@apollo-annotation/mst 0.1.19 → 0.1.21

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 +93 -0
  2. package/dist/AnnotationFeatureModel.js +236 -0
  3. package/dist/AnnotationFeatureModel.js.map +1 -0
  4. package/dist/ApolloAssembly.d.ts +404 -0
  5. package/dist/ApolloAssembly.js +30 -0
  6. package/dist/ApolloAssembly.js.map +1 -0
  7. package/dist/ApolloRefSeq.d.ts +71 -0
  8. package/dist/ApolloRefSeq.js +87 -0
  9. package/dist/ApolloRefSeq.js.map +1 -0
  10. package/dist/CheckResult.d.ts +57 -0
  11. package/dist/CheckResult.js +16 -0
  12. package/dist/CheckResult.js.map +1 -0
  13. package/dist/index.d.ts +4 -0
  14. package/dist/index.js +8 -0
  15. package/dist/index.js.map +1 -0
  16. package/dist/tsconfig.tsbuildinfo +1 -0
  17. package/package.json +1 -1
package/dist/ApolloAssembly.d.ts ADDED
@@ -0,0 +1,404 @@
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+ import { Instance, SnapshotIn } from 'mobx-state-tree';
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+ export type BackendDriverType = 'CollaborationServerDriver' | 'InMemoryFileDriver' | 'DesktopFileDriver';
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+ export declare const ApolloAssembly: import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ refSeqs: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ name: import("mobx-state-tree").ISimpleType<string>;
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+ description: import("mobx-state-tree").IType<string | undefined, string, string>;
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+ features: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ refSeq: import("mobx-state-tree").ISimpleType<string>;
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+ type: import("mobx-state-tree").ISimpleType<string>;
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+ min: import("mobx-state-tree").ISimpleType<number>;
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+ max: import("mobx-state-tree").ISimpleType<number>;
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+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
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+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
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+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
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+ }, {
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+ readonly length: number;
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+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
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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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+ } & {
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+ setAttributes(attributes: Map<string, string[]>): void;
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+ setAttribute(key: string, value: string[]): void;
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+ setType(type: string): void;
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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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+ addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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+ deleteChild(childFeatureId: string): void;
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+ } & {
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+ update({ children, max, min, refSeq, strand, }: {
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+ refSeq: string;
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+ min: number;
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+ max: number;
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+ strand?: 1 | -1;
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+ children?: import("mobx-state-tree").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>;
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+ }): void;
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+ } & {
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+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
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+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
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+ readonly assemblyId: string;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ sequence: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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+ start: import("mobx-state-tree").ISimpleType<number>;
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+ stop: import("mobx-state-tree").ISimpleType<number>;
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+ sequence: import("mobx-state-tree").ISimpleType<string>;
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+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ }, {
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+ addFeature(feature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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+ deleteFeature(featureId: string): boolean;
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+ setDescription(description: string): void;
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+ addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
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+ } & {
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+ getSequence(start: number, stop: number): string;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ comments: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
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+ backendDriverType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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+ }, {
