@rcsb/rcsb-saguaro-app 6.3.2 → 6.3.4

package/lib/RcsbUtils/PairwiseAlignmentTools/PairwiseAlignmentBuilder.js

@@ -1,291 +0,0 @@
-import { RcsbAnnotationConstants } from "../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { SequenceReference } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { FeatureTools } from "../../RcsbCollectTools/FeatureTools/FeatureTools";
-import { TrackUtils } from "../../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
-export 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.provenanceName.userInput : TrackUtils.transformSourceFromTarget(this.targetId, SequenceReference.PdbEntity),
-                    sourceId: this.targetId,
-                    provenanceName: RcsbAnnotationConstants.provenanceName.mmseqs,
-                    provenanceColor: RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
-                    type: "ALIGNED_BLOCK",
-                    title: "ALIGNED REGION"
-                });
-                blockQueryStart = 0;
-            }
-            if (q != "-" && t != "-") {
-                targetSequence.push({
-                    begin: currentQueryIndex,
-                    oriBegin: currentTargetIndex,
-                    source: this.isTargetExternal ? RcsbAnnotationConstants.provenanceName.userInput : TrackUtils.transformSourceFromTarget(this.targetId, SequenceReference.PdbEntity),
-                    sourceId: this.targetId,
-                    provenanceName: TrackUtils.getProvenanceConfigFormTarget(this.targetId, this.targetId).name,
-                    provenanceColor: 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.provenanceName.userInput : TrackUtils.transformSourceFromTarget(this.targetId, SequenceReference.PdbEntity),
-                        sourceId: this.targetId,
-                        provenanceName: RcsbAnnotationConstants.provenanceName.mmseqs,
-                        provenanceColor: 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.provenanceName.userInput : TrackUtils.transformSourceFromTarget(this.targetId, SequenceReference.PdbEntity),
-                sourceId: this.targetId,
-                provenanceName: RcsbAnnotationConstants.provenanceName.mmseqs,
-                provenanceColor: 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.getProvenanceConfigFormTarget(this.queryId, SequenceReference.PdbEntity).color,
-            rowTitle: this.queryId,
-            nonEmptyDisplay: true,
-            trackData: this.querySequence.split('').map((s, n) => ({
-                source: this.isQueryExternal ? RcsbAnnotationConstants.provenanceName.userInput : TrackUtils.transformSourceFromTarget(this.queryId, SequenceReference.PdbEntity),
-                sourceId: this.queryId,
-                provenanceName: TrackUtils.getProvenanceConfigFormTarget(this.queryId, this.queryId).name,
-                provenanceColor: 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.getProvenanceConfigFormTarget(this.targetId, 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.provenanceName.mmseqs,
-                        provenanceColor: 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.provenanceName.mmseqs,
-                    provenanceColor: RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
-                    type: "MISMATCH",
-                    title: "MISMATCH"
-                });
-            }
-            querySeq.push({
-                begin: i + 1,
-                label: q,
-                source: RcsbAnnotationConstants.provenanceName.userInput,
-                sourceId: this.queryId,
-                provenanceName: this.queryId,
-                provenanceColor: RcsbAnnotationConstants.provenanceColorCode.external,
-                oriBegin: q != "-" ? currentQueryIndex : undefined
-            });
-            if (q != "-") {
-                currentQueryIndex++;
-            }
-            targetSeq.push({
-                begin: i + 1,
-                label: t,
-                source: TrackUtils.transformSourceFromTarget(this.targetId, SequenceReference.PdbEntity),
-                sourceId: this.targetId,
-                provenanceName: TrackUtils.getProvenanceConfigFormTarget(this.targetId, SequenceReference.PdbEntity).name,
-                provenanceColor: TrackUtils.getProvenanceConfigFormTarget(this.targetId, SequenceReference.PdbEntity).color,
-                oriBegin: t != "-" ? currentTargetIndex : undefined
-            });
-            if (t != "-") {
-                currentTargetIndex++;
-            }
-        });
-        if (start > 0) {
-            alignedBlocks.push({
-                begin: start,
-                end: this.alignmentLength,
-                provenanceName: RcsbAnnotationConstants.provenanceName.mmseqs,
-                provenanceColor: 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.getProvenanceConfigFormTarget(this.queryId, 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.getProvenanceConfigFormTarget(this.targetId, 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.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.mergeBlocks(alignedBlocks);
-    }
-}

