@jbrowse/plugin-alignments 2.10.2 → 2.11.0

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Files changed (29) hide show
  1. package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts +1 -1
  2. package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js +3 -3
  3. package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts +1 -1
  4. package/dist/BamAdapter/BamAdapter.js +7 -8
  5. package/dist/CramAdapter/CramAdapter.js +14 -18
  6. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +18 -4
  7. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +1 -1
  8. package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts +1 -1
  9. package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -1
  10. package/dist/LinearPileupDisplay/model.d.ts +26 -12
  11. package/dist/LinearPileupDisplay/model.js +11 -2
  12. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +11 -2
  13. package/dist/PileupRenderer/components/PileupRendering.d.ts +6 -6
  14. package/dist/shared/BaseDisplayComponent.js +3 -1
  15. package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts +1 -1
  16. package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js +3 -3
  17. package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts +1 -1
  18. package/esm/BamAdapter/BamAdapter.js +7 -8
  19. package/esm/CramAdapter/CramAdapter.js +15 -19
  20. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts +18 -4
  21. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +1 -1
  22. package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts +1 -1
  23. package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts +1 -1
  24. package/esm/LinearPileupDisplay/model.d.ts +26 -12
  25. package/esm/LinearPileupDisplay/model.js +11 -2
  26. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +11 -2
  27. package/esm/PileupRenderer/components/PileupRendering.d.ts +6 -6
  28. package/esm/shared/BaseDisplayComponent.js +3 -1
  29. package/package.json +2 -2
package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts CHANGED
@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
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  model: AlignmentFeatureWidgetModel;
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  feature: SimpleFeatureSerialized;
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  viewType: ViewType;
9
- }): React.JSX.Element;
9
+ }): React.JSX.Element | null;
package/dist/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js CHANGED
@@ -65,7 +65,7 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
65
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  ret.push([res[i], res[i + 1]]);
66
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  }
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  }
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- return (react_1.default.createElement(react_1.default.Fragment, null, ret.length ? (react_1.default.createElement("div", null,
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+ return ret.length ? (react_1.default.createElement("div", null,
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  react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
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  error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
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  react_1.default.createElement("ul", null, ret.map((arg, index) => {
@@ -82,11 +82,11 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
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  f1.refName,
83
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  ":",
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  (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start),
85
- " ->",
86
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  ' ',
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+ "-> ",
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  f2.refName,
88
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  ":",
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  (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end)))));
90
- })))) : null));
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+ })))) : null;
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  }
92
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  exports.default = LaunchBreakpointSplitViewPanel;
package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts CHANGED
@@ -37,8 +37,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
38
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  maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
39
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  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
40
- type: "BaseFeatureWidget";
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  id: string;
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+ type: "BaseFeatureWidget";
