@teselagen/ove 0.0.13 → 0.0.15
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/index.umd.js +164751 -135808
- package/package.json +78 -2
- package/src/AlignmentTool/index.js +16 -0
- package/src/AlignmentView/AlignmentVisibilityTool.js +105 -0
- package/src/AlignmentView/EditTrackNameDialog.js +34 -0
- package/src/AlignmentView/HorizontalPanelDragHandle.js +35 -0
- package/src/AlignmentView/Minimap.js +520 -0
- package/src/AlignmentView/Mismatches.js +134 -0
- package/src/AlignmentView/PairwiseAlignmentView.js +68 -0
- package/src/AlignmentView/PerformantSelectionLayer.js +32 -0
- package/src/AlignmentView/coerceInitialValue.js +7 -0
- package/src/AlignmentView/getGapMap.js +12 -0
- package/src/AlignmentView/getGaps.js +27 -0
- package/src/AlignmentView/getPairwiseOverviewLinearViewOptions.js +38 -0
- package/src/AlignmentView/getTrackFromEvent.js +25 -0
- package/src/AlignmentView/index.js +2058 -0
- package/src/AlignmentView/isTargetWithinEl.js +6 -0
- package/src/AlignmentView/style.css +100 -0
- package/src/AlignmentView/updateTrackHelper.js +58 -0
- package/src/AutoAnnotate.js +500 -0
- package/src/AutoAnnotateBpMatchingDialog.js +208 -0
- package/src/CircularView/Axis.js +40 -0
- package/src/CircularView/AxisNumbers.js +35 -0
- package/src/CircularView/Caret.js +63 -0
- package/src/CircularView/CircularDnaSequence.js +73 -0
- package/src/CircularView/CircularZoomMinimap.js +16 -0
- package/src/CircularView/Cutsite.js +18 -0
- package/src/CircularView/Cutsites.js +113 -0
- package/src/CircularView/DeletionLayer.js +28 -0
- package/src/CircularView/Feature.js +83 -0
- package/src/CircularView/Labels/index.js +536 -0
- package/src/CircularView/Labels/relaxLabelAngles.js +157 -0
- package/src/CircularView/Labels/relaxLabels_DEPRECATED.js +105 -0
- package/src/CircularView/Labels/style.css +55 -0
- package/src/CircularView/Orf.js +25 -0
- package/src/CircularView/Part.js +34 -0
- package/src/CircularView/PositionAnnotationOnCircle.js +26 -0
- package/src/CircularView/Primer.js +41 -0
- package/src/CircularView/RotateCircularViewSlider.js +82 -0
- package/src/CircularView/SelectionLayer.js +132 -0
- package/src/CircularView/VeTopRightContainer.js +12 -0
- package/src/CircularView/ZoomCircularViewSlider.js +62 -0
- package/src/CircularView/drawAnnotations.js +433 -0
- package/src/CircularView/drawDirectedPiePiece.js +142 -0
- package/src/CircularView/getAngleForPositionMidpoint.js +3 -0
- package/src/CircularView/getInternalLabel.js +40 -0
- package/src/CircularView/getRangeAnglesSpecial.js +12 -0
- package/src/CircularView/getYOffset.js +15 -0
- package/src/CircularView/index.d.ts +20 -0
- package/src/CircularView/index.js +930 -0
- package/src/CircularView/normalizeAngle.js +3 -0
- package/src/CircularView/normalizeAngleRange.js +9 -0
- package/src/CircularView/positionCutsites.js +6 -0
- package/src/CircularView/shouldFlipText.js +4 -0
- package/src/CircularView/style.css +47 -0
- package/src/CircularView/utils/polarToSpecialCartesian.js +7 -0
- package/src/CreateAnnotationsPage.js +96 -0
- package/src/CreateCustomEnzyme/index.js +337 -0
- package/src/CreateCustomEnzyme/style.css +100 -0
- package/src/CutsiteFilter/AdditionalCutsiteInfoDialog.js +599 -0
- package/src/CutsiteFilter/index.js +408 -0
- package/src/CutsiteFilter/style.css +23 -0
- package/src/CutsiteFilter/withRestrictionEnzymes.js +15 -0
- package/src/DigestTool/AddLaddersDialog.js +82 -0
- package/src/DigestTool/DigestTool.js +223 -0
- package/src/DigestTool/Ladder.css +20 -0
