@apollo-annotation/mst 0.3.4 → 0.3.6

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 (17) hide show
  1. package/dist/AnnotationFeatureModel.d.ts +4 -2
  2. package/dist/AnnotationFeatureModel.js +91 -2
  3. package/dist/AnnotationFeatureModel.js.map +1 -1
  4. package/dist/ApolloAssembly.d.ts +15 -1
  5. package/dist/ApolloAssembly.js.map +1 -1
  6. package/dist/ApolloRefSeq.d.ts +4 -2
  7. package/dist/ApolloRefSeq.js +14 -3
  8. package/dist/ApolloRefSeq.js.map +1 -1
  9. package/dist/CheckResult.d.ts +4 -1
  10. package/dist/CheckResult.js +1 -0
  11. package/dist/CheckResult.js.map +1 -1
  12. package/dist/tsconfig.tsbuildinfo +1 -1
  13. package/package.json +1 -1
  14. package/src/AnnotationFeatureModel.ts +101 -8
  15. package/src/ApolloAssembly.ts +1 -1
  16. package/src/ApolloRefSeq.ts +23 -9
  17. package/src/CheckResult.ts +2 -1
package/dist/AnnotationFeatureModel.d.ts CHANGED
@@ -1,10 +1,10 @@
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- import { IAnyModelType, IMSTMap, Instance, SnapshotIn, SnapshotOrInstance } from 'mobx-state-tree';
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+ import { type IAnyModelType, type IMSTMap, type Instance, type SnapshotIn, type SnapshotOrInstance } from 'mobx-state-tree';
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  export interface TranscriptPartLocation {
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  min: number;
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  max: number;
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  }
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  export interface TranscriptPartNonCoding extends TranscriptPartLocation {
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- type: 'fivePrimeUTR' | 'threePrimeUTR' | 'intron';
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+ type: 'fivePrimeUTR' | 'threePrimeUTR' | 'intron' | 'exon';
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  }
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  export interface TranscriptPartCoding extends TranscriptPartLocation {
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  type: 'CDS';
@@ -63,9 +63,11 @@ export declare const AnnotationFeatureModel: import("mobx-state-tree").IModelTyp
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  */
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  readonly maxWithChildren: number;
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  hasDescendant(featureId: string): boolean;
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+ readonly transcriptExonParts: TranscriptParts;
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  readonly transcriptParts: TranscriptParts[];
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  } & {
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  readonly cdsLocations: TranscriptPartCoding[][];
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+ readonly looksLikeGene: boolean;
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
package/dist/AnnotationFeatureModel.js CHANGED
@@ -96,6 +96,54 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  }
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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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+ 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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+ 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;
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+ if (!children) {
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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;
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+ const parts = [];
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+ for (const child of sortedChildren) {
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+ if (child.min > lastMax) {
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+ parts.push({
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+ min: lastMax,
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+ max: child.min,
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+ type: 'intron',
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+ });
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+ }