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  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
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  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
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  trackId: string | undefined;
package/dist/BamAdapter/BamAdapter.js CHANGED
@@ -65,14 +65,13 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  const idToName = [];
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  const nameToId = {};
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  samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
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- sqLine.data.forEach(item => {
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- if (item.tag === 'SN') {
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- // this is the ref name
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- const refName = item.value;
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- nameToId[refName] = refId;
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- idToName[refId] = refName;
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- }
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- });
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+ const SN = sqLine.data.find(item => item.tag === 'SN');
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+ if (SN) {
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+ // this is the ref name
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+ const refName = SN.value;
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+ nameToId[refName] = refId;
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+ idToName[refId] = refName;
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+ }
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  });
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  return { idToName, nameToId };
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  });
package/dist/CramAdapter/CramAdapter.js CHANGED
@@ -22,12 +22,6 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  async configurePre() {
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  const cramLocation = this.getConf('cramLocation');
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  const craiLocation = this.getConf('craiLocation');
25
- if (!cramLocation) {
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- throw new Error('missing cramLocation argument');
27
- }
28
- if (!craiLocation) {
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- throw new Error('missing craiLocation argument');
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- }
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  const pm = this.pluginManager;
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  const cram = new cram_1.IndexedCramFile({
33
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  cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
@@ -40,6 +34,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
40
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  throw new Error('Error getting subadapter');
41
35
  }
42
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  const seqConf = this.getConf('sequenceAdapter');
37
+ if (!seqConf) {
38
+ throw new Error('no sequenceAdapter supplied to CramAdapter config');
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+ }
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  const subadapter = await this.getSubAdapter(seqConf);
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  return {
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  cram,
@@ -86,8 +83,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  return chunkSeq.slice(trimStart, trimStart + trimLength);
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  })
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  .join('');
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- if (sequence.length !== end - start) {
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- throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
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+ const qlen = end - start;
87
+ if (sequence.length !== qlen) {
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+ throw new Error(`fetching ${refName}:${(0, util_1.toLocale)(start - 1)}-${(0, util_1.toLocale)(end)} returned ${(0, util_1.toLocale)(sequence.length)} bases, should have returned ${(0, util_1.toLocale)(qlen)}`);
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  }
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  return sequence;
93
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  }
@@ -104,14 +102,12 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  samHeader
105
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  .filter(l => l.tag === 'SQ')
106
104
  .forEach((sqLine, refId) => {
107
- sqLine.data.forEach(item => {
108
- if (item.tag === 'SN') {
109
- // this is the ref name
110
- const refName = item.value;
