@apollo-annotation/shared 0.1.19 → 0.1.20

package/dist/GFF3/gff3ToAnnotationFeature.js

@@ -0,0 +1,211 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.gff3ToAnnotationFeature = gff3ToAnnotationFeature;
+const tslib_1 = require("tslib");
+const util_1 = require("@jbrowse/core/util");
+const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
+const gffReservedKeys_1 = require("./gffReservedKeys");
+function gff3ToAnnotationFeature(gff3Feature, refSeq, featureIds) {
+    const [firstFeature] = gff3Feature;
+    const { end, seq_id: refName, start, strand, type } = firstFeature;
+    if (!refName) {
+        throw new Error(`feature does not have seq_id: ${JSON.stringify(firstFeature)}`);
+    }
+    if (!type) {
+        throw new Error(`feature does not have type: ${JSON.stringify(firstFeature)}`);
+    }
+    if (start === null) {
+        throw new Error(`feature does not have start: ${JSON.stringify(firstFeature)}`);
+    }
+    if (end === null) {
+        throw new Error(`feature does not have end: ${JSON.stringify(firstFeature)}`);
+    }
+    const [min, max] = getFeatureMinMax(gff3Feature);
+    const convertedChildren = convertChildren(gff3Feature, refSeq, featureIds);
+    const convertedAttributes = convertFeatureAttributes(gff3Feature);
+    const feature = {
+        _id: new bson_objectid_1.default().toHexString(),
+        refSeq: refSeq ?? refName,
+        type,
+        min,
+        max,
+    };
+    if (strand) {
+        if (strand === '+') {
+            feature.strand = 1;
+        }
+        else if (strand === '-') {
+            feature.strand = -1;
+        }
+        else {
+            throw new Error(`Unknown strand: "${strand}"`);
+        }
+    }
+    if (convertedChildren) {
+        feature.children = convertedChildren;
+    }
+    if (convertedAttributes) {
+        feature.attributes = convertedAttributes;
+    }
+    if (featureIds) {
+        featureIds.push(feature._id);
+    }
+    return feature;
+}
+function getFeatureMinMax(gff3Feature) {
+    if (gff3Feature.length > 1 && !gff3Feature.every((f) => f.type === 'CDS')) {
+        throw new Error('GFF3 features has multiple locations but is not a CDS');
+    }
+    const mins = gff3Feature.map((f) => f.start).filter((m) => m !== null);
+    const maxes = gff3Feature.map((f) => f.end).filter((m) => m !== null);
+    const min = Math.min(...mins);
+    const max = Math.max(...maxes);
+    return [min - 1, max];
+}
+function convertFeatureAttributes(gff3Feature) {
+    const convertedAttributes = {};
+    const scores = gff3Feature
+        .map((f) => f.score)
+        .filter((score) => score !== null);
+    const sources = gff3Feature
+        .map((f) => f.source)
+        .filter((source) => source !== null);
+    const attributesCollections = gff3Feature
+        .map((f) => f.attributes)
+        .filter((attributes) => attributes !== null);
+    if (scores.length > 0) {
+        let [score] = scores;
+        if (scores.length > 1) {
+            const scoresSum = scores.reduce((accumulator, currentValue) => accumulator + currentValue, 0);
+            // Average score
+            score = scoresSum / scores.length;
+        }
+        convertedAttributes.gff_score = [String(score)];
+    }
+    if (sources.length > 0) {
+        let [source] = sources;
+        if (sources.length > 1) {
+            const sourceSet = new Set(sources);
+            source = [...sourceSet].join(',');
+        }
+        convertedAttributes.gff_source = [source];
+    }
+    if (attributesCollections.length > 0) {
+        for (const attributesCollection of attributesCollections) {
+            for (const [key, val] of Object.entries(attributesCollection)) {
+                if (!val || key === 'Parent') {
+                    continue;
+                }
+                const newKey = (0, gffReservedKeys_1.isGFFReservedAttribute)(key) ? gffReservedKeys_1.gffToInternal[key] : key;
+                const existingVal = convertedAttributes[newKey];
+                if (existingVal) {
+                    const valSet = new Set([...existingVal, ...val]);
+                    convertedAttributes[newKey] = [...valSet];
+                }
+                else {
+                    convertedAttributes[newKey] = val;
+                }
+            }
+        }
+    }
+    if (Object.keys(convertedAttributes).length > 0) {
+        return convertedAttributes;