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+ parts.push({
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+ min: child.min,
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+ max: child.max,
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+ type: 'exon',
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+ });
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+ lastMax = child.max;
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+ }
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+ if (lastMax < self.max) {
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+ parts.push({
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+ min: lastMax,
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+ max: self.max,
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+ type: 'intron',
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+ });
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+ }
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+ if (self.strand === -1) {
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+ parts.reverse();
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+ }
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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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  const session = (0, util_1.getSession)(self);
@@ -114,10 +162,11 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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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 transcriptParts = [];
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  if (cdsChildren.length === 0) {
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- throw new Error('no CDS in transcript');
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+ transcriptParts.push(this.transcriptExonParts);
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+ return transcriptParts;
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  }
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- const transcriptParts = [];
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  for (const cds of cdsChildren) {
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  const { max: cdsMax, min: cdsMin } = cds;
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  const parts = [];
@@ -191,6 +240,46 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  const { transcriptParts } = self;
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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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+ 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;
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+ }
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+ const children = self.children;
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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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+ 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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+ 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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+ }
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+ }
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+ return false;
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+ },
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  }))
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  .actions((self) => ({
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  setAttributes(attributes) {
package/dist/AnnotationFeatureModel.js.map CHANGED
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package/dist/ApolloAssembly.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import { Instance, SnapshotIn } from 'mobx-state-tree';
1
+ import { type Instance, type SnapshotIn } from 'mobx-state-tree';
2
2
  export type BackendDriverType = 'CollaborationServerDriver' | 'InMemoryFileDriver' | 'DesktopFileDriver';
3
3
  export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
4
4
  _id: import("mobx-state-tree").ISimpleType<string>;
@@ -21,9 +21,11 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
21
21
  readonly minWithChildren: number;
22