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- nameToId[refName] = refId;
112
- idToName[refId] = refName;
113
- }
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- });
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+ const SN = sqLine.data.find(item => item.tag === 'SN');
106
+ if (SN) {
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+ const refName = SN.value;
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+ nameToId[refName] = refId;
109
+ idToName[refId] = refName;
110
+ }
115
111
  });
116
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  const readGroups = samHeader
117
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  .filter(l => l.tag === 'RG')
@@ -161,7 +157,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
161
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  const { signal, filterBy, statusCallback = () => { } } = opts || {};
162
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  const { refName, start, end, originalRefName } = region;
163
159
  return (0, rxjs_1.ObservableCreate)(async (observer) => {
164
- const { cram } = await this.setup(opts);
160
+ const { cram, samHeader } = await this.setup(opts);
165
161
  const refId = this.refNameToId(refName);
166
162
  if (refId === undefined) {
167
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  console.warn('Unknown refName', refName);
@@ -183,7 +179,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
183
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  }
184
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  if (tagFilter) {
185
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  const v = tagFilter.tag === 'RG'
186
- ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
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+ ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
187
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  : record.tags[tagFilter.tag];
188
184
  if (!(tagFilter.value === '*'
189
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  ? v !== undefined
package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts CHANGED
@@ -46,8 +46,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
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  message: string | undefined;
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  maxHeightReached: boolean;
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  ReactComponent: ({ model, }: {
49
- model: any;
50
- }) => any;
49
+ model: {
50
+ error?: unknown;
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+ reload: () => void;
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+ message: import("react").ReactNode;
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+ filled?: boolean | undefined;
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+ status?: string | undefined;
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+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
56
+ };
57
+ }) => import("react").JSX.Element | undefined;
51
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  renderProps: any;
52
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  } & {
53
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  doReload(): void;
@@ -453,8 +460,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
453
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  message: string | undefined;
454
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  maxHeightReached: boolean;
455
462
  ReactComponent: ({ model, }: {
456
- model: any;
457
- }) => any;
463
+ model: {
464
+ error?: unknown;
465
+ reload: () => void;
466
+ message: import("react").ReactNode;
467
+ filled?: boolean | undefined;
468
+ status?: string | undefined;
469
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
470
+ };
471
+ }) => import("react").JSX.Element | undefined;
458
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  renderProps: any;
459
473
  } & {
460
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  doReload(): void;
package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -538,7 +538,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
538
538
  }
539
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  catch (e) {
540
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  console.error(e);
541
- session.notify(`${e}`, 'error');
541
+ session.notifyError(`${e}`, e);
542
542
  }
543
543
  }));
544
544
  },
package/dist/LinearPileupDisplay/components/ColorByModifications.d.ts CHANGED
@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
8
8
  modificationTagMap: ObservableMap<string, string>;
9
9
  colorBy?: {
10
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  type: string;
11
- } | undefined;
11
+ };
12
12
  };
13
13
  handleClose: () => void;
14
14
  }) => React.JSX.Element;
package/dist/LinearPileupDisplay/components/SetFeatureHeight.d.ts CHANGED
@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
4
4
  setFeatureHeight: (arg?: number) => void;
