@jbrowse/plugin-linear-comparative-view 2.11.2 → 2.12.0

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 (23) hide show
  1. package/dist/LGVSyntenyDisplay/components/util.js +1 -1
  2. package/dist/LinearComparativeView/model.d.ts +10 -36
  3. package/dist/LinearComparativeView/model.js +0 -23
  4. package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.js +54 -101
  5. package/dist/LinearSyntenyDisplay/components/util.d.ts +10 -0
  6. package/dist/LinearSyntenyDisplay/components/util.js +87 -1
  7. package/dist/LinearSyntenyView/components/ImportForm/index.js +1 -0
  8. package/dist/LinearSyntenyView/model.d.ts +36 -139
  9. package/dist/LinearSyntenyView/model.js +0 -8
  10. package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +5 -3
  11. package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js +2 -4
  12. package/esm/LGVSyntenyDisplay/components/util.js +1 -1
  13. package/esm/LinearComparativeView/model.d.ts +10 -36
  14. package/esm/LinearComparativeView/model.js +1 -24
  15. package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.js +54 -101
  16. package/esm/LinearSyntenyDisplay/components/util.d.ts +10 -0
  17. package/esm/LinearSyntenyDisplay/components/util.js +84 -1
  18. package/esm/LinearSyntenyView/components/ImportForm/index.js +1 -0
  19. package/esm/LinearSyntenyView/model.d.ts +36 -139
  20. package/esm/LinearSyntenyView/model.js +0 -8
  21. package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +5 -3
  22. package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js +2 -4
  23. package/package.json +2 -2
package/dist/LinearSyntenyView/model.d.ts CHANGED
@@ -32,7 +32,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
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  trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
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  showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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- linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  middleComparativeHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
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  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
@@ -45,20 +44,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  type: import("mobx-state-tree").IType<string | undefined, string, string>;
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  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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- refName: import("mobx-state-tree").ISimpleType<string>;
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- start: import("mobx-state-tree").ISimpleType<number>;
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- end: import("mobx-state-tree").ISimpleType<number>; /**
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- * #property/
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- */
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- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- } & {
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- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
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- * #action
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- */
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- }, {
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- setRefName(newRefName: string): void;
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- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
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  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
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  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -216,14 +202,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  } | undefined;
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  lowerCaseRefNameAliases: {
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  [x: string]: string | undefined;
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- } | undefined;
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+ } | undefined; /**
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+ * #property
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+ */
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
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- readonly initialized: boolean; /**
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- * #property/
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- */
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+ readonly initialized: boolean;
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  readonly name: string;
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  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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  readonly aliases: string[];
@@ -280,14 +266,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  } | undefined;
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  lowerCaseRefNameAliases: {
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  [x: string]: string | undefined;
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- } | undefined;
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+ } | undefined; /**
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+ * #property
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+ */
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
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  } & {
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  getConf(arg: string): any;
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  } & {
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- readonly initialized: boolean; /**
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- * #property/
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- */
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+ readonly initialized: boolean;
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  readonly name: string;
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  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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  readonly aliases: string[];
@@ -357,7 +343,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  offset: number;
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  start: number;
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  end: number;
