react-msaview 4.4.2 → 4.4.4
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/bundle/index.js +10 -10
- package/bundle/index.js.LICENSE.txt +5 -5
- package/bundle/index.js.map +1 -1
- package/dist/DataModel.d.ts +34 -0
- package/dist/DataModel.js +46 -0
- package/dist/DataModel.js.map +1 -0
- package/dist/DialogQueue.d.ts +25 -0
- package/dist/DialogQueue.js +44 -0
- package/dist/DialogQueue.js.map +1 -0
- package/dist/SelectedStructuresMixin.d.ts +46 -0
- package/dist/SelectedStructuresMixin.js +52 -0
- package/dist/SelectedStructuresMixin.js.map +1 -0
- package/dist/StructureModel.d.ts +9 -0
- package/dist/StructureModel.js +11 -0
- package/dist/StructureModel.js.map +1 -0
- package/dist/UniprotTrack.d.ts +27 -0
- package/dist/UniprotTrack.js +53 -0
- package/dist/UniprotTrack.js.map +1 -0
- package/dist/components/BoxTrack.d.ts +7 -0
- package/dist/components/BoxTrack.js +15 -0
- package/dist/components/BoxTrack.js.map +1 -0
- package/dist/components/BoxTrackBlock.d.ts +8 -0
- package/dist/components/BoxTrackBlock.js +136 -0
- package/dist/components/BoxTrackBlock.js.map +1 -0
- package/dist/components/ExportSVGDialog.d.ts +6 -0
- package/dist/components/ExportSVGDialog.js +39 -0
- package/dist/components/ExportSVGDialog.js.map +1 -0
- package/dist/components/Header.d.ts +6 -0
- package/dist/components/Header.js +62 -0
- package/dist/components/Header.js.map +1 -0
- package/dist/components/HeaderInfoArea.d.ts +6 -0
- package/dist/components/HeaderInfoArea.js +12 -0
- package/dist/components/HeaderInfoArea.js.map +1 -0
- package/dist/components/ImportForm/ImportFormExamples.d.ts +6 -0
- package/dist/components/ImportForm/ImportFormExamples.js +50 -0
- package/dist/components/ImportForm/ImportFormExamples.js.map +1 -0
- package/dist/components/ImportForm/data/seq2.d.ts +3 -0
- package/dist/components/ImportForm/data/seq2.js +33 -0
- package/dist/components/ImportForm/data/seq2.js.map +1 -0
- package/dist/components/ImportForm/index.d.ts +6 -0
- package/dist/components/ImportForm/index.js +31 -0
- package/dist/components/ImportForm/index.js.map +1 -0
- package/dist/components/ImportForm/util.d.ts +3 -0
- package/dist/components/ImportForm/util.js +16 -0
- package/dist/components/ImportForm/util.js.map +1 -0
- package/dist/components/MSACanvas.d.ts +6 -0
- package/dist/components/MSACanvas.js +141 -0
- package/dist/components/MSACanvas.js.map +1 -0
- package/dist/components/MSAPanel/Loading.d.ts +2 -0
- package/dist/components/MSAPanel/Loading.js +12 -0
- package/dist/components/MSAPanel/Loading.js.map +1 -0
- package/dist/components/MSAPanel/MSABlock.d.ts +8 -0
- package/dist/components/MSAPanel/MSABlock.js +62 -0
- package/dist/components/MSAPanel/MSABlock.js.map +1 -0
- package/dist/components/MSAPanel/MSACanvas.d.ts +7 -0
- package/dist/components/MSAPanel/MSACanvas.js +69 -0
- package/dist/components/MSAPanel/MSACanvas.js.map +1 -0
- package/dist/components/MSAPanel/MSAMouseoverCanvas.d.ts +6 -0
- package/dist/components/MSAPanel/MSAMouseoverCanvas.js +27 -0
- package/dist/components/MSAPanel/MSAMouseoverCanvas.js.map +1 -0
- package/dist/components/MSAPanel/index.d.ts +5 -0
- package/dist/components/MSAPanel/index.js +9 -0
- package/dist/components/MSAPanel/index.js.map +1 -0
- package/dist/components/MSAPanel/renderMSABlock.d.ts +9 -0
- package/dist/components/MSAPanel/renderMSABlock.js +89 -0
- package/dist/components/MSAPanel/renderMSABlock.js.map +1 -0
- package/dist/components/MSAPanel/renderMSABlock_BACKUP_139826.d.ts +9 -0
- package/dist/components/MSAPanel/renderMSABlock_BACKUP_139826.js +89 -0
- package/dist/components/MSAPanel/renderMSABlock_BACKUP_139826.js.map +1 -0
- package/dist/components/MSAPanel/renderMSABlock_BASE_139826.d.ts +13 -0
- package/dist/components/MSAPanel/renderMSABlock_BASE_139826.js +82 -0
- package/dist/components/MSAPanel/renderMSABlock_BASE_139826.js.map +1 -0
- package/dist/components/MSAPanel/renderMSABlock_LOCAL_139826.d.ts +9 -0
- package/dist/components/MSAPanel/renderMSABlock_LOCAL_139826.js +89 -0
- package/dist/components/MSAPanel/renderMSABlock_LOCAL_139826.js.map +1 -0
- package/dist/components/MSAPanel/renderMSABlock_REMOTE_139826.d.ts +0 -0
- package/dist/components/MSAPanel/renderMSABlock_REMOTE_139826.js +2 -0
- package/dist/components/MSAPanel/renderMSABlock_REMOTE_139826.js.map +1 -0
- package/dist/components/MSAPanel/renderMSAMouseover.d.ts +5 -0
- package/dist/components/MSAPanel/renderMSAMouseover.js +30 -0
- package/dist/components/MSAPanel/renderMSAMouseover.js.map +1 -0
- package/dist/components/Minimap.d.ts +6 -0
- package/dist/components/Minimap.js +72 -0
- package/dist/components/Minimap.js.map +1 -0
- package/dist/components/MinimapSVG.d.ts +6 -0
- package/dist/components/MinimapSVG.js +25 -0
- package/dist/components/MinimapSVG.js.map +1 -0
- package/dist/components/MultiAlignmentSelector.d.ts +6 -0
- package/dist/components/MultiAlignmentSelector.js +13 -0
- package/dist/components/MultiAlignmentSelector.js.map +1 -0
- package/dist/components/TreePanel/TreeBranchMenu.d.ts +14 -0
- package/dist/components/TreePanel/TreeBranchMenu.js +26 -0
- package/dist/components/TreePanel/TreeBranchMenu.js.map +1 -0
- package/dist/components/TreePanel/TreeCanvas.d.ts +6 -0
- package/dist/components/TreePanel/TreeCanvas.js +100 -0
- package/dist/components/TreePanel/TreeCanvas.js.map +1 -0
- package/dist/components/TreePanel/TreeCanvasBlock.d.ts +7 -0
- package/dist/components/TreePanel/TreeCanvasBlock.js +118 -0
- package/dist/components/TreePanel/TreeCanvasBlock.js.map +1 -0
- package/dist/components/TreePanel/TreeNodeMenu.d.ts +13 -0
- package/dist/components/TreePanel/TreeNodeMenu.js +74 -0
- package/dist/components/TreePanel/TreeNodeMenu.js.map +1 -0