+    }
+    return;
+}
+function convertChildren(gff3Feature, refSeq, featureIds) {
+    const convertedChildren = {};
+    const locationsWithChildren = gff3Feature.filter((feature) => feature.child_features.length > 0);
+    if (locationsWithChildren.length > 1) {
+        throw new Error('Features with multiple locations may not have children');
+    }
+    if (locationsWithChildren.length === 0) {
+        return;
+    }
+    const [firstFeature] = locationsWithChildren;
+    const { child_features: childFeatures } = firstFeature;
+    const cdsFeatures = [];
+    for (const childFeature of childFeatures) {
+        const [firstChildFeatureLocation] = childFeature;
+        if (firstChildFeatureLocation.type === 'three_prime_UTR' ||
+            firstChildFeatureLocation.type === 'five_prime_UTR' ||
+            firstChildFeatureLocation.type === 'intron' ||
+            firstChildFeatureLocation.type === 'start_codon' ||
+            firstChildFeatureLocation.type === 'stop_codon') {
+            continue;
+        }
+        if (firstChildFeatureLocation.type === 'CDS') {
+            cdsFeatures.push(childFeature);
+        }
+        else {
+            const child = gff3ToAnnotationFeature(childFeature, refSeq, featureIds);
+            convertedChildren[child._id] = child;
+        }
+    }
+    const processedCDS = cdsFeatures.length > 0 ? processCDS(cdsFeatures, refSeq, featureIds) : [];
+    for (const cds of processedCDS) {
+        convertedChildren[cds._id] = cds;
+    }
+    if (Object.keys(convertedChildren).length > 0) {
+        return convertedChildren;
+    }
+    return;
+}
+/**
+ * If a GFF3 file has CDS features that either (1) don't have an ID or (2) have
+ * different IDs for each CDS, we have to do a bit of guessing about how they
+ * should be represented in our internal structure
+ * @param cdsFeatures -
+ */
+function processCDS(cdsFeatures, refSeq, featureIds) {
+    const locationCounts = cdsFeatures.map((cds) => cds.length);
+    // If any CDS have multiple locations, assume it really is multiple CDS
+    // (e.g. the mRNA has multiple alternative translational start sites)
+    // and process normally.
+    if (locationCounts.some((count) => count > 1)) {
+        return cdsFeatures.map((cds) => gff3ToAnnotationFeature(cds, refSeq, featureIds));
+    }
+    // If all CDS have a single location, we guess that this GFF3 represented CDS
+    // as multiple features instead of a single feature with multiple locations.
+    // To figure out if it's actually representing one vs. multiple CDS features,
+    // first check to see if any of the CDS overlap
+    const sortedCDSLocations = cdsFeatures
+        .map((cds) => cds[0])
+        .filter((cds) => cds.start !== null && cds.end !== null)
+        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+        .sort((cdsA, cdsB) => cdsA.start - cdsB.start);
+    const overlapping = sortedCDSLocations.some((loc, idx) => {
+        const nextLoc = sortedCDSLocations.at(idx + 1);
+        if (!nextLoc) {
+            return false;
+        }
+        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+        return (0, util_1.doesIntersect2)(loc.start, loc.end, nextLoc.start, nextLoc.end);
+    });
+    // If no overlaps, assume it's a single CDS feature
+    if (!overlapping) {
+        return [gff3ToAnnotationFeature(sortedCDSLocations, refSeq, featureIds)];
+    }
+    // Some CDS locations overlap, the best we can do is use the original order to
+    // guess how to group the locations into features
+    const cdsLocations = cdsFeatures.map((cds) => cds[0]);
+    const groupedLocations = [];
+    for (const location of cdsLocations) {
+        const lastGroup = groupedLocations.at(-1);
+        if (!lastGroup) {
+            groupedLocations.push([location]);
+            continue;
+        }
+        const overlaps = lastGroup.some((lastGroupLoc) => (0, util_1.doesIntersect2)(
+        /* eslint-disable @typescript-eslint/no-non-null-assertion */
+        lastGroupLoc.start, lastGroupLoc.end, location.start, location.end));
+        if (overlaps) {
+            groupedLocations.push([location]);
+        }
+        else {
+            lastGroup.push(location);
+        }
+    }
+    return groupedLocations.map((group) => gff3ToAnnotationFeature(group, refSeq, featureIds));
+}
+//# sourceMappingURL=gff3ToAnnotationFeature.js.map