5
5
  setNoSpacing: (arg?: boolean) => void;
6
6
  featureHeightSetting: number;
7
- noSpacing?: boolean | undefined;
7
+ noSpacing?: boolean;
8
8
  };
9
9
  handleClose: () => void;
10
10
  }) => React.JSX.Element;
package/dist/LinearPileupDisplay/model.d.ts CHANGED
@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
5
5
  * #stateModel LinearPileupDisplay
6
6
  * #category display
7
7
  * extends
8
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
8
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
9
9
  */
10
10
  declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
11
11
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -43,8 +43,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
43
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  message: string | undefined;
44
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  maxHeightReached: boolean;
45
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  ReactComponent: ({ model, }: {
46
- model: any;
47
- }) => any;
46
+ model: {
47
+ error?: unknown;
48
+ reload: () => void;
49
+ message: import("react").ReactNode;
50
+ filled?: boolean | undefined;
51
+ status?: string | undefined;
52
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
53
+ };
54
+ }) => import("react").JSX.Element | undefined;
48
55
  renderProps: any;
49
56
  } & {
50
57
  doReload(): void;
@@ -89,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
89
96
  } & {
90
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  configuration: AnyConfigurationSchemaType;
91
98
  featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
92
- /**
93
- * #action
94
- */
95
99
  noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
96
100
  fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
97
101
  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
98
102
  colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
99
103
  type: import("mobx-state-tree").ISimpleType<string>;
100
104
  tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
101
- extra: import("mobx-state-tree").IType<any, any, any>;
105
+ extra: import("mobx-state-tree").IType<any, any, any>; /**
106
+ * #action
107
+ */
102
108
  }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
103
109
  filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
104
110
  flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -178,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
178
184
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
179
185
  regionCannotBeRendered(): null;
180
186
  } & {
181
- setMessage(arg?: string | undefined): void; /**
182
- * #getter
183
- */
187
+ setMessage(arg?: string | undefined): void;
184
188
  setError(error?: unknown): void;
185
189
  setRpcDriverName(rpcDriverName: string): void;
186
190
  reload(): void;
@@ -230,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
230
234
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
231
235
  } & {
232
236
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
233
- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
237
+ readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
238
+ * #getter
239
+ */
234
240
  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
235
241
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
236
242
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -239,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
239
245
  deleteBlock(key: string): void;
240
246
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
241
247
  clearFeatureSelection(): void;
242
- setFeatureIdUnderMouse(feature?: string | undefined): void;
248
+ setFeatureIdUnderMouse(feature?: string | undefined): void; /**
249
+ * #method
250
+ */
243
251
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
244
252
  } & {
245
253
  reload(): Promise<void>;
@@ -368,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
368
376
  * #action
369
377
  */
370
378
  setSortedBy(type: string, tag?: string): void;
379
+ /**
380
+ * #action
381
+ * overrides base from SharedLinearPileupDisplay to make sortReady false
382
+ * since changing feature height destroys the sort-induced layout
383
+ */
384
+ setFeatureHeight(n?: number): void;
371
385
  } & {
372
386
  /**
373
387
  * #action
package/dist/LinearPileupDisplay/model.js CHANGED
@@ -39,14 +39,14 @@ const Sort_1 = __importDefault(require("@mui/icons-material/Sort"));
39
39
  // locals
40
40
  const SharedLinearPileupDisplayMixin_1 = require("./SharedLinearPileupDisplayMixin");
41
41
  const mobx_1 = require("mobx");
42
- // async
42
+ // lzies
43
43
  const SortByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SortByTag'))));
44
44
  const ModificationsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByModifications'))));
45
45
  /**
46
46
  * #stateModel LinearPileupDisplay
47
47
  * #category display
48
48
  * extends
49
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
49
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
