@apollo-annotation/mst 0.3.11 → 0.3.12

package/dist/AnnotationFeatureModel.d.ts

@@ -1,4 +1,4 @@
-import { type IAnyModelType, type IMSTMap, type Instance, type SnapshotIn, type SnapshotOrInstance } from 'mobx-state-tree';
+import { type IAnyModelType, type IMSTMap, type Instance, type SnapshotIn, type SnapshotOrInstance } from '@jbrowse/mobx-state-tree';
 export interface TranscriptPartLocation {
     min: number;
     max: number;
@@ -12,44 +12,44 @@ export interface TranscriptPartCoding extends TranscriptPartLocation {
 }
 export type TranscriptPart = TranscriptPartCoding | TranscriptPartNonCoding;
 type TranscriptParts = TranscriptPart[];
-export declare const AnnotationFeatureModel: import("mobx-state-tree").IModelType<{
-    _id: import("mobx-state-tree").ISimpleType<string>;
+export declare const AnnotationFeatureModel: import("@jbrowse/mobx-state-tree").IModelType<{
+    _id: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     /** Unique ID of the reference sequence on which this feature is located */
-    refSeq: import("mobx-state-tree").ISimpleType<string>;
+    refSeq: import("@jbrowse/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>;
+    type: import("@jbrowse/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>;
+    min: import("@jbrowse/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>;
+    max: import("@jbrowse/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>>;
+    strand: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/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>>;
+    children: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/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>>>;
+    attributes: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/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;
+    readonly featureId: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").ISimpleType<string>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/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
@@ -84,13 +84,13 @@ export declare const AnnotationFeatureModel: import("mobx-state-tree").IModelTyp
         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>;
+        children?: SnapshotOrInstance<(IMSTMap<IAnyModelType> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/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>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type Children = IMSTMap<typeof AnnotationFeatureModel> | undefined;
 interface AnnotationFeatureRaw extends Instance<typeof AnnotationFeatureModel> {
 }
@@ -104,3 +104,4 @@ export interface AnnotationFeatureSnapshot extends AnnotationFeatureSnapshotRaw
     children?: Record<string, AnnotationFeatureSnapshot>;
 }
 export {};
+//# sourceMappingURL=AnnotationFeatureModel.d.ts.map

package/dist/AnnotationFeatureModel.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AnnotationFeatureModel.d.ts","sourceRoot":"","sources":["../src/AnnotationFeatureModel.ts"],"names":[],"mappings":"AAIA,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,OAAO,EACZ,KAAK,QAAQ,EACb,KAAK,UAAU,EACf,KAAK,kBAAkB,EAKxB,MAAM,0BAA0B,CAAA;AAQjC,MAAM,WAAW,sBAAsB;IACrC,GAAG,EAAE,MAAM,CAAA;IACX,GAAG,EAAE,MAAM,CAAA;CACZ;AAED,MAAM,WAAW,uBAAwB,SAAQ,sBAAsB;IACrE,IAAI,EAAE,cAAc,GAAG,eAAe,GAAG,QAAQ,GAAG,MAAM,CAAA;CAC3D;AAED,MAAM,WAAW,oBAAqB,SAAQ,sBAAsB;IAClE,IAAI,EAAE,KAAK,CAAA;IACX,KAAK,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;CACjB;AAED,MAAM,MAAM,cAAc,GAAG,oBAAoB,GAAG,uBAAuB,CAAA;AAE3E,KAAK,eAAe,GAAG,cAAc,EAAE,CAAA;AAEvC,eAAO,MAAM,sBAAsB;;IAG/B,2EAA2E;;IAE3E;;;;OAIG;;IAEH;;;;OAIG;;IAEH;;;;OAIG;;IAEH;;;;OAIG;;IAEH,qCAAqC;;IAErC;;;OAGG;;;;;IAUH;;;;OAIG;;IAYH;;;;OAIG;;6BAYsB,MAAM;;;;;;;8BAqNL,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC;sBAM7B,MAAM,SAAS,MAAM,EAAE;kBAG3B,MAAM;sBAGF,MAAM;gBAGZ,MAAM;gBAQN,MAAM;uBAQC,CAAC,GAAG,CAAC,CAAC;2BAGF,yBAAyB;gCAiBpB,MAAM;;oDAW/B;QACD,MAAM,EAAE,MAAM,CAAA;QACd,GAAG,EAAE,MAAM,CAAA;QACX,GAAG,EAAE,MAAM,CAAA;QACX,MAAM,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;QACf,QAAQ,CAAC,EAAE,kBAAkB,iMAAsB,CAAA;KACpD;;;8BAiCmB,iBAAiB;;wGAKpC,CAAA;AAEL,MAAM,MAAM,QAAQ,GAAG,OAAO,CAAC,OAAO,sBAAsB,CAAC,GAAG,SAAS,CAAA;AAKzE,UAAU,oBACR,SAAQ,QAAQ,CAAC,OAAO,sBAAsB,CAAC;CAAG;AAGpD,MAAM,WAAW,iBACf,SAAQ,IAAI,CAAC,oBAAoB,EAAE,UAAU,CAAC;IAC9C,QAAQ,CAAC,EAAE,GAAG,CAAC,MAAM,GAAG,MAAM,EAAE,iBAAiB,CAAC,CAAA;CACnD;AAED,UAAU,4BACR,SAAQ,UAAU,CAAC,OAAO,sBAAsB,CAAC;CAAG;AACtD,MAAM,WAAW,yBACf,SAAQ,4BAA4B;IACpC,qCAAqC;IACrC,QAAQ,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,yBAAyB,CAAC,CAAA;CACrD"}