package/lib/RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite.d.ts

@@ -1,2 +0,0 @@
-import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
-export declare function alignmentGlobalLigandBindingSite(): ExternalTrackBuilderInterface;

package/lib/RcsbUtils/TrackGenerators/AlignmentGlobalBindingSite.js

@@ -1,99 +0,0 @@
-import { __awaiter } from "tslib";
-import { RcsbAnnotationConstants } from "../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { groupExternalTrackBuilder } from "./GroupExternalTrackBuilder";
-import { Assertions } from "../Helpers/Assertions";
-var assertDefined = Assertions.assertDefined;
-export function alignmentGlobalLigandBindingSite() {
-    const trackName = "GLOBAL BINDING";
-    const bindingSiteMap = new Map();
-    let max = 0;
-    const groupTrackBuilder = groupExternalTrackBuilder();
-    return {
-        addTo(tracks) {
-            return __awaiter(this, void 0, void 0, function* () {
-                var _a;
-                if (Array.from(bindingSiteMap.values()).length > 0)
-                    tracks.annotationTracks.unshift({
-                        trackId: "annotationTrack_GLOBAL_BINDINGS",
-                        trackHeight: 40,
-                        displayType: "area" /* RcsbFvDisplayTypes.AREA */,
-                        overlap: true,
-                        trackColor: "#F9F9F9",
-                        displayColor: "#c4124b",
-                        titleFlagColor: RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
-                        rowTitle: trackName,
-                        displayDomain: [0, max],
-                        interpolationType: "step" /* InterpolationTypes.STEP */,
-                        trackData: Array.from(bindingSiteMap.values())
-                    });
-                yield ((_a = groupTrackBuilder.addTo) === null || _a === void 0 ? void 0 : _a.call(groupTrackBuilder, tracks));
-            });
-        },
-        processAlignmentAndFeatures(data) {
-            return __awaiter(this, void 0, void 0, function* () {
-                var _a;
-                yield ((_a = groupTrackBuilder.processAlignmentAndFeatures) === null || _a === void 0 ? void 0 : _a.call(groupTrackBuilder, data));
-                processFeatures(data.annotations);
-            });
-        },
-        filterFeatures(data) {
-            return __awaiter(this, void 0, void 0, function* () {
-                var _a, _b;
-                const annotations = (_b = yield ((_a = groupTrackBuilder.filterFeatures) === null || _a === void 0 ? void 0 : _a.call(groupTrackBuilder, data))) !== null && _b !== void 0 ? _b : [];
-                annotations.forEach(ann => {
-                    var _a;
-                    ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => { var _a; return f ? (_a = f.name) === null || _a === void 0 ? void 0 : _a.includes("ligand") : false; });
-                });
-                return new Promise((resolve => {
-                    resolve(annotations);
-                }));
-            });
-        },
-        filterAlignments(data) {
-            assertDefined(groupTrackBuilder.filterAlignments);
-            return groupTrackBuilder.filterAlignments(data);
-        }
-    };
-    function processFeatures(annotations) {
-        // position > ligand name
-        const ligandMap = new Map();
-        annotations.forEach(ann => {
-            var _a;
-            (_a = ann.features) === null || _a === void 0 ? void 0 : _a.forEach(d => {
-                var _a;
-                if (d)
-                    (_a = d.feature_positions) === null || _a === void 0 ? void 0 : _a.forEach(p => {
-                        var _a;
-                        if (p === null || p === void 0 ? void 0 : p.beg_seq_id)
-                            (_a = p.values) === null || _a === void 0 ? void 0 : _a.forEach((v, n) => {
-                                var _a, _b;
-                                const key = (p.beg_seq_id + n).toString();
-                                if (!ligandMap.has(key))
-                                    ligandMap.set(key, new Set());
-                                else if (d.name && !((_a = ligandMap.get(key)) === null || _a === void 0 ? void 0 : _a.has(d.name)))
-                                    (_b = ligandMap.get(key)) === null || _b === void 0 ? void 0 : _b.add(d.name);
-                                else
-                                    return;
-                                const bs = bindingSiteMap.get(key);
-                                if (!bs) {
-                                    bindingSiteMap.set(key, {
-                                        begin: p.beg_seq_id + n,
-                                        type: trackName,
-                                        value: 1
-                                    });
-                                    if (max == 0)
-                                        max = 1;
-                                }
-                                else {
-                                    if (bs) {
-                                        bs.value += 1;
-                                        if (bs.value > max)
-                                            max = bs.value;
-                                    }
-                                }
-                            });
-                    });
-            });
-        });
-    }
-}