- package/src/DigestTool/Ladder.js +303 -0
- package/src/DigestTool/createFragmentLines.js +120 -0
- package/src/DigestTool/ladderDefaults.js +26 -0
- package/src/DigestTool/ruler.css +89 -0
- package/src/Editor/CommandHotkeyHandler.js +44 -0
- package/src/Editor/DropHandler.css +21 -0
- package/src/Editor/DropHandler.js +64 -0
- package/src/Editor/FillWindow.js +46 -0
- package/src/Editor/darkmode.css +98 -0
- package/src/Editor/index.js +1005 -0
- package/src/Editor/style.css +235 -0
- package/src/Editor/userDefinedHandlersAndOpts.js +56 -0
- package/src/EnzymeViewer/index.js +81 -0
- package/src/EnzymeViewer/style.css +6 -0
- package/src/FindBar/index.js +411 -0
- package/src/FindBar/style.css +46 -0
- package/src/GlobalDialog.js +66 -0
- package/src/GlobalDialogUtils.js +85 -0
- package/src/LinearView/SequenceName.js +15 -0
- package/src/LinearView/ZoomLinearView.js +47 -0
- package/src/LinearView/index.js +374 -0
- package/src/LinearView/style.css +12 -0
- package/src/ManageEnzymes/index.js +326 -0
- package/src/ManageEnzymes/style.css +100 -0
- package/src/MenuBar/defaultConfig.js +149 -0
- package/src/MenuBar/index.js +98 -0
- package/src/MenuBar/viewSubmenu.js +479 -0
- package/src/PCRTool/PCRTool.js +173 -0
- package/src/Reflex/Browser.js +107 -0
- package/src/Reflex/ReflexContainer.js +802 -0
- package/src/Reflex/ReflexElement.js +160 -0
- package/src/Reflex/ReflexEvents.js +77 -0
- package/src/Reflex/ReflexSplitter.js +205 -0
- package/src/Reflex/index.js +5 -0
- package/src/Reflex/reflex-styles.css +128 -0
- package/src/Reflex/reflex-styles.css.map +9 -0
- package/src/RowItem/AnnotationContainerHolder.js +20 -0
- package/src/RowItem/AnnotationPositioner.js +27 -0
- package/src/RowItem/Axis.js +149 -0
- package/src/RowItem/Caret/index.js +64 -0
- package/src/RowItem/Caret/style.css +8 -0
- package/src/RowItem/Chromatograms/Chromatogram.js +289 -0
- package/src/RowItem/CutsiteSelectionLayers.js +47 -0
- package/src/RowItem/Cutsites.js +271 -0
- package/src/RowItem/DeletionLayers/index.js +113 -0
- package/src/RowItem/DeletionLayers/style.css +5 -0
- package/src/RowItem/Labels.js +327 -0
- package/src/RowItem/Orf.js +109 -0
- package/src/RowItem/Orfs.js +35 -0
- package/src/RowItem/ReplacementLayers/style.css +5 -0
- package/src/RowItem/SelectionLayer/index.js +184 -0
- package/src/RowItem/SelectionLayer/style.css +21 -0
- package/src/RowItem/Sequence.js +269 -0
- package/src/RowItem/StackedAnnotations/PointedAnnotation.js +347 -0
- package/src/RowItem/StackedAnnotations/getStructuredBases.js +97 -0
- package/src/RowItem/StackedAnnotations/index.js +182 -0
- package/src/RowItem/StackedAnnotations/primerBases.js +218 -0
- package/src/RowItem/StackedAnnotations/style.css +14 -0
- package/src/RowItem/Translations/AASliver.js +190 -0
- package/src/RowItem/Translations/Translation.js +162 -0
- package/src/RowItem/Translations/index.js +54 -0
- package/src/RowItem/Translations/style.css +3 -0
- package/src/RowItem/constants.js +3 -0
- package/src/RowItem/getCutsiteLabelHeights.js +56 -0
- package/src/RowItem/getXStartAndWidthFromNonCircularRange.js +12 -0
- package/src/RowItem/getXStartAndWidthOfRangeWrtRow.js +27 -0
- package/src/RowItem/getXStartAndWidthOfRowAnnotation.js +19 -0
- package/src/RowItem/index.js +647 -0
- package/src/RowItem/partOverhangs.js +6 -0
- package/src/RowItem/style.css +103 -0
- package/src/RowItem/utils.js +32 -0
- package/src/RowView/estimateRowHeight.js +184 -0
- package/src/RowView/index.d.ts +10 -0
- package/src/RowView/index.js +554 -0
