@apollo-annotation/mst 0.1.18 → 0.1.20

package/dist/AnnotationFeatureModel.d.ts

@@ -0,0 +1,93 @@
+import { IAnyModelType, IMSTMap, Instance, SnapshotIn, SnapshotOrInstance } from 'mobx-state-tree';
+export declare const AnnotationFeatureModel: import("mobx-state-tree").IModelType<{
+    _id: import("mobx-state-tree").ISimpleType<string>;
+    /** Unique ID of the reference sequence on which this feature is located */
+    refSeq: import("mobx-state-tree").ISimpleType<string>;
+    /**
+     * Type of feature. Can be any string, but is usually an ontology term,
+     * e.g. "gene" from the
+     * {@link http://sequenceontology.org/browser/current_release/term/SO:0000704 |Sequence Ontology}.
+     */
+    type: import("mobx-state-tree").ISimpleType<string>;
+    /**
+     * Coordinate of the edge of the feature that is closer to the beginning of
+     * the reference sequence. This can be thought of as the "start" of features
+     * on the positive strand. Uses interbase (0-based half-open) coordinates.
+     */
+    min: import("mobx-state-tree").ISimpleType<number>;
+    /**
+     * Coordinate of the edge of the feature that is closer to the end of the
+     * reference sequence. This can be thought of as the "end" of features on
+     * the positive strand. Uses interbase (0-based half-open) coordinates.
+     */
+    max: import("mobx-state-tree").ISimpleType<number>;
+    /**
+     * The strand on which the feature is located. `+1` for the positive (a.k.a.
+     * plus or forward) and `-1` for the negative (a.k.a minus or reverse)
+     * strand.
+     */
+    strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
+    /** Child features of this feature */
+    children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<IAnyModelType>>;
+    /**
+     * Additional attributes of the feature. This could include name, source,
+     * note, dbxref, etc.
+     */
+    attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
+}, {
+    readonly length: number;
+    readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
+    /**
+     * Possibly different from `min` because "The GFF3 format does not enforce a
+     * rule in which features must be wholly contained within the location of
+     * their parents"
+     */
+    readonly minWithChildren: number;
+    /**
+     * Possibly different from `max` because "The GFF3 format does not enforce a
+     * rule in which features must be wholly contained within the location of
+     * their parents"
+     */
+    readonly maxWithChildren: number;
+    hasDescendant(featureId: string): boolean;
+    readonly cdsLocations: {
+        min: number;
+        max: number;
+        phase: 0 | 1 | 2;
+    }[][];
+} & {
+    setAttributes(attributes: Map<string, string[]>): void;
+    setAttribute(key: string, value: string[]): void;
+    setType(type: string): void;
+    setRefSeq(refSeq: string): void;
+    setMin(min: number): void;
+    setMax(max: number): void;
+    setStrand(strand?: 1 | -1 | undefined): void;
+    addChild(childFeature: AnnotationFeatureSnapshot): void;
+    deleteChild(childFeatureId: string): void;
+} & {
+    update({ children, max, min, refSeq, strand, }: {
+        refSeq: string;
+        min: number;
+        max: number;
+        strand?: 1 | -1;
+        children?: SnapshotOrInstance<(IMSTMap<IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<IAnyModelType>>>) | undefined>;
+    }): void;
+} & {
+    readonly parent: AnnotationFeature | undefined;
+    readonly topLevelFeature: AnnotationFeature;
+    readonly assemblyId: string;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type Children = IMSTMap<typeof AnnotationFeatureModel> | undefined;
+interface AnnotationFeatureRaw extends Instance<typeof AnnotationFeatureModel> {
+}
+export interface AnnotationFeature extends Omit<AnnotationFeatureRaw, 'children'> {
+    children?: Map<string, AnnotationFeature>;
+}
+interface AnnotationFeatureSnapshotRaw extends SnapshotIn<typeof AnnotationFeatureModel> {
+}
+export interface AnnotationFeatureSnapshot extends AnnotationFeatureSnapshotRaw {
+    /** Child features of this feature */
+    children?: Record<string, AnnotationFeatureSnapshot>;
+}
+export {};