package/dist/GFF3/gff3ToAnnotationFeature.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"gff3ToAnnotationFeature.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.ts"],"names":[],"mappings":";;AAOA,0DA4DC;;AAjED,6CAAmD;AACnD,0EAAoC;AAEpC,uDAAyE;AAEzE,SAAgB,uBAAuB,CACrC,WAAwB,EACxB,MAAe,EACf,UAAqB;IAErB,MAAM,CAAC,YAAY,CAAC,GAAG,WAAW,CAAA;IAClC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,YAAY,CAAA;IAClE,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,MAAM,IAAI,KAAK,CACb,iCAAiC,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,EAAE,CAChE,CAAA;IACH,CAAC;IACD,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CACb,+BAA+B,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,EAAE,CAC9D,CAAA;IACH,CAAC;IACD,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;QACnB,MAAM,IAAI,KAAK,CACb,gCAAgC,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,EAAE,CAC/D,CAAA;IACH,CAAC;IACD,IAAI,GAAG,KAAK,IAAI,EAAE,CAAC;QACjB,MAAM,IAAI,KAAK,CACb,8BAA8B,IAAI,CAAC,SAAS,CAAC,YAAY,CAAC,EAAE,CAC7D,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,gBAAgB,CAAC,WAAW,CAAC,CAAA;IAEhD,MAAM,iBAAiB,GAAG,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,CAAC,CAAA;IAE1E,MAAM,mBAAmB,GAAG,wBAAwB,CAAC,WAAW,CAAC,CAAA;IAEjE,MAAM,OAAO,GAA8B;QACzC,GAAG,EAAE,IAAI,uBAAQ,EAAE,CAAC,WAAW,EAAE;QACjC,MAAM,EAAE,MAAM,IAAI,OAAO;QACzB,IAAI;QACJ,GAAG;QACH,GAAG;KACJ,CAAA;IACD,IAAI,MAAM,EAAE,CAAC;QACX,IAAI,MAAM,KAAK,GAAG,EAAE,CAAC;YACnB,OAAO,CAAC,MAAM,GAAG,CAAC,CAAA;QACpB,CAAC;aAAM,IAAI,MAAM,KAAK,GAAG,EAAE,CAAC;YAC1B,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,oBAAoB,MAAM,GAAG,CAAC,CAAA;QAChD,CAAC;IACH,CAAC;IACD,IAAI,iBAAiB,EAAE,CAAC;QACtB,OAAO,CAAC,QAAQ,GAAG,iBAAiB,CAAA;IACtC,CAAC;IACD,IAAI,mBAAmB,EAAE,CAAC;QACxB,OAAO,CAAC,UAAU,GAAG,mBAAmB,CAAA;IAC1C,CAAC;IACD,IAAI,UAAU,EAAE,CAAC;QACf,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IAC9B,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,SAAS,gBAAgB,CAAC,WAAwB;IAChD,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;QAC1E,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAA;IAC1E,CAAC;IACD,MAAM,IAAI,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,IAAI,CAAC,CAAA;IACtE,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,IAAI,CAAC,CAAA;IACrE,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,CAAA;IAC7B,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,CAAA;IAC9B,OAAO,CAAC,GAAG,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;AACvB,CAAC;AAED,SAAS,wBAAwB,CAC/B,WAAwB;IAExB,MAAM,mBAAmB,GACvB,EAAE,CAAA;IACJ,MAAM,MAAM,GAAG,WAAW;SACvB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC;SACnB,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,KAAK,IAAI,CAAC,CAAA;IACpC,MAAM,OAAO,GAAG,WAAW;SACxB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC;SACpB,MAAM,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,KAAK,IAAI,CAAC,CAAA;IACtC,MAAM,qBAAqB,GAAG,WAAW;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC;SACxB,MAAM,CAAC,CAAC,UAAU,EAAE,EAAE,CAAC,UAAU,KAAK,IAAI,CAAC,CAAA;IAC9C,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtB,IAAI,CAAC,KAAK,CAAC,GAAG,MAAM,CAAA;QACpB,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACtB,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAC7B,CAAC,WAAW,EAAE,YAAY,EAAE,EAAE,CAAC,WAAW,GAAG,YAAY,EACzD,CAAC,CACF,CAAA;YACD,gBAAgB;YAChB,KAAK,GAAG,SAAS,GAAG,MAAM,CAAC,MAAM,CAAA;QACnC,CAAC;QACD,mBAAmB,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAA;IACjD,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACvB,IAAI,CAAC,MAAM,CAAC,GAAG,OAAO,CAAA;QACtB,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACvB,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAA;YAClC,MAAM,GAAG,CAAC,GAAG,SAAS,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACnC,CAAC;QACD,mBAAmB,CAAC,UAAU,GAAG,CAAC,MAAM,CAAC,CAAA;IAC3C,CAAC;IACD,IAAI,qBAAqB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrC,KAAK,MAAM,oBAAoB,IAAI,qBAAqB,EAAE,CAAC;YACzD,KAAK,MAAM,CAAC,GAAG,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,oBAAoB,CAAC,EAAE,CAAC;gBAC9D,IAAI,CAAC,GAAG,IAAI,GAAG,KAAK,QAAQ,EAAE,CAAC;oBAC7B,SAAQ;gBACV,CAAC;gBACD,MAAM,MAAM,GAAG,IAAA,wCAAsB,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,+BAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