@apollo-annotation/mst 0.1.21 → 0.2.0

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 (13) hide show
  1. package/dist/AnnotationFeatureModel.d.ts +17 -6
  2. package/dist/AnnotationFeatureModel.js +57 -11
  3. package/dist/AnnotationFeatureModel.js.map +1 -1
  4. package/dist/ApolloAssembly.d.ts +28 -42
  5. package/dist/ApolloRefSeq.d.ts +4 -6
  6. package/dist/CheckResult.d.ts +4 -6
  7. package/dist/tsconfig.tsbuildinfo +1 -1
  8. package/package.json +1 -1
  9. package/src/AnnotationFeatureModel.ts +86 -15
  10. package/src/ApolloAssembly.ts +2 -2
  11. package/src/ApolloRefSeq.ts +2 -2
  12. package/src/CheckResult.ts +2 -2
  13. package/tsconfig.json +1 -1
package/dist/AnnotationFeatureModel.d.ts CHANGED
@@ -1,4 +1,17 @@
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  import { IAnyModelType, IMSTMap, Instance, SnapshotIn, 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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+ }
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+ export interface TranscriptPartCoding extends TranscriptPartLocation {
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+ type: 'CDS';
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+ phase: 0 | 1 | 2;
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+ }
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+ export type TranscriptPart = TranscriptPartCoding | TranscriptPartNonCoding;
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+ type TranscriptParts = TranscriptPart[];
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  export declare const AnnotationFeatureModel: import("mobx-state-tree").IModelType<{
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  _id: import("mobx-state-tree").ISimpleType<string>;
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  /** Unique ID of the reference sequence on which this feature is located */
@@ -50,11 +63,9 @@ 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 cdsLocations: {
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- min: number;
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- max: number;
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- phase: 0 | 1 | 2;
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- }[][];
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+ readonly transcriptParts: TranscriptParts[];
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+ } & {
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+ readonly cdsLocations: TranscriptPartCoding[][];
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
@@ -62,7 +73,7 @@ export declare const AnnotationFeatureModel: import("mobx-state-tree").IModelTyp
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  setRefSeq(refSeq: string): void;
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  setMin(min: number): void;
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  setMax(max: number): void;
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- setStrand(strand?: 1 | -1 | undefined): void;
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+ setStrand(strand?: 1 | -1): void;
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  addChild(childFeature: AnnotationFeatureSnapshot): void;
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  deleteChild(childFeatureId: string): void;
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  } & {
package/dist/AnnotationFeatureModel.js CHANGED
@@ -96,7 +96,7 @@ 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 cdsLocations() {
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+ get transcriptParts() {
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  if (self.type !== 'mRNA') {
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  throw new Error('Only features of type "mRNA" or equivalent can calculate CDS locations');
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  }
@@ -108,32 +108,78 @@ exports.AnnotationFeatureModel = mobx_state_tree_1.types
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  if (cdsChildren.length === 0) {
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  throw new Error('no CDS in mRNA');
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  }
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- const cdsLocations = [];
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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 locs = [];
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+ const parts = [];
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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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- if (child.type !== 'exon') {
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- continue;
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+ if (child.type === 'exon') {
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+ exonLocations.push({ min: child.min, max: child.max });
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+ }
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+ }
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+ exonLocations.sort(({ min: a }, { min: b }) => a - b);
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+ for (const child of exonLocations) {
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+ const lastPart = parts.at(-1);
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+ if (lastPart) {
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+ parts.push({ min: lastPart.max, max: child.min, type: 'intron' });
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  }
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  const [start, end] = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max);
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+ let utrType;
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+ if (hasIntersected) {
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+ utrType = self.strand === 1 ? 'threePrimeUTR' : 'fivePrimeUTR';
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+ }
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+ else {
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+ utrType = self.strand === 1 ? 'fivePrimeUTR' : 'threePrimeUTR';
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+ }
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  if (start !== undefined && end !== undefined) {
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- locs.push({ min: start, max: end });
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+ hasIntersected = true;
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+ if (start === child.min && end === child.max) {
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+ parts.push({ min: start, max: end, phase: 0, type: 'CDS' });
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+ }
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+ else if (start === child.min) {
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+ parts.push({ min: start, max: end, phase: 0, type: 'CDS' }, { min: end, max: child.max, type: utrType });
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+ }
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+ else if (end === child.max) {
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+ parts.push({ min: child.min, max: start, type: utrType }, { min: start, max: end, phase: 0, type: 'CDS' });
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+ }
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+ else {
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+ parts.push({ min: child.min, max: start, type: utrType }, { min: start, max: end, phase: 0, type: 'CDS' }, {
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+ min: end,
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+ max: child.max,
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+ type: utrType === 'fivePrimeUTR'
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+ ? 'threePrimeUTR'
