@jbrowse/plugin-alignments 4.1.13 → 4.1.15

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 (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 +11 -11
package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts CHANGED
@@ -3,9 +3,9 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
3
3
  export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
4
4
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
5
5
  type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
6
- 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>;
6
+ featureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
7
7
  formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
8
- 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>;
8
+ unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
9
9
  view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
10
10
  track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
11
11
  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(
53
53
  } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
54
54
  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
55
55
  type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
56
- 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>;
56
+ featureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
57
57
  formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
58
- 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>;
58
+ unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
59
59
  view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
60
60
  track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
61
61
  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
8
8
  };
9
9
  index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
10
10
  indexType: {
11
- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
11
+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"BAI" | "CSI">;
12
12
  type: string;
13
13
  defaultValue: string;
14
14
  };
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts CHANGED
@@ -1097,6 +1097,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
1097
1097
  onMouseMove(_: unknown, featureId?: string): void;
1098
1098
  onMouseLeave(_: unknown): void;
1099
1099
  onContextMenu(_: unknown): void;
1100
+ onFeatureClick(_: unknown, featureId?: string): void;
1100
1101
  };
1101
1102
  renderProps(): any;
1102
1103
  } & {
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -1,5 +1,5 @@
1
1
  import { lazy } from 'react';
2
- import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
2
+ import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
3
3
  import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
4
4
  import { SimpleFeature, getContainingTrack, getContainingView, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
5
5
  import { getRpcSessionId } from '@jbrowse/core/util/tracks';
@@ -158,12 +158,12 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
158
158
  const { featureHeight, noSpacing, hideSmallIndels, hideMismatches, hideLargeIndels, trackMaxHeight, rendererTypeName, } = self;
159
159
  const conf = self.configuration.renderers?.[rendererTypeName];
160
160
  return {
161
- height: featureHeight ?? readConfObject(conf, 'height'),
162
- noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
163
- maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
164
- hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
165
- hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
166
- hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
161
+ height: featureHeight ?? conf?.height?.value,
162
+ noSpacing: noSpacing ?? conf?.noSpacing?.value,
163
+ maxHeight: trackMaxHeight ?? conf?.maxHeight?.value,
164
+ hideSmallIndels: hideSmallIndels ?? conf?.hideSmallIndels?.value,
165
+ hideMismatches: hideMismatches ?? conf?.hideMismatches?.value,
166
+ hideLargeIndels: hideLargeIndels ?? conf?.hideLargeIndels?.value,
167
167
  };
168
168
  },
169
169
  }))
package/esm/LinearPileupDisplay/configSchema.d.ts CHANGED
@@ -2,7 +2,7 @@ import type PluginManager from '@jbrowse/core/PluginManager';
2
2
  declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
3
3
  defaultRendering: {
4
4
  type: string;
5
- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
5
+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"pileup">;
6
6
  defaultValue: string;
7
7
  };
8
8
  renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -1100,6 +1100,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
1100
1100
  onMouseMove(_: unknown, featureId?: string): void;
1101
1101
  onMouseLeave(_: unknown): void;
1102
1102
  onContextMenu(_: unknown): void;
1103
