@jbrowse/plugin-linear-comparative-view 2.11.1 → 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 (27) hide show
  1. package/dist/LGVSyntenyDisplay/components/util.js +1 -1
  2. package/dist/LGVSyntenyDisplay/configSchemaF.d.ts +5 -0
  3. package/dist/LGVSyntenyDisplay/model.d.ts +7 -3
  4. package/dist/LinearComparativeView/model.d.ts +11 -36
  5. package/dist/LinearComparativeView/model.js +0 -23
  6. package/dist/LinearSyntenyDisplay/components/LinearSyntenyRendering.js +54 -101
  7. package/dist/LinearSyntenyDisplay/components/util.d.ts +10 -0
  8. package/dist/LinearSyntenyDisplay/components/util.js +87 -1
  9. package/dist/LinearSyntenyView/components/ImportForm/index.js +1 -0
  10. package/dist/LinearSyntenyView/model.d.ts +39 -139
  11. package/dist/LinearSyntenyView/model.js +0 -8
  12. package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +5 -3
  13. package/dist/SyntenyFeatureDetail/SyntenyFeatureDetail.js +2 -4
  14. package/esm/LGVSyntenyDisplay/components/util.js +1 -1
  15. package/esm/LGVSyntenyDisplay/configSchemaF.d.ts +5 -0
  16. package/esm/LGVSyntenyDisplay/model.d.ts +7 -3
  17. package/esm/LinearComparativeView/model.d.ts +11 -36
  18. package/esm/LinearComparativeView/model.js +1 -24
  19. package/esm/LinearSyntenyDisplay/components/LinearSyntenyRendering.js +54 -101
  20. package/esm/LinearSyntenyDisplay/components/util.d.ts +10 -0
  21. package/esm/LinearSyntenyDisplay/components/util.js +84 -1
  22. package/esm/LinearSyntenyView/components/ImportForm/index.js +1 -0
  23. package/esm/LinearSyntenyView/model.d.ts +39 -139
  24. package/esm/LinearSyntenyView/model.js +0 -8
  25. package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts +5 -3
  26. package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js +2 -4
  27. 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>;
@@ -159,6 +145,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
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  start: number;
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  end: number;
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+ type: string;
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  regionNumber?: number | undefined;
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  reversed?: boolean | undefined;
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  refName: string;
@@ -215,14 +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[];
@@ -279,14 +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[];
@@ -356,7 +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;
@@ -367,7 +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;
@@ -380,20 +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>;
@@ -427,7 +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;
@@ -440,20 +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
453
- */
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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>;
@@ -473,33 +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>; /**
485
- * #action
486
- */
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- }, {
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- setRefName(newRefName: string): void;
489
- }, 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<{
490
- refName: import("mobx-state-tree").ISimpleType<string>;
491
- start: import("mobx-state-tree").ISimpleType<number>;
492
- end: import("mobx-state-tree").ISimpleType<number>; /**
493
- * #property/
494
- */
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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
499
- */
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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]>>;
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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;
505
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  hideHeaderOverview: boolean;
@@ -600,6 +534,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
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  getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
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  start: number;
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  end: number;
537
+ type: string;
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  regionNumber?: number | undefined;
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  reversed?: boolean | undefined;
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  refName: string;
@@ -656,14 +591,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
656
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  } | undefined;
657
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  lowerCaseRefNameAliases: {
658
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  [x: string]: string | undefined;
659
- } | undefined;
594
+ } | undefined; /**
595
+ * #property
596
+ */
660
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
661
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  } & {
662
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  getConf(arg: string): any;
663
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  } & {
664
- readonly initialized: boolean; /**
665
- * #property/
666
- */
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+ readonly initialized: boolean;
667
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  readonly name: string;
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  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
669
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  readonly aliases: string[];
@@ -720,14 +655,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
720
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  } | undefined;
721
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  lowerCaseRefNameAliases: {
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  [x: string]: string | undefined;
723
- } | undefined;
658
+ } | undefined; /**
659
+ * #property
660
+ */
724
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
725
662
  } & {
726
663
  getConf(arg: string): any;
727
664
  } & {
728
- readonly initialized: boolean; /**
729
- * #property/
730
- */
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+ readonly initialized: boolean;
731
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  readonly name: string;
732
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  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