package/dist/AnnotationFeatureModel.js

@@ -0,0 +1,236 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.AnnotationFeatureModel = void 0;
+const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const _1 = require(".");
+const LateAnnotationFeature = mobx_state_tree_1.types.late(() => exports.AnnotationFeatureModel);
+exports.AnnotationFeatureModel = mobx_state_tree_1.types
+    .model('AnnotationFeatureModel', {
+    _id: mobx_state_tree_1.types.identifier,
+    /** Unique ID of the reference sequence on which this feature is located */
+    refSeq: mobx_state_tree_1.types.string,
+    /**
+     * Type of feature. Can be any string, but is usually an ontology term,
+     * e.g. "gene" from the
+     * {@link http://sequenceontology.org/browser/current_release/term/SO:0000704 |Sequence Ontology}.
+     */
+    type: mobx_state_tree_1.types.string,
+    /**
+     * Coordinate of the edge of the feature that is closer to the beginning of
+     * the reference sequence. This can be thought of as the "start" of features
+     * on the positive strand. Uses interbase (0-based half-open) coordinates.
+     */
+    min: mobx_state_tree_1.types.number,
+    /**
+     * Coordinate of the edge of the feature that is closer to the end of the
+     * reference sequence. This can be thought of as the "end" of features on
+     * the positive strand. Uses interbase (0-based half-open) coordinates.
+     */
+    max: mobx_state_tree_1.types.number,
+    /**
+     * The strand on which the feature is located. `+1` for the positive (a.k.a.
+     * plus or forward) and `-1` for the negative (a.k.a minus or reverse)
+     * strand.
+     */
+    strand: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.union(mobx_state_tree_1.types.literal(1), mobx_state_tree_1.types.literal(-1))),
+    /** Child features of this feature */
+    children: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.map(LateAnnotationFeature)),
+    /**
+     * Additional attributes of the feature. This could include name, source,
+     * note, dbxref, etc.
+     */
+    attributes: mobx_state_tree_1.types.map(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string)),
+})
+    .views((self) => ({
+    get length() {
+        return self.max - self.min;
+    },
+    get featureId() {
+        return self.attributes.get('id');
+    },
+    /**
+     * Possibly different from `min` because "The GFF3 format does not enforce a
+     * rule in which features must be wholly contained within the location of
+     * their parents"
+     */
+    get minWithChildren() {
+        let { min } = self;
+        const children = self.children;
+        if (!children) {
+            return min;
+        }
+        for (const [, child] of children) {
+            min = Math.min(min, child.min);
+        }
+        return min;
+    },
+    /**
+     * Possibly different from `max` because "The GFF3 format does not enforce a
+     * rule in which features must be wholly contained within the location of
+     * their parents"
+     */
+    get maxWithChildren() {
+        let { max } = self;
+        const children = self.children;
+        if (!children) {
+            return max;
+        }
+        for (const [, child] of children) {
+            max = Math.max(max, child.max);
+        }
+        return max;
+    },
+    hasDescendant(featureId) {
+        const children = self.children;
+        if (!children) {
+            return false;
+        }
+        for (const [id, child] of children) {
+            if (id === featureId) {
+                return true;
+            }
+            if (child.hasDescendant(featureId)) {
+                return true;
+            }
+        }
+        return false;
+    },
+    get cdsLocations() {
+        if (self.type !== 'mRNA') {
+            throw new Error('Only features of type "mRNA" or equivalent can calculate CDS locations');
+        }
+        const children = self.children;
+        if (!children) {
+            throw new Error('no CDS or exons in mRNA');
+        }
+        const cdsChildren = [...children.values()].filter((child) => child.type === 'CDS');