;gBACrE,MAAM,WAAW,GAAG,mBAAmB,CAAC,MAAM,CAAC,CAAA;gBAC/C,IAAI,WAAW,EAAE,CAAC;oBAChB,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,WAAW,EAAE,GAAG,GAAG,CAAC,CAAC,CAAA;oBAChD,mBAAmB,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,CAAA;gBAC3C,CAAC;qBAAM,CAAC;oBACN,mBAAmB,CAAC,MAAM,CAAC,GAAG,GAAG,CAAA;gBACnC,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IACD,IAAI,MAAM,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAChD,OAAO,mBAAmB,CAAA;IAC5B,CAAC;IACD,OAAM;AACR,CAAC;AAED,SAAS,eAAe,CACtB,WAAwB,EACxB,MAAe,EACf,UAAqB;IAErB,MAAM,iBAAiB,GAA8C,EAAE,CAAA;IACvE,MAAM,qBAAqB,GAAG,WAAW,CAAC,MAAM,CAC9C,CAAC,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,cAAc,CAAC,MAAM,GAAG,CAAC,CAC/C,CAAA;IACD,IAAI,qBAAqB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrC,MAAM,IAAI,KAAK,CAAC,wDAAwD,CAAC,CAAA;IAC3E,CAAC;IACD,IAAI,qBAAqB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAM;IACR,CAAC;IACD,MAAM,CAAC,YAAY,CAAC,GAAG,qBAAqB,CAAA;IAC5C,MAAM,EAAE,cAAc,EAAE,aAAa,EAAE,GAAG,YAAY,CAAA;IAEtD,MAAM,WAAW,GAAkB,EAAE,CAAA;IACrC,KAAK,MAAM,YAAY,IAAI,aAAa,EAAE,CAAC;QACzC,MAAM,CAAC,yBAAyB,CAAC,GAAG,YAAY,CAAA;QAChD,IACE,yBAAyB,CAAC,IAAI,KAAK,iBAAiB;YACpD,yBAAyB,CAAC,IAAI,KAAK,gBAAgB;YACnD,yBAAyB,CAAC,IAAI,KAAK,QAAQ;YAC3C,yBAAyB,CAAC,IAAI,KAAK,aAAa;YAChD,yBAAyB,CAAC,IAAI,KAAK,YAAY,EAC/C,CAAC;YACD,SAAQ;QACV,CAAC;QACD,IAAI,yBAAyB,CAAC,IAAI,KAAK,KAAK,EAAE,CAAC;YAC7C,WAAW,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAChC,CAAC;aAAM,CAAC;YACN,MAAM,KAAK,GAAG,uBAAuB,CAAC,YAAY,EAAE,MAAM,EAAE,UAAU,CAAC,CAAA;YACvE,iBAAiB,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,KAAK,CAAA;QACtC,CAAC;IACH,CAAC;IACD,MAAM,YAAY,GAChB,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;IAC3E,KAAK,MAAM,GAAG,IAAI,YAAY,EAAE,CAAC;QAC/B,iBAAiB,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,CAAA;IAClC,CAAC;IAED,IAAI,MAAM,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC9C,OAAO,iBAAiB,CAAA;IAC1B,CAAC;IACD,OAAM;AACR,CAAC;AAED;;;;;GAKG;AACH,SAAS,UAAU,CACjB,WAA0B,EAC1B,MAAe,EACf,UAAqB;IAErB,MAAM,cAAc,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAC3D,uEAAuE;IACvE,qEAAqE;IACrE,wBAAwB;IACxB,IAAI,cAAc,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,GAAG,CAAC,CAAC,EAAE,CAAC;QAC9C,OAAO,WAAW,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAC7B,uBAAuB,CAAC,GAAG,EAAE,MAAM,EAAE,UAAU,CAAC,CACjD,CAAA;IACH,CAAC;IACD,6EAA6E;IAC7E,4EAA4E;IAC5E,6EAA6E;IAC7E,+CAA+C;IAC/C,MAAM,kBAAkB,GAAG,WAAW;SACnC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;SACpB,MAAM,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,KAAK,KAAK,IAAI,IAAI,GAAG,CAAC,GAAG,KAAK,IAAI,CAAC;QACxD,oEAAoE;SACnE,IAAI,CAAC,CAAC,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,KAAM,GAAG,IAAI,CAAC,KAAM,CAAC,CAAA;IAClD,MAAM,WAAW,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;QACvD,MAAM,OAAO,GAAG,kBAAkB,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAA;QAC9C,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,OAAO,KAAK,CAAA;QACd,CAAC;QACD,oEAAoE;QACpE,OAAO,IAAA,qBAAc,EAAC,GAAG,CAAC,KAAM,EAAE,GAAG,CAAC,GAAI,EAAE,OAAO,CAAC,KAAM,EAAE,OAAO,CAAC,GAAI,CAAC,CAAA;IAC3E,CAAC,CAAC,CAAA;IACF,mDAAmD;IACnD,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,OAAO,CAAC,uBAAuB,CAAC,kBAAkB,EAAE,MAAM,EAAE,UAAU,CAAC,CAAC,CAAA;IAC1E,CAAC;IACD,8EAA8E;IAC9E,iDAAiD;IACjD,MAAM,YAAY,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACrD,MAAM,gBAAgB,GAAgC,EAAE,CAAA;IACxD,KAAK,MAAM,QAAQ,IAAI,YAAY,EAAE,CAAC;QACpC,MAAM,SAAS,GAAG,gBAAgB,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QACzC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,gBAAgB,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAA;YACjC,SAAQ;QACV,CAAC;QACD,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,YAAY,EAAE,EAAE,CAC/C,IAAA,qBAAc;QACZ,6DAA6D;QAC7D,YAAY,CAAC,KAAM,EACnB,YAAY,CAAC,GAAI,EACjB,QAAQ,CAAC,KAAM,EACf,QAAQ,CAAC,GAAI,CAEd,CACF,CAAA;QACD,IAAI,QAAQ,EAAE,CAAC;YACb,gBAAgB,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAA;QACnC,CAAC;aAAM,CAAC;YACN,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QAC1B,CAAC;IACH,CAAC;IACD,OAAO,gBAAgB,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CACpC,uBAAuB,CAAC,KAAK,EAAE,MAAM,EAAE,UAAU,CAAC,CACnD,CAAA;AACH,CAAC"}