733
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  readonly aliases: string[];
@@ -797,7 +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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  end: number;
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- reversed: boolean;
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+ reversed?: boolean | undefined;
801
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  };
802
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  readonly centerLineInfo: {
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  coord: number;
@@ -808,7 +743,7 @@ 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;
811
- reversed: boolean;
746
+ reversed?: boolean | undefined;
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  } | undefined;
813
748
  } & {
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  afterCreate(): void;
@@ -821,20 +756,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
821
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  type: import("mobx-state-tree").IType<string | undefined, string, string>;
822
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  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
823
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  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
824
- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
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- refName: import("mobx-state-tree").ISimpleType<string>;
826
- start: import("mobx-state-tree").ISimpleType<number>;
827
- end: import("mobx-state-tree").ISimpleType<number>; /**
828
- * #property/
829
- */
830
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
831
- } & {
832
- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
833
- * #action
834
- */
835
- }, {
836
- setRefName(newRefName: string): void;
837
- }, 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]>;
838
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  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
839
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  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
840
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  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -935,6 +857,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
935
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  getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
936
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  start: number;
937
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  end: number;
860
+ type: string;
938
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  regionNumber?: number | undefined;
939
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  reversed?: boolean | undefined;
940
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  refName: string;
@@ -991,14 +914,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
991
914
  } | undefined;
992
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  lowerCaseRefNameAliases: {
993
916
  [x: string]: string | undefined;
994
- } | undefined;
917
+ } | undefined; /**
918
+ * #property
919
+ */
995
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  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
996
921
  } & {
997
922
  getConf(arg: string): any;
998
923
  } & {
999
- readonly initialized: boolean; /**
1000
- * #property/
1001
- */
924
+ readonly initialized: boolean;
1002
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  readonly name: string;
1003
926
  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1004
927
  readonly aliases: string[];
@@ -1055,14 +978,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1055
978
  } | undefined;
1056
979
  lowerCaseRefNameAliases: {
1057
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  [x: string]: string | undefined;
1058
- } | undefined;
981
+ } | undefined; /**
982
+ * #property
983
+ */
1059
984
  cytobands: import("@jbrowse/core/util").Feature[] | undefined;
1060
985
  } & {
1061
986
  getConf(arg: string): any;
1062
987
  } & {
1063
- readonly initialized: boolean; /**
1064
- * #property/
1065
- */
988
+ readonly initialized: boolean;
1066
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  readonly name: string;
1067
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  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
1068
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  readonly aliases: string[];
@@ -1132,7 +1055,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1132
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  offset: number;
1133
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  start: number;
1134
1057
  end: number;
1135
- reversed: boolean;
1058
+ reversed?: boolean | undefined;
1136
1059
  };
1137
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  readonly centerLineInfo: {
1138
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  coord: number;
@@ -1143,7 +1066,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1143
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  offset: number;
1144
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  start: number;
1145
1068
  end: number;
1146
- reversed: boolean;
1069
+ reversed?: boolean | undefined;
1147
1070
  } | undefined;
1148
1071
  } & {
1149
1072
  afterCreate(): void;
@@ -1156,20 +1079,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1156
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  type: import("mobx-state-tree").IType<string | undefined, string, string>;
1157
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  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1158
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  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
1159
- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
1160
- refName: import("mobx-state-tree").ISimpleType<string>;
1161
- start: import("mobx-state-tree").ISimpleType<number>;
1162
- end: import("mobx-state-tree").ISimpleType<number>; /**
1163
- * #property/
1164
- */
1165
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
1166
- } & {
1167
- assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
1168
- * #action
1169
- */
1170
- }, {
1171
- setRefName(newRefName: string): void;
1172
- }, 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]>;
1173
1083
  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