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- reversed: boolean;
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+ reversed?: boolean | undefined;
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  };
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  readonly centerLineInfo: {
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  coord: number;
@@ -368,7 +354,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  offset: number;
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  start: number;
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  end: number;
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- reversed: boolean;
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+ reversed?: boolean | undefined;
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  } | undefined;
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  } & {
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  afterCreate(): void;
@@ -381,20 +367,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  type: import("mobx-state-tree").IType<string | undefined, string, string>;
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  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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- refName: import("mobx-state-tree").ISimpleType<string>;
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- start: import("mobx-state-tree").ISimpleType<number>;
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- end: import("mobx-state-tree").ISimpleType<number>; /**
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- * #property/
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- */
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- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- } & {
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- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
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- * #action
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- */
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- }, {
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- setRefName(newRefName: string): void;
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- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
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  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
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  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -428,7 +401,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  readonly refNames: string[][];
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  readonly assemblyNames: string[];
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  } & {
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- afterAttach(): void;
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  beforeDestroy(): void;
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  onSubviewAction(actionName: string, path: string, args?: unknown[] | undefined): void;
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  setWidth(newWidth: number): void;
@@ -441,20 +413,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  type: import("mobx-state-tree").IType<string | undefined, string, string>;
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  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
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- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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- refName: import("mobx-state-tree").ISimpleType<string>;
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- start: import("mobx-state-tree").ISimpleType<number>;
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- end: import("mobx-state-tree").ISimpleType<number>; /**
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- * #property/
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- */
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- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- } & {
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- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
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- * #action
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- */
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- }, {
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- setRefName(newRefName: string): void;
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- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
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+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
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  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
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  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
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  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -474,33 +433,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  type: string;
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  offsetPx: number;
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  bpPerPx: number;
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- displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
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- refName: import("mobx-state-tree").ISimpleType<string>;
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- start: import("mobx-state-tree").ISimpleType<number>;
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- end: import("mobx-state-tree").ISimpleType<number>; /**
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- * #property/
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- */
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- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- } & {
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- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
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- * #action
487
- */
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- }, {
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- setRefName(newRefName: string): void;
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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<{
491
- refName: import("mobx-state-tree").ISimpleType<string>;
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- start: import("mobx-state-tree").ISimpleType<number>;
