@apollo-annotation/jbrowse-plugin-apollo 0.1.18 → 0.1.20
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.
- package/dist/index.esm.js +3189 -3575
- package/dist/index.esm.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.cjs.development.js +3185 -3570
- package/dist/jbrowse-plugin-apollo.cjs.development.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.cjs.production.min.js +1 -1
- package/dist/jbrowse-plugin-apollo.cjs.production.min.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.umd.development.js +14884 -15905
- package/dist/jbrowse-plugin-apollo.umd.development.js.map +1 -1
- package/dist/jbrowse-plugin-apollo.umd.production.min.js +1 -1
- package/dist/jbrowse-plugin-apollo.umd.production.min.js.map +1 -1
- package/package.json +33 -33
- package/src/ApolloInternetAccount/addMenuItems.ts +18 -0
- package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx +1 -0
- package/src/ApolloInternetAccount/configSchema.ts +5 -2
- package/src/ApolloInternetAccount/model.ts +14 -5
- package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts +94 -0
- package/src/ApolloRefNameAliasAdapter/configSchema.ts +12 -0
- package/src/ApolloRefNameAliasAdapter/index.ts +21 -0
- package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts +1 -0
- package/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx +10 -10
- package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts +35 -32
- package/src/BackendDrivers/BackendDriver.ts +8 -0
- package/src/BackendDrivers/CollaborationServerDriver.ts +49 -1
- package/src/BackendDrivers/DesktopFileDriver.ts +14 -1
- package/src/BackendDrivers/InMemoryFileDriver.ts +17 -1
- package/src/ChangeManager.ts +1 -1
- package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx +5 -25
- package/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx +82 -0
- package/src/FeatureDetailsWidget/Attributes.tsx +11 -3
- package/src/FeatureDetailsWidget/BasicInformation.tsx +38 -30
- package/src/FeatureDetailsWidget/Sequence.tsx +7 -7
- package/src/FeatureDetailsWidget/TranscriptBasic.tsx +446 -0
- package/src/FeatureDetailsWidget/TranscriptSequence.tsx +365 -0
- package/src/FeatureDetailsWidget/index.ts +2 -0
- package/src/FeatureDetailsWidget/model.ts +77 -9
- package/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx +0 -2
- package/src/LinearApolloDisplay/glyphs/BoxGlyph.ts +453 -380
- package/src/LinearApolloDisplay/glyphs/GeneGlyph.ts +520 -0
- package/src/LinearApolloDisplay/glyphs/GenericChildGlyph.ts +138 -134
- package/src/LinearApolloDisplay/glyphs/Glyph.ts +38 -370
- package/src/LinearApolloDisplay/glyphs/index.ts +1 -2
- package/src/LinearApolloDisplay/stateModel/base.ts +3 -6
- package/src/LinearApolloDisplay/stateModel/getGlyph.ts +30 -30
- package/src/LinearApolloDisplay/stateModel/index.ts +5 -1
- package/src/LinearApolloDisplay/stateModel/layouts.ts +32 -24
- package/src/LinearApolloDisplay/stateModel/mouseEvents.ts +206 -217
- package/src/LinearApolloDisplay/stateModel/rendering.ts +43 -67
- package/src/OntologyManager/OntologyStore/fulltext.ts +1 -1
- package/src/OntologyManager/OntologyStore/index.ts +2 -1
- package/src/OntologyManager/index.ts +6 -2
- package/src/OntologyManager/util.ts +2 -2
- package/src/SixFrameFeatureDisplay/stateModel.ts +15 -10
- package/src/TabularEditor/HybridGrid/ChangeHandling.ts +21 -46
- package/src/TabularEditor/HybridGrid/Feature.tsx +31 -82
- package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx +3 -2
- package/src/TabularEditor/HybridGrid/HybridGrid.tsx +2 -3
- package/src/TabularEditor/HybridGrid/NumberCell.tsx +1 -0
- package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts +46 -5
- package/src/TabularEditor/model.ts +5 -3
- package/src/components/AddAssembly.tsx +15 -9
- package/src/components/AddChildFeature.tsx +7 -73
- package/src/components/AddFeature.tsx +2 -57
- package/src/components/AddRefSeqAliases.tsx +285 -0
- package/src/components/CopyFeature.tsx +16 -33
- package/src/components/DeleteFeature.tsx +4 -6
- package/src/components/ImportFeatures.tsx +6 -3
- package/src/components/LogOut.tsx +105 -0
- package/src/components/ManageChecks.tsx +1 -0
- package/src/components/ManageUsers.tsx +21 -1
- package/src/components/ModifyFeatureAttribute.tsx +2 -2
- package/src/components/OntologyTermAutocomplete.tsx +0 -2
- package/src/components/OntologyTermMultiSelect.tsx +1 -0
- package/src/components/OpenLocalFile.tsx +6 -5
- package/src/components/ViewChangeLog.tsx +1 -0
- package/src/components/ViewCheckResults.tsx +1 -0
- package/src/components/index.ts +4 -0
- package/src/extensions/annotationFromPileup.ts +10 -16
- package/src/index.ts +57 -3
- package/src/session/ClientDataStore.ts +49 -46
- package/src/session/session.ts +186 -114
- package/src/util/loadAssemblyIntoClient.ts +4 -210
- package/src/FeatureDetailsWidget/RelatedFeature.tsx +0 -97
- package/src/LinearApolloDisplay/glyphs/CanonicalGeneGlyph.ts +0 -1204
- package/src/LinearApolloDisplay/glyphs/ImplicitExonGeneGlyph.ts +0 -716
- package/src/LinearApolloDisplay/stateModel/glyphs.ts +0 -47
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/* eslint-disable @typescript-eslint/no-unsafe-argument */
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/* eslint-disable @typescript-eslint/no-unsafe-return */
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import { AnnotationFeatureI } from '@apollo-annotation/mst'
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import { ObservableMap, observable } from 'mobx'
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import { types } from 'mobx-state-tree'
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import { BoxGlyph } from '../glyphs/BoxGlyph'
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import { Glyph } from '../glyphs/Glyph'
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export default function Glyphs() {
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return types
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.model({})
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.volatile(() => ({
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glyphs: observable.map<number, ObservableMap<string, Glyph>>(),
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}))
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.actions((s) => {
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const self = s
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return {
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getGlyphsForZoomLevel(bpPerPx: number): ObservableMap<string, Glyph> {
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const existingZoomLevel = self.glyphs.get(bpPerPx)
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if (existingZoomLevel) {
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return existingZoomLevel
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}
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const newZoomLevel = observable.map()
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self.glyphs.set(bpPerPx, newZoomLevel)
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return newZoomLevel
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},
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createGlyph() {
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return new BoxGlyph()
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},
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/** get the appropriate glyph for the given top-level feature */
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getGlyph(feature: AnnotationFeatureI, bpPerPx: number) {
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const glyphsForZoomLevel = this.getGlyphsForZoomLevel(bpPerPx)
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const glyphForFeature = glyphsForZoomLevel.get(feature._id)
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if (glyphForFeature) {
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return glyphForFeature
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}
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const newGlyph = this.createGlyph()
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glyphsForZoomLevel.set(feature._id, newGlyph)
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return newGlyph
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},
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afterAttach() {
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// autorun to clean up old glyph zoom levels
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},
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}
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})
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}
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