- package/dist/components/TreePanel/TreeRuler.d.ts +6 -0
- package/dist/components/TreePanel/TreeRuler.js +8 -0
- package/dist/components/TreePanel/TreeRuler.js.map +1 -0
- package/dist/components/TreePanel/dialogs/TreeNodeInfoDialog.d.ts +9 -0
- package/dist/components/TreePanel/dialogs/TreeNodeInfoDialog.js +16 -0
- package/dist/components/TreePanel/dialogs/TreeNodeInfoDialog.js.map +1 -0
- package/dist/components/TreePanel/index.d.ts +6 -0
- package/dist/components/TreePanel/index.js +10 -0
- package/dist/components/TreePanel/index.js.map +1 -0
- package/dist/components/TreePanel/renderTreeCanvas.d.ts +46 -0
- package/dist/components/TreePanel/renderTreeCanvas.js +180 -0
- package/dist/components/TreePanel/renderTreeCanvas.js.map +1 -0
- package/dist/components/VerticalGuide.d.ts +7 -0
- package/dist/components/VerticalGuide.js +30 -0
- package/dist/components/VerticalGuide.js.map +1 -0
- package/dist/components/ZoomControls.d.ts +6 -0
- package/dist/components/ZoomControls.js +59 -0
- package/dist/components/ZoomControls.js.map +1 -0
- package/dist/components/header/Header.js +1 -1
- package/dist/components/header/Header.js.map +1 -1
- package/dist/components/header/SettingsMenu.js +1 -1
- package/dist/components/header/SettingsMenu.js.map +1 -1
- package/dist/components/msa/MSACanvas_BACKUP_139826.d.ts +7 -0
- package/dist/components/msa/MSACanvas_BACKUP_139826.js +68 -0
- package/dist/components/msa/MSACanvas_BACKUP_139826.js.map +1 -0
- package/dist/components/msa/MSACanvas_BASE_139826.d.ts +6 -0
- package/dist/components/msa/MSACanvas_BASE_139826.js +107 -0
- package/dist/components/msa/MSACanvas_BASE_139826.js.map +1 -0
- package/dist/components/msa/MSACanvas_LOCAL_139826.d.ts +7 -0
- package/dist/components/msa/MSACanvas_LOCAL_139826.js +69 -0
- package/dist/components/msa/MSACanvas_LOCAL_139826.js.map +1 -0
- package/dist/components/msa/MSACanvas_REMOTE_139826.d.ts +6 -0
- package/dist/components/msa/MSACanvas_REMOTE_139826.js +106 -0
- package/dist/components/msa/MSACanvas_REMOTE_139826.js.map +1 -0
- package/dist/sansserif.d.ts +3 -0
- package/dist/sansserif.js +1583 -0
- package/dist/sansserif.js.map +1 -0
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +7 -2
- package/src/components/header/Header.tsx +1 -1
- package/src/components/header/SettingsMenu.tsx +1 -1
- package/src/version.ts +1 -1
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/**
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* #stateModel DataModel
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* the data stored for the model. this is sometimes temporary in the case that
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* e.g. msaFilehandle is available on the parent model, because then the msa
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* data will not be persisted in saved session snapshots, it will be fetched
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* from msaFilehandle at startup
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*/
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export declare function DataModelF(): import("mobx-state-tree").IModelType<{
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/**
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* #property
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*/
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tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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/**
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* #property
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*/
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msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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/**
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* #property
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*/
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treeMetadata: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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}, {
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/**
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* #action
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*/
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setTree(tree?: string): void;
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/**
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* #action
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*/
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setMSA(msa?: string): void;
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/**
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* #action
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*/
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setTreeMetadata(treeMetadata?: string): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
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import { types } from 'mobx-state-tree';
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/**
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* #stateModel DataModel
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* the data stored for the model. this is sometimes temporary in the case that
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* e.g. msaFilehandle is available on the parent model, because then the msa
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* data will not be persisted in saved session snapshots, it will be fetched
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* from msaFilehandle at startup
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*/