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+ getByRefName(refName: string): ({
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+ _id: string;
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+ name: string;
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+ description: string;
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+ features: import("mobx-state-tree").IMSTMap<import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ refSeq: import("mobx-state-tree").ISimpleType<string>;
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+ type: import("mobx-state-tree").ISimpleType<string>;
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+ min: import("mobx-state-tree").ISimpleType<number>;
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+ max: import("mobx-state-tree").ISimpleType<number>;
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+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
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+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
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+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
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+ }, {
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+ readonly length: number;
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+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
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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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+ } & {
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+ setAttributes(attributes: Map<string, string[]>): void;
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+ setAttribute(key: string, value: string[]): void;
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+ setType(type: string): void;
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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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+ addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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+ deleteChild(childFeatureId: string): void;
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+ } & {
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+ update({ children, max, min, refSeq, strand, }: {
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+ refSeq: string;
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+ min: number;
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+ max: number;
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+ strand?: 1 | -1;
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+ children?: import("mobx-state-tree").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>;
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+ }): void;
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+ } & {
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+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
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+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
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+ readonly assemblyId: string;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ refSeq: import("mobx-state-tree").ISimpleType<string>;
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+ type: import("mobx-state-tree").ISimpleType<string>;
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+ min: import("mobx-state-tree").ISimpleType<number>;
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+ max: import("mobx-state-tree").ISimpleType<number>;
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+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
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+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
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+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
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+ }, {
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+ readonly length: number;
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+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
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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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+ } & {
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+ setAttributes(attributes: Map<string, string[]>): void;
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+ setAttribute(key: string, value: string[]): void;
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+ setType(type: string): void;
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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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+ addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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+ deleteChild(childFeatureId: string): void;
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+ } & {
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+ update({ children, max, min, refSeq, strand, }: {
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+ refSeq: string;
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+ min: number;
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+ max: number;
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+ strand?: 1 | -1;
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+ children?: import("mobx-state-tree").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>;
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+ }): void;
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+ } & {
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+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