+ onFeatureClick(_: unknown, featureId?: string): void;
1103
1104
  };
1104
1105
  renderProps(): any;
1105
1106
  } & {
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -1,5 +1,5 @@
1
1
  import { lazy } from 'react';
2
- import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
2
+ import { ConfigurationReference } from '@jbrowse/core/configuration';
3
3
  import { getContainingView, getSession } from '@jbrowse/core/util';
4
4
  import { types } from '@jbrowse/mobx-state-tree';
5
5
  import ColorLensIcon from '@mui/icons-material/ColorLens';
@@ -94,13 +94,13 @@ function stateModelFactory(configSchema) {
94
94
  const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, hideSmallIndels, hideMismatches, hideLargeIndels, } = self;
95
95
  const conf = self.configuration.renderers?.PileupRenderer;
96
96
  return {
97
- height: featureHeight ?? readConfObject(conf, 'height'),
98
- noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
99
- maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
100
- mismatchAlpha: mismatchAlpha ?? readConfObject(conf, 'mismatchAlpha'),
101
- hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
102
- hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
103
- hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
97
+ height: featureHeight ?? conf?.height?.value,
98
+ noSpacing: noSpacing ?? conf?.noSpacing?.value,
99
+ maxHeight: trackMaxHeight ?? conf?.maxHeight?.value,
100
+ mismatchAlpha: mismatchAlpha ?? conf?.mismatchAlpha?.value,
101
+ hideSmallIndels: hideSmallIndels ?? conf?.hideSmallIndels?.value,
102
+ hideMismatches: hideMismatches ?? conf?.hideMismatches?.value,
103
+ hideLargeIndels: hideLargeIndels ?? conf?.hideLargeIndels?.value,
104
104
  };
105
105
  },
106
106
  }))
package/esm/LinearSNPCoverageDisplay/configSchema.d.ts CHANGED
@@ -3,7 +3,7 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
3
3
  autoscale: {
4
4
  type: string;
5
5
  defaultValue: string;
6
- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
6
+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"local">;
7
7
  description: string;
8
8
  };
9
9
  minScore: {
@@ -18,7 +18,7 @@ export default function SNPCoverageConfigFactory(pluginManager: PluginManager):
18
18
  };
19
19
  scaleType: {
20
20
  type: string;
21
- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
21
+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"linear" | "log">;
22
22
  description: string;
23
23
  defaultValue: string;
24
24
  };
package/esm/LinearSNPCoverageDisplay/model.js CHANGED
@@ -1,5 +1,5 @@
1
1
  import { lazy } from 'react';
2
- import { getConf, readConfObject } from '@jbrowse/core/configuration';
2
+ import { getConf } from '@jbrowse/core/configuration';
3
3
  import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
4
4
  import { getContainingView, getSession } from '@jbrowse/core/util';
5
5
  import { cast, getSnapshot, isAlive, types } from '@jbrowse/mobx-state-tree';
@@ -64,11 +64,9 @@ function stateModelFactory(pluginManager, configSchema) {
64
64
  const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
65
65
  const conf = self.configuration.renderers?.[self.rendererTypeName];
66
66
  return {
67
- showInterbaseCounts: showInterbaseCounts ??
68
- readConfObject(conf, 'showInterbaseCounts'),
69
- showInterbaseIndicators: showInterbaseIndicators ??
70
- readConfObject(conf, 'showInterbaseIndicators'),
71
- showArcs: showArcs ?? readConfObject(conf, 'showArcs'),
67
+ showInterbaseCounts: showInterbaseCounts ?? conf?.showInterbaseCounts?.value,
68
+ showInterbaseIndicators: showInterbaseIndicators ?? conf?.showInterbaseIndicators?.value,
69
+ showArcs: showArcs ?? conf?.showArcs?.value,
72
70
  };
73
71
  },
74
72
  get showArcsSetting() {
package/esm/ModificationParser/consts.js CHANGED
@@ -1 +1 @@
1
- export const modificationRegex = new RegExp(/([A-Z])([-+])([a-z]+|[0-9]+)([.?]?)/);
1
+ 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
7
7
  };
8
8
  orientationType: {
9
9
  type: string;
10
- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
10
+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"fr" | "ff" | "rf">;
11
11
  defaultValue: string;
12
12
  description: string;
13
13
  };
14
14
  displayMode: {
15
15
  type: string;
16
- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
16
+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"normal" | "collapse" | "compact">;
17
17
  description: string;
18
18
  defaultValue: string;
19
19
  };
package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.d.ts CHANGED
@@ -8,7 +8,7 @@ export interface CloudTicks {
8
8
  height: number;
9
9
  maxDistance: number;
10
10
  }
11