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export function DataModelF() {
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return types
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.model({
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/**
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* #property
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*/
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tree: types.maybe(types.string),
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/**
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* #property
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*/
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msa: types.maybe(types.string),
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/**
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* #property
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*/
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treeMetadata: types.maybe(types.string),
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})
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.actions(self => ({
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/**
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* #action
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*/
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setTree(tree) {
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self.tree = tree;
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},
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/**
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* #action
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*/
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setMSA(msa) {
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self.msa = msa;
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},
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/**
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* #action
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*/
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setTreeMetadata(treeMetadata) {
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self.treeMetadata = treeMetadata;
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},
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}));
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}
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//# sourceMappingURL=DataModel.js.map
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import { DialogComponentType } from '@jbrowse/core/util';
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/**
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* #stateModel DialogQueueSessionMixin
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*/
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export declare function DialogQueueSessionMixin(): import("mobx-state-tree").IModelType<{}, {
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queueOfDialogs: [DialogComponentType, any][];
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} & {
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/**
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* #getter
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*/
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readonly DialogComponent: DialogComponentType;
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/**
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* #getter
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*/
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readonly DialogProps: any;
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} & {
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/**
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* #action
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*/
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removeActiveDialog(): void;
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/**
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* #action
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*/
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queueDialog(cb: (doneCallback: () => void) => [DialogComponentType, unknown]): void;
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}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
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import { types } from 'mobx-state-tree';
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/**
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* #stateModel DialogQueueSessionMixin
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*/
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export function DialogQueueSessionMixin() {
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return types
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.model('DialogQueueSessionMixin', {})
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// eslint-disable-next-line @typescript-eslint/no-explicit-any
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queueOfDialogs: [],
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}))
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.views(self => ({
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*/
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get DialogComponent() {
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return self.queueOfDialogs[0]?.[0];
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},
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* #getter
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*/
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get DialogProps() {
