@jbrowse/plugin-alignments 4.1.14 → 4.1.15

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Files changed (16) hide show
  1. package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts +4 -4
  2. package/esm/BamAdapter/configSchema.d.ts +1 -1
  3. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +1 -0
  4. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +7 -7
  5. package/esm/LinearPileupDisplay/configSchema.d.ts +1 -1
  6. package/esm/LinearPileupDisplay/model.d.ts +1 -0
  7. package/esm/LinearPileupDisplay/model.js +8 -8
  8. package/esm/LinearSNPCoverageDisplay/configSchema.d.ts +2 -2
  9. package/esm/LinearSNPCoverageDisplay/model.js +4 -6
  10. package/esm/ModificationParser/consts.js +1 -1
  11. package/esm/PileupRenderer/configSchema.d.ts +2 -2
  12. package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.d.ts +1 -1
  13. package/esm/shared/legendUtils.d.ts +2 -2
  14. package/esm/shared/menuItems.d.ts +7 -3
  15. package/esm/shared/menuItems.js +2 -2
  16. package/package.json +10 -10
package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts CHANGED
@@ -3,9 +3,9 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
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  export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
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- featureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ featureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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- unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -53,9 +53,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
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- featureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ featureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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- unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
package/esm/BamAdapter/configSchema.d.ts CHANGED
@@ -8,7 +8,7 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
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  };
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  index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  indexType: {
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"BAI" | "CSI">;
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  type: string;
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  defaultValue: string;
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  };
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts CHANGED
@@ -1097,6 +1097,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -1,5 +1,5 @@
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  import { lazy } from 'react';
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- import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
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+ import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
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  import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
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  import { SimpleFeature, getContainingTrack, getContainingView, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
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  import { getRpcSessionId } from '@jbrowse/core/util/tracks';
@@ -158,12 +158,12 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
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  const { featureHeight, noSpacing, hideSmallIndels, hideMismatches, hideLargeIndels, trackMaxHeight, rendererTypeName, } = self;
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  const conf = self.configuration.renderers?.[rendererTypeName];
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  return {
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- height: featureHeight ?? readConfObject(conf, 'height'),
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- noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
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- maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
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- hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
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- hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
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- hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
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+ height: featureHeight ?? conf?.height?.value,
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+ noSpacing: noSpacing ?? conf?.noSpacing?.value,
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+ maxHeight: trackMaxHeight ?? conf?.maxHeight?.value,
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+ hideSmallIndels: hideSmallIndels ?? conf?.hideSmallIndels?.value,
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+ hideMismatches: hideMismatches ?? conf?.hideMismatches?.value,
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+ hideLargeIndels: hideLargeIndels ?? conf?.hideLargeIndels?.value,
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  };
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  },
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  }))
package/esm/LinearPileupDisplay/configSchema.d.ts CHANGED
@@ -2,7 +2,7 @@ import type PluginManager from '@jbrowse/core/PluginManager';
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  declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  defaultRendering: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"pileup">;
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  defaultValue: string;
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  };
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  renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -1100,6 +1100,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -1,5 +1,5 @@
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  import { lazy } from 'react';
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- import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
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+ import { ConfigurationReference } from '@jbrowse/core/configuration';
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  import { getContainingView, getSession } from '@jbrowse/core/util';
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  import { types } from '@jbrowse/mobx-state-tree';
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  import ColorLensIcon from '@mui/icons-material/ColorLens';
@@ -94,13 +94,13 @@ function stateModelFactory(configSchema) {
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  const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, hideSmallIndels, hideMismatches, hideLargeIndels, } = self;
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  const conf = self.configuration.renderers?.PileupRenderer;
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  return {
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- height: featureHeight ?? readConfObject(conf, 'height'),
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- noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
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- maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
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- mismatchAlpha: mismatchAlpha ?? readConfObject(conf, 'mismatchAlpha'),