package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/GFF3/gff3ToAnnotationFeature.test.js

@@ -0,0 +1,174 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tslib_1 = require("tslib");
+/* eslint-disable @typescript-eslint/no-floating-promises */
+const node_test_1 = require("node:test");
+const node_fs_1 = require("node:fs");
+const gff_1 = tslib_1.__importDefault(require("@gmod/gff"));
+const chai_1 = require("chai");
+const chai_exclude_1 = tslib_1.__importDefault(require("chai-exclude"));
+const gff3ToAnnotationFeature_1 = require("./gff3ToAnnotationFeature");
+(0, chai_1.use)(chai_exclude_1.default);
+const testCases = [
+    [
+        'a feature with no children',
+        'ctgA	example	remark	1000	2000	.	.	.	Name=Remark:hga;Alias=hga\n',
+        {
+            _id: '66c51f3e002c683eaf98a223',
+            refSeq: 'ctgA',
+            type: 'remark',
+            min: 999,
+            max: 2000,
+            attributes: {
+                gff_source: ['example'],
+                gff_name: ['Remark:hga'],
+                gff_alias: ['hga'],
+            },
+        },
+    ],
+    [
+        'a feature with two children',
+        `ctgA	est	EST_match	1050	3202	.	+	.	ID=Match1;Name=agt830.5;Target=agt830.5 1 654
+ctgA	est	match_part	1050	1500	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 1 451
+ctgA	est	match_part	3000	3202	.	+	.	Parent=Match1;Name=agt830.5;Target=agt830.5 452 654
+`,
+        {
+            _id: '66cf9fbb4e947fa2c27d3d6a',
+            refSeq: 'ctgA',
+            type: 'EST_match',
+            min: 1049,
+            max: 3202,
+            strand: 1,
+            children: {
+                '66cf9fbb4e947fa2c27d3d68': {
+                    _id: '66cf9fbb4e947fa2c27d3d68',
+                    refSeq: 'ctgA',
+                    type: 'match_part',
+                    min: 1049,
+                    max: 1500,
+                    strand: 1,
+                    attributes: {
+                        gff_source: ['est'],
+                        gff_name: ['agt830.5'],
+                        gff_target: ['agt830.5 1 451'],
+                    },
+                },
+                '66cf9fbb4e947fa2c27d3d69': {
+                    _id: '66cf9fbb4e947fa2c27d3d69',
+                    refSeq: 'ctgA',
+                    type: 'match_part',
+                    min: 2999,
+                    max: 3202,
+                    strand: 1,
+                    attributes: {
+                        gff_source: ['est'],
+                        gff_name: ['agt830.5'],
+                        gff_target: ['agt830.5 452 654'],
+                    },
+                },
+            },
+            attributes: {
+                gff_source: ['est'],
+                gff_id: ['Match1'],
+                gff_name: ['agt830.5'],
+                gff_target: ['agt830.5 1 654'],
+            },
+        },
+    ],
+];
+function childrenToArray(feature) {
+    const { children } = feature;
+    if (!children) {
+        return feature;
+    }
+    const childrenArray = Object.values(children).map((child) => childrenToArray(child));
+    return { ...feature, children: childrenArray };
+}
+function compareFeatures(feature1, feature2) {
+    chai_1.assert.deepEqualExcludingEvery(childrenToArray(feature1), childrenToArray(feature2), '_id');
+}
+function readFeatureFile(fn) {
+    const lines = (0, node_fs_1.readFileSync)(fn).toString().split('\n');
+    const feature = [];
+    for (const line of lines) {
+        if (!line.startsWith('#')) {
+            feature.push(line);
+        }
+    }
+    const inGff = gff_1.default.parseStringSync(feature.join('\n'));
+    return inGff;
+}
+function readAnnotationFeatureSnapshot(fn) {
+    const lines = (0, node_fs_1.readFileSync)(fn).toString();
+    return JSON.parse(lines);
+}
+const [ex1, ex2, ex3, ex4] = readFeatureFile('test_data/gene_representations.gff3');
+(0, node_test_1.describe)('gff3ToAnnotationFeature examples', () => {
+    (0, node_test_1.it)('Convert one CDS', () => {
+        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/one_cds.gff3')[0]);
+        const expected = readAnnotationFeatureSnapshot('test_data/one_cds.json');
+        compareFeatures(actual, expected);
+    });
+    (0, node_test_1.it)('Convert two CDSs', () => {
+        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(readFeatureFile('test_data/two_cds.gff3')[0]);
+        const expected = readAnnotationFeatureSnapshot('test_data/two_cds.json');
+        compareFeatures(actual, expected);
+    });
+    (0, node_test_1.it)('Convert example 1', () => {
+        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(ex1);
+        const txt = JSON.stringify(actual, null, 2);
+        chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
+        chai_1.assert.equal(txt.match(/"type": "TF_binding_site"/g)?.length, 1);
+        const expected = readAnnotationFeatureSnapshot('test_data/example01.json');
+        compareFeatures(actual, expected);
+    });
+    (0, node_test_1.it)('Convert example 2', () => {
+        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(ex2);
+        const txt = JSON.stringify(actual, null, 2);
+        chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
+        const expected = readAnnotationFeatureSnapshot('test_data/example02.json');
+        compareFeatures(actual, expected);
+    });
+    (0, node_test_1.it)('Convert example 3', () => {
+        // NB: In example 3 (and in the other examples) mRNA10003 produces two proteins.
+        // In the other examples the two proteins are identified by sharing the same cds id.
+        // In example 3 instead each cds has a unique id so the two proteins are identified by the order they
+        // appear in the gff.
+        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(ex3);
+        const txt = JSON.stringify(actual, null, 2);
+        chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
+        // const expected = readAnnotationFeatureSnapshot('test_data/example03.json')
+        // compareFeatures(actual, expected)
+    });
+    (0, node_test_1.it)('Convert example 4', () => {
+        const ft = JSON.stringify(ex4, null, 2);
+        chai_1.assert.equal(ft.match(/"type": "five_prime_UTR"/g)?.length, 6);
+        chai_1.assert.equal(ft.match(/"type": "three_prime_UTR"/g)?.length, 3);
+        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(ex4);
+        const txt = JSON.stringify(actual, null, 2);
+        chai_1.assert.equal(txt.match(/"type": "CDS"/g)?.length, 4);
+        chai_1.assert.equal(txt.match(/prime_UTR/g), null);
+        const expected = readAnnotationFeatureSnapshot('test_data/example04.json');
+        compareFeatures(actual, expected);
+    });
+    (0, node_test_1.it)('Convert braker gff', () => {
+        const [gffFeature] = readFeatureFile('test_data/braker.gff');
+        const actual = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gffFeature);
+        const txt = JSON.stringify(actual, null, 2);
+        chai_1.assert.equal(txt.match(/intron/g), null);
+        chai_1.assert.equal(txt.match(/_codon/g), null);
+    });
+});
+(0, node_test_1.describe)('gff3ToAnnotationFeature', () => {
+    for (const testCase of testCases) {
+        const [description, featureLine, convertedFeature] = testCase;
+        (0, node_test_1.it)(`converts ${description}`, () => {
+            const gff3Feature = gff_1.default.parseStringSync(featureLine, {
+                parseSequences: false,
+            });
+            const feature = (0, gff3ToAnnotationFeature_1.gff3ToAnnotationFeature)(gff3Feature[0]);
+            compareFeatures(convertedFeature, feature);
+        });
+    }
+});
+//# sourceMappingURL=gff3ToAnnotationFeature.test.js.map