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return self.queueOfDialogs[0]?.[1];
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},
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}))
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.actions(self => ({
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/**
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* #action
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*/
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removeActiveDialog() {
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},
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queueDialog(cb) {
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const [component, props] = cb(() => {
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this.removeActiveDialog();
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});
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self.queueOfDialogs = [...self.queueOfDialogs, [component, props]];
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},
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}));
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}
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//# sourceMappingURL=DialogQueue.js.map
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{"version":3,"file":"DialogQueue.js","sourceRoot":"","sources":["../src/DialogQueue.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,MAAM,UAAU,uBAAuB;IACrC,OAAO,KAAK;SACT,KAAK,CAAC,yBAAyB,EAAE,EAAE,CAAC;SACpC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,8DAA8D;QAC9D,cAAc,EAAE,EAAkC;KACnD,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,eAAe;YACjB,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;QACD;;WAEG;QACH,IAAI,WAAW;YACb,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,kBAAkB;YAChB,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACpD,CAAC;QACD;;WAEG;QACH,WAAW,CACT,EAAgE;YAEhE,MAAM,CAAC,SAAS,EAAE,KAAK,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE;gBACjC,IAAI,CAAC,kBAAkB,EAAE,CAAA;YAC3B,CAAC,CAAC,CAAA;YACF,IAAI,CAAC,cAAc,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,EAAE,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC,CAAA;QACpE,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
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import { SnapshotIn } from 'mobx-state-tree';
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import { StructureModel } from './StructureModel';
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export type StructureSnap = SnapshotIn<typeof StructureModel>;
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export declare function SelectedStructuresMixin(): import("mobx-state-tree").IModelType<{
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/**
|
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6
|
+
* #property
|
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7
|
+
* currently "selected" structures, generally PDB 3-D protein structures
|
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8
|
+
*/
|
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9
|
+
selectedStructures: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
|
|
10
|
+
id: import("mobx-state-tree").ISimpleType<string>;
|
|
11
|
+
structure: import("mobx-state-tree").IModelType<{
|
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12
|
+
pdb: import("mobx-state-tree").ISimpleType<string>;
|
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13
|
+
startPos: import("mobx-state-tree").ISimpleType<number>;
|
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14
|
+
endPos: import("mobx-state-tree").ISimpleType<number>;
|
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15
|
+
}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
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16
|
+
range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
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17
|
+
}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
|
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+
}, {
|
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|
+
/**
|
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+
* #action
|
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21
|
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* add to the selected structures
|
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22
|
+
*/
|
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23
|
+
addStructureToSelection(elt: StructureSnap): void;
|
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24
|
+
/**
|
|
25
|
+
* #action
|
|
26
|
+
* remove from the selected structures
|
|
27
|
+
*/
|
|
28
|
+
removeStructureFromSelection(elt: StructureSnap): void;
|
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29
|
+
/**
|
|
30
|
+
* #action
|
|
31
|
+
* toggle a structure from the selected structures list
|
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32
|
+
*/
|
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|
+
toggleStructureSelection(elt: {
|
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|
+
id: string;
|
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35
|
+
structure: {
|
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+
startPos: number;
|
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+
endPos: number;
|
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+
pdb: string;
|
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+
};
|
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+
}): void;
|
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41
|
+
/**
|
|
42
|
+
* #action
|
|
43
|
+
* clear all selected structures
|
|
44
|
