@apollo-annotation/mst 0.3.6 → 0.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (12) 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/CheckResult.d.ts +1 -0
  8. package/dist/tsconfig.tsbuildinfo +1 -1
  9. package/package.json +2 -2
  10. package/src/AnnotationFeatureModel.ts +17 -25
  11. package/src/ApolloRefSeq.ts +11 -1
  12. package/src/CheckResult.ts +2 -0
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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package/dist/CheckResult.d.ts CHANGED
@@ -56,3 +56,4 @@ export interface CheckResultI extends Instance<typeof CheckResult> {
56
56
  }
57
57
  export interface CheckResultSnapshot extends SnapshotIn<typeof CheckResult> {
58
58
  }
59
+ export type CheckResultIdsType = Instance<typeof CheckResult>['ids'];