package/dist/GFF3/gff3ToAnnotationFeature.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":";;;AAAA,4DAA4D;AAC5D,yCAAwC;AACxC,qCAAsC;AAEtC,4DAA4C;AAC5C,+BAAkC;AAClC,wEAAsC;AAEtC,uEAAmE;AAGnE,IAAA,UAAG,EAAC,sBAAW,CAAC,CAAA;AAEhB,MAAM,SAAS,GAAkD;IAC/D;QACE,4BAA4B;QAC5B,iEAAiE;QACjE;YACE,GAAG,EAAE,0BAA0B;YAC/B,MAAM,EAAE,MAAM;YACd,IAAI,EAAE,QAAQ;YACd,GAAG,EAAE,GAAG;YACR,GAAG,EAAE,IAAI;YACT,UAAU,EAAE;gBACV,UAAU,EAAE,CAAC,SAAS,CAAC;gBACvB,QAAQ,EAAE,CAAC,YAAY,CAAC;gBACxB,SAAS,EAAE,CAAC,KAAK,CAAC;aACnB;SACF;KACF;IACD;QACE,6BAA6B;QAC7B;;;CAGH;QACG;YACE,GAAG,EAAE,0BAA0B;YAC/B,MAAM,EAAE,MAAM;YACd,IAAI,EAAE,WAAW;YACjB,GAAG,EAAE,IAAI;YACT,GAAG,EAAE,IAAI;YACT,MAAM,EAAE,CAAC;YACT,QAAQ,EAAE;gBACR,0BAA0B,EAAE;oBAC1B,GAAG,EAAE,0BAA0B;oBAC/B,MAAM,EAAE,MAAM;oBACd,IAAI,EAAE,YAAY;oBAClB,GAAG,EAAE,IAAI;oBACT,GAAG,EAAE,IAAI;oBACT,MAAM,EAAE,CAAC;oBACT,UAAU,EAAE;wBACV,UAAU,EAAE,CAAC,KAAK,CAAC;wBACnB,QAAQ,EAAE,CAAC,UAAU,CAAC;wBACtB,UAAU,EAAE,CAAC,gBAAgB,CAAC;qBAC/B;iBACF;gBACD,0BAA0B,EAAE;oBAC1B,GAAG,EAAE,0BAA0B;oBAC/B,MAAM,EAAE,MAAM;oBACd,IAAI,EAAE,YAAY;oBAClB,GAAG,EAAE,IAAI;oBACT,GAAG,EAAE,IAAI;oBACT,MAAM,EAAE,CAAC;oBACT,UAAU,EAAE;wBACV,UAAU,EAAE,CAAC,KAAK,CAAC;wBACnB,QAAQ,EAAE,CAAC,UAAU,CAAC;wBACtB,UAAU,EAAE,CAAC,kBAAkB,CAAC;qBACjC;iBACF;aACF;YACD,UAAU,EAAE;gBACV,UAAU,EAAE,CAAC,KAAK,CAAC;gBACnB,MAAM,EAAE,CAAC,QAAQ,CAAC;gBAClB,QAAQ,EAAE,CAAC,UAAU,CAAC;gBACtB,UAAU,EAAE,CAAC,gBAAgB,CAAC;aAC/B;SACF;KACF;CACF,CAAA;AAOD,SAAS,eAAe,CACtB,OAAkC;IAElC,MAAM,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAA;IAC5B,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,OAAqD,CAAA;IAC9D,CAAC;IACD,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAC1D,eAAe,CAAC,KAAK,CAAC,CACvB,CAAA;IACD,OAAO,EAAE,GAAG,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAA;AAChD,CAAC;AAED,SAAS,eAAe,CACtB,QAAmC,EACnC,QAAmC;IAEnC,aAAM,CAAC,uBAAuB,CAC5B,eAAe,CAAC,QAAQ,CAAC,EACzB,eAAe,CAAC,QAAQ,CAAC,EACzB,KAAK,CACN,CAAA;AACH,CAAC;AAED,SAAS,eAAe,CAAC,EAAU;IACjC,MAAM,KAAK,GAAG,IAAA,sBAAY,EAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IACrD,MAAM,OAAO,GAAa,EAAE,CAAA;IAC5B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC1B,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,MAAM,KAAK,GAAG,aAAG,CAAC,eAAe,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAkB,CAAA;IACtE,OAAO,KAAK,CAAA;AACd,CAAC;AAED,SAAS,6BAA6B,CAAC,EAAU;IAC/C,MAAM,KAAK,GAAG,IAAA,sBAAY,EAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;IACzC,OAAO,IAAI,CAAC,KAAK,CAAC,KAAK,CAA8B,CAAA;AACvD,CAAC;AAED,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,eAAe,CAC1C,qCAAqC,CACtC,CAAA;AAED,IAAA,oBAAQ,EAAC,kCAAkC,EAAE,GAAG,EAAE;IAChD,IAAA,cAAE,EAAC,iBAAiB,EAAE,GAAG,EAAE;QACzB,MAAM,MAAM,GAAG,IAAA,iDAAuB,EACpC,eAAe,CAAC,wBAAwB,CAAC,CAAC,CAAC,CAAC,CAC7C,CAAA;QACD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,wBAAwB,CAAC,CAAA;QACxE,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,kBAAkB,EAAE,GAAG,EAAE;QAC1B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EACpC,eAAe,CAAC,wBAAwB,CAAC,CAAC,CAAC,CAAC,CAC7C,CAAA;QACD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,wBAAwB,CAAC,CAAA;QACxE,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAE3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEhE,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,gFAAgF;QAChF,oFAAoF;QACpF,qGAAqG;QACrG,qBAAqB;QACrB,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEpD,6EAA6E;QAC7E,oCAAoC;IACtC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QACvC,aAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,2BAA2B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAC9D,aAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAE/D,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,EAAE,IAAI,CAAC,CAAA;QAE3C,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,oBAAoB,EAAE,GAAG,EAAE;QAC5B,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAAC,sBAAsB,CAAC,CAAA;QAC5D,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAA,oBAAQ,EAAC,yBAAyB,EAAE,GAAG,EAAE;IACvC,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE,CAAC;QACjC,MAAM,CAAC,WAAW,EAAE,WAAW,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAA;QAC7D,IAAA,cAAE,EAAC,YAAY,WAAW,EAAE,EAAE,GAAG,EAAE;YACjC,MAAM,WAAW,GAAG,aAAG,CAAC,eAAe,CAAC,WAAW,EAAE;gBACnD,cAAc,EAAE,KAAK;aACtB,CAAC,CAAA;YACF,MAAM,OAAO,GAAG,IAAA,iDAAuB,EAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;YACvD,eAAe,CAAC,gBAAgB,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC,CAAC,CAAA"}