- package/src/RowView/style.css +12 -0
- package/src/SimpleCircularOrLinearView.js +379 -0
- package/src/SimpleOligoPreview.js +39 -0
- package/src/StatusBar/MeltingTemp.js +81 -0
- package/src/StatusBar/index.js +275 -0
- package/src/StatusBar/style.css +38 -0
- package/src/ToolBar/ToolbarItem.js +194 -0
- package/src/ToolBar/alignmentTool.js +503 -0
- package/src/ToolBar/array_move.js +10 -0
- package/src/ToolBar/cutsiteTool.js +88 -0
- package/src/ToolBar/downloadTool.js +38 -0
- package/src/ToolBar/editTool.js +26 -0
- package/src/ToolBar/featureTool.js +34 -0
- package/src/ToolBar/findTool.js +2 -0
- package/src/ToolBar/importTool.js +27 -0
- package/src/ToolBar/index.js +231 -0
- package/src/ToolBar/inlineFindTool.js +38 -0
- package/src/ToolBar/oligoTool.js +30 -0
- package/src/ToolBar/orfTool.js +141 -0
- package/src/ToolBar/partTool.js +47 -0
- package/src/ToolBar/printTool.js +31 -0
- package/src/ToolBar/redoTool.js +30 -0
- package/src/ToolBar/saveTool.js +48 -0
- package/src/ToolBar/style.css +138 -0
- package/src/ToolBar/undoTool.js +30 -0
- package/src/ToolBar/veToolbarIcons/find.png +0 -0
- package/src/ToolBar/veToolbarIcons/fullscreen.png +0 -0
- package/src/ToolBar/veToolbarIcons/linear.png +0 -0
- package/src/ToolBar/veToolbarIcons/pie.png +0 -0
- package/src/ToolBar/veToolbarIcons/print.png +0 -0
- package/src/ToolBar/veToolbarIcons/save.png +0 -0
- package/src/ToolBar/veToolbarIcons/show_cut_sites.png +0 -0
- package/src/ToolBar/veToolbarIcons/show_features.png +0 -0
- package/src/ToolBar/veToolbarIcons/show_orfs.png +0 -0
- package/src/ToolBar/veToolbarIcons/show_primers.png +0 -0
- package/src/ToolBar/veToolbarIcons/toggle_views.svg +1 -0
- package/src/ToolBar/versionHistoryTool.js +20 -0
- package/src/ToolBar/visibilityTool.js +39 -0
- package/src/VersionHistoryView/index.js +215 -0
- package/src/addAlignment.js +6 -0
- package/src/commands/getOveHotkeyDefs.js +12 -0
- package/src/commands/index.js +1585 -0
- package/src/constants/constants.js +2 -0
- package/src/constants/dnaToColor.js +17 -0
- package/src/constants/draggableClassnames.js +5 -0
- package/src/constants/findToolConstants.js +1 -0
- package/src/constants/orfFrameToColorMap.js +10 -0
- package/src/constants/rowviewContants.js +3 -0
- package/src/constants/specialCutsiteFilterOptions.js +22 -0
- package/src/constants.js +1 -0
- package/src/createVectorEditor/index.js +138 -0
- package/src/createVectorEditor/makeStore.js +34 -0
- package/src/fileUtils.js +103 -0
- package/src/helperComponents/AddOrEditAnnotationDialog/index.js +711 -0
- package/src/helperComponents/AddOrEditAnnotationDialog/style.css +11 -0
- package/src/helperComponents/AddOrEditFeatureDialog/index.js +58 -0
- package/src/helperComponents/AddOrEditPartDialog/index.js +101 -0
- package/src/helperComponents/AddOrEditPrimerDialog/EditCaretPosition.js +234 -0
- package/src/helperComponents/AddOrEditPrimerDialog/index.js +329 -0
- package/src/helperComponents/AddOrEditPrimerDialog/style.css +41 -0
- package/src/helperComponents/EnzymesDialog/index.js +904 -0
- package/src/helperComponents/EnzymesDialog/style.css +21 -0
- package/src/helperComponents/GoToDialog.js +21 -0
- package/src/helperComponents/MergeFeaturesDialog/index.js +253 -0
- package/src/helperComponents/MergeFeaturesDialog/style.css +3 -0
- package/src/helperComponents/MultipleSeqsDetectedOnImportDialog.js +74 -0
- package/src/helperComponents/PinchHelper/PinchHelper.js +24 -0
- package/src/helperComponents/PrintDialog/index.js +396 -0