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- end: import("mobx-state-tree").ISimpleType<number>; /**
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- * #property/
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- */
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- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
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- } & {
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- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
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- * #action
500
- */
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- }, {
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- setRefName(newRefName: string): void;
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- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
436
+ displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
504
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  tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
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  hideHeader: boolean;
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  hideHeaderOverview: boolean;
@@ -658,14 +591,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  } | undefined;
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  lowerCaseRefNameAliases: {
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  [x: string]: string | undefined;
661
- } | undefined;
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+ } | undefined; /**
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+ * #property
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+ */
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
663
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  } & {
664
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  getConf(arg: string): any;
665
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  } & {
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- readonly initialized: boolean; /**
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- * #property/
668
- */
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+ readonly initialized: boolean;
669
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  readonly name: string;
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  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
671
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  readonly aliases: string[];
@@ -722,14 +655,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  } | undefined;
723
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  lowerCaseRefNameAliases: {
724
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  [x: string]: string | undefined;
725
- } | undefined;
658
+ } | undefined; /**
659
+ * #property
660
+ */
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
727
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  } & {
728
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  getConf(arg: string): any;
729
664
  } & {
730
- readonly initialized: boolean; /**
731
- * #property/
732
- */
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+ readonly initialized: boolean;
733
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  readonly name: string;
734
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  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
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  readonly aliases: string[];
@@ -799,7 +732,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  offset: number;
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  start: number;
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734
  end: number;
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- reversed: boolean;
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+ reversed?: boolean | undefined;
803
736
  };
804
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  readonly centerLineInfo: {
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  coord: number;
@@ -810,7 +743,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  offset: number;
811
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  start: number;
812
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  end: number;
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- reversed: boolean;
746
+ reversed?: boolean | undefined;
814
747
  } | undefined;
815
748
  } & {
816
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  afterCreate(): void;
@@ -823,20 +756,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
823
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  type: import("mobx-state-tree").IType<string | undefined, string, string>;
824
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  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
825
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  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
826
- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
827
- refName: import("mobx-state-tree").ISimpleType<string>;
828
- start: import("mobx-state-tree").ISimpleType<number>;
829
- end: import("mobx-state-tree").ISimpleType<number>; /**
830
- * #property/
831
- */
832
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
833
- } & {
834
- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
835
- * #action
836
- */
837
- }, {
838
- setRefName(newRefName: string): void;
839
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
759
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
840
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  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
841
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  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
842
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  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -994,14 +914,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
994
914
  } | undefined;
995
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  lowerCaseRefNameAliases: {
996
916
  [x: string]: string | undefined;
997
- } | undefined;
917
+ } | undefined; /**
918
+ * #property
919
+ */
998
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
999
921
  } & {
1000
922
  getConf(arg: string): any;
1001
923
  } & {
1002
- readonly initialized: boolean; /**
1003
- * #property/
1004
- */
924
+ readonly initialized: boolean;
1005
925
  readonly name: string;
1006
926
  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1007
927
  readonly aliases: string[];