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+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
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+ readonly assemblyId: string;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
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+ sequence: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
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+ start: import("mobx-state-tree").ISimpleType<number>;
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+ stop: import("mobx-state-tree").ISimpleType<number>;
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+ sequence: import("mobx-state-tree").ISimpleType<string>;
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+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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+ start: import("mobx-state-tree").ISimpleType<number>;
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+ stop: import("mobx-state-tree").ISimpleType<number>;
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+ sequence: import("mobx-state-tree").ISimpleType<string>;
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+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
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+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
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+ addFeature(feature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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+ deleteFeature(featureId: string): boolean;
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+ setDescription(description: string): void;
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+ addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
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+ } & {
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+ getSequence(start: number, stop: number): string;
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+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ name: import("mobx-state-tree").ISimpleType<string>;
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+ description: import("mobx-state-tree").IType<string | undefined, string, string>;
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+ features: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ refSeq: import("mobx-state-tree").ISimpleType<string>;
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+ type: import("mobx-state-tree").ISimpleType<string>;
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+ min: import("mobx-state-tree").ISimpleType<number>;
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+ max: import("mobx-state-tree").ISimpleType<number>;
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+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
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+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
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+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
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+ }, {
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+ readonly length: number;
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+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
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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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+ } & {
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+ setAttributes(attributes: Map<string, string[]>): void;
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+ setAttribute(key: string, value: string[]): void;
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+ setType(type: string): void;
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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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+ addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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+ deleteChild(childFeatureId: string): void;
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+ } & {
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+ update({ children, max, min, refSeq, strand, }: {
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+ refSeq: string;
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+ min: number;
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+ max: number;
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+ strand?: 1 | -1;
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+ children?: import("mobx-state-tree").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>;
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+ }): void;
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+ } & {
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+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
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+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
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+ readonly assemblyId: string;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ sequence: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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+ start: import("mobx-state-tree").ISimpleType<number>;
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+ stop: import("mobx-state-tree").ISimpleType<number>;
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+ sequence: import("mobx-state-tree").ISimpleType<string>;
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+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ }, {
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+ addFeature(feature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
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+ deleteFeature(featureId: string): boolean;