- package/src/helperComponents/PrintDialog/style.css +4 -0
- package/src/helperComponents/PropertiesDialog/ColorPicker.js +30 -0
- package/src/helperComponents/PropertiesDialog/CutsiteProperties.js +185 -0
- package/src/helperComponents/PropertiesDialog/FeatureProperties.js +6 -0
- package/src/helperComponents/PropertiesDialog/GenbankView.js +74 -0
- package/src/helperComponents/PropertiesDialog/GeneralProperties.js +140 -0
- package/src/helperComponents/PropertiesDialog/GenericAnnotationProperties.js +406 -0
- package/src/helperComponents/PropertiesDialog/OrfProperties.js +117 -0
- package/src/helperComponents/PropertiesDialog/PartProperties.js +9 -0
- package/src/helperComponents/PropertiesDialog/PrimerProperties.js +19 -0
- package/src/helperComponents/PropertiesDialog/SingleEnzymeCutsiteInfo.js +131 -0
- package/src/helperComponents/PropertiesDialog/TranslationProperties.js +149 -0
- package/src/helperComponents/PropertiesDialog/index.js +166 -0
- package/src/helperComponents/PropertiesDialog/style.css +68 -0
- package/src/helperComponents/PropertiesDialog/typeField.js +24 -0
- package/src/helperComponents/PropertiesDialog/utils.js +37 -0
- package/src/helperComponents/RemoveDuplicates/index.js +194 -0
- package/src/helperComponents/RenameSequenceDialog.js +7 -0
- package/src/helperComponents/SelectDialog.js +150 -0
- package/src/helperComponents/UncontrolledSliderWithPlusMinusBtns.css +5 -0
- package/src/helperComponents/UncontrolledSliderWithPlusMinusBtns.js +134 -0
- package/src/helperComponents/VeWarning/index.js +22 -0
- package/src/helperComponents/VeWarning/style.css +10 -0
- package/src/helperComponents/createSimpleDialog.js +89 -0
- package/src/helperComponents/partTagSearch.js +72 -0
- package/src/helperComponents/simpleDialog.css +13 -0
- package/src/helperComponents/withHover.js +90 -0
- package/src/index.js +60 -0
- package/src/redux/alignments.js +373 -0
- package/src/redux/annotationLabelVisibility.js +53 -0
- package/src/redux/annotationVisibility.js +196 -0
- package/src/redux/annotationsToSupport.js +104 -0
- package/src/redux/caretPosition.js +27 -0
- package/src/redux/charWidth.js +22 -0
- package/src/redux/copyOptions.js +34 -0
- package/src/redux/createYourOwnEnzyme.js +39 -0
- package/src/redux/deletionLayers.js +36 -0
- package/src/redux/digestTool.js +34 -0
- package/src/redux/featureLengthsToHide.js +27 -0
- package/src/redux/findTool.js +79 -0
- package/src/redux/frameTranslations.js +52 -0
- package/src/redux/hoveredAnnotation.js +24 -0
- package/src/redux/index.js +196 -0
- package/src/redux/labelLineIntensity.js +25 -0
- package/src/redux/labelSize.js +23 -0
- package/src/redux/lastSavedId.js +20 -0
- package/src/redux/middleware.js +112 -0
- package/src/redux/minimumOrfSize.js +24 -0
- package/src/redux/modalActions.js +3 -0
- package/src/redux/panelsShown.js +273 -0
- package/src/redux/partLengthsToHide.js +23 -0
- package/src/redux/primerLengthsToHide.js +27 -0
- package/src/redux/propertiesTool.js +40 -0
- package/src/redux/readOnly.js +28 -0
- package/src/redux/replacementLayers.js +36 -0
- package/src/redux/restrictionEnzymes.js +52 -0
- package/src/redux/selectedAnnotations.js +89 -0
- package/src/redux/selectedPartTags.js +21 -0
- package/src/redux/selectionLayer.js +46 -0
- package/src/redux/sequenceData/circular.js +19 -0
- package/src/redux/sequenceData/description.js +21 -0
- package/src/redux/sequenceData/features.js +19 -0
- package/src/redux/sequenceData/index.js +81 -0