package/dist/GFF3/gffReservedKeys.d.ts

@@ -0,0 +1,5 @@
+export type GFFReservedAttribute = 'ID' | 'Name' | 'Alias' | 'Parent' | 'Target' | 'Gap' | 'Derives_from' | 'Note' | 'Dbxref' | 'Ontology_term' | 'Is_circular';
+export type GFFInternalAttribute = 'gff_id' | 'gff_name' | 'gff_alias' | 'gff_parent' | 'gff_target' | 'gff_gap' | 'gff_derives_from' | 'gff_note' | 'gff_dbxref' | 'gff_ontology_term' | 'gff_is_circular';
+export declare const gffToInternal: Record<GFFReservedAttribute, GFFInternalAttribute>;
+export declare function isGFFReservedAttribute(attribute: string): attribute is GFFReservedAttribute;
+export declare const internalToGFF: Record<GFFInternalAttribute, GFFReservedAttribute>;

package/dist/GFF3/gffReservedKeys.js

@@ -0,0 +1,34 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.internalToGFF = exports.gffToInternal = void 0;
+exports.isGFFReservedAttribute = isGFFReservedAttribute;
+exports.gffToInternal = {
+    ID: 'gff_id',
+    Name: 'gff_name',
+    Alias: 'gff_alias',
+    Parent: 'gff_parent',
+    Target: 'gff_target',
+    Gap: 'gff_gap',
+    Derives_from: 'gff_derives_from',
+    Note: 'gff_note',
+    Dbxref: 'gff_dbxref',
+    Ontology_term: 'gff_ontology_term',
+    Is_circular: 'gff_is_circular',
+};
+function isGFFReservedAttribute(attribute) {
+    return attribute in exports.gffToInternal;
+}
+exports.internalToGFF = {
+    gff_id: 'ID',
+    gff_name: 'Name',
+    gff_alias: 'Alias',
+    gff_parent: 'Parent',
+    gff_target: 'Target',
+    gff_gap: 'Gap',
+    gff_derives_from: 'Derives_from',
+    gff_note: 'Note',
+    gff_dbxref: 'Dbxref',
+    gff_ontology_term: 'Ontology_term',
+    gff_is_circular: 'Is_circular',
+};
+//# sourceMappingURL=gffReservedKeys.js.map

package/dist/GFF3/gffReservedKeys.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"gffReservedKeys.js","sourceRoot":"","sources":["../../src/GFF3/gffReservedKeys.ts"],"names":[],"mappings":";;;AAyCA,wDAIC;AAnBY,QAAA,aAAa,GACxB;IACE,EAAE,EAAE,QAAQ;IACZ,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;IACpB,MAAM,EAAE,YAAY;IACpB,GAAG,EAAE,SAAS;IACd,YAAY,EAAE,kBAAkB;IAChC,IAAI,EAAE,UAAU;IAChB,MAAM,EAAE,YAAY;IACpB,aAAa,EAAE,mBAAmB;IAClC,WAAW,EAAE,iBAAiB;CAC/B,CAAA;AAEH,SAAgB,sBAAsB,CACpC,SAAiB;IAEjB,OAAO,SAAS,IAAI,qBAAa,CAAA;AACnC,CAAC;AAEY,QAAA,aAAa,GACxB;IACE,MAAM,EAAE,IAAI;IACZ,QAAQ,EAAE,MAAM;IAChB,SAAS,EAAE,OAAO;IAClB,UAAU,EAAE,QAAQ;IACpB,UAAU,EAAE,QAAQ;IACpB,OAAO,EAAE,KAAK;IACd,gBAAgB,EAAE,cAAc;IAChC,QAAQ,EAAE,MAAM;IAChB,UAAU,EAAE,QAAQ;IACpB,iBAAiB,EAAE,eAAe;IAClC,eAAe,EAAE,aAAa;CAC/B,CAAA"}

package/dist/GFF3/index.d.ts

@@ -0,0 +1,2 @@
+export * from './gffReservedKeys';
+export * from './gff3ToAnnotationFeature';

package/dist/GFF3/index.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tslib_1 = require("tslib");
+tslib_1.__exportStar(require("./gffReservedKeys"), exports);
+tslib_1.__exportStar(require("./gff3ToAnnotationFeature"), exports);
+//# sourceMappingURL=index.js.map

package/dist/GFF3/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GFF3/index.ts"],"names":[],"mappings":";;;AAAA,4DAAiC;AACjC,oEAAyC"}

package/dist/Messages.d.ts

@@ -0,0 +1,28 @@
+import { SerializedChange } from '@apollo-annotation/common';
+import { CheckResultSnapshot } from '@apollo-annotation/mst';
+interface BaseMessage {
+    channel: string;
+    userName: string;
+    userSessionId: string;
+}
+export interface ChangeMessage extends BaseMessage {
+    changeInfo: SerializedChange;
+    changeSequence: number;
+}
+export interface CheckResultUpdate extends BaseMessage {
+    checkResult: CheckResultSnapshot;
+    deleted?: boolean;
+}
+export interface UserLocation {
+    assemblyId: string;
+    refSeq: string;
+    start: number;
+    end: number;
+}
+export interface UserLocationMessage extends BaseMessage {
+    locations: UserLocation[];
+}
+export interface RequestUserInformationMessage extends BaseMessage {
+    readonly reqType: 'CURRENT_LOCATION';
+}
+export {};

package/dist/Messages.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=Messages.js.map

package/dist/Messages.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"Messages.js","sourceRoot":"","sources":["../src/Messages.ts"],"names":[],"mappings":""}

package/dist/Operations/GetAssembliesOperation.d.ts

@@ -0,0 +1,13 @@
+import { LocalGFF3DataStore, Operation, SerializedOperation, ServerDataStore } from '@apollo-annotation/common';
+interface SerializedGetAssembliesOperation extends SerializedOperation {
+    typeName: 'GetAssembliesOperation';
+}
+export declare class GetAssembliesOperation extends Operation {
+    typeName: "GetAssembliesOperation";
+    toJSON(): SerializedGetAssembliesOperation;
+    executeOnServer(backend: ServerDataStore): Promise<(import("mongoose").Document<unknown, any, import("@apollo-annotation/schemas").AssemblyDocument> & Omit<import("@apollo-annotation/schemas").Assembly & Document & {
+        _id: import("mongoose").Types.ObjectId;
+    }, never>)[]>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
+}
+export {};