22
  readonly maxWithChildren: number;
23
23
  hasDescendant(featureId: string): boolean;
24
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
24
25
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
25
26
  } & {
26
27
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
28
+ readonly looksLikeGene: boolean;
27
29
  } & {
28
30
  setAttributes(attributes: Map<string, string[]>): void;
29
31
  setAttribute(key: string, value: string[]): void;
@@ -82,9 +84,11 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
82
84
  readonly minWithChildren: number;
83
85
  readonly maxWithChildren: number;
84
86
  hasDescendant(featureId: string): boolean;
87
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
85
88
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
86
89
  } & {
87
90
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
91
+ readonly looksLikeGene: boolean;
88
92
  } & {
89
93
  setAttributes(attributes: Map<string, string[]>): void;
90
94
  setAttribute(key: string, value: string[]): void;
@@ -122,9 +126,11 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
122
126
  readonly minWithChildren: number;
123
127
  readonly maxWithChildren: number;
124
128
  hasDescendant(featureId: string): boolean;
129
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
125
130
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
126
131
  } & {
127
132
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
133
+ readonly looksLikeGene: boolean;
128
134
  } & {
129
135
  setAttributes(attributes: Map<string, string[]>): void;
130
136
  setAttribute(key: string, value: string[]): void;
@@ -183,9 +189,11 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
183
189
  readonly minWithChildren: number;
184
190
  readonly maxWithChildren: number;
185
191
  hasDescendant(featureId: string): boolean;
192
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
186
193
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
187
194
  } & {
188
195
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
196
+ readonly looksLikeGene: boolean;
189
197
  } & {
190
198
  setAttributes(attributes: Map<string, string[]>): void;
191
199
  setAttribute(key: string, value: string[]): void;
@@ -242,9 +250,11 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
242
250
  readonly minWithChildren: number;
243
251
  readonly maxWithChildren: number;
244
252
  hasDescendant(featureId: string): boolean;
253
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
245
254
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
246
255
  } & {
247
256
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
257
+ readonly looksLikeGene: boolean;
248
258
  } & {
249
259
  setAttributes(attributes: Map<string, string[]>): void;
250
260
  setAttribute(key: string, value: string[]): void;
@@ -282,9 +292,11 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
282
292
  readonly minWithChildren: number;
283
293
  readonly maxWithChildren: number;
284
294
  hasDescendant(featureId: string): boolean;
295
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
285
296
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
286
297
  } & {
287
298
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
299
+ readonly looksLikeGene: boolean;
288
300
  } & {
289
301
  setAttributes(attributes: Map<string, string[]>): void;
290
302
  setAttribute(key: string, value: string[]): void;
@@ -343,9 +355,11 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
343
355
  readonly minWithChildren: number;
344
356
  readonly maxWithChildren: number;
345
357
  hasDescendant(featureId: string): boolean;
358
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
346
359
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
347
360
  } & {
348
361
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
362
+ readonly looksLikeGene: boolean;
349
363
  } & {
350
364
  setAttributes(attributes: Map<string, string[]>): void;
351
365
  setAttribute(key: string, value: string[]): void;