@@ -1058,14 +978,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1058
978
  } | undefined;
1059
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  lowerCaseRefNameAliases: {
1060
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  [x: string]: string | undefined;
1061
- } | undefined;
981
+ } | undefined; /**
982
+ * #property
983
+ */
1062
984
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1063
985
  } & {
1064
986
  getConf(arg: string): any;
1065
987
  } & {
1066
- readonly initialized: boolean; /**
1067
- * #property/
1068
- */
988
+ readonly initialized: boolean;
1069
989
  readonly name: string;
1070
990
  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1071
991
  readonly aliases: string[];
@@ -1135,7 +1055,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1135
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  offset: number;
1136
1056
  start: number;
1137
1057
  end: number;
1138
- reversed: boolean;
1058
+ reversed?: boolean | undefined;
1139
1059
  };
1140
1060
  readonly centerLineInfo: {
1141
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  coord: number;
@@ -1146,7 +1066,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1146
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  offset: number;
1147
1067
  start: number;
1148
1068
  end: number;
1149
- reversed: boolean;
1069
+ reversed?: boolean | undefined;
1150
1070
  } | undefined;
1151
1071
  } & {
1152
1072
  afterCreate(): void;
@@ -1159,20 +1079,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1159
1079
  type: import("mobx-state-tree").IType<string | undefined, string, string>;
1160
1080
  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1161
1081
  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1162
- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1163
- refName: import("mobx-state-tree").ISimpleType<string>;
1164
- start: import("mobx-state-tree").ISimpleType<number>;
1165
- end: import("mobx-state-tree").ISimpleType<number>; /**
1166
- * #property/
1167
- */
1168
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1169
- } & {
1170
- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
1171
- * #action
1172
- */
1173
- }, {
1174
- setRefName(newRefName: string): void;
1175
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
1082
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
1176
1083
  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
1177
1084
  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1178
1085
  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1187,7 +1094,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1187
1094
  }>>, import("mobx-state-tree")._NotCustomized>>): void;
1188
1095
  closeView(): void;
1189
1096
  setMiddleComparativeHeight(n: number): number;
1190
- toggleLinkViews(): void;
1191
1097
  activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
1192
1098
  toggleTrack(trackId: string): boolean;
1193
1099
  showTrack(trackId: string, initialSnapshot?: {}): void;
@@ -1244,15 +1150,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1244
1150
  type: string;
1245
1151
  description: string;
1246
1152
  icon?: undefined;
1247
- } | {
1248
- label: string;
1249
- type: string;
1250
- checked: boolean;
1251
- onClick: () => void;
1252
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1253
- muiName: string;
1254
- };
1255
- description?: undefined;
1256
1153
  } | {
1257
1154
  label: string;
1258
1155
  type: string;
package/dist/LinearSyntenyView/model.js CHANGED
@@ -33,7 +33,6 @@ const util_1 = require("@jbrowse/core/util");
33
33
  const file_saver_1 = require("file-saver");
34
34
  // icons
35
35
  const CropFree_1 = __importDefault(require("@mui/icons-material/CropFree"));
36
- const Link_1 = __importDefault(require("@mui/icons-material/Link"));
37
36
  const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
38
37
  const PhotoCamera_1 = __importDefault(require("@mui/icons-material/PhotoCamera"));
39
38
  const Icons_1 = require("./components/Icons");
@@ -126,13 +125,6 @@ function stateModelFactory(pluginManager) {
126
125
  type: 'checkbox',
127
126
  description: 'Draws per-base CIGAR level alignments',
128
127
  },
129
- {
130
- label: 'Link views',
131
- type: 'checkbox',
132
- checked: self.linkViews,
133
- onClick: self.toggleLinkViews,
134
- icon: Link_1.default,
135
- },
136
128
  {
137
129
  label: 'Use curved lines',
138
130
  type: 'checkbox',
package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts CHANGED
@@ -1,5 +1,7 @@
1
1
  import React from 'react';
2
- declare const BreakpointAlignmentsFeatureDetail: ({ model }: {
3
- model: any;
2
+ declare const SyntenyFeatureDetail: ({ model, }: {
3
+ model: {
4
+ featureData: unknown;
5
+ };
4
6
  }) => React.JSX.Element;
5
- export default BreakpointAlignmentsFeatureDetail;
7
+ export default SyntenyFeatureDetail;
package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js CHANGED
@@ -52,9 +52,7 @@ function Formatter({ value }) {
52
52
  function CustomFeatureDetails(props) {
53
53
  return (react_1.default.createElement(BaseFeatureDetail_1.BaseAttributes, { ...props, formatter: (value) => react_1.default.createElement(Formatter, { value: value }) }));
54
54
  }
55
- const BreakpointAlignmentsFeatureDetail = (0, mobx_react_1.observer)(
56
- // eslint-disable-next-line @typescript-eslint/no-explicit-any
57
- ({ model }) => {
55
+ const SyntenyFeatureDetail = (0, mobx_react_1.observer)(function ({ model, }) {
58
56
  const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
59
57
  return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
60
58
  react_1.default.createElement(BaseFeatureDetail_1.BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
@@ -62,4 +60,4 @@ const BreakpointAlignmentsFeatureDetail = (0, mobx_react_1.observer)(
62
60
  react_1.default.createElement(CustomFeatureDetails, { feature: feature1 }),
63
61
  react_1.default.createElement(CustomFeatureDetails, { feature: feature2 })));
64
62
  });
65
- exports.default = BreakpointAlignmentsFeatureDetail;
63
+ exports.default = SyntenyFeatureDetail;
package/esm/LGVSyntenyDisplay/components/util.js CHANGED
@@ -21,7 +21,7 @@ function findPosInCigar(cigar, startX) {
21
21
  else if (op === 'D') {
22
22
  featX += min;
23
23
  }
24
- else if (op === 'M') {
24
+ else if (op === 'M' || op === '=' || op === 'X') {
25
25
  mateX += min;
26
26
  featX += min;
27
27
  }
package/esm/LinearComparativeView/model.d.ts CHANGED
@@ -17,7 +17,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
