};
const alignmentTrack = {
trackId: "targetSequenceTrack",
rowTitle: this.targetId,
displayType: "composite" /* RcsbFvDisplayTypes.COMPOSITE */,
trackColor: "#F9F9F9",
titleFlagColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity).color,
displayConfig: [alignmentDisplay, mismatchDisplay, targetSequenceDisplay]
};
return [queryTrack, alignmentTrack];
}
buildPairwiseAlignment() {
const qA = this.queryAlignment.split('');
const tA = this.targetAlignment.split('');
const alignedBlocks = [];
const mismatchData = [];
const querySeq = [];
const targetSeq = [];
let currentQueryIndex = this.queryBegin;
let currentTargetIndex = this.targetBegin;
let start = 1;
qA.forEach((q, i) => {
const t = tA[i];
if (q === "-" || t === "-") {
if (start > 0 && i > start) {
alignedBlocks.push({
begin: start,
end: i,
provenanceName: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.mmseqs,
provenanceColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
type: "ALIGNED_BLOCK",
title: "ALIGNED REGION"
});
start = 0;
}
}
else if (q != "-" && t != "-" && start == 0) {
start = i + 1;
}
if (q != "-" && t != "-" && q != t && start > 0) {
mismatchData.push({
begin: i + 1,
provenanceName: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.mmseqs,
provenanceColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
type: "MISMATCH",
title: "MISMATCH"
});
}
querySeq.push({
begin: i + 1,
label: q,
source: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.userInput,
sourceId: this.queryId,
provenanceName: this.queryId,
provenanceColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.external,
oriBegin: q != "-" ? currentQueryIndex : undefined
});
if (q != "-") {
currentQueryIndex++;
}
targetSeq.push({
begin: i + 1,
label: t,
source: TrackUtils_1.TrackUtils.transformSourceFromTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity),
sourceId: this.targetId,
provenanceName: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity).name,
provenanceColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity).color,
oriBegin: t != "-" ? currentTargetIndex : undefined
});
if (t != "-") {
currentTargetIndex++;
}
});
if (start > 0) {
alignedBlocks.push({
begin: start,
end: this.alignmentLength,
provenanceName: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceName.mmseqs,
provenanceColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
type: "ALIGNED_BLOCK",
title: "ALIGNED REGION"
});
}
const queryTrack = {
trackId: "query_sequence",
displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
trackColor: "#F9F9F9",
displayColor: "#000000",
rowTitle: this.queryId,
titleFlagColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.queryId, GqlTypes_1.SequenceReference.PdbEntity).color,
nonEmptyDisplay: true,
trackData: querySeq
};
const targetTrack = {
trackId: "target_sequence",
displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
trackColor: "#F9F9F9",
displayColor: "#000000",
rowTitle: this.targetId,
titleFlagColor: TrackUtils_1.TrackUtils.getProvenanceConfigFormTarget(this.targetId, GqlTypes_1.SequenceReference.PdbEntity).color,
nonEmptyDisplay: true,
trackData: targetSeq
};
const mismatchDisplay = {
displayType: "pin" /* RcsbFvDisplayTypes.PIN */,
displayColor: "#FF9999",
displayData: mismatchData,
minRatio: 5
};
const blockColor = "rgb(" + gradient([153, 153, 255], [50, 50, 50], this.sequenceId).join(",") + ")";
const alignmentDisplay = {
displayType: "block" /* RcsbFvDisplayTypes.BLOCK */,
displayColor: blockColor,
displayData: alignedBlocks
};
const alignmentTrack = {
trackId: "targetSequenceTrack",
displayType: "composite" /* RcsbFvDisplayTypes.COMPOSITE */,
trackColor: "#F9F9F9",
rowTitle: " ",
titleFlagColor: RcsbAnnotationConstants_1.RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
displayConfig: [alignmentDisplay, mismatchDisplay]
};
return [queryTrack, alignmentTrack, targetTrack];
}
addBlockTerminalTags(alignedBlocks) {
var _a;
if ((_a = alignedBlocks[0].oriBegin) !== null && _a !== void 0 ? _a : 0 > 1) {
alignedBlocks[0].openBegin = true;
}
for (let n = 0; n < (alignedBlocks.length - 1); n++) {
const oriEnd = alignedBlocks[n].oriEnd;
if (oriEnd && oriEnd + 1 != alignedBlocks[n + 1].oriBegin) {
alignedBlocks[n].openEnd = true;
alignedBlocks[n + 1].openBegin = true;
}
}
const oriEnd = alignedBlocks[alignedBlocks.length - 1].oriEnd;
if (oriEnd && oriEnd < this.targetSequence.length) {
alignedBlocks[alignedBlocks.length - 1].openEnd = true;
}
FeatureTools_1.FeatureTools.mergeBlocks(alignedBlocks);
}
}
exports.PairwiseAlignmentBuilder = PairwiseAlignmentBuilder;