package/dist/ApolloAssembly.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"ApolloAssembly.js","sourceRoot":"","sources":["../src/ApolloAssembly.ts"],"names":[],"mappings":";;;AAAA,qDAAuE;AAEvE,iDAA6C;AAOhC,QAAA,cAAc,GAAG,uBAAK;KAChC,KAAK,CAAC,gBAAgB,EAAE;IACvB,GAAG,EAAE,uBAAK,CAAC,UAAU;IACrB,OAAO,EAAE,uBAAK,CAAC,GAAG,CAAC,2BAAY,CAAC;IAChC,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;IACnC,iBAAiB,EAAE,uBAAK,CAAC,QAAQ,CAC/B,uBAAK,CAAC,WAAW,CAAC,mBAAmB,EAAE;QACrC,2BAA2B;QAC3B,oBAAoB;QACpB,mBAAmB;KACpB,CAAC,EACF,2BAA2B,CAC5B;CACF,CAAC;KACD,KAAK,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAChB,YAAY,CAAC,OAAe;QAC1B,OAAO,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,IAAI,KAAK,OAAO,CAAC,CAAA;IACvE,CAAC;CACF,CAAC,CAAC;KACF,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAClB,SAAS,CAAC,EAAU,EAAE,IAAY,EAAE,WAAoB;QACtD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,CAAC,CAAA;IACzD,CAAC;IACD,UAAU,CAAC,OAAe;QACxB,OAAO,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;CACF,CAAC,CAAC,CAAA"}
package/dist/ApolloRefSeq.d.ts CHANGED
@@ -1,5 +1,5 @@
1
- import { Instance, SnapshotIn, SnapshotOrInstance } from 'mobx-state-tree';
2
- import { AnnotationFeatureSnapshot } from './AnnotationFeatureModel';
1
+ import { type Instance, type SnapshotIn, type SnapshotOrInstance } from 'mobx-state-tree';
2
+ import { 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>;
@@ -24,9 +24,11 @@ export declare const ApolloRefSeq: import("mobx-state-tree").IModelType<{
24
24
  readonly minWithChildren: number;
25
25
  readonly maxWithChildren: number;
26
26
  hasDescendant(featureId: string): boolean;
27
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
27
28
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
28
29
  } & {
29
30
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
31
+ readonly looksLikeGene: boolean;
30
32
  } & {
31
33
  setAttributes(attributes: Map<string, string[]>): void;
32
34
  setAttribute(key: string, value: string[]): void;
package/dist/ApolloRefSeq.js CHANGED
@@ -29,7 +29,7 @@ exports.ApolloRefSeq = mobx_state_tree_1.types
29
29
  },
30
30
  addSequence(seq) {
31
31
  if (seq.sequence.length !== seq.stop - seq.start) {
32
- throw new Error('sequence does not match declared length');
32
+ throw new Error(`sequence does not match declared length: ${JSON.stringify(seq)}`);
33
33
  }
34
34
  if (self.sequence.length === 0) {
35
35
  self.sequence.push(seq);
@@ -45,7 +45,12 @@ exports.ApolloRefSeq = mobx_state_tree_1.types
45
45
  stop: seq.stop,
46
46
  sequence: seq.sequence,
47
47
  });
48
- newSequences.sort((s1, s2) => s1.start - s2.start);
48
+ newSequences.sort((s1, s2) => {
49
+ if (s1.start === s2.start) {
50
+ return s1.stop - s2.stop;
51
+ }
52
+ return s1.start - s2.start;
53
+ });
49
54
  // eslint-disable-next-line unicorn/no-array-reduce
50
55
  const consolidatedSequences = newSequences.reduce((result, current) => {
51
56
  const lastRange = result.at(-1);
@@ -54,8 +59,9 @@ exports.ApolloRefSeq = mobx_state_tree_1.types
54
59
  }
55
60
  if (lastRange.stop >= current.start) {
56
61
  if (current.stop > lastRange.stop) {
62
+ const overlapLength = lastRange.stop - current.start;
57
63
  lastRange.stop = current.stop;
58
- lastRange.sequence += current.sequence.slice(current.stop - lastRange.stop);
64
+ lastRange.sequence += current.sequence.slice(overlapLength);
59
65
  }
60
66
  }
61
67
  else {
@@ -63,6 +69,11 @@ exports.ApolloRefSeq = mobx_state_tree_1.types
63
69
  }
64
70
  return result;
65
71
  }, []);
72
+ for (const seq of consolidatedSequences) {
73
+ if (seq.sequence.length !== seq.stop - seq.start) {
74
+ throw new Error('Consolidated sequence does not match declared length');
75
+ }
76
+ }
66
77
  if (self.sequence.length === consolidatedSequences.length &&
67
78
  self.sequence.every((s, idx) => s.start === consolidatedSequences[idx].start &&
68
79
  s.stop === consolidatedSequences[idx].stop)) {