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+ : 'fivePrimeUTR',
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+ });
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+ }
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+ }
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+ else {
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+ parts.push({ min: child.min, max: child.max, type: utrType });
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  }
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  }
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- locs.sort(({ min: a }, { min: b }) => a - b);
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+ parts.sort(({ min: a }, { min: b }) => a - b);
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  if (self.strand === -1) {
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- locs.reverse();
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+ parts.reverse();
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  }
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  let nextPhase = 0;
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- const phasedLocs = locs.map((loc) => {
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+ const phasedParts = parts.map((loc) => {
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+ if (loc.type !== 'CDS') {
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+ return loc;
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+ }
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  const phase = nextPhase;
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  nextPhase = ((3 - ((loc.max - loc.min - phase + 3) % 3)) % 3);
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  return { ...loc, phase };
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  });
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- cdsLocations.push(phasedLocs);
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+ transcriptParts.push(phasedParts);
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  }
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- return cdsLocations;
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+ return transcriptParts;
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+ },
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+ }))
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+ .views((self) => ({
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+ get cdsLocations() {
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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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  }))
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  .actions((self) => ({
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package/dist/ApolloAssembly.d.ts CHANGED
@@ -21,11 +21,9 @@ 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 cdsLocations: {
25
- min: number;
26
- max: number;
27
- phase: 0 | 1 | 2;
28
- }[][];
24
+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
25
+ } & {
26
+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
29
27
  } & {
30
28
  setAttributes(attributes: Map<string, string[]>): void;
31
29
  setAttribute(key: string, value: string[]): void;
@@ -33,7 +31,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
33
31
  setRefSeq(refSeq: string): void;
34
32
  setMin(min: number): void;
35
33
  setMax(max: number): void;
36
- setStrand(strand?: 1 | -1 | undefined): void;
34
+ setStrand(strand?: 1 | -1): void;
37
35
  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
38
36
  deleteChild(childFeatureId: string): void;
39
37
  } & {
@@ -84,11 +82,9 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
84
82
  readonly minWithChildren: number;
85
83
  readonly maxWithChildren: number;
86
84
  hasDescendant(featureId: string): boolean;
87
- readonly cdsLocations: {
88
- min: number;
89
- max: number;
90
- phase: 0 | 1 | 2;
91
- }[][];
85
+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
86
+ } & {
87
+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
92
88
  } & {
93
89
  setAttributes(attributes: Map<string, string[]>): void;
94
90
  setAttribute(key: string, value: string[]): void;
@@ -96,7 +92,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
96
92
  setRefSeq(refSeq: string): void;
97
93
  setMin(min: number): void;
98
94
  setMax(max: number): void;
99
- setStrand(strand?: 1 | -1 | undefined): void;
95
+ setStrand(strand?: 1 | -1): void;
100
96
  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
101
97
  deleteChild(childFeatureId: string): void;
102
98
  } & {
@@ -126,11 +122,9 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
126
122
  readonly minWithChildren: number;
127
123
  readonly maxWithChildren: number;
128
124
  hasDescendant(featureId: string): boolean;
129
- readonly cdsLocations: {
130
- min: number;
131
- max: number;
132
- phase: 0 | 1 | 2;
133
- }[][];
125
+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
126
+ } & {
127
+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
134
128
  } & {
135
129
  setAttributes(attributes: Map<string, string[]>): void;
136
130
  setAttribute(key: string, value: string[]): void;
@@ -138,7 +132,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
138
132
  setRefSeq(refSeq: string): void;
139
133
  setMin(min: number): void;
140
134
  setMax(max: number): void;
141
- setStrand(strand?: 1 | -1 | undefined): void;
135
+ setStrand(strand?: 1 | -1): void;
142
136
  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
143
137
  deleteChild(childFeatureId: string): void;
144
138
  } & {
@@ -189,11 +183,9 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
189
183
  readonly minWithChildren: number;
190
184
  readonly maxWithChildren: number;
191
185
  hasDescendant(featureId: string): boolean;
192
- readonly cdsLocations: {
193
- min: number;
194
- max: number;
195
- phase: 0 | 1 | 2;
196
- }[][];
186
+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
187
+ } & {
188
+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
197
189
  } & {
198
190
  setAttributes(attributes: Map<string, string[]>): void;
199
191
  setAttribute(key: string, value: string[]): void;
@@ -201,7 +193,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
201
193
  setRefSeq(refSeq: string): void;
202
194
  setMin(min: number): void;
203
195
  setMax(max: number): void;
204
- setStrand(strand?: 1 | -1 | undefined): void;
196
+ setStrand(strand?: 1 | -1): void;
205
197
  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
206
198
  deleteChild(childFeatureId: string): void;
207
199
  } & {
@@ -250,11 +242,9 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
250
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  readonly minWithChildren: number;
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  readonly maxWithChildren: number;
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  hasDescendant(featureId: string): boolean;
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- readonly cdsLocations: {
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- min: number;
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- max: number;
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- phase: 0 | 1 | 2;
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- }[][];
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+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
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+ } & {
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+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
@@ -262,7 +252,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
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  setRefSeq(refSeq: string): void;
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  setMin(min: number): void;
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  setMax(max: number): void;