package/dist/AnnotationFeatureModel.js

@@ -1,49 +1,46 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.AnnotationFeatureModel = void 0;
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
-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
+import { getSession, intersection2 } from '@jbrowse/core/util';
+import { cast, getParentOfType, getSnapshot, types, } from '@jbrowse/mobx-state-tree';
+import { ApolloAssembly } from './index.js';
+const LateAnnotationFeature = types.late(() => AnnotationFeatureModel);
+export const AnnotationFeatureModel = types
     .model('AnnotationFeatureModel', {
-    _id: mobx_state_tree_1.types.identifier,
+    _id: types.identifier,
     /** Unique ID of the reference sequence on which this feature is located */
-    refSeq: mobx_state_tree_1.types.string,
+    refSeq: 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,
+    type: 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,
+    min: 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,
+    max: 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))),
+    strand: types.maybe(types.union(types.literal(1), types.literal(-1))),
     /** Child features of this feature */
-    children: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.map(LateAnnotationFeature)),
+    children: types.maybe(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)),
+    attributes: types.map(types.array(types.string)),
 })
     .views((self) => ({
     get length() {
@@ -101,7 +98,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
     },
     get transcriptExonParts() {
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const session = (0, util_1.getSession)(self);
+        const session = getSession(self);
         const { apolloDataStore } = session;
         const { featureTypeOntology } = apolloDataStore.ontologyManager;
         if (!featureTypeOntology.isTypeOf(self.type, 'transcript') &&
@@ -146,7 +143,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
     },
     get transcriptParts() {
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const session = (0, util_1.getSession)(self);
+        const session = getSession(self);
         const { apolloDataStore } = session;
         const { featureTypeOntology } = apolloDataStore.ontologyManager;
         if (!featureTypeOntology.isTypeOf(self.type, 'transcript') &&
@@ -179,7 +176,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
                 if (lastPart) {
                     parts.push({ min: lastPart.max, max: child.min, type: 'intron' });
                 }
-                const [start, end] = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max);
+                const [start, end] = intersection2(cdsMin, cdsMax, child.min, child.max);
                 let utrType;
                 if (hasIntersected) {
                     utrType = self.strand === 1 ? 'threePrimeUTR' : 'fivePrimeUTR';
@@ -237,7 +234,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
     },
     get looksLikeGene() {
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        const session = (0, util_1.getSession)(self);
+        const session = getSession(self);
         const { apolloDataStore } = session;
         const { featureTypeOntology } = apolloDataStore.ontologyManager;
         if (!featureTypeOntology) {
@@ -302,7 +299,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
     },
     addChild(childFeature) {
         if (self.children && self.children.size > 0) {
-            const existingChildren = (0, mobx_state_tree_1.getSnapshot)(self.children);
+            const existingChildren = getSnapshot(self.children);
             self.children.clear();
             for (const [, child] of Object.entries({
                 ...existingChildren,
@@ -312,7 +309,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
             }
         }
         else {
-            self.children = (0, mobx_state_tree_1.cast)({});
+            self.children = cast({});
             self.children?.put(childFeature);
         }
     },
@@ -327,7 +324,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
         self.setMax(max);
         self.setStrand(strand);
         if (children) {
-            self.children = (0, mobx_state_tree_1.cast)(children);
+            self.children = cast(children);
         }
     },
 }))
@@ -337,7 +334,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
     get parent() {
         let parent;
         try {
-            parent = (0, mobx_state_tree_1.getParentOfType)(self, exports.AnnotationFeatureModel);
+            parent = getParentOfType(self, AnnotationFeatureModel);
         }
         catch {
             // pass
@@ -349,7 +346,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
         let parent;
         do {
             try {
-                parent = (0, mobx_state_tree_1.getParentOfType)(feature, exports.AnnotationFeatureModel);
+                parent = getParentOfType(feature, AnnotationFeatureModel);
                 feature = parent;
             }
             catch {
@@ -359,7 +356,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
         return feature;
     },
     get assemblyId() {
-        return (0, mobx_state_tree_1.getParentOfType)(self, _1.ApolloAssembly)._id;
+        return getParentOfType(self, ApolloAssembly)._id;
     },
 }));
 //# sourceMappingURL=AnnotationFeatureModel.js.map

package/dist/AnnotationFeatureModel.js.map

@@ -1 +1 @@
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