+        if (cdsChildren.length === 0) {
+            throw new Error('no CDS in mRNA');
+        }
+        const cdsLocations = [];
+        for (const cds of cdsChildren) {
+            const { max: cdsMax, min: cdsMin } = cds;
+            const locs = [];
+            for (const [, child] of children) {
+                if (child.type !== 'exon') {
+                    continue;
+                }
+                const [start, end] = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max);
+                if (start !== undefined && end !== undefined) {
+                    locs.push({ min: start, max: end });
+                }
+            }
+            locs.sort(({ min: a }, { min: b }) => a - b);
+            if (self.strand === -1) {
+                locs.reverse();
+            }
+            let nextPhase = 0;
+            const phasedLocs = locs.map((loc) => {
+                const phase = nextPhase;
+                nextPhase = ((3 - ((loc.max - loc.min - phase + 3) % 3)) % 3);
+                return { ...loc, phase };
+            });
+            cdsLocations.push(phasedLocs);
+        }
+        return cdsLocations;
+    },
+}))
+    .actions((self) => ({
+    setAttributes(attributes) {
+        self.attributes.clear();
+        for (const [key, value] of attributes.entries()) {
+            self.attributes.set(key, value);
+        }
+    },
+    setAttribute(key, value) {
+        self.attributes.merge({ [key]: value });
+    },
+    setType(type) {
+        self.type = type;
+    },
+    setRefSeq(refSeq) {
+        self.refSeq = refSeq;
+    },
+    setMin(min) {
+        if (min > self.max) {
+            throw new Error(`Min "${min}" is greater than max "${self.max}"`);
+        }
+        if (self.min !== min) {
+            self.min = min;
+        }
+    },
+    setMax(max) {
+        if (max < self.min) {
+            throw new Error(`Max "${max}" is less than Min "${self.min}"`);
+        }
+        if (self.max !== max) {
+            self.max = max;
+        }
+    },
+    setStrand(strand) {
+        self.strand = strand;
+    },
+    addChild(childFeature) {
+        if (self.children && self.children.size > 0) {
+            const existingChildren = (0, mobx_state_tree_1.getSnapshot)(self.children);
+            self.children.clear();
+            for (const [, child] of Object.entries({
+                ...existingChildren,
+                [childFeature._id]: childFeature,
+            }).sort(([, a], [, b]) => a.min - b.min)) {
+                self.children.put(child);
+            }
+        }
+        else {
+            self.children = (0, mobx_state_tree_1.cast)({});
+            self.children?.put(childFeature);
+        }
+    },
+    deleteChild(childFeatureId) {
+        self.children?.delete(childFeatureId);
+    },
+}))
+    .actions((self) => ({
+    update({ children, max, min, refSeq, strand, }) {
+        self.setRefSeq(refSeq);
+        self.setMin(min);
+        self.setMax(max);
+        self.setStrand(strand);
+        if (children) {
+            self.children = (0, mobx_state_tree_1.cast)(children);
+        }
+    },
+}))
+    // This views block has to be last to avoid:
+    // "'parent' is referenced directly or indirectly in its own type annotation."
+    .views((self) => ({
+    get parent() {
+        let parent;
+        try {
+            parent = (0, mobx_state_tree_1.getParentOfType)(self, exports.AnnotationFeatureModel);
+        }
+        catch {
+            // pass
+        }
+        return parent;
+    },
+    get topLevelFeature() {
+        let feature = self;
+        let parent;
+        do {
+            try {
+                parent = (0, mobx_state_tree_1.getParentOfType)(feature, exports.AnnotationFeatureModel);
+                feature = parent;
+            }
+            catch {
+                parent = undefined;
+            }
+        } while (parent);
+        return feature;
+    },
+    get assemblyId() {
+        return (0, mobx_state_tree_1.getParentOfType)(self, _1.ApolloAssembly)._id;
+    },
+}));
+//# sourceMappingURL=AnnotationFeatureModel.js.map

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