50
50
  */
51
51
  function stateModelFactory(configSchema) {
52
52
  return mobx_state_tree_1.types
@@ -153,6 +153,15 @@ function stateModelFactory(configSchema) {
153
153
  tag,
154
154
  };
155
155
  },
156
+ /**
157
+ * #action
158
+ * overrides base from SharedLinearPileupDisplay to make sortReady false
159
+ * since changing feature height destroys the sort-induced layout
160
+ */
161
+ setFeatureHeight(n) {
162
+ self.sortReady = false;
163
+ self.featureHeight = n;
164
+ },
156
165
  }))
157
166
  .actions(self => {
158
167
  // resets the sort object and refresh whole display on reload
package/dist/LinearSNPCoverageDisplay/models/model.d.ts CHANGED
@@ -42,8 +42,17 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
42
42
  message: string | undefined;
43
43
  maxHeightReached: boolean;
44
44
  ReactComponent: ({ model, }: {
45
- model: any;
46
- }) => any;
45
+ model: {
46
+ error?: unknown;
47
+ reload: () => void;
48
+ message: import("react").ReactNode; /**
49
+ * #property
50
+ */
51
+ filled?: boolean | undefined;
52
+ status?: string | undefined;
53
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
54
+ };
55
+ }) => import("react").JSX.Element | undefined;
47
56
  renderProps: any;
48
57
  } & {
49
58
  doReload(): void;
package/dist/PileupRenderer/components/PileupRendering.d.ts CHANGED
@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
12
12
  type: string;
13
13
  pos: number;
14
14
  refName: string;
15
- } | undefined;
15
+ };
16
16
  colorBy?: {
17
17
  type: string;
18
- tag?: string | undefined;
19
- } | undefined;
18
+ tag?: string;
19
+ };
20
20
  filterBy?: {
21
21
  tagFilter?: {
22
22
  tag: string;
23
- } | undefined;
24
- } | undefined;
25
- onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
23
+ };
24
+ };
25
+ onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
26
26
  }) => React.JSX.Element;
27
27
  export default PileupRendering;
package/dist/shared/BaseDisplayComponent.js CHANGED
@@ -9,6 +9,7 @@ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view"
9
9
  const mui_1 = require("tss-react/mui");
10
10
  const mobx_react_1 = require("mobx-react");
11
11
  const util_1 = require("@jbrowse/core/util");
12
+ const material_1 = require("@mui/material");
12
13
  const useStyles = (0, mui_1.makeStyles)()(theme => ({
13
14
  loading: {
14
15
  backgroundColor: theme.palette.background.default,
@@ -24,7 +25,8 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
24
25
  }));
25
26
  const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, children, }) {
26
27
  const { error, regionTooLarge } = model;
27
- return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
28
+ return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: react_1.default.createElement(material_1.Tooltip, { title: "Reload" },
29
+ react_1.default.createElement(material_1.Button, { "data-testid": "reload_button", onClick: () => model.reload() }, "Reload")) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (react_1.default.createElement(DataDisplay, { model: model }, children));
28
30
  });
29
31
  const DataDisplay = (0, mobx_react_1.observer)(function ({ model, children, }) {
30
32
  const { drawn, loading } = model;
package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.d.ts CHANGED
@@ -6,4 +6,4 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
6
6
  model: AlignmentFeatureWidgetModel;
7
7
  feature: SimpleFeatureSerialized;
8
8
  viewType: ViewType;
9
- }): React.JSX.Element;
9
+ }): React.JSX.Element | null;
package/esm/AlignmentsFeatureDetail/LaunchBreakpointSplitViewPanel.js CHANGED
@@ -40,7 +40,7 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
40
40
  ret.push([res[i], res[i + 1]]);
41
41
  }
42
42
  }
43
- return (React.createElement(React.Fragment, null, ret.length ? (React.createElement("div", null,
43
+ return ret.length ? (React.createElement("div", null,
44
44
  React.createElement(Typography, null, "Launch split views with breakend source and target"),
45
45
  error ? React.createElement(ErrorMessage, { error: error }) : null,
46
46
  React.createElement("ul", null, ret.map((arg, index) => {
@@ -57,10 +57,10 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
57
57
  f1.refName,
58
58
  ":",
59
59
  toLocale(f1.strand === 1 ? f1.end : f1.start),
60
- " ->",
61
60
  ' ',
61
+ "-> ",
62
62
  f2.refName,
63
63
  ":",
64
64
  toLocale(f2.strand === 1 ? f2.start : f2.end)))));
65
- })))) : null));
65
+ })))) : null;
66
66
  }
package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts CHANGED
@@ -37,8 +37,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
37
37
  trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
38
38
  maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
39
39
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
40
- type: "BaseFeatureWidget";
41
40
  id: string;
41
+ type: "BaseFeatureWidget";
42
42
  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
43
43