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+ setDescription(description: string): void;
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+ addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
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+ } & {
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+ getSequence(start: number, stop: number): string;
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+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
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+ } & {
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+ addRefSeq(id: string, name: string, description?: string): {
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+ _id: string;
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+ name: string;
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+ description: string;
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+ features: import("mobx-state-tree").IMSTMap<import("mobx-state-tree").IModelType<{
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+ _id: import("mobx-state-tree").ISimpleType<string>;
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+ refSeq: import("mobx-state-tree").ISimpleType<string>;
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+ type: import("mobx-state-tree").ISimpleType<string>;
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+ min: import("mobx-state-tree").ISimpleType<number>;
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+ max: import("mobx-state-tree").ISimpleType<number>;
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+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
245
+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
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+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
247
+ }, {
248
+ readonly length: number;
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+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
250
+ readonly minWithChildren: number;
251
+ readonly maxWithChildren: number;
252
+ hasDescendant(featureId: string): boolean;
253
+ readonly cdsLocations: {
254
+ min: number;
255
+ max: number;
256
+ phase: 0 | 1 | 2;
257
+ }[][];
258
+ } & {
259
+ setAttributes(attributes: Map<string, string[]>): void;
260
+ setAttribute(key: string, value: string[]): void;
261
+ setType(type: string): void;
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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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+ addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
267
+ deleteChild(childFeatureId: string): void;
268
+ } & {
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+ update({ children, max, min, refSeq, strand, }: {
270
+ refSeq: string;
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+ min: number;
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+ max: number;
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+ strand?: 1 | -1;
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+ children?: import("mobx-state-tree").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>;
275
+ }): void;
276
+ } & {
277
+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
278
+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
279
+ readonly assemblyId: string;
280
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
281
+ _id: import("mobx-state-tree").ISimpleType<string>;
282
+ refSeq: import("mobx-state-tree").ISimpleType<string>;
283
+ type: import("mobx-state-tree").ISimpleType<string>;
284
+ min: import("mobx-state-tree").ISimpleType<number>;
285
+ max: import("mobx-state-tree").ISimpleType<number>;
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+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
287
+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
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+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
289
+ }, {
290
+ readonly length: number;
291
+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
292
+ readonly minWithChildren: number;
293
+ readonly maxWithChildren: number;
294
+ hasDescendant(featureId: string): boolean;
295
+ readonly cdsLocations: {
296
+ min: number;
297
+ max: number;
298
+ phase: 0 | 1 | 2;
299
+ }[][];
300
+ } & {
301
+ setAttributes(attributes: Map<string, string[]>): void;
302
+ setAttribute(key: string, value: string[]): void;
303
+ setType(type: string): void;
304
+ setRefSeq(refSeq: string): void;
305
+ setMin(min: number): void;
306
+ setMax(max: number): void;
307
+ setStrand(strand?: 1 | -1 | undefined): void;
308
+ addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
309
+ deleteChild(childFeatureId: string): void;
310
+ } & {
311
+ update({ children, max, min, refSeq, strand, }: {
312
+ refSeq: string;
313
+ min: number;
314
+ max: number;
315
+ strand?: 1 | -1;
316
+ children?: import("mobx-state-tree").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>;
317
+ }): void;
318
+ } & {
319
+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
320
+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
321
+ readonly assemblyId: string;
322
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
323
+ sequence: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
324
+ start: import("mobx-state-tree").ISimpleType<number>;
325
+ stop: import("mobx-state-tree").ISimpleType<number>;
326
+ sequence: import("mobx-state-tree").ISimpleType<string>;
327
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
328
+ start: import("mobx-state-tree").ISimpleType<number>;
329
+ stop: import("mobx-state-tree").ISimpleType<number>;
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+ sequence: import("mobx-state-tree").ISimpleType<string>;
331
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
332