package/dist/Operations/GetAssembliesOperation.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.GetAssembliesOperation = void 0;
+/* eslint-disable @typescript-eslint/require-await */
+const common_1 = require("@apollo-annotation/common");
+class GetAssembliesOperation extends common_1.Operation {
+    typeName = 'GetAssembliesOperation';
+    toJSON() {
+        const { typeName } = this;
+        return { typeName };
+    }
+    executeOnServer(backend) {
+        return backend.assemblyModel.find({ status: 0 }).exec();
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+}
+exports.GetAssembliesOperation = GetAssembliesOperation;
+//# sourceMappingURL=GetAssembliesOperation.js.map

package/dist/Operations/GetAssembliesOperation.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"GetAssembliesOperation.js","sourceRoot":"","sources":["../../src/Operations/GetAssembliesOperation.ts"],"names":[],"mappings":";;;AAAA,qDAAqD;AACrD,sDAKkC;AAMlC,MAAa,sBAAuB,SAAQ,kBAAS;IACnD,QAAQ,GAAG,wBAAiC,CAAA;IAE5C,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACzB,OAAO,EAAE,QAAQ,EAAE,CAAA;IACrB,CAAC;IAED,eAAe,CAAC,OAAwB;QACtC,OAAO,OAAO,CAAC,aAAa,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,CAAA;IACzD,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;CACF;AAfD,wDAeC"}

package/dist/Operations/GetFeaturesOperation.d.ts

@@ -0,0 +1,26 @@
+import { LocalGFF3DataStore, Operation, OperationOptions, SerializedOperation, ServerDataStore } from '@apollo-annotation/common';
+interface SerializedGetFeaturesOperation extends SerializedOperation {
+    typeName: 'GetFeaturesOperation';
+    refSeq: string;
+    start: number;
+    end: number;
+}
+export declare class GetFeaturesOperation extends Operation {
+    typeName: "GetFeaturesOperation";
+    refSeq: string;
+    start: number;
+    end: number;
+    constructor(json: SerializedGetFeaturesOperation, options?: OperationOptions);
+    toJSON(): SerializedGetFeaturesOperation;
+    /**
+     * Fetch features based on Reference seq, Start and End -values
+     * @param request - Contain search criteria i.e. refSeq, start and end -parameters
+     * @returns Return Array of features if search was successful
+     * or if search data was not found or in case of error throw exception
+     */
+    executeOnServer(backend: ServerDataStore): Promise<(import("@apollo-annotation/schemas").FeatureDocument & Required<{
+        _id: import("mongoose").Types.ObjectId;
+    }>)[]>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
+}
+export {};

package/dist/Operations/GetFeaturesOperation.js

@@ -0,0 +1,42 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.GetFeaturesOperation = void 0;
+/* eslint-disable @typescript-eslint/require-await */
+const common_1 = require("@apollo-annotation/common");
+class GetFeaturesOperation extends common_1.Operation {
+    typeName = 'GetFeaturesOperation';
+    refSeq;
+    start;
+    end;
+    constructor(json, options) {
+        super(json, options);
+        this.refSeq = json.refSeq;
+        this.start = json.start;
+        this.end = json.end;
+    }
+    toJSON() {
+        const { end, refSeq, start, typeName } = this;
+        return { typeName, refSeq, start, end };
+    }
+    /**
+     * Fetch features based on Reference seq, Start and End -values
+     * @param request - Contain search criteria i.e. refSeq, start and end -parameters
+     * @returns Return Array of features if search was successful
+     * or if search data was not found or in case of error throw exception
+     */
+    executeOnServer(backend) {
+        return backend.featureModel
+            .find({
+            refSeq: this.refSeq,
+            min: { $lte: this.end },
+            max: { $gte: this.start },
+            status: 0,
+        })
+            .exec();
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+}
+exports.GetFeaturesOperation = GetFeaturesOperation;
+//# sourceMappingURL=GetFeaturesOperation.js.map

package/dist/Operations/GetFeaturesOperation.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"GetFeaturesOperation.js","sourceRoot":"","sources":["../../src/Operations/GetFeaturesOperation.ts"],"names":[],"mappings":";;;AAAA,qDAAqD;AACrD,sDAMkC;AASlC,MAAa,oBAAqB,SAAQ,kBAAS;IACjD,QAAQ,GAAG,sBAA+B,CAAA;IAC1C,MAAM,CAAQ;IACd,KAAK,CAAQ;IACb,GAAG,CAAQ;IAEX,YACE,IAAoC,EACpC,OAA0B;QAE1B,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACzB,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;QACvB,IAAI,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAA;IACrB,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,CAAA;IACzC,CAAC;IAED;;;;;OAKG;IACH,eAAe,CAAC,OAAwB;QACtC,OAAO,OAAO,CAAC,YAAY;aACxB,IAAI,CAAC;YACJ,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,GAAG,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,GAAG,EAAE;YACvB,GAAG,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,EAAE;YACzB,MAAM,EAAE,CAAC;SACV,CAAC;aACD,IAAI,EAAE,CAAA;IACX,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;CACF;AAzCD,oDAyCC"}

package/dist/Operations/index.d.ts

@@ -0,0 +1,8 @@
+import { GetAssembliesOperation } from './GetAssembliesOperation';
+import { GetFeaturesOperation } from './GetFeaturesOperation';
+export declare const operations: {
+    GetAssembliesOperation: typeof GetAssembliesOperation;
+    GetFeaturesOperation: typeof GetFeaturesOperation;
+};
+export * from './GetAssembliesOperation';
+export * from './GetFeaturesOperation';

package/dist/Operations/index.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.operations = void 0;
+const tslib_1 = require("tslib");
+const GetAssembliesOperation_1 = require("./GetAssembliesOperation");
+const GetFeaturesOperation_1 = require("./GetFeaturesOperation");
+exports.operations = { GetAssembliesOperation: GetAssembliesOperation_1.GetAssembliesOperation, GetFeaturesOperation: GetFeaturesOperation_1.GetFeaturesOperation };
+tslib_1.__exportStar(require("./GetAssembliesOperation"), exports);
+tslib_1.__exportStar(require("./GetFeaturesOperation"), exports);
+//# sourceMappingURL=index.js.map