  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
44
44
  trackId: string | undefined;
package/esm/BamAdapter/BamAdapter.js CHANGED
@@ -60,14 +60,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
60
60
  const idToName = [];
61
61
  const nameToId = {};
62
62
  samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
63
- sqLine.data.forEach(item => {
64
- if (item.tag === 'SN') {
65
- // this is the ref name
66
- const refName = item.value;
67
- nameToId[refName] = refId;
68
- idToName[refId] = refName;
69
- }
70
- });
63
+ const SN = sqLine.data.find(item => item.tag === 'SN');
64
+ if (SN) {
65
+ // this is the ref name
66
+ const refName = SN.value;
67
+ nameToId[refName] = refId;
68
+ idToName[refId] = refName;
69
+ }
71
70
  });
72
71
  return { idToName, nameToId };
73
72
  });
package/esm/CramAdapter/CramAdapter.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import { CraiIndex, IndexedCramFile } from '@gmod/cram';
2
2
  import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
3
- import { checkAbortSignal, updateStatus, } from '@jbrowse/core/util';
3
+ import { checkAbortSignal, updateStatus, toLocale, } from '@jbrowse/core/util';
4
4
  import { openLocation } from '@jbrowse/core/util/io';
5
5
  import { ObservableCreate } from '@jbrowse/core/util/rxjs';
6
6
  import { toArray } from 'rxjs/operators';
@@ -17,12 +17,6 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
17
17
  async configurePre() {
18
18
  const cramLocation = this.getConf('cramLocation');
19
19
  const craiLocation = this.getConf('craiLocation');
20
- if (!cramLocation) {
21
- throw new Error('missing cramLocation argument');
22
- }
23
- if (!craiLocation) {
24
- throw new Error('missing craiLocation argument');
25
- }
26
20
  const pm = this.pluginManager;
27
21
  const cram = new IndexedCramFile({
28
22
  cramFilehandle: openLocation(cramLocation, pm),
@@ -35,6 +29,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
35
29
  throw new Error('Error getting subadapter');
36
30
  }
37
31
  const seqConf = this.getConf('sequenceAdapter');
32
+ if (!seqConf) {
33
+ throw new Error('no sequenceAdapter supplied to CramAdapter config');
34
+ }
38
35
  const subadapter = await this.getSubAdapter(seqConf);
39
36
  return {
40
37
  cram,
@@ -81,8 +78,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
81
78
  return chunkSeq.slice(trimStart, trimStart + trimLength);
82
79
  })
83
80
  .join('');
84
- if (sequence.length !== end - start) {
85
- throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
81
+ const qlen = end - start;
82
+ if (sequence.length !== qlen) {
83
+ throw new Error(`fetching ${refName}:${toLocale(start - 1)}-${toLocale(end)} returned ${toLocale(sequence.length)} bases, should have returned ${toLocale(qlen)}`);
86
84
  }
87
85
  return sequence;
88
86
  }
@@ -99,14 +97,12 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
99
97
  samHeader
100
98
  .filter(l => l.tag === 'SQ')
101
99
  .forEach((sqLine, refId) => {
102
- sqLine.data.forEach(item => {
103
- if (item.tag === 'SN') {
104
- // this is the ref name
105
- const refName = item.value;
106
- nameToId[refName] = refId;
107
- idToName[refId] = refName;
108
- }
109
- });
100
+ const SN = sqLine.data.find(item => item.tag === 'SN');
101
+ if (SN) {
102
+ const refName = SN.value;
103
+ nameToId[refName] = refId;
104
+ idToName[refId] = refName;
105
+ }
110
106
  });
111
107
  const readGroups = samHeader
112
108
  .filter(l => l.tag === 'RG')
@@ -156,7 +152,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
156
152
  const { signal, filterBy, statusCallback = () => { } } = opts || {};
157
153
  const { refName, start, end, originalRefName } = region;
158
154
  return ObservableCreate(async (observer) => {
159
- const { cram } = await this.setup(opts);
155
+ const { cram, samHeader } = await this.setup(opts);
160
156
  const refId = this.refNameToId(refName);
161
157
  if (refId === undefined) {
162
158
  console.warn('Unknown refName', refName);
@@ -178,7 +174,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
178
174
  }
179
175
  if (tagFilter) {
180
176
  const v = tagFilter.tag === 'RG'
181
- ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
177
+ ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
182
178
  : record.tags[tagFilter.tag];
183
179
  if (!(tagFilter.value === '*'
184
180
  ? v !== undefined
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts CHANGED
@@ -46,8 +46,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
46
46
  message: string | undefined;
47
47
  maxHeightReached: boolean;
48
48
  ReactComponent: ({ model, }: {
49
- model: any;
50
- }) => any;
49
+ model: {
50
+ error?: unknown;
51
+ reload: () => void;
52
+ message: import("react").ReactNode;
53
+ filled?: boolean | undefined;
54
+ status?: string | undefined;
55
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
56
+ };
57
+ }) => import("react").JSX.Element | undefined;
51
58
  renderProps: any;
52
59
  } & {
53
60