1174
1084
  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
1175
1085
  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1184,7 +1094,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1184
1094
  }>>, import("mobx-state-tree")._NotCustomized>>): void;
1185
1095
  closeView(): void;
1186
1096
  setMiddleComparativeHeight(n: number): number;
1187
- toggleLinkViews(): void;
1188
1097
  activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
1189
1098
  toggleTrack(trackId: string): boolean;
1190
1099
  showTrack(trackId: string, initialSnapshot?: {}): void;
@@ -1241,15 +1150,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
1241
1150
  type: string;
1242
1151
  description: string;
1243
1152
  icon?: undefined;
1244
- } | {
1245
- label: string;
1246
- type: string;
1247
- checked: boolean;
1248
- onClick: () => void;
1249
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
1250
- muiName: string;
1251
- };
1252
- description?: undefined;
1253
1153
  } | {
1254
1154
  label: string;
1255
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/LGVSyntenyDisplay/configSchemaF.d.ts CHANGED
@@ -48,5 +48,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
48
48
  defaultValue: string;
49
49
  contextVariable: string[];
50
50
  };
51
+ jexlFilters: {
52
+ type: string;
53
+ description: string;
54
+ defaultValue: never[];
55
+ };
51
56
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>, undefined>>;
52
57
  export default configSchemaF;
package/esm/LGVSyntenyDisplay/model.d.ts CHANGED
@@ -85,9 +85,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
85
85
  height: {
86
86
  type: string;
87
87
  defaultValue: number;
88
- description: string; /**
89
- * #method
90
- */
88
+ description: string;
91
89
  };
92
90
  mouseover: {
93
91
  type: string;
@@ -95,6 +93,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
95
93
  defaultValue: string;
96
94
  contextVariable: string[];
97
95
  };
96
+ jexlFilters: {
97
+ type: string;
98
+ description: string;
99
+ defaultValue: never[];
100
+ };
98
101
  }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
99
102
  } & {
100
103
  configuration: AnyConfigurationSchemaType;
@@ -240,6 +243,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
240
243
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
241
244
  deleteBlock(key: string): void;
242
245
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
246
+ navToFeature(feature: import("@jbrowse/core/util").Feature): void;
243
247
  clearFeatureSelection(): void;
244
248
  setFeatureIdUnderMouse(feature?: string | undefined): void;
245
249
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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>;
@@ -140,6 +130,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
140
130
  getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
141
131
  start: number;
142
132
  end: number;
133
+ type: string;
143
134
  regionNumber?: number | undefined;
144
135
  reversed?: boolean | undefined;
145
136
  refName: string;
@@ -197,14 +188,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
197
188
  lowerCaseRefNameAliases: {
198
189
  [x: string]: string | undefined;
199
190
  } | undefined;
200
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
191
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
192
+ * #property
193
+ */
201
194
  } & {
202
195
  getConf(arg: string): any;
203
196
  } & {
204
197
  readonly initialized: boolean;
205
- /**
206
- * #property
207
- */
208
198
  readonly name: string;
209
199
  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
210
200
  readonly aliases: string[];
@@ -262,14 +252,13 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
262
252
  lowerCaseRefNameAliases: {
263
253
  [x: string]: string | undefined;
264
254
  } | undefined;
265
- cytobands: import("@jbrowse/core/util").Feature[] | undefined;
255
+ cytobands: import("@jbrowse/core/util").Feature[] | undefined; /**
256
+ * #property
257
+ */
266
258
  } & {
267
259
  getConf(arg: string): any;
268
260
  } & {
269
261
  readonly initialized: boolean;
270
- /**
271
- * #property
272
- */
273
262
  readonly name: string;
274
263
  readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
275
264
  readonly aliases: string[];
@@ -339,7 +328,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
339
328
  offset: number;
340
329
  start: number;
341
330
  end: number;
342
- reversed: boolean;
331
+ reversed?: boolean | undefined;
343
332
  };
344
333
  readonly centerLineInfo: {
345
334
  coord: number;
@@ -350,7 +339,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
350
339
  offset: number;
351
340
  start: number;
352
341
  end: number;
353
- reversed: boolean;
342
+ reversed?: boolean | undefined;
354
343
  } | undefined;
355
344
  } & {
356
345
  afterCreate(): void;
@@ -363,16 +352,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
363
352
  type: import("mobx-state-tree").IType<string | undefined, string, string>;
364
353
  offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
365
354
  bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
366
- displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
367
- refName: import("mobx-state-tree").ISimpleType<string>;
368
- start: import("mobx-state-tree").ISimpleType<number>;
369
- end: import("mobx-state-tree").ISimpleType<number>;
370
- reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
371
- } & {
372
- assemblyName: import("mobx-state-tree").ISimpleType<string>;
373
- }, {
374
- setRefName(newRefName: string): void;
375
- }, 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]>;
376
356
  tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
377
357
  hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
378
358
  hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -414,7 +394,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
414
394
  */
415
395
  readonly assemblyNames: string[];
416
396
  } & {
417
- afterAttach(): void;
418
397
  beforeDestroy(): void;
419
398
  onSubviewAction(actionName: string, path: string, args?: unknown[]): void;
420
399
  /**
@@ -439,10 +418,6 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
439
418
  * #action
440
419
  */
441
420
  setMiddleComparativeHeight(n: number): number;
442
- /**
443
- * #action
444
- */
445
- toggleLinkViews(): void;
446
421
  /**
447
422
  * #action
448
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
  */