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
333
+ addFeature(feature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
334
+ deleteFeature(featureId: string): boolean;
335
+ setDescription(description: string): void;
336
+ addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
337
+ } & {
338
+ getSequence(start: number, stop: number): string;
339
+ } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
340
+ _id: import("mobx-state-tree").ISimpleType<string>;
341
+ name: import("mobx-state-tree").ISimpleType<string>;
342
+ description: import("mobx-state-tree").IType<string | undefined, string, string>;
343
+ features: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
344
+ _id: import("mobx-state-tree").ISimpleType<string>;
345
+ refSeq: import("mobx-state-tree").ISimpleType<string>;
346
+ type: import("mobx-state-tree").ISimpleType<string>;
347
+ min: import("mobx-state-tree").ISimpleType<number>;
348
+ max: import("mobx-state-tree").ISimpleType<number>;
349
+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
350
+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
351
+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
352
+ }, {
353
+ readonly length: number;
354
+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
355
+ readonly minWithChildren: number;
356
+ readonly maxWithChildren: number;
357
+ hasDescendant(featureId: string): boolean;
358
+ readonly cdsLocations: {
359
+ min: number;
360
+ max: number;
361
+ phase: 0 | 1 | 2;
362
+ }[][];
363
+ } & {
364
+ setAttributes(attributes: Map<string, string[]>): void;
365
+ setAttribute(key: string, value: string[]): void;
366
+ setType(type: string): void;
367
+ setRefSeq(refSeq: string): void;
368
+ setMin(min: number): void;
369
+ setMax(max: number): void;
370
+ setStrand(strand?: 1 | -1 | undefined): void;
371
+ addChild(childFeature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
372
+ deleteChild(childFeatureId: string): void;
373
+ } & {
374
+ update({ children, max, min, refSeq, strand, }: {
375
+ refSeq: string;
376
+ min: number;
377
+ max: number;
378
+ strand?: 1 | -1;
379
+ children?: import("mobx-state-tree").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>;
380
+ }): void;
381
+ } & {
382
+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
383
+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
384
+ readonly assemblyId: string;
385
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
386
+ sequence: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
387
+ start: import("mobx-state-tree").ISimpleType<number>;
388
+ stop: import("mobx-state-tree").ISimpleType<number>;
389
+ sequence: import("mobx-state-tree").ISimpleType<string>;
390
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
391
+ }, {
392
+ addFeature(feature: import("./AnnotationFeatureModel").AnnotationFeatureSnapshot): void;
393
+ deleteFeature(featureId: string): boolean;
394
+ setDescription(description: string): void;
395
+ addSequence(seq: import("mobx-state-tree").SnapshotOrInstance<typeof import("./ApolloRefSeq").Sequence>): void;
396
+ } & {
397
+ getSequence(start: number, stop: number): string;
398
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
399
+ addComment(comment: string): number;
400
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
401
+ export interface ApolloAssemblyI extends Instance<typeof ApolloAssembly> {
402
+ }
403
+ export interface ApolloAssemblySnapshot extends SnapshotIn<typeof ApolloAssembly> {
404
+ }
package/dist/ApolloAssembly.js ADDED
@@ -0,0 +1,30 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.ApolloAssembly = void 0;
4
+ const mobx_state_tree_1 = require("mobx-state-tree");
5
+ const ApolloRefSeq_1 = require("./ApolloRefSeq");
6
+ exports.ApolloAssembly = mobx_state_tree_1.types
7
+ .model('ApolloAssembly', {
8
+ _id: mobx_state_tree_1.types.identifier,
9
+ refSeqs: mobx_state_tree_1.types.map(ApolloRefSeq_1.ApolloRefSeq),
10
+ comments: mobx_state_tree_1.types.array(mobx_state_tree_1.types.string),
11
+ backendDriverType: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.enumeration('backendDriverType', [
12
+ 'CollaborationServerDriver',
13
+ 'InMemoryFileDriver',
14
+ 'DesktopFileDriver',
15
+ ]), 'CollaborationServerDriver'),
16
+ })
17
+ .views((self) => ({
18
+ getByRefName(refName) {
19
+ return [...self.refSeqs.values()].find((val) => val.name === refName);
20
+ },
21
+ }))
22
+ .actions((self) => ({
23
+ addRefSeq(id, name, description) {
24
+ return self.refSeqs.put({ _id: id, name, description });
25
+ },
26
+ addComment(comment) {
27
+ return self.comments.push(comment);
28
+ },
29
+ }));
30
+ //# sourceMappingURL=ApolloAssembly.js.map
package/dist/ApolloAssembly.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"ApolloAssembly.js","sourceRoot":"","sources":["../src/ApolloAssembly.ts"],"names":[],"mappings":";;;AAAA,qDAA6D;AAE7D,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 ADDED
@@ -0,0 +1,71 @@
1
+ import { Instance, SnapshotIn, SnapshotOrInstance } from 'mobx-state-tree';
2
+ import { AnnotationFeatureSnapshot } from './AnnotationFeatureModel';
3
+ export declare const Sequence: import("mobx-state-tree").IModelType<{
4
+ start: import("mobx-state-tree").ISimpleType<number>;
5
+ stop: import("mobx-state-tree").ISimpleType<number>;
6
+ sequence: import("mobx-state-tree").ISimpleType<string>;
7
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
8
+ export declare const ApolloRefSeq: import("mobx-state-tree").IModelType<{
9
+ _id: import("mobx-state-tree").ISimpleType<string>;
10
+ name: import("mobx-state-tree").ISimpleType<string>;
11
+ description: import("mobx-state-tree").IType<string | undefined, string, string>;
12
+ features: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
13
+ _id: import("mobx-state-tree").ISimpleType<string>;
14
+ refSeq: import("mobx-state-tree").ISimpleType<string>;