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- hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
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- hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
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- hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
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+ height: featureHeight ?? conf?.height?.value,
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+ noSpacing: noSpacing ?? conf?.noSpacing?.value,
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+ maxHeight: trackMaxHeight ?? conf?.maxHeight?.value,
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+ mismatchAlpha: mismatchAlpha ?? conf?.mismatchAlpha?.value,
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+ hideSmallIndels: hideSmallIndels ?? conf?.hideSmallIndels?.value,
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+ hideMismatches: hideMismatches ?? conf?.hideMismatches?.value,
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+ hideLargeIndels: hideLargeIndels ?? conf?.hideLargeIndels?.value,
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  };
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  },
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  }))
package/esm/LinearSNPCoverageDisplay/configSchema.d.ts CHANGED
@@ -3,7 +3,7 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
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  autoscale: {
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  type: string;
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  defaultValue: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"local">;
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  description: string;
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  };
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  minScore: {
@@ -18,7 +18,7 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
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  };
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  scaleType: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"linear" | "log">;
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  description: string;
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  defaultValue: string;
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  };
package/esm/LinearSNPCoverageDisplay/model.js CHANGED
@@ -1,5 +1,5 @@
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  import { lazy } from 'react';
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- import { getConf, readConfObject } from '@jbrowse/core/configuration';
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+ import { getConf } from '@jbrowse/core/configuration';
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  import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
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  import { getContainingView, getSession } from '@jbrowse/core/util';
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  import { cast, getSnapshot, isAlive, types } from '@jbrowse/mobx-state-tree';
@@ -64,11 +64,9 @@ function stateModelFactory(pluginManager, configSchema) {
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  const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
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  const conf = self.configuration.renderers?.[self.rendererTypeName];
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  return {
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- showInterbaseCounts: showInterbaseCounts ??
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- readConfObject(conf, 'showInterbaseCounts'),
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- showInterbaseIndicators: showInterbaseIndicators ??
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- readConfObject(conf, 'showInterbaseIndicators'),
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- showArcs: showArcs ?? readConfObject(conf, 'showArcs'),
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+ showInterbaseCounts: showInterbaseCounts ?? conf?.showInterbaseCounts?.value,
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+ showInterbaseIndicators: showInterbaseIndicators ?? conf?.showInterbaseIndicators?.value,
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+ showArcs: showArcs ?? conf?.showArcs?.value,
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  };
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  },
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  get showArcsSetting() {
package/esm/ModificationParser/consts.js CHANGED
@@ -1 +1 @@
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- export const modificationRegex = new RegExp(/([A-Z])([-+])([a-z]+|[0-9]+)([.?]?)/);
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+ export const modificationRegex = new RegExp(/([ACGTUN])([-+])([a-z]+|[A-Z]|[0-9]+)([.?]?)/);
package/esm/PileupRenderer/configSchema.d.ts CHANGED
@@ -7,13 +7,13 @@ declare const PileupRenderer: import("@jbrowse/core/configuration/configurationS
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  };
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  orientationType: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"fr" | "ff" | "rf">;
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  defaultValue: string;
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  description: string;
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  };
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  displayMode: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"normal" | "collapse" | "compact">;
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  description: string;
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  defaultValue: string;
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  };
package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.d.ts CHANGED
@@ -8,7 +8,7 @@ export interface CloudTicks {
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  height: number;
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  maxDistance: number;
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  }
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- export declare function createCloudScale(maxDistance: number, height: number): import("d3-scale").ScaleLogarithmic<number, number, never>;
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+ export declare function createCloudScale(maxDistance: number, height: number): import("@mui/x-charts-vendor/d3-scale").ScaleLogarithmic<number, number, never>;
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  export declare function calculateCloudTicks(maxDistance: number, height: number): CloudTicks;
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  export declare function calculateCloudYOffsetsUtil(computedChains: ComputedChain[], height: number): {
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  chainYOffsets: Map<string, number>;
package/esm/shared/legendUtils.d.ts CHANGED
@@ -4,5 +4,5 @@ import type { Theme } from '@mui/material';
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  export { calculateSvgLegendWidth } from '@jbrowse/plugin-linear-genome-view';
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  export type { LegendItem } from '@jbrowse/plugin-linear-genome-view';
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  export declare function getPileupLegendItems(colorBy: ColorBy | undefined, theme: Theme): LegendItem[];