package/lib/RcsbUtils/TrackGenerators/BurialFraction.d.ts

@@ -1,3 +0,0 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function burialFraction(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
-export declare function burialFractionFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;

package/lib/RcsbUtils/TrackGenerators/BurialFraction.js

@@ -1,62 +0,0 @@
-import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { cloneDeep } from "lodash";
-import { FeatureType } from "../../RcsbExport/FeatureType";
-export function burialFraction(annotations) {
-    const burialFractionOut = new Array();
-    const asaUnboundAnn = cloneDeep(annotations).map(ann => {
-        var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === Type.AsaUnbound));
-        return ann;
-    }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
-    const asaBoundAnn = cloneDeep(annotations).map(ann => {
-        var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) === Type.AsaBound));
-        return ann;
-    }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
-    asaUnboundAnn.forEach((asaUnbound) => {
-        var _a, _b, _c;
-        const asaBound = asaBoundAnn.find((ann) => { var _a, _b, _c, _d; return (((_a = ann.target_identifiers) === null || _a === void 0 ? void 0 : _a.target_id) === ((_b = asaUnbound.target_identifiers) === null || _b === void 0 ? void 0 : _b.target_id) && ((_c = ann.target_identifiers) === null || _c === void 0 ? void 0 : _c.interface_partner_index) === ((_d = asaUnbound.target_identifiers) === null || _d === void 0 ? void 0 : _d.interface_partner_index)); });
-        if (asaUnbound && asaBound) {
-            if (((_a = asaBound.features) === null || _a === void 0 ? void 0 : _a.length) != ((_b = asaUnbound.features) === null || _b === void 0 ? void 0 : _b.length))
-                throw "Inconsistent bound and unbound ASA features, different array lengths";
-            const burialFraction = cloneDeep(asaUnbound);
-            burialFraction.features = [];
-            (_c = asaUnbound.features) === null || _c === void 0 ? void 0 : _c.forEach((uF, l) => {
-                var _a, _b, _c, _d;
-                const bF = (_b = (_a = asaBound.features) === null || _a === void 0 ? void 0 : _a[l]) !== null && _b !== void 0 ? _b : undefined;
-                if (bF && uF) {
-                    const feature = cloneDeep(uF);
-                    feature.type = FeatureType.BurialFraction;
-                    feature.name = "Interface residues buried fraction";
-                    feature.description = "(1 - bASA/uASA)";
-                    feature.feature_positions = [];
-                    (_c = uF === null || uF === void 0 ? void 0 : uF.feature_positions) === null || _c === void 0 ? void 0 : _c.forEach((uP, n) => {
-                        var _a, _b, _c, _d;
-                        const bP = (_b = (_a = bF.feature_positions) === null || _a === void 0 ? void 0 : _a[n]) !== null && _b !== void 0 ? _b : undefined;
-                        if (bP)
-                            (_c = feature.feature_positions) === null || _c === void 0 ? void 0 : _c.push({
-                                beg_seq_id: uP === null || uP === void 0 ? void 0 : uP.beg_seq_id,
-                                values: (_d = uP === null || uP === void 0 ? void 0 : uP.values) === null || _d === void 0 ? void 0 : _d.map((uV, m) => {
-                                    var _a, _b;
-                                    const bV = (_b = (_a = bP.values) === null || _a === void 0 ? void 0 : _a[m]) !== null && _b !== void 0 ? _b : 0;
-                                    if (uV === 0)
-                                        return 0;
-                                    return Math.floor((1 - bV / (uV !== null && uV !== void 0 ? uV : 1)) * 100) / 100;
-                                })
-                            });
-                    });
-                    (_d = burialFraction.features) === null || _d === void 0 ? void 0 : _d.push(feature);
-                }
-            });
-            burialFractionOut.push(burialFraction);
-        }
-    });
-    return burialFractionOut;
-}
-export function burialFractionFilter(annotations) {
-    return cloneDeep(annotations).map(ann => {
-        var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => (ann.source !== Source.PdbInterface || (f === null || f === void 0 ? void 0 : f.type) === FeatureType.BurialFraction));
-        return ann;
-    }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
-}