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- setStrand(strand?: 1 | -1 | undefined): void;
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+ setStrand(strand?: 1 | -1): void;
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  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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  deleteChild(childFeatureId: string): void;
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  } & {
@@ -292,11 +282,9 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
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  readonly minWithChildren: number;
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  readonly maxWithChildren: number;
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  hasDescendant(featureId: string): boolean;
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- readonly cdsLocations: {
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- min: number;
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- max: number;
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- phase: 0 | 1 | 2;
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- }[][];
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+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
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+ } & {
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+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
@@ -304,7 +292,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
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  setRefSeq(refSeq: string): void;
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  setMin(min: number): void;
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  setMax(max: number): void;
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- setStrand(strand?: 1 | -1 | undefined): void;
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+ setStrand(strand?: 1 | -1): void;
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  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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  deleteChild(childFeatureId: string): void;
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  } & {
@@ -355,11 +343,9 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
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  readonly minWithChildren: number;
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  readonly maxWithChildren: number;
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  hasDescendant(featureId: string): boolean;
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- readonly cdsLocations: {
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- min: number;
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- max: number;
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- phase: 0 | 1 | 2;
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- }[][];
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+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
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+ } & {
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+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
@@ -367,7 +353,7 @@ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
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  setRefSeq(refSeq: string): void;
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  setMin(min: number): void;
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  setMax(max: number): void;
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- setStrand(strand?: 1 | -1 | undefined): void;
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+ setStrand(strand?: 1 | -1): void;
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  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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  deleteChild(childFeatureId: string): void;
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  } & {
package/dist/ApolloRefSeq.d.ts CHANGED
@@ -24,11 +24,9 @@ export declare const ApolloRefSeq: import("mobx-state-tree").IModelType<{
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  readonly minWithChildren: number;
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  readonly maxWithChildren: number;
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  hasDescendant(featureId: string): boolean;
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- readonly cdsLocations: {
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- min: number;
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- max: number;
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- phase: 0 | 1 | 2;
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- }[][];
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+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
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+ } & {
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+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
@@ -36,7 +34,7 @@ export declare const ApolloRefSeq: import("mobx-state-tree").IModelType<{
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  setRefSeq(refSeq: string): void;
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  setMin(min: number): void;
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  setMax(max: number): void;
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- setStrand(strand?: 1 | -1 | undefined): void;
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+ setStrand(strand?: 1 | -1): void;
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  addChild(childFeature: AnnotationFeatureSnapshot): void;
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  deleteChild(childFeatureId: string): void;
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  } & {
package/dist/CheckResult.d.ts CHANGED
@@ -17,11 +17,9 @@ export declare const CheckResult: import("mobx-state-tree").IModelType<{
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  readonly minWithChildren: number;
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  readonly maxWithChildren: number;
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  hasDescendant(featureId: string): boolean;
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- readonly cdsLocations: {
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- min: number;
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- max: number;
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- phase: 0 | 1 | 2;
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- }[][];
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+ readonly transcriptParts: import("./AnnotationFeatureModel").TranscriptPart[][];
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+ } & {
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+ readonly cdsLocations: import("./AnnotationFeatureModel").TranscriptPartCoding[][];
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  } & {
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  setAttributes(attributes: Map<string, string[]>): void;
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  setAttribute(key: string, value: string[]): void;
@@ -29,7 +27,7 @@ export declare const CheckResult: import("mobx-state-tree").IModelType<{
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  setRefSeq(refSeq: string): void;
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  setMin(min: number): void;
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  setMax(max: number): void;
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- setStrand(strand?: 1 | -1 | undefined): void;
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+ setStrand(strand?: 1 | -1): void;
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  addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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  deleteChild(childFeatureId: string): void;
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  } & {