- export declare function createCloudScale(maxDistance: number, height: number): import("d3-scale").ScaleLogarithmic<number, number, never>;
11
+ export declare function createCloudScale(maxDistance: number, height: number): import("@mui/x-charts-vendor/d3-scale").ScaleLogarithmic<number, number, never>;
12
12
  export declare function calculateCloudTicks(maxDistance: number, height: number): CloudTicks;
13
13
  export declare function calculateCloudYOffsetsUtil(computedChains: ComputedChain[], height: number): {
14
14
  chainYOffsets: Map<string, number>;
package/esm/shared/legendUtils.d.ts CHANGED
@@ -4,5 +4,5 @@ import type { Theme } from '@mui/material';
4
4
  export { calculateSvgLegendWidth } from '@jbrowse/plugin-linear-genome-view';
5
5
  export type { LegendItem } from '@jbrowse/plugin-linear-genome-view';
6
6
  export declare function getPileupLegendItems(colorBy: ColorBy | undefined, theme: Theme): LegendItem[];
7
- export declare function getSNPCoverageLegendItems(colorBy: ColorBy | undefined, visibleModifications: Map<string, ModificationTypeWithColor>, theme: Theme): LegendItem[];
8
- export declare function getReadDisplayLegendItems(colorBy: ColorBy | undefined, visibleModifications?: Map<string, ModificationTypeWithColor>): LegendItem[];
7
+ export declare function getSNPCoverageLegendItems(colorBy: ColorBy | undefined, visibleModifications: ReadonlyMap<string, ModificationTypeWithColor>, theme: Theme): LegendItem[];
8
+ export declare function getReadDisplayLegendItems(colorBy: ColorBy | undefined, visibleModifications?: ReadonlyMap<string, ModificationTypeWithColor>): LegendItem[];
package/esm/shared/menuItems.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- import type { ColorBy } from './types.ts';
1
+ import type { ColorBy, FilterBy } from './types.ts';
2
2
  interface LinearReadDisplayModel {
3
3
  setColorScheme: (colorBy: ColorBy) => void;
4
4
  }
@@ -62,14 +62,18 @@ export declare function getColorSchemeMenuItem(model: LinearReadDisplayModel): {
62
62
  onClick: () => void;
63
63
  })[];
64
64
  };
65
- export declare function getFilterByMenuItem(model: unknown): {
65
+ interface FilterByModel {
66
+ filterBy: FilterBy;
67
+ setFilterBy: (arg: FilterBy) => void;
68
+ }
69
+ export declare function getFilterByMenuItem(model: FilterByModel): {
66
70
  label: string;
67
71
  icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
68
72
  muiName: string;
69
73
  };
70
74
  onClick: () => void;
71
75
  };
72
- interface EditFiltersModel {
76
+ interface EditFiltersModel extends FilterByModel {
73
77
  drawSingletons: boolean;
74
78
  drawProperPairs: boolean;
75
79
  setDrawSingletons: (arg: boolean) => void;
package/esm/shared/menuItems.js CHANGED
@@ -152,7 +152,7 @@ export function getFilterByMenuItem(model) {
152
152
  label: 'Filter by',
153
153
  icon: ClearAllIcon,
154
154
  onClick: () => {
155
- getSession(model).queueDialog((handleClose) => [
155
+ getSession(model).queueDialog(handleClose => [
156
156
  FilterByTagDialog,
157
157
  { model, handleClose },
158
158
  ]);
@@ -185,7 +185,7 @@ export function getEditFiltersMenuItem(model) {
185
185
  {
186
186
  label: 'Edit filters...',
187
187
  onClick: () => {
188
- getSession(model).queueDialog((handleClose) => [
188
+ getSession(model).queueDialog(handleClose => [
189
189
  FilterByTagDialog,
190
190
  { model, handleClose },
191
191
  ]);
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "4.1.13",
3
+ "version": "4.1.15",
4
4
  "type": "module",
5
5
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
6
6
  "keywords": [
@@ -21,23 +21,23 @@
21
21
  "esm"
22
22
  ],
23
23
  "dependencies": {
24
- "@gmod/bam": "^7.1.17",
25
- "@gmod/cram": "^8.0.4",
26
- "@jbrowse/mobx-state-tree": "^5.5.0",
27
- "@mui/icons-material": "^7.3.8",
28
- "@mui/material": "^7.3.8",
24
+ "@gmod/bam": "^7.1.20",
25
+ "@gmod/cram": "^8.0.5",
26
+ "@jbrowse/mobx-state-tree": "^5.6.0",
27
+ "@mui/icons-material": "^7.3.9",
28
+ "@mui/material": "^7.3.9",
29
29
  "@mui/x-charts-vendor": "^8.26.0",
30
30
  "canvas2svg": "^1.0.16",
31
31
  "copy-to-clipboard": "^3.3.3",
32
32
  "fast-deep-equal": "^3.1.3",
33
- "generic-filehandle2": "^2.0.18",
33
+ "generic-filehandle2": "^2.1.4",
34
34
  "mobx": "^6.15.0",
35
35
  "mobx-react": "^9.2.1",
36
36
  "rxjs": "^7.8.2",
37
- "@jbrowse/plugin-linear-genome-view": "^4.1.13",
38
- "@jbrowse/plugin-wiggle": "^4.1.13",
39
- "@jbrowse/core": "^4.1.13",
40
- "@jbrowse/sv-core": "^4.1.13"
37
+ "@jbrowse/plugin-linear-genome-view": "^4.1.15",
38
+ "@jbrowse/plugin-wiggle": "^4.1.15",
39
+ "@jbrowse/core": "^4.1.15",
40
+ "@jbrowse/sv-core": "^4.1.15"
41
41
  },
42
42
  "peerDependencies": {
43
43
  "react": ">=18.0.0"