package/lib/RcsbUtils/TrackGenerators/BuriedResidues.d.ts

@@ -1,3 +0,0 @@
-import { AnnotationFeatures } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare function buriedResidues(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;
-export declare function buriedResiduesFilter(annotations: Array<AnnotationFeatures>): Array<AnnotationFeatures>;

package/lib/RcsbUtils/TrackGenerators/BuriedResidues.js

@@ -1,47 +0,0 @@
-import { Source, Type } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-import { cloneDeep } from "lodash";
-import { FeatureType } from "../../RcsbExport/FeatureType";
-export function buriedResidues(annotations) {
-    var _a, _b;
-    const accThr = 6;
-    let buriedResidues = {};
-    let nBuried = 0;
-    mainloop: for (const ann of annotations) {
-        if (ann.source === Source.PdbInstance) {
-            for (const f of (_a = ann.features) !== null && _a !== void 0 ? _a : []) {
-                if ((f === null || f === void 0 ? void 0 : f.type) === Type.Asa) {
-                    buriedResidues = cloneDeep(ann);
-                    buriedResidues.source = Source.PdbInstance;
-                    const feature = cloneDeep(f);
-                    feature.type = FeatureType.BuriedResidues;
-                    feature.name = "Unbound chain core residues";
-                    feature.description = `Residue accessibility lower than ${accThr}Å`;
-                    (_b = feature.feature_positions) === null || _b === void 0 ? void 0 : _b.forEach(p => {
-                        var _a;
-                        if (p)
-                            p.values = (_a = p.values) === null || _a === void 0 ? void 0 : _a.map((v) => {
-                                if (v) {
-                                    const acc = (v < accThr ? Math.floor(v * 100) / 100 : 0);
-                                    nBuried += acc;
-                                    return acc;
-                                }
-                                else {
-                                    return 0;
-                                }
-                            });
-                    });
-                    buriedResidues.features = [feature];
-                    break mainloop;
-                }
-            }
-        }
-    }
-    return nBuried > 0 && buriedResidues ? [buriedResidues] : [];
-}
-export function buriedResiduesFilter(annotations) {
-    return cloneDeep(annotations).map(ann => {
-        var _a;
-        ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.type) !== Type.Asa));
-        return ann;
-    }).filter(ann => { var _a, _b; return (((_b = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.length) !== null && _b !== void 0 ? _b : 0) > 0); });
-}

package/lib/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.d.ts

@@ -1,2 +0,0 @@
-import { ExternalTrackBuilderInterface } from "../../RcsbCollectTools/FeatureTools/ExternalTrackBuilderInterface";
-export declare function groupExternalTrackBuilder(): ExternalTrackBuilderInterface;