17
17
  type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
18
18
  trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
19
19
  showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
20
- linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
21
20
  interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
22
21
  middleComparativeHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
23
22
  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
@@ -30,16 +29,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
30
29
  type: import("mobx-state-tree").IType<string | undefined, string, string>;
31
30
  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
32
31
  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
33
- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
34
- refName: import("mobx-state-tree").ISimpleType<string>;
35
- start: import("mobx-state-tree").ISimpleType<number>;
36
- end: import("mobx-state-tree").ISimpleType<number>;
37
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
38
- } & {
39
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
40
- }, {
41
- setRefName(newRefName: string): void;
42
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
32
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
43
33
  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
44
34
  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
45
35
  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -198,14 +188,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
198
188
  lowerCaseRefNameAliases: {
199
189
  [x: string]: string | undefined;
200
190
  } | undefined;
201
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
191
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
192
+ * #property
193
+ */
202
194
  } & {
203
195
  getConf(arg: string): any;
204
196
  } & {
205
197
  readonly initialized: boolean;
206
- /**
207
- * #property
208
- */
209
198
  readonly name: string;
210
199
  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
211
200
  readonly aliases: string[];
@@ -263,14 +252,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
263
252
  lowerCaseRefNameAliases: {
264
253
  [x: string]: string | undefined;
265
254
  } | undefined;
266
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
255
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
256
+ * #property
257
+ */
267
258
  } & {
268
259
  getConf(arg: string): any;
269
260
  } & {
270
261
  readonly initialized: boolean;
271
- /**
272
- * #property
273
- */
274
262
  readonly name: string;
275
263
  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
276
264
  readonly aliases: string[];
@@ -340,7 +328,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
340
328
  offset: number;
341
329
  start: number;
342
330
  end: number;
343
- reversed: boolean;
331
+ reversed?: boolean | undefined;
344
332
  };
345
333
  readonly centerLineInfo: {
346
334
  coord: number;
@@ -351,7 +339,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
351
339
  offset: number;
352
340
  start: number;
353
341
  end: number;
354
- reversed: boolean;
342
+ reversed?: boolean | undefined;
355
343
  } | undefined;
356
344
  } & {
357
345
  afterCreate(): void;
@@ -364,16 +352,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
364
352
  type: import("mobx-state-tree").IType<string | undefined, string, string>;
365
353
  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
366
354
  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
367
- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
368
- refName: import("mobx-state-tree").ISimpleType<string>;
369
- start: import("mobx-state-tree").ISimpleType<number>;
370
- end: import("mobx-state-tree").ISimpleType<number>;
371
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
372
- } & {
373
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
374
- }, {
375
- setRefName(newRefName: string): void;
376
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
355
+ displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
377
356
  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
378
357
  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
379
358
  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -415,7 +394,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
415
394
  */
416
395
  readonly assemblyNames: string[];
417
396
  } & {
418
- afterAttach(): void;
419
397
  beforeDestroy(): void;
420
398
  onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
421
399
  /**
@@ -440,10 +418,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
440
418
  * #action
441
419
  */
442
420
  setMiddleComparativeHeight(n: number): number;
443
- /**
444
- * #action
445
- */
446
- toggleLinkViews(): void;
447
421
  /**
448
422
  * #action
449
423
  */
package/esm/LinearComparativeView/model.js CHANGED
@@ -1,5 +1,5 @@
1
1
  import { lazy } from 'react';
2
- import { addDisposer, cast, getParent, getPath, getRoot, onAction, resolveIdentifier, types, } from 'mobx-state-tree';
2
+ import { addDisposer, cast, getParent, getPath, getRoot, resolveIdentifier, types, } from 'mobx-state-tree';
3
3
  import { autorun, transaction } from 'mobx';
4
4
  // jbrowse
5
5
  import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel';
@@ -34,10 +34,6 @@ function stateModelFactory(pluginManager) {
34
34
  * #property
35
35
  */
36
36
  showIntraviewLinks: true,
37
- /**
38
- * #property
39
- */
40
- linkViews: false,
41
37
  /**
42
38
  * #property
43
39
  */
@@ -98,19 +94,6 @@ function stateModelFactory(pluginManager) {
98
94
  },
99
95
  }))
100
96
  .actions(self => ({
101
- afterAttach() {
102
- addDisposer(self, onAction(self, param => {
103
- if (self.linkViews) {
104
- const { name, path, args } = param;
105
- // doesn't link showTrack/hideTrack, doesn't make sense in
106
- // synteny views most time
107
- const actions = ['horizontalScroll', 'zoomTo', 'setScaleFactor'];
108
- if (actions.includes(name) && path) {
109
- this.onSubviewAction(name, path, args);
110
- }
111
- }
112
- }));
113
- },
114
97
  // automatically removes session assemblies associated with this view
115
98
  // e.g. read vs ref
116
99
  beforeDestroy() {
@@ -163,12 +146,6 @@ function stateModelFactory(pluginManager) {
163
146
  self.middleComparativeHeight = n;
164
147
  return self.middleComparativeHeight;
165
148
  },
166
- /**
167
- * #action
168
- */
169
- toggleLinkViews() {
170
- self.linkViews = !self.linkViews;
171
- },
172
149
  /**
173
150
  * #action
174
151
  */