+
*/
|
|
45
|
+
clearSelectedStructures(): void;
|
|
46
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
@@ -0,0 +1,52 @@
|
|
|
1
|
+
import { cast, types } from 'mobx-state-tree';
|
|
2
|
+
import { StructureModel } from './StructureModel';
|
|
3
|
+
export function SelectedStructuresMixin() {
|
|
4
|
+
return types
|
|
5
|
+
.model({
|
|
6
|
+
/**
|
|
7
|
+
* #property
|
|
8
|
+
* currently "selected" structures, generally PDB 3-D protein structures
|
|
9
|
+
*/
|
|
10
|
+
selectedStructures: types.array(StructureModel),
|
|
11
|
+
})
|
|
12
|
+
.actions(self => ({
|
|
13
|
+
/**
|
|
14
|
+
* #action
|
|
15
|
+
* add to the selected structures
|
|
16
|
+
*/
|
|
17
|
+
addStructureToSelection(elt) {
|
|
18
|
+
self.selectedStructures.push(elt);
|
|
19
|
+
},
|
|
20
|
+
/**
|
|
21
|
+
* #action
|
|
22
|
+
* remove from the selected structures
|
|
23
|
+
*/
|
|
24
|
+
removeStructureFromSelection(elt) {
|
|
25
|
+
const r = self.selectedStructures.find(node => node.id === elt.id);
|
|
26
|
+
if (r) {
|
|
27
|
+
self.selectedStructures.remove(r);
|
|
28
|
+
}
|
|
29
|
+
},
|
|
30
|
+
/**
|
|
31
|
+
* #action
|
|
32
|
+
* toggle a structure from the selected structures list
|
|
33
|
+
*/
|
|
34
|
+
toggleStructureSelection(elt) {
|
|
35
|
+
const r = self.selectedStructures.find(node => node.id === elt.id);
|
|
36
|
+
if (r) {
|
|
37
|
+
self.selectedStructures.remove(r);
|
|
38
|
+
}
|
|
39
|
+
else {
|
|
40
|
+
self.selectedStructures.push(elt);
|
|
41
|
+
}
|
|
42
|
+
},
|
|
43
|
+
/**
|
|
44
|
+
* #action
|
|
45
|
+
* clear all selected structures
|
|
46
|
+
*/
|
|
47
|
+
clearSelectedStructures() {
|
|
48
|
+
self.selectedStructures = cast([]);
|
|
49
|
+
},
|
|
50
|
+
}));
|
|
51
|
+
}
|
|
52
|
+
//# sourceMappingURL=SelectedStructuresMixin.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"SelectedStructuresMixin.js","sourceRoot":"","sources":["../src/SelectedStructuresMixin.ts"],"names":[],"mappings":"AAAA,OAAO,EAAc,IAAI,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACzD,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAA;AAIjD,MAAM,UAAU,uBAAuB;IACrC,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;;WAGG;QACH,kBAAkB,EAAE,KAAK,CAAC,KAAK,CAAC,cAAc,CAAC;KAChD,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;WAGG;QACH,uBAAuB,CAAC,GAAkB;YACxC,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACnC,CAAC;QAED;;;WAGG;QACH,4BAA4B,CAAC,GAAkB;YAC7C,MAAM,CAAC,GAAG,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;YAClE,IAAI,CAAC,EAAE,CAAC;gBACN,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;QAED;;;WAGG;QACH,wBAAwB,CAAC,GAGxB;YACC,MAAM,CAAC,GAAG,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC,CAAA;YAClE,IAAI,CAAC,EAAE,CAAC;gBACN,IAAI,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;YACnC,CAAC;iBAAM,CAAC;gBACN,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YACnC,CAAC;QACH,CAAC;QAED;;;WAGG;QACH,uBAAuB;YACrB,IAAI,CAAC,kBAAkB,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACpC,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
|
|
@@ -0,0 +1,9 @@
|
|
|
1
|
+
export declare const StructureModel: import("mobx-state-tree").IModelType<{
|
|
2
|
+
id: import("mobx-state-tree").ISimpleType<string>;
|
|
3
|
+
structure: import("mobx-state-tree").IModelType<{
|
|
4
|
+
pdb: import("mobx-state-tree").ISimpleType<string>;
|
|
5
|
+
startPos: import("mobx-state-tree").ISimpleType<number>;
|
|
6
|
+
endPos: import("mobx-state-tree").ISimpleType<number>;
|
|
7
|
+
}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
8
|
+
range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
9
|
+
}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
@@ -0,0 +1,11 @@
|
|
|
1
|
+
import { types } from 'mobx-state-tree';
|
|
2
|
+
export const StructureModel = types.model({
|
|
3
|
+
id: types.identifier,
|
|
4
|
+
structure: types.model({
|
|
5
|
+
pdb: types.string,
|
|
6
|
+
startPos: types.number,
|
|
7
|
+
endPos: types.number,
|
|
8
|
+
}),
|
|
9
|
+
range: types.maybe(types.string),
|
|
10
|
+
});
|
|
11
|
+
//# sourceMappingURL=StructureModel.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"StructureModel.js","sourceRoot":"","sources":["../src/StructureModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,MAAM,CAAC,MAAM,cAAc,GAAG,KAAK,CAAC,KAAK,CAAC;IACxC,EAAE,EAAE,KAAK,CAAC,UAAU;IACpB,SAAS,EAAE,KAAK,CAAC,KAAK,CAAC;QACrB,GAAG,EAAE,KAAK,CAAC,MAAM;QACjB,QAAQ,EAAE,KAAK,CAAC,MAAM;QACtB,MAAM,EAAE,KAAK,CAAC,MAAM;KACrB,CAAC;IACF,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;CACjC,CAAC,CAAA"}
|
|
@@ -0,0 +1,27 @@
|
|
|
1
|
+
export declare const UniprotTrack: import("mobx-state-tree").IModelType<{
|
|
2
|
+
id: import("mobx-state-tree").ISimpleType<string>;
|
|
3
|
+
accession: import("mobx-state-tree").ISimpleType<string>;
|
|
4
|
+
name: import("mobx-state-tree").ISimpleType<string>;
|
|
5
|
+
associatedRowName: import("mobx-state-tree").ISimpleType<string>;
|
|
6
|
+
height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
|
|
7
|
+
}, {
|
|
8
|
+
error: unknown;
|
|
9
|
+
data: string | undefined;
|
|
10
|
+
} & {
|
|
11
|
+
setError(error: unknown): void;
|
|
12
|
+
setData(data: string): void;
|
|
13
|
+
} & {
|
|
14
|
+
afterCreate(): void;
|
|
15
|
+
} & {
|
|
16
|
+
readonly loading: boolean;
|
|
17
|
+
readonly features: {
|
|
18
|
+
seq_id: string;
|
|
19
|
+
source: string;
|
|
20
|
+
type: string;
|
|
21
|
+
start: number;
|
|
22
|
+
end: number;
|
|
23
|
+
score: number;
|
|
24
|
+
strand: string;
|
|
25
|
+
phase: string;
|
|
26
|
+
}[] | undefined;
|
|
27
|
+
}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
|
|
@@ -0,0 +1,53 @@
|
|
|
1
|
+
import { types, addDisposer } from 'mobx-state-tree';
|
|
2
|
+
import { autorun } from 'mobx';
