@apollo-annotation/mst 0.3.6 → 0.3.7

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Files changed (10) hide show
  1. package/dist/AnnotationFeatureModel.js +15 -31
  2. package/dist/AnnotationFeatureModel.js.map +1 -1
  3. package/dist/ApolloAssembly.d.ts +5 -0
  4. package/dist/ApolloRefSeq.d.ts +4 -3
  5. package/dist/ApolloRefSeq.js +9 -0
  6. package/dist/ApolloRefSeq.js.map +1 -1
  7. package/dist/tsconfig.tsbuildinfo +1 -1
  8. package/package.json +1 -1
  9. package/src/AnnotationFeatureModel.ts +17 -25
  10. package/src/ApolloRefSeq.ts +11 -1
package/dist/AnnotationFeatureModel.js CHANGED
@@ -1,6 +1,9 @@
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  "use strict";
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  Object.defineProperty(exports, "__esModule", { value: true });
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  exports.AnnotationFeatureModel = void 0;
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+ /* eslint-disable @typescript-eslint/no-unsafe-assignment */
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+ /* eslint-disable @typescript-eslint/no-unsafe-member-access */
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+ /* eslint-disable @typescript-eslint/no-unsafe-call */
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  const util_1 = require("@jbrowse/core/util");
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  const mobx_state_tree_1 = require("mobx-state-tree");
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  const _1 = require(".");
@@ -97,14 +100,12 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  return false;
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  },
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  get transcriptExonParts() {
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
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+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
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  const session = (0, util_1.getSession)(self);
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
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  const { apolloDataStore } = session;
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
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  const { featureTypeOntology } = apolloDataStore.ontologyManager;
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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- if (!featureTypeOntology.isTypeOf(self.type, 'transcript')) {
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+ if (!featureTypeOntology.isTypeOf(self.type, 'transcript') &&
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+ !featureTypeOntology.isTypeOf(self.type, 'pseudogenic_transcript')) {
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  throw new Error('Feature is not a transcript or equivalent, cannot calculate exon locations');
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  }
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  const children = self.children;
@@ -112,7 +113,6 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  throw new Error('No exons in transcript');
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  }
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  const sortedChildren = [...children.values()]
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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  .filter((child) => featureTypeOntology.isTypeOf(child.type, 'exon'))
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  .sort((a, b) => a.min - b.min);
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  let lastMax = self.min;
@@ -145,23 +145,19 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  return parts;
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  },
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  get transcriptParts() {
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
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+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
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  const session = (0, util_1.getSession)(self);
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
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  const { apolloDataStore } = session;
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
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  const { featureTypeOntology } = apolloDataStore.ontologyManager;
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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- if (!featureTypeOntology.isTypeOf(self.type, 'transcript')) {
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+ if (!featureTypeOntology.isTypeOf(self.type, 'transcript') &&
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+ !featureTypeOntology.isTypeOf(self.type, 'pseudogenic_transcript')) {
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  throw new Error('Only features of type "transcript" or equivalent can calculate CDS locations');
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  }
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  const children = self.children;
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  if (!children) {
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  throw new Error('no CDS or exons in transcript');
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  }
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- const cdsChildren = [...children.values()].filter(
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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- (child) => featureTypeOntology.isTypeOf(child.type, 'CDS'));
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+ const cdsChildren = [...children.values()].filter((child) => featureTypeOntology.isTypeOf(child.type, 'CDS'));
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  const transcriptParts = [];
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  if (cdsChildren.length === 0) {
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  transcriptParts.push(this.transcriptExonParts);
@@ -173,7 +169,6 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  let hasIntersected = false;
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  const exonLocations = [];
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  for (const [, child] of children) {
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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  if (featureTypeOntology.isTypeOf(child.type, 'exon')) {
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  exonLocations.push({ min: child.min, max: child.max });
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  }
@@ -241,11 +236,9 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  return transcriptParts.map((transcript) => transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'));
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  },
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  get looksLikeGene() {
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-explicit-any
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+ // eslint-disable-next-line @typescript-eslint/no-explicit-any
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  const session = (0, util_1.getSession)(self);
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
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  const { apolloDataStore } = session;
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
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  const { featureTypeOntology } = apolloDataStore.ontologyManager;
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  if (!featureTypeOntology) {
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  return false;
@@ -254,28 +247,19 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  if (!children?.size) {
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  return false;