  doReload(): void;
@@ -453,8 +460,15 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
453
460
  message: string | undefined;
454
461
  maxHeightReached: boolean;
455
462
  ReactComponent: ({ model, }: {
456
- model: any;
457
- }) => any;
463
+ model: {
464
+ error?: unknown;
465
+ reload: () => void;
466
+ message: import("react").ReactNode;
467
+ filled?: boolean | undefined;
468
+ status?: string | undefined;
469
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
470
+ };
471
+ }) => import("react").JSX.Element | undefined;
458
472
  renderProps: any;
459
473
  } & {
460
474
  doReload(): void;
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -509,7 +509,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
509
509
  }
510
510
  catch (e) {
511
511
  console.error(e);
512
- session.notify(`${e}`, 'error');
512
+ session.notifyError(`${e}`, e);
513
513
  }
514
514
  }));
515
515
  },
package/esm/LinearPileupDisplay/components/ColorByModifications.d.ts CHANGED
@@ -8,7 +8,7 @@ declare const ColorByModificationsDialog: ({ model, handleClose, }: {
8
8
  modificationTagMap: ObservableMap<string, string>;
9
9
  colorBy?: {
10
10
  type: string;
11
- } | undefined;
11
+ };
12
12
  };
13
13
  handleClose: () => void;
14
14
  }) => React.JSX.Element;
package/esm/LinearPileupDisplay/components/SetFeatureHeight.d.ts CHANGED
@@ -4,7 +4,7 @@ declare const SetFeatureHeightDialog: (props: {
4
4
  setFeatureHeight: (arg?: number) => void;
5
5
  setNoSpacing: (arg?: boolean) => void;
6
6
  featureHeightSetting: number;
7
- noSpacing?: boolean | undefined;
7
+ noSpacing?: boolean;
8
8
  };
9
9
  handleClose: () => void;
10
10
  }) => React.JSX.Element;
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -5,7 +5,7 @@ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
5
5
  * #stateModel LinearPileupDisplay
6
6
  * #category display
7
7
  * extends
8
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
8
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
9
9
  */
10
10
  declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
11
11
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -43,8 +43,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
43
43
  message: string | undefined;
44
44
  maxHeightReached: boolean;
45
45
  ReactComponent: ({ model, }: {
46
- model: any;
47
- }) => any;
46
+ model: {
47
+ error?: unknown;
48
+ reload: () => void;
49
+ message: import("react").ReactNode;
50
+ filled?: boolean | undefined;
51
+ status?: string | undefined;
52
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
53
+ };
54
+ }) => import("react").JSX.Element | undefined;
48
55
  renderProps: any;
49
56
  } & {
50
57
  doReload(): void;
@@ -89,16 +96,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
89
96
  } & {
90
97
  configuration: AnyConfigurationSchemaType;
91
98
  featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
92
- /**
93
- * #action
94
- */
95
99
  noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
96
100
  fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
97
101
  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
98
102
  colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
99
103
  type: import("mobx-state-tree").ISimpleType<string>;
100
104
  tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
101
- extra: import("mobx-state-tree").IType<any, any, any>;
105
+ extra: import("mobx-state-tree").IType<any, any, any>; /**
106
+ * #action
107
+ */
102
108
  }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
103
109
  filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
104
110
  flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -178,9 +184,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
178
184
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
179
185
  regionCannotBeRendered(): null;
180
186
  } & {
181
- setMessage(arg?: string | undefined): void; /**
182
- * #getter
183
- */
187
+ setMessage(arg?: string | undefined): void;
184
188
  setError(error?: unknown): void;
185
189
  setRpcDriverName(rpcDriverName: string): void;
186
190
  reload(): void;
@@ -230,7 +234,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
230
234
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
231
235
  } & {
232
236
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
233
- readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
237
+ readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined; /**
238
+ * #getter
239
+ */
234
240
  getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
235
241
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
236
242
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
@@ -239,7 +245,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
239
245
  deleteBlock(key: string): void;
240
246
  selectFeature(feature: import("@jbrowse/core/util").Feature): void;
241
247
  clearFeatureSelection(): void;
242
- setFeatureIdUnderMouse(feature?: string | undefined): void;
248