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- export declare function getSNPCoverageLegendItems(colorBy: ColorBy | undefined, visibleModifications: Map<string, ModificationTypeWithColor>, theme: Theme): LegendItem[];
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- export declare function getReadDisplayLegendItems(colorBy: ColorBy | undefined, visibleModifications?: Map<string, ModificationTypeWithColor>): LegendItem[];
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+ export declare function getSNPCoverageLegendItems(colorBy: ColorBy | undefined, visibleModifications: ReadonlyMap<string, ModificationTypeWithColor>, theme: Theme): LegendItem[];
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+ export declare function getReadDisplayLegendItems(colorBy: ColorBy | undefined, visibleModifications?: ReadonlyMap<string, ModificationTypeWithColor>): LegendItem[];
package/esm/shared/menuItems.d.ts CHANGED
@@ -1,4 +1,4 @@
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- import type { ColorBy } from './types.ts';
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+ import type { ColorBy, FilterBy } from './types.ts';
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  interface LinearReadDisplayModel {
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  setColorScheme: (colorBy: ColorBy) => void;
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  }
@@ -62,14 +62,18 @@ export declare function getColorSchemeMenuItem(model: LinearReadDisplayModel): {
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  onClick: () => void;
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  })[];
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  };
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- export declare function getFilterByMenuItem(model: unknown): {
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+ interface FilterByModel {
66
+ filterBy: FilterBy;
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+ setFilterBy: (arg: FilterBy) => void;
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+ }
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+ export declare function getFilterByMenuItem(model: FilterByModel): {
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  label: string;
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  icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
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  muiName: string;
69
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  };
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  onClick: () => void;
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  };
72
- interface EditFiltersModel {
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+ interface EditFiltersModel extends FilterByModel {
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  drawSingletons: boolean;
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  drawProperPairs: boolean;
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  setDrawSingletons: (arg: boolean) => void;
package/esm/shared/menuItems.js CHANGED
@@ -152,7 +152,7 @@ export function getFilterByMenuItem(model) {
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  label: 'Filter by',
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  icon: ClearAllIcon,
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  onClick: () => {
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- getSession(model).queueDialog((handleClose) => [
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+ getSession(model).queueDialog(handleClose => [
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  FilterByTagDialog,
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  { model, handleClose },
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  ]);
@@ -185,7 +185,7 @@ export function getEditFiltersMenuItem(model) {
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  {
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  label: 'Edit filters...',
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  onClick: () => {
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- getSession(model).queueDialog((handleClose) => [
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+ getSession(model).queueDialog(handleClose => [
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  FilterByTagDialog,
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  { model, handleClose },
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  ]);
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-alignments",
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- "version": "4.1.14",
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+ "version": "4.1.15",
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  "type": "module",
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  "description": "JBrowse 2 alignments adapters, tracks, etc.",
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  "keywords": [
@@ -21,23 +21,23 @@
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  "esm"
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  ],
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  "dependencies": {
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- "@gmod/bam": "^7.1.19",
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+ "@gmod/bam": "^7.1.20",
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  "@gmod/cram": "^8.0.5",
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- "@jbrowse/mobx-state-tree": "^5.5.0",
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- "@mui/icons-material": "^7.3.8",
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- "@mui/material": "^7.3.8",
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+ "@jbrowse/mobx-state-tree": "^5.6.0",
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+ "@mui/icons-material": "^7.3.9",
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+ "@mui/material": "^7.3.9",
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  "@mui/x-charts-vendor": "^8.26.0",
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  "canvas2svg": "^1.0.16",
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  "copy-to-clipboard": "^3.3.3",
32
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  "fast-deep-equal": "^3.1.3",
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- "generic-filehandle2": "^2.0.18",
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+ "generic-filehandle2": "^2.1.4",
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  "mobx": "^6.15.0",
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  "mobx-react": "^9.2.1",
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  "rxjs": "^7.8.2",
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- "@jbrowse/plugin-wiggle": "^4.1.14",
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- "@jbrowse/core": "^4.1.14",
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- "@jbrowse/sv-core": "^4.1.14",
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- "@jbrowse/plugin-linear-genome-view": "^4.1.14"
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+ "@jbrowse/plugin-linear-genome-view": "^4.1.15",
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+ "@jbrowse/plugin-wiggle": "^4.1.15",
39
+ "@jbrowse/core": "^4.1.15",
40
+ "@jbrowse/sv-core": "^4.1.15"
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  },
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  "peerDependencies": {
43
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  "react": ">=18.0.0"