package/dist/ApolloRefSeq.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"ApolloRefSeq.js","sourceRoot":"","sources":["../src/ApolloRefSeq.ts"],"names":[],"mappings":";;;AAAA,6CAAsD;AACtD,qDAKwB;AAExB,qEAGiC;AAEpB,QAAA,QAAQ,GAAG,uBAAK,CAAC,KAAK,CAAC;IAClC,KAAK,EAAE,uBAAK,CAAC,MAAM;IACnB,IAAI,EAAE,uBAAK,CAAC,MAAM;IAClB,QAAQ,EAAE,uBAAK,CAAC,MAAM;CACvB,CAAC,CAAA;AAQW,QAAA,YAAY,GAAG,uBAAK;KAC9B,KAAK,CAAC,cAAc,EAAE;IACrB,GAAG,EAAE,uBAAK,CAAC,UAAU;IACrB,IAAI,EAAE,uBAAK,CAAC,MAAM;IAClB,WAAW,EAAE,EAAE;IACf,QAAQ,EAAE,uBAAK,CAAC,GAAG,CAAC,+CAAsB,CAAC;IAC3C,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,gBAAQ,CAAC;CAChC,CAAC;KACD,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAClB,UAAU,CAAC,OAAkC;QAC3C,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAC5B,CAAC;IACD,aAAa,CAAC,SAAiB;QAC7B,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACxC,CAAC;IACD,cAAc,CAAC,WAAmB;QAChC,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IACD,WAAW,CAAC,GAAwC;QAClD,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,KAAK,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,KAAK,EAAE,CAAC;YACjD,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAA;QAC5D,CAAC;QACD,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC/B,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACvB,OAAM;QACR,CAAC;QACD,MAAM,YAAY,GAAuB,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjE,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,QAAQ,EAAE,CAAC,CAAC,QAAQ;SACrB,CAAC,CAAC,CAAA;QACH,YAAY,CAAC,IAAI,CAAC;YAChB,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,IAAI,EAAE,GAAG,CAAC,IAAI;YACd,QAAQ,EAAE,GAAG,CAAC,QAAQ;SACvB,CAAC,CAAA;QACF,YAAY,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,KAAK,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;QAClD,mDAAmD;QACnD,MAAM,qBAAqB,GAAG,YAAY,CAAC,MAAM,CAC/C,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE;YAClB,MAAM,SAAS,GAAG,MAAM,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;YAC/B,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,OAAO,CAAC,OAAO,CAAC,CAAA;YAClB,CAAC;YACD,IAAI,SAAS,CAAC,IAAI,IAAI,OAAO,CAAC,KAAK,EAAE,CAAC;gBACpC,IAAI,OAAO,CAAC,IAAI,GAAG,SAAS,CAAC,IAAI,EAAE,CAAC;oBAClC,SAAS,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI,CAAA;oBAC7B,SAAS,CAAC,QAAQ,IAAI,OAAO,CAAC,QAAQ,CAAC,KAAK,CAC1C,OAAO,CAAC,IAAI,GAAG,SAAS,CAAC,IAAI,CAC9B,CAAA;gBACH,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACtB,CAAC;YACD,OAAO,MAAM,CAAA;QACf,CAAC,EACD,EAAE,CACH,CAAA;QACD,IACE,IAAI,CAAC,QAAQ,CAAC,MAAM,KAAK,qBAAqB,CAAC,MAAM;YACrD,IAAI,CAAC,QAAQ,CAAC,KAAK,CACjB,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CACT,CAAC,CAAC,KAAK,KAAK,qBAAqB,CAAC,GAAG,CAAC,CAAC,KAAK;gBAC5C,CAAC,CAAC,IAAI,KAAK,qBAAqB,CAAC,GAAG,CAAC,CAAC,IAAI,CAC7C,EACD,CAAC;YACD,0BAA0B;YAC1B,OAAM;QACR,CAAC;QACD,IAAI,CAAC,QAAQ,CAAC,KAAK,EAAE,CAAA;QACrB,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,qBAAqB,CAAC,CAAA;IAC9C,CAAC;CACF,CAAC,CAAC;KACF,KAAK,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAChB,WAAW,CAAC,KAAa,EAAE,IAAY;QACrC,KAAK,MAAM,EACT,QAAQ,EACR,KAAK,EAAE,QAAQ,EACf,IAAI,EAAE,OAAO,GACd,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YACnB,yCAAyC;YACzC,IAAI,IAAA,wBAAiB,EAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,EAAE,CAAC;gBACtD,OAAO,QAAQ,CAAC,KAAK,CAAC,KAAK,GAAG,QAAQ,EAAE,IAAI,GAAG,QAAQ,CAAC,CAAA;YAC1D,CAAC;QACH,CAAC;QACD,OAAO,EAAE,CAAA;IACX,CAAC;CACF,CAAC,CAAC,CAAA"}
1
+ {"version":3,"file":"ApolloRefSeq.js","sourceRoot":"","sources":["../src/ApolloRefSeq.ts"],"names":[],"mappings":";;;AAAA,6CAAsD;AACtD,qDAKwB;AAExB,qEAGiC;AAEpB,QAAA,QAAQ,GAAG,uBAAK,CAAC,KAAK,CAAC;IAClC,KAAK,EAAE,uBAAK,CAAC,MAAM;IACnB,IAAI,EAAE,uBAAK,CAAC,MAAM;IAClB,QAAQ,EAAE,uBAAK,CAAC,MAAM;CACvB,CAAC,CAAA;AAQW,QAAA,YAAY,GAAG,uBAAK;KAC9B,KAAK,CAAC,cAAc,EAAE;IACrB,GAAG,EAAE,uBAAK,CAAC,UAAU;IACrB,IAAI,EAAE,uBAAK,CAAC,MAAM;IAClB,WAAW,EAAE,EAAE;IACf,QAAQ,EAAE,uBAAK,CAAC,GAAG,CAAC,+CAAsB,CAAC;IAC3C,QAAQ,EAAE,uBAAK,CAAC,KAAK,CAAC,gBAAQ,CAAC;CAChC,CAAC;KACD,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAClB,UAAU,CAAC,OAAkC;QAC3C,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAC5B,CAAC;IACD,aAAa,CAAC,SAAiB;QAC7B,OAAO,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,CAAC,CAAA;IACxC,CAAC;IACD,cAAc,CAAC,WAAmB;QAChC,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IACD,WAAW,CAAC,GAAwC;QAClD,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,KAAK,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,KAAK,EAAE,CAAC;YACjD,MAAM,IAAI,KAAK,CACb,4CAA4C,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAClE,CAAA;QACH,CAAC;QACD,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC/B,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACvB,OAAM;QACR,CAAC;QACD,MAAM,YAAY,GAAuB,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjE,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,QAAQ,EAAE,CAAC,CAAC,QAAQ;SACrB,CAAC,CAAC,CAAA;QACH,YAAY,CAAC,IAAI,CAAC;YAChB,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,IAAI,EAAE,GAAG,CAAC,IAAI;YACd,QAAQ,EAAE,GAAG,CAAC,QAAQ;SACvB,CAAC,CAAA;QACF,YAAY,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;YAC3B,IAAI,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,KAAK,EAAE,CAAC;gBAC1B,OAAO,EAAE,CAAC,IAAI,GAAG,EAAE,CAAC,IAAI,CAAA;YAC1B,CAAC;YACD,OAAO,EAAE,CAAC,KAAK,GAAG,EAAE,CAAC,KAAK,CAAA;QAC5B,CAAC,CAAC,CAAA;QAEF,mDAAmD;QACnD,MAAM,qBAAqB,GAAG,YAAY,CAAC,MAAM,CAC/C,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE;YAClB,MAAM,SAAS,GAAG,MAAM,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;YAC/B,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,OAAO,CAAC,OAAO,CAAC,CAAA;YAClB,CAAC;YACD,IAAI,SAAS,CAAC,IAAI,IAAI,OAAO,CAAC,KAAK,EAAE,CAAC;gBACpC,IAAI,OAAO,CAAC,IAAI,GAAG,SAAS,CAAC,IAAI,EAAE,CAAC;oBAClC,MAAM,aAAa,GAAG,SAAS,CAAC,IAAI,GAAG,OAAO,CAAC,KAAK,CAAA;oBACpD,SAAS,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI,CAAA;oBAC7B,SAAS,CAAC,QAAQ,IAAI,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAC,aAAa,CAAC,CAAA;gBAC7D,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACtB,CAAC;YACD,OAAO,MAAM,CAAA;QACf,CAAC,EACD,EAAE,CACH,CAAA;QACD,KAAK,MAAM,GAAG,IAAI,qBAAqB,EAAE,CAAC;YACxC,IAAI,GAAG,CAAC,QAAQ,CAAC,MAAM,KAAK,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,KAAK,EAAE,CAAC;gBACjD,MAAM,IAAI,KAAK,CACb,sDAAsD,CACvD,CAAA;YACH,CAAC;QACH,CAAC;QACD,IACE,IAAI,CAAC,QAAQ,CAAC,MAAM,KAAK,qBAAqB,CAAC,MAAM;YACrD,IAAI,CAAC,QAAQ,CAAC,KAAK,CACjB,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE,CACT,CAAC,CAAC,KAAK,KAAK,qBAAqB,CAAC,GAAG,CAAC,CAAC,KAAK;gBAC5C,CAAC,CAAC,IAAI,KAAK,qBAAqB,CAAC,GAAG,CAAC,CAAC,IAAI,CAC7C,EACD,CAAC;YACD,0BAA0B;YAC1B,OAAM;QACR,CAAC;QACD,IAAI,CAAC,QAAQ,CAAC,KAAK,EAAE,CAAA;QACrB,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,GAAG,qBAAqB,CAAC,CAAA;IAC9C,CAAC;CACF,CAAC,CAAC;KACF,KAAK,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IAChB,WAAW,CAAC,KAAa,EAAE,IAAY;QACrC,KAAK,MAAM,EACT,QAAQ,EACR,KAAK,EAAE,QAAQ,EACf,IAAI,EAAE,OAAO,GACd,IAAI,IAAI,CAAC,QAAQ,EAAE,CAAC;YACnB,yCAAyC;YACzC,IAAI,IAAA,wBAAiB,EAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,EAAE,CAAC;gBACtD,OAAO,QAAQ,CAAC,KAAK,CAAC,KAAK,GAAG,QAAQ,EAAE,IAAI,GAAG,QAAQ,CAAC,CAAA;YAC1D,CAAC;QACH,CAAC;QACD,OAAO,EAAE,CAAA;IACX,CAAC;CACF,CAAC,CAAC,CAAA"}
package/dist/CheckResult.d.ts CHANGED
@@ -1,7 +1,8 @@
1
- import { Instance, SnapshotIn } from 'mobx-state-tree';
1
+ import { type Instance, type SnapshotIn } from 'mobx-state-tree';
2
2
  export declare const CheckResult: import("mobx-state-tree").IModelType<{
3
3
  _id: import("mobx-state-tree").ISimpleType<string>;
4
4
  name: import("mobx-state-tree").ISimpleType<string>;
5
+ cause: import("mobx-state-tree").ISimpleType<string>;
5
6
  ids: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IModelType<{
6
7
  _id: import("mobx-state-tree").ISimpleType<string>;
7
8
  refSeq: import("mobx-state-tree").ISimpleType<string>;
@@ -17,9 +18,11 @@ export declare const CheckResult: import("mobx-state-tree").IModelType<{
17
18
  readonly minWithChildren: number;
18
19
  readonly maxWithChildren: number;
19
20
  hasDescendant(featureId: string): boolean;
21
+ readonly transcriptExonParts: import("./AnnotationFeatureModel").TranscriptPart[];
20
22
  readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
21
23
  } & {
22
24
  readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
25
+ readonly looksLikeGene: boolean;
23
26
  } & {
24
27
  setAttributes(attributes: Map<string, string[]>): void;
25
28
  setAttribute(key: string, value: string[]): void;
package/dist/CheckResult.js CHANGED
@@ -6,6 +6,7 @@ const AnnotationFeatureModel_1 = require("./AnnotationFeatureModel");
6
6
  exports.CheckResult = mobx_state_tree_1.types.model('CheckResult', {
7
7
  _id: mobx_state_tree_1.types.identifier,
8
8
  name: mobx_state_tree_1.types.string,
9
+ cause: mobx_state_tree_1.types.string,
9
10
  ids: mobx_state_tree_1.types.array(mobx_state_tree_1.types.safeReference(AnnotationFeatureModel_1.AnnotationFeatureModel)),
10
11
  refSeq: mobx_state_tree_1.types.string,
11
12
  start: mobx_state_tree_1.types.number,
package/dist/CheckResult.js.map CHANGED
@@ -1 +1 @@
1
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