+ setFeatureIdUnderMouse(feature?: string | undefined): void; /**
249
+ * #method
250
+ */
243
251
  setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
244
252
  } & {
245
253
  reload(): Promise<void>;
@@ -368,6 +376,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
368
376
  * #action
369
377
  */
370
378
  setSortedBy(type: string, tag?: string): void;
379
+ /**
380
+ * #action
381
+ * overrides base from SharedLinearPileupDisplay to make sortReady false
382
+ * since changing feature height destroys the sort-induced layout
383
+ */
384
+ setFeatureHeight(n?: number): void;
371
385
  } & {
372
386
  /**
373
387
  * #action
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -11,14 +11,14 @@ import SortIcon from '@mui/icons-material/Sort';
11
11
  // locals
12
12
  import { SharedLinearPileupDisplayMixin } from './SharedLinearPileupDisplayMixin';
13
13
  import { observable } from 'mobx';
14
- // async
14
+ // lzies
15
15
  const SortByTagDialog = lazy(() => import('./components/SortByTag'));
16
16
  const ModificationsDialog = lazy(() => import('./components/ColorByModifications'));
17
17
  /**
18
18
  * #stateModel LinearPileupDisplay
19
19
  * #category display
20
20
  * extends
21
- *- [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
21
+ * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
22
22
  */
23
23
  function stateModelFactory(configSchema) {
24
24
  return types
@@ -125,6 +125,15 @@ function stateModelFactory(configSchema) {
125
125
  tag,
126
126
  };
127
127
  },
128
+ /**
129
+ * #action
130
+ * overrides base from SharedLinearPileupDisplay to make sortReady false
131
+ * since changing feature height destroys the sort-induced layout
132
+ */
133
+ setFeatureHeight(n) {
134
+ self.sortReady = false;
135
+ self.featureHeight = n;
136
+ },
128
137
  }))
129
138
  .actions(self => {
130
139
  // resets the sort object and refresh whole display on reload
package/esm/LinearSNPCoverageDisplay/models/model.d.ts CHANGED
@@ -42,8 +42,17 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
42
42
  message: string | undefined;
43
43
  maxHeightReached: boolean;
44
44
  ReactComponent: ({ model, }: {
45
- model: any;
46
- }) => any;
45
+ model: {
46
+ error?: unknown;
47
+ reload: () => void;
48
+ message: import("react").ReactNode; /**
49
+ * #property
50
+ */
51
+ filled?: boolean | undefined;
52
+ status?: string | undefined;
53
+ reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
54
+ };
55
+ }) => import("react").JSX.Element | undefined;
47
56
  renderProps: any;
48
57
  } & {
49
58
  doReload(): void;
package/esm/PileupRenderer/components/PileupRendering.d.ts CHANGED
@@ -12,16 +12,16 @@ declare const PileupRendering: (props: {
12
12
  type: string;
13
13
  pos: number;
14
14
  refName: string;
15
- } | undefined;
15
+ };
16
16
  colorBy?: {
17
17
  type: string;
18
- tag?: string | undefined;
19
- } | undefined;
18
+ tag?: string;
19
+ };
20
20
  filterBy?: {
21
21
  tagFilter?: {
22
22
  tag: string;
23
- } | undefined;
24
- } | undefined;
25
- onMouseMove?: ((event: React.MouseEvent, featureId?: string) => void) | undefined;
23
+ };
24
+ };
25
+ onMouseMove?: (event: React.MouseEvent, featureId?: string) => void;
26
26
  }) => React.JSX.Element;
27
27
  export default PileupRendering;
package/esm/shared/BaseDisplayComponent.js CHANGED
@@ -4,6 +4,7 @@ import { BlockMsg, } from '@jbrowse/plugin-linear-genome-view';
4
4
  import { makeStyles } from 'tss-react/mui';
5
5
  import { observer } from 'mobx-react';
6
6
  import { getContainingView } from '@jbrowse/core/util';
7
+ import { Button, Tooltip } from '@mui/material';
7
8
  const useStyles = makeStyles()(theme => ({
8
9
  loading: {
9
10
  backgroundColor: theme.palette.background.default,
@@ -19,7 +20,8 @@ const useStyles = makeStyles()(theme => ({
19
20
  }));
20
21
  const BaseDisplayComponent = observer(function ({ model, children, }) {
21
22
  const { error, regionTooLarge } = model;
22
- return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", buttonText: "Reload", action: model.reload })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
23
+ return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", action: React.createElement(Tooltip, { title: "Reload" },
24
+ React.createElement(Button, { "data-testid": "reload_button", onClick: () => model.reload() }, "Reload")) })) : regionTooLarge ? (model.regionCannotBeRendered()) : (React.createElement(DataDisplay, { model: model }, children));
23
25
  });
24
26
  const DataDisplay = observer(function ({ model, children, }) {
25
27
  const { drawn, loading } = model;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "2.10.2",
3
+ "version": "2.11.0",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -63,5 +63,5 @@
63
63
  "distModule": "esm/index.js",
64
64
  "srcModule": "src/index.ts",
65
65
  "module": "esm/index.js",
66
- "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
66
+ "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
67
67
  }