|
|
3
|
+
// locals
|
|
4
|
+
import { parseGFF } from './util';
|
|
5
|
+
export const UniprotTrack = types
|
|
6
|
+
.model({
|
|
7
|
+
id: types.string,
|
|
8
|
+
accession: types.string,
|
|
9
|
+
name: types.string,
|
|
10
|
+
associatedRowName: types.string,
|
|
11
|
+
height: types.optional(types.number, 100),
|
|
12
|
+
})
|
|
13
|
+
.volatile(() => ({
|
|
14
|
+
error: undefined,
|
|
15
|
+
data: undefined,
|
|
16
|
+
}))
|
|
17
|
+
.actions(self => ({
|
|
18
|
+
setError(error) {
|
|
19
|
+
self.error = error;
|
|
20
|
+
},
|
|
21
|
+
setData(data) {
|
|
22
|
+
self.data = data;
|
|
23
|
+
},
|
|
24
|
+
}))
|
|
25
|
+
.actions(self => ({
|
|
26
|
+
afterCreate() {
|
|
27
|
+
addDisposer(self, autorun(async () => {
|
|
28
|
+
try {
|
|
29
|
+
const { accession } = self;
|
|
30
|
+
const accessionSansVersion = accession?.replace(/\.[^/.]+$/, '');
|
|
31
|
+
const url = `https://rest.uniprot.org/uniprotkb/${accessionSansVersion}.gff`;
|
|
32
|
+
const res = await fetch(url);
|
|
33
|
+
if (!res.ok) {
|
|
34
|
+
throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
|
|
35
|
+
}
|
|
36
|
+
self.setData(await res.text());
|
|
37
|
+
}
|
|
38
|
+
catch (e) {
|
|
39
|
+
console.error(e);
|
|
40
|
+
self.setError(e);
|
|
41
|
+
}
|
|
42
|
+
}));
|
|
43
|
+
},
|
|
44
|
+
}))
|
|
45
|
+
.views(self => ({
|
|
46
|
+
get loading() {
|
|
47
|
+
return !self.data;
|
|
48
|
+
},
|
|
49
|
+
get features() {
|
|
50
|
+
return parseGFF(self.data);
|
|
51
|
+
},
|
|
52
|
+
}));
|
|
53
|
+
//# sourceMappingURL=UniprotTrack.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"UniprotTrack.js","sourceRoot":"","sources":["../src/UniprotTrack.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AACpD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B,SAAS;AACT,OAAO,EAAE,QAAQ,EAAE,MAAM,QAAQ,CAAA;AAEjC,MAAM,CAAC,MAAM,YAAY,GAAG,KAAK;KAC9B,KAAK,CAAC;IACL,EAAE,EAAE,KAAK,CAAC,MAAM;IAChB,SAAS,EAAE,KAAK,CAAC,MAAM;IACvB,IAAI,EAAE,KAAK,CAAC,MAAM;IAClB,iBAAiB,EAAE,KAAK,CAAC,MAAM;IAC/B,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;CAC1C,CAAC;KACD,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;IACf,KAAK,EAAE,SAAoB;IAC3B,IAAI,EAAE,SAA+B;CACtC,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,QAAQ,CAAC,KAAc;QACrB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;IACpB,CAAC;IACD,OAAO,CAAC,IAAY;QAClB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;IAClB,CAAC;CACF,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,WAAW;QACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,KAAK,IAAI,EAAE;YACjB,IAAI,CAAC;gBACH,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAA;gBAC1B,MAAM,oBAAoB,GAAG,SAAS,EAAE,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAA;gBAChE,MAAM,GAAG,GAAG,sCAAsC,oBAAoB,MAAM,CAAA;gBAC5E,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;gBAC5B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;oBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;gBACH,CAAC;gBACD,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,CAAA;YAChC,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAC,CACH,CAAA;IACH,CAAC;CACF,CAAC,CAAC;KACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACd,IAAI,OAAO;QACT,OAAO,CAAC,IAAI,CAAC,IAAI,CAAA;IACnB,CAAC;IAED,IAAI,QAAQ;QACV,OAAO,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC5B,CAAC;CACF,CAAC,CAAC,CAAA"}
|
|
@@ -0,0 +1,15 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
|
+
import { observer } from 'mobx-react';
|
|
3
|
+
import BoxTrackBlock from './BoxTrackBlock';
|
|
4
|
+
const BoxTrack = observer(function ({ model, track, }) {
|
|
5
|
+
const { blocksX, msaAreaWidth } = model;
|
|
6
|
+
const { height } = track.model;
|
|
7
|
+
return (React.createElement("div", { style: {
|
|
8
|
+
position: 'relative',
|
|
9
|
+
height,
|
|
10
|
+
width: msaAreaWidth,
|
|
11
|
+
overflow: 'hidden',
|
|
12
|
+
} }, blocksX.map(bx => (React.createElement(BoxTrackBlock, { track: track, key: bx, model: model, offsetX: bx })))));
|
|
13
|
+
});
|
|
14
|
+
export default BoxTrack;
|
|
15
|
+
//# sourceMappingURL=BoxTrack.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"BoxTrack.js","sourceRoot":"","sources":["../../src/components/BoxTrack.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAE3C,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IACvC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAC9B,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM;YACN,KAAK,EAAE,YAAY;YACnB,QAAQ,EAAE,QAAQ;SACnB,IAEA,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,CACjB,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,GAAI,CACpE,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}
|
|
@@ -0,0 +1,8 @@
|
|
|
1
|
+
import React from 'react';
|
|
2
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+
import { IBoxTrack, MsaViewModel } from '../model';
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3
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+
declare const BoxTrackBlock: ({ track, model, offsetX, }: {
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4
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+
track: IBoxTrack;
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5
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+
model: MsaViewModel;
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6
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+
offsetX: number;
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7
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+
}) => React.JSX.Element | null;
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8
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+
export default BoxTrackBlock;
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@@ -0,0 +1,136 @@