15
+ type: import("mobx-state-tree").ISimpleType<string>;
16
+ min: import("mobx-state-tree").ISimpleType<number>;
17
+ max: import("mobx-state-tree").ISimpleType<number>;
18
+ strand: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ITypeUnion<1 | -1, 1 | -1, 1 | -1>>;
19
+ children: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IMapType<import("mobx-state-tree").IAnyModelType>>;
20
+ attributes: import("mobx-state-tree").IMapType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
21
+ }, {
22
+ readonly length: number;
23
+ readonly featureId: (import("mobx-state-tree").IMSTArray<import("mobx-state-tree").ISimpleType<string>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>) | undefined;
24
+ readonly minWithChildren: number;
25
+ readonly maxWithChildren: number;
26
+ hasDescendant(featureId: string): boolean;
27
+ readonly cdsLocations: {
28
+ min: number;
29
+ max: number;
30
+ phase: 0 | 1 | 2;
31
+ }[][];
32
+ } & {
33
+ setAttributes(attributes: Map<string, string[]>): void;
34
+ setAttribute(key: string, value: string[]): void;
35
+ setType(type: string): void;
36
+ setRefSeq(refSeq: string): void;
37
+ setMin(min: number): void;
38
+ setMax(max: number): void;
39
+ setStrand(strand?: 1 | -1 | undefined): void;
40
+ addChild(childFeature: AnnotationFeatureSnapshot): void;
41
+ deleteChild(childFeatureId: string): void;
42
+ } & {
43
+ update({ children, max, min, refSeq, strand, }: {
44
+ refSeq: string;
45
+ min: number;
46
+ max: number;
47
+ strand?: 1 | -1;
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
+ }): void;
50
+ } & {
51
+ readonly parent: import("./AnnotationFeatureModel").AnnotationFeature | undefined;
52
+ readonly topLevelFeature: import("./AnnotationFeatureModel").AnnotationFeature;
53
+ readonly assemblyId: string;
54
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
55
+ sequence: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
56
+ start: import("mobx-state-tree").ISimpleType<number>;
57
+ stop: import("mobx-state-tree").ISimpleType<number>;
58
+ sequence: import("mobx-state-tree").ISimpleType<string>;
59
+ }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
60
+ }, {
61
+ addFeature(feature: AnnotationFeatureSnapshot): void;
62
+ deleteFeature(featureId: string): boolean;
63
+ setDescription(description: string): void;
64
+ addSequence(seq: SnapshotOrInstance<typeof Sequence>): void;
65
+ } & {
66
+ getSequence(start: number, stop: number): string;
67
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
68
+ export interface ApolloRefSeqI extends Instance<typeof ApolloRefSeq> {
69
+ }
70
+ export interface ApolloRefSeqSnapshot extends SnapshotIn<typeof ApolloRefSeq> {
71
+ }
package/dist/ApolloRefSeq.js ADDED
@@ -0,0 +1,87 @@
1
+ "use strict";
2
+ Object.defineProperty(exports, "__esModule", { value: true });
3
+ exports.ApolloRefSeq = exports.Sequence = void 0;
4
+ const util_1 = require("@jbrowse/core/util");
5
+ const mobx_state_tree_1 = require("mobx-state-tree");
6
+ const AnnotationFeatureModel_1 = require("./AnnotationFeatureModel");
7
+ exports.Sequence = mobx_state_tree_1.types.model({
8
+ start: mobx_state_tree_1.types.number,
9
+ stop: mobx_state_tree_1.types.number,
10
+ sequence: mobx_state_tree_1.types.string,
11
+ });
12
+ exports.ApolloRefSeq = mobx_state_tree_1.types
13
+ .model('ApolloRefSeq', {
14
+ _id: mobx_state_tree_1.types.identifier,
15
+ name: mobx_state_tree_1.types.string,
16
+ description: '',
17
+ features: mobx_state_tree_1.types.map(AnnotationFeatureModel_1.AnnotationFeatureModel),
18
+ sequence: mobx_state_tree_1.types.array(exports.Sequence),
19
+ })
20
+ .actions((self) => ({
21
+ addFeature(feature) {
22
+ self.features.put(feature);
23
+ },
24
+ deleteFeature(featureId) {
25
+ return self.features.delete(featureId);
26
+ },
27
+ setDescription(description) {
28
+ self.description = description;
29
+ },
30
+ addSequence(seq) {
31
+ if (seq.sequence.length !== seq.stop - seq.start) {
32
+ throw new Error('sequence does not match declared length');
33
+ }
34
+ if (self.sequence.length === 0) {
35
+ self.sequence.push(seq);
36
+ return;
37
+ }
38
+ const newSequences = self.sequence.map((s) => ({
39
+ start: s.start,
40
+ stop: s.stop,
41
+ sequence: s.sequence,
42
+ }));
43
+ newSequences.push({
44
+ start: seq.start,
45
+ stop: seq.stop,
46
+ sequence: seq.sequence,
47
+ });
48
+ newSequences.sort((s1, s2) => s1.start - s2.start);
49
+ // eslint-disable-next-line unicorn/no-array-reduce
50
+ const consolidatedSequences = newSequences.reduce((result, current) => {
51
+ const lastRange = result.at(-1);
52
+ if (lastRange === undefined) {
53
+ return [current];
54
+ }
55
+ if (lastRange.stop >= current.start) {
56
+ if (current.stop > lastRange.stop) {
57
+ lastRange.stop = current.stop;
58
+ lastRange.sequence += current.sequence.slice(current.stop - lastRange.stop);
59
+ }
60
+ }
61
+ else {
62
+ result.push(current);
63
+ }
64
+ return result;
65
+ }, []);
66
+ if (self.sequence.length === consolidatedSequences.length &&
67
+ self.sequence.every((s, idx) => s.start === consolidatedSequences[idx].start &&
68
+ s.stop === consolidatedSequences[idx].stop)) {
69
+ // sequences was unchanged
70
+ return;
71
+ }
72
+ self.sequence.clear();
73
+ self.sequence.push(...consolidatedSequences);
74
+ },
75
+ }))
76
+ .views((self) => ({
77
+ getSequence(start, stop) {
78
+ for (const { sequence, start: seqStart, stop: seqStop, } of self.sequence) {
79
+ // adjacent to existing sequence - modify
80
+ if ((0, util_1.isContainedWithin)(start, stop, seqStart, seqStop)) {
81
+ return sequence.slice(start - seqStart, stop - seqStart);
82
+ }
83
+ }
84
+ return '';
85
+ },
86
+ }));
87
+ //# sourceMappingURL=ApolloRefSeq.js.map
package/dist/ApolloRefSeq.js.map ADDED
@@ -0,0 +1 @@
1
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