package/lib/RcsbUtils/TrackGenerators/GroupExternalTrackBuilder.js

@@ -1,96 +0,0 @@
-import { Logo } from "./Logo";
-import { RcsbAnnotationConstants } from "../../RcsbAnnotationConfig/RcsbAnnotationConstants";
-import { Assertions } from "../Helpers/Assertions";
-var assertElementListDefined = Assertions.assertElementListDefined;
-import { GroupGapLessTransformer } from "../Groups/GroupGapLessTransformer";
-export function groupExternalTrackBuilder() {
-    const seqName = "CONSENSUS SEQUENCE";
-    const conservationName = "SEQUENCE VARIATION";
-    const querySequenceLogo = new Array();
-    const gapLessTransformer = new GroupGapLessTransformer();
-    let variationRowData;
-    return {
-        addTo(tracks) {
-            if (querySequenceLogo.length == 0)
-                return new Promise((resolve) => {
-                    resolve();
-                });
-            variationRowData.forEach(track => tracks.alignmentTracks.unshift(track));
-            return new Promise((resolve) => {
-                resolve();
-            });
-        },
-        processAlignmentAndFeatures(data) {
-            return new Promise((resolve) => {
-                resolve();
-            });
-        },
-        filterFeatures(data) {
-            gapLessTransformer.gapLessFeatures(data.annotations);
-            data.annotations.forEach(ann => {
-                var _a;
-                ann.features = (_a = ann.features) === null || _a === void 0 ? void 0 : _a.filter(f => ((f === null || f === void 0 ? void 0 : f.name) != "automated matches"));
-            });
-            return new Promise((resolve) => {
-                resolve(data.annotations);
-            });
-        },
-        filterAlignments(data) {
-            gapLessTransformer.gapLessAlignments(data.alignments);
-            processAlignments(data.alignments);
-            return new Promise((resolve) => {
-                resolve(data.alignments);
-            });
-        }
-    };
-    function processAlignments(alignment) {
-        var _a, _b;
-        if (querySequenceLogo.length > 0) {
-            return;
-        }
-        if (alignment.alignment_length && alignment.alignment_logo && alignment.alignment_length != ((_a = alignment.alignment_logo) === null || _a === void 0 ? void 0 : _a.length))
-            throw new Error("ERROR Alignment length and logo should match");
-        (_b = alignment.alignment_logo) === null || _b === void 0 ? void 0 : _b.forEach(al => {
-            assertElementListDefined(al);
-            querySequenceLogo.push(new Logo(al));
-        });
-        const sequenceRowData = querySequenceLogo.map((s, n) => {
-            const nFreq = 5;
-            const maxFreqList = s.frequency().filter(f => f.symbol != "-").slice(0, nFreq).map(f => Math.trunc(f.value * 100) / 100);
-            const gapFreq = Math.trunc(s.frequency().filter(f => f.symbol == "-")[0].value * 100) / 100;
-            return {
-                begin: n + 1,
-                values: maxFreqList.map((f, n) => maxFreqList.slice(0, (n + 1)).reduce((v, n) => v + n)).concat([1 - gapFreq, 1]),
-                value: s.frequency()[0].symbol != "-" ? Math.trunc(s.frequency()[0].value * 100) / 100 : 0
-            };
-        });
-        const logoRowData = querySequenceLogo.map((s, n) => ({
-            begin: n + 1,
-            label: s.mode(),
-            description: [s.frequency().filter(s => (s.value >= 0.01)).slice(0, 14).map(s => (s.symbol.replace("-", "gap") + ": " + Math.trunc(s.value * 100) / 100)).join(", ")]
-        }));
-        variationRowData = [{
-                trackId: "annotationTrack_ALIGNMENT_FREQ",
-                displayType: "multi-area" /* RcsbFvDisplayTypes.MULTI_AREA */,
-                overlap: true,
-                trackColor: "#F9F9F9",
-                displayColor: {
-                    thresholds: [],
-                    colors: ["#5289e9", "#76bbf6", "#91cef6", "#b9d9f8", "#d6eafd", "#e6f5fd", "#f9f9f9"]
-                },
-                trackHeight: 20,
-                titleFlagColor: RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
-                rowTitle: conservationName,
-                trackData: sequenceRowData
-            }, {
-                trackId: "annotationTrack_ALIGNMENT_MODE",
-                displayType: "sequence" /* RcsbFvDisplayTypes.SEQUENCE */,
-                overlap: true,
-                trackColor: "#F9F9F9",
-                titleFlagColor: RcsbAnnotationConstants.provenanceColorCode.rcsbPdb,
-                rowTitle: seqName,
-                nonEmptyDisplay: true,
-                trackData: logoRowData
-            }];
-    }
-}

package/lib/RcsbUtils/TrackGenerators/Logo.d.ts

@@ -1,16 +0,0 @@
-import { AlignmentLogo } from "@rcsb/rcsb-api-tools/build/RcsbGraphQL/Types/Borrego/GqlTypes";
-export declare class Logo<T extends string> {
-    private readonly symbols;
-    private n;
-    constructor(logo: AlignmentLogo[]);
-    private aaTypes;
-    get(aa: T): number;
-    total(): number;
-    forEach(callback: (aa: T, n: number) => void): void;
-    mode(): T;
-    frequency(): {
-        symbol: T;
-        value: number;
-    }[];
-    entropy(): number;
-}