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1
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+
import React, { useRef, useMemo, useEffect } from 'react';
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2
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+
import { observer } from 'mobx-react';
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3
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+
import { getSnapshot, isStateTreeNode } from 'mobx-state-tree';
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4
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+
import Layout from '../layout';
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5
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+
const BoxTrackBlock = observer(function ({ track, model, offsetX, }) {
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6
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+
const { blockSize, colWidth, blanks, rowHeight, highResScaleFactor, fontSize, scrollX, } = model;
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7
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+
const { height, features, associatedRowName } = track.model;
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8
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+
const feats = isStateTreeNode(features)
|
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9
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+
? // @ts-expect-error
|
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10
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+
getSnapshot(features)
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11
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+
: features;
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12
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+
const layout = useMemo(() => {
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13
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+
const temp = new Layout();
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14
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+
feats?.forEach((feature, index) => {
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15
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+
const { start, end } = feature;
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16
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+
if (associatedRowName) {
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17
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+
const s = model.rowSpecificBpToPx(associatedRowName, start - 1);
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18
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+
const e = model.rowSpecificBpToPx(associatedRowName, end);
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+
temp.addRect(`${index}`, s, e, rowHeight, feature);
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20
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+
}
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21
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+
else {
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22
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+
const s = model.globalBpToPx(start - 1);
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23
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+
const e = model.globalBpToPx(end);
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24
|
+
temp.addRect(`${index}`, s, e, rowHeight, feature);
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25
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+
}
|
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26
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+
});
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27
|
+
return temp;
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28
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+
// might convert to autorun based drawing
|
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29
|
+
// eslint-disable-next-line react-hooks/exhaustive-deps
|
|
30
|
+
}, [rowHeight, feats, associatedRowName, model, blanks]);
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31
|
+
const ref = useRef(null);
|
|
32
|
+
const labelRef = useRef(null);
|
|
33
|
+
const mouseoverRef = useRef(null);
|
|
34
|
+
useEffect(() => {
|
|
35
|
+
if (!ref.current) {
|
|
36
|
+
return;
|
|
37
|
+
}
|
|
38
|
+
const ctx = ref.current.getContext('2d');
|
|
39
|
+
if (!ctx) {
|
|
40
|
+
return;
|
|
41
|
+
}
|
|
42
|
+
ctx.resetTransform();
|
|
43
|
+
ctx.scale(highResScaleFactor, highResScaleFactor);
|
|
44
|
+
ctx.clearRect(0, 0, blockSize, height);
|
|
45
|
+
ctx.translate(-offsetX, 0);
|
|
46
|
+
ctx.textAlign = 'center';
|
|
47
|
+
ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
|
|
48
|
+
const xStart = Math.max(0, Math.floor(offsetX / colWidth));
|
|
49
|
+
ctx.fillStyle = 'goldenrod';
|
|
50
|
+
layout.rectangles.forEach(value => {
|
|
51
|
+
const { minX, maxX, minY, maxY } = value;
|
|
52
|
+
const x1 = (minX - xStart) * colWidth + offsetX - (offsetX % colWidth);
|
|
53
|
+
const x2 = (maxX - xStart) * colWidth + offsetX - (offsetX % colWidth);
|
|
54
|
+
if (x2 - x1 > 0) {
|
|
55
|
+
ctx.fillRect(x1, minY, x2 - x1, (maxY - minY) / 2);
|
|
56
|
+
}
|
|
57
|
+
});
|
|
58
|
+
}, [
|
|
59
|
+
associatedRowName,
|
|
60
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+
fontSize,
|
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61
|
+
blockSize,
|
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62
|
+
colWidth,
|
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63
|
+