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  }
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
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- const isGene =
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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- featureTypeOntology.isTypeOf(self.type, 'gene') ||
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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+ const isGene = featureTypeOntology.isTypeOf(self.type, 'gene') ||
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  featureTypeOntology.isTypeOf(self.type, 'pseudogene');
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  if (!isGene) {
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  return false;
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  }
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  for (const [, child] of children) {
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- if (
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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- featureTypeOntology.isTypeOf(child.type, 'transcript') ||
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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+ if (featureTypeOntology.isTypeOf(child.type, 'transcript') ||
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  featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')) {
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  const { children: grandChildren } = child;
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  if (!grandChildren?.size) {
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  return false;
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  }
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- return [...grandChildren.values()].some((grandchild) =>
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- // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
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- featureTypeOntology.isTypeOf(grandchild.type, 'exon'));
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+ return [...grandChildren.values()].some((grandchild) => featureTypeOntology.isTypeOf(grandchild.type, 'exon'));
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  }
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  }
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  return false;
@@ -299,7 +283,7 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  },
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  setMin(min) {
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  if (min > self.max) {
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- throw new Error(`Min "${min}" is greater than max "${self.max}"`);
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+ throw new Error(`Min "${min + 1}" is greater than max "${self.max}"`);
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  }
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  if (self.min !== min) {
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  self.min = min;
package/dist/AnnotationFeatureModel.js.map CHANGED
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package/dist/ApolloAssembly.d.ts CHANGED
@@ -61,6 +61,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
61
61
  addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
62
62
  } & {
63
63
  getSequence(start: number, stop: number): string;
64
+ getFeatures(min: number, max: number): import("./AnnotationFeatureModel").AnnotationFeature[];
64
65
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
65
66
  comments: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
66
67
  backendDriverType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -170,6 +171,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
170
171
  addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
171
172
  } & {
172
173
  getSequence(start: number, stop: number): string;
174
+ getFeatures(min: number, max: number): import("./AnnotationFeatureModel").AnnotationFeature[];
173
175
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
174
176
  _id: import("mobx-state-tree").ISimpleType<string>;
175
177
  name: import("mobx-state-tree").ISimpleType<string>;
@@ -229,6 +231,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
229
231
  addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
230
232
  } & {
231
233
  getSequence(start: number, stop: number): string;
234
+ getFeatures(min: number, max: number): import("./AnnotationFeatureModel").AnnotationFeature[];
232
235
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
233
236
  } & {
234
237
  addRefSeq(id: string, name: string, description?: string): {
@@ -336,6 +339,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
336
339
  addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
337
340
  } & {
338
341
  getSequence(start: number, stop: number): string;
342
+ getFeatures(min: number, max: number): import("./AnnotationFeatureModel").AnnotationFeature[];
339
343
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
340
344
  _id: import("mobx-state-tree").ISimpleType<string>;
341
345
  name: import("mobx-state-tree").ISimpleType<string>;
@@ -395,6 +399,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
395
399
  addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
396
400
  } & {
397
401
  getSequence(start: number, stop: number): string;
402
+ getFeatures(min: number, max: number): import("./AnnotationFeatureModel").AnnotationFeature[];
398
403
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
399
404
  addComment(comment: string): number;
400
405
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
package/dist/ApolloRefSeq.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import { type Instance, type SnapshotIn, type SnapshotOrInstance } from 'mobx-state-tree';
2
- import { type AnnotationFeatureSnapshot } from './AnnotationFeatureModel';
2
+ import { type AnnotationFeature, type AnnotationFeatureSnapshot } from './AnnotationFeatureModel';
3
3
  export declare const Sequence: import("mobx-state-tree").IModelType<{
4
4
  start: import("mobx-state-tree").ISimpleType<number>;
5
5
  stop: import("mobx-state-tree").ISimpleType<number>;
@@ -48,8 +48,8 @@ export declare const ApolloRefSeq: import("mobx-state-tree").IModelType<{
48
48
  children?: SnapshotOrInstance<(import("mobx-state-tree").IMSTMap<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>>) | undefined>;
49
49
  }): void;
50
50
  } & {
51
- readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
52
- readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
51
+ readonly parent: AnnotationFeature | undefined;
52
+ readonly topLevelFeature: AnnotationFeature;
53
53
  readonly assemblyId: string;
54
54
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
55
55
  sequence: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -64,6 +64,7 @@ export declare const ApolloRefSeq: import("mobx-state-tree").IModelType<{
64
64
  addSequence(seq: SnapshotOrInstance<typeof Sequence>): void;
65
65
  } & {
66
66
  getSequence(start: number, stop: number): string;
67
+ getFeatures(min: number, max: number): AnnotationFeature[];
67
68
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
68
69
  export interface ApolloRefSeqI extends Instance<typeof ApolloRefSeq> {
69
70
  }
package/dist/ApolloRefSeq.js CHANGED
@@ -94,5 +94,14 @@ exports.ApolloRefSeq = mobx_state_tree_1.types
94
94
  }
95
95
  return '';
96
96
  },
97
+ getFeatures(min, max) {
98
+ const features = [];
99
+ for (const [, feature] of self.features) {
100
+ if ((0, util_1.doesIntersect2)(feature.min, feature.max, min, max)) {
101
+ features.push(feature);
102
+ }
103
+ }
104
+ return features;
105
+ },
97
106
  }));
98
107
  //# sourceMappingURL=ApolloRefSeq.js.map
package/dist/ApolloRefSeq.js.map CHANGED
@@ -1 +1 @@
1
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