layout.rectangles,
|
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64
|
+
model,
|
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65
|
+
rowHeight,
|
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66
|
+
height,
|
|
67
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+
offsetX,
|
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68
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+
highResScaleFactor,
|
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69
|
+
features,
|
|
70
|
+
blanks,
|
|
71
|
+
]);
|
|
72
|
+
useEffect(() => {
|
|
73
|
+
if (!labelRef.current) {
|
|
74
|
+
return;
|
|
75
|
+
}
|
|
76
|
+
const ctx = labelRef.current.getContext('2d');
|
|
77
|
+
if (!ctx) {
|
|
78
|
+
return;
|
|
79
|
+
}
|
|
80
|
+
// this logic is very similar to MSACanvas
|
|
81
|
+
ctx.resetTransform();
|
|
82
|
+
ctx.scale(highResScaleFactor, highResScaleFactor);
|
|
83
|
+
ctx.clearRect(0, 0, blockSize, height);
|
|
84
|
+
ctx.translate(-offsetX, 0);
|
|
85
|
+
ctx.textAlign = 'center';
|
|
86
|
+
ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
|
|
87
|
+
ctx.fillStyle = 'black';
|
|
88
|
+
ctx.textAlign = 'left';
|
|
89
|
+
for (const value of layout.rectangles.values()) {
|
|
90
|
+
const { minX, maxX, maxY, minY, data } = value;
|
|
91
|
+
const x1 = minX * colWidth;
|
|
92
|
+
const x2 = maxX * colWidth;
|
|
93
|
+
// eslint-disable-next-line @typescript-eslint/no-explicit-any
|
|
94
|
+
const feature = data;
|
|
95
|
+
if (x2 - x1 > 0) {
|
|
96
|
+
const note = feature.attributes?.Note?.[0];
|
|
97
|
+
const name = feature.attributes?.Name?.[0];
|
|
98
|
+
const type = feature.type;
|
|
99
|
+
ctx.fillText([type, name, note].filter(f => !!f).join(' - '), Math.max(Math.min(-scrollX, x2), x1), minY + (maxY - minY));
|
|
100
|
+
}
|
|
101
|
+
}
|
|
102
|
+
}, [
|
|
103
|
+
blockSize,
|
|
104
|
+
colWidth,
|
|
105
|
+
scrollX,
|
|
106
|
+
highResScaleFactor,
|
|
107
|
+
height,
|
|
108
|
+
layout.rectangles,
|
|
109
|
+
offsetX,
|
|
110
|
+
features,
|
|
111
|
+
model,
|
|
112
|
+
rowHeight,
|
|
113
|
+
blanks,
|
|
114
|
+
]);
|
|
115
|
+
return !features ? null : (React.createElement(React.Fragment, null,
|
|
116
|
+
React.createElement("canvas", { ref: ref, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
|
|
117
|
+
position: 'absolute',
|
|
118
|
+
left: scrollX + offsetX,
|
|
119
|
+
width: blockSize,
|
|
120
|
+
height,
|
|
121
|
+
} }),
|
|
122
|
+
React.createElement("canvas", { ref: labelRef, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
|
|
123
|
+
position: 'absolute',
|
|
124
|
+
left: scrollX + offsetX,
|
|
125
|
+
width: blockSize,
|
|
126
|
+
height,
|
|
127
|
+
} }),
|
|
128
|
+
React.createElement("canvas", { ref: mouseoverRef, height: height * highResScaleFactor, width: blockSize * highResScaleFactor, style: {
|
|
129
|
+
position: 'absolute',
|
|
130
|
+
left: scrollX + offsetX,
|
|
131
|
+
width: blockSize,
|
|
132
|
+
height,
|
|
133
|
+
} })));
|
|
134
|
+
});
|
|
135
|
+
export default BoxTrackBlock;
|
|
136
|
+
//# sourceMappingURL=BoxTrackBlock.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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|
|
@@ -0,0 +1,39 @@
|
|
|
1
|
+
import React, { useState } from 'react';
|
|
2
|
+
import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
|
|
3
|
+
import { Button, Checkbox, DialogContent, DialogActions, FormControlLabel, FormControl, FormLabel, RadioGroup, Radio, Typography, useTheme, } from '@mui/material';
|
|
4
|
+
export default function ExportSVGDialog({ model, onClose, }) {
|
|
5
|
+
const [includeMinimap, setIncludeMinimap] = useState(true);
|
|
6
|
+
const [exportType, setExportType] = useState('viewport');
|
|
7
|
+
const [error, setError] = useState();
|
|
8
|
+
const theme = useTheme();
|
|
9
|
+
return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Export SVG" },
|
|
10
|
+
React.createElement(DialogContent, null,
|
|
11
|
+
error ? React.createElement(ErrorMessage, { error: error }) : null,
|
|
12
|
+
React.createElement(Typography, null, "Settings:"),
|
|
13
|
+
React.createElement("div", null,
|
|
14
|
+
React.createElement(FormControl, null,
|
|
15
|
+
React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: includeMinimap, onChange: event => setIncludeMinimap(event.target.checked) }), disabled: exportType === 'entire', label: "Include minimap?" }))),
|
|
16
|
+
React.createElement("div", null,
|
|
17
|
+
React.createElement(FormControl, null,
|
|
18
|
+
React.createElement(FormLabel, null, "Export type"),
|
|
19
|
+
React.createElement(RadioGroup, { value: exportType, onChange: event => setExportType(event.target.value) },
|
|
20
|
+
React.createElement(FormControlLabel, { value: "entire", control: React.createElement(Radio, null), label: "Entire MSA" }),
|
|
21
|
+
React.createElement(FormControlLabel, { value: "viewport", control: React.createElement(Radio, null), label: "Current viewport only" }))))),
|
|
22
|
+
React.createElement(DialogActions, null,
|
|
23
|
+
React.createElement(Button, { variant: "contained", color: "primary", onClick: async () => {
|
|
24
|
+
try {
|
|
25
|
+
await model.exportSVG({
|
|
26
|
+
theme,
|
|
27
|
+
includeMinimap: exportType === 'entire' ? false : includeMinimap,
|
|
28
|
+
exportType,
|
|
29
|
+
});
|
|
30
|
+
}
|
|
31
|
+
catch (e) {
|
|
32
|
+
console.error(e);
|
|
33
|
+
setError(e);
|
|
34
|
+
}
|
|
35
|
+
onClose();
|
|
36
|
+
} }, "Submit"),
|
|
37
|
+
React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => onClose() }, "Cancel"))));
|
|
38
|
+
}
|
|
39
|
+
//# sourceMappingURL=ExportSVGDialog.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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|