- package/src/redux/sequenceData/lineageLines.js +11 -0
- package/src/redux/sequenceData/materiallyAvailable.js +19 -0
- package/src/redux/sequenceData/name.js +19 -0
- package/src/redux/sequenceData/parts.js +19 -0
- package/src/redux/sequenceData/primers.js +19 -0
- package/src/redux/sequenceData/sequence.js +12 -0
- package/src/redux/sequenceData/sharedActionCreators.js +0 -0
- package/src/redux/sequenceData/translations.js +20 -0
- package/src/redux/sequenceData/upsertDeleteActionGenerator.js +31 -0
- package/src/redux/sequenceDataHistory.js +43 -0
- package/src/redux/showGCContent.js +23 -0
- package/src/redux/toolBar.js +25 -0
- package/src/redux/uppercaseSequenceMapFont.js +25 -0
- package/src/redux/useAdditionalOrfStartCodons.js +24 -0
- package/src/redux/utils/addDashesForMatchStartAndEndForTracks/index.js +71 -0
- package/src/redux/utils/addMetaToActionCreators.js +12 -0
- package/src/redux/utils/createMergedDefaultStateReducer.js +30 -0
- package/src/redux/utils/createMetaAction.js +12 -0
- package/src/redux/versionHistory.js +27 -0
- package/src/selectors/annotationLabelVisibility.js +2 -0
- package/src/selectors/annotationSearchSelector.js +24 -0
- package/src/selectors/cdsFeaturesSelector.js +9 -0
- package/src/selectors/circularSelector.js +4 -0
- package/src/selectors/cutsiteLabelColorSelector.js +6 -0
- package/src/selectors/cutsitesByRangeSelector.js +5 -0
- package/src/selectors/cutsitesSelector.js +61 -0
- package/src/selectors/editorSelector.js +2 -0
- package/src/selectors/featuresSelector.js +8 -0
- package/src/selectors/filteredCutsitesSelector.js +137 -0
- package/src/selectors/filteredFeaturesSelector.js +32 -0
- package/src/selectors/filteredPartsSelector.js +57 -0
- package/src/selectors/filteredPrimersSelector.js +27 -0
- package/src/selectors/filteredRestrictionEnzymesSelector.js +1 -0
- package/src/selectors/getAdditionalEnzymesSelector.js +46 -0
- package/src/selectors/index.js +41 -0
- package/src/selectors/isEnzymeFilterAndSelector.js +1 -0
- package/src/selectors/minimumOrfSizeSelector.js +2 -0
- package/src/selectors/orfsSelector.js +15 -0
- package/src/selectors/partsSelector.js +8 -0
- package/src/selectors/primersSelector.js +8 -0
- package/src/selectors/restrictionEnzymesSelector.js +34 -0
- package/src/selectors/searchLayersSelector.js +71 -0
- package/src/selectors/selectedAnnotationsSelector.js +1 -0
- package/src/selectors/selectedCutsitesSelector.js +21 -0
- package/src/selectors/sequenceDataSelector.js +2 -0
- package/src/selectors/sequenceLengthSelector.js +5 -0
- package/src/selectors/sequenceSelector.js +4 -0
- package/src/selectors/tagsToBoldSelector.js +2 -0
- package/src/selectors/translationSearchMatchesSelector.js +14 -0
- package/src/selectors/translationsRawSelector.js +8 -0
- package/src/selectors/translationsSelector.js +137 -0
- package/src/style.css +82 -0
- package/src/updateEditor.js +198 -0
- package/src/utils/PassThrough.js +3 -0
- package/src/utils/addWrappedAddons.js +20 -0
- package/src/utils/annotationTypes.js +37 -0
- package/src/utils/arrayUtils.js +19 -0
- package/src/utils/calculateTickMarkPositionsForGivenRange.js +47 -0
- package/src/utils/cleanSequenceData_DEPRECATED/arrayToObjWithIds.js +17 -0
- package/src/utils/combineReducersDontIgnoreKeys.js +12 -0
- package/src/utils/commandUtils.js +18 -0
- package/src/utils/editorUtils.js +223 -0
- package/src/utils/getAnnotationClassnames.js +12 -0
- package/src/utils/getAnnotationNameAndStartStopString.js +61 -0
- package/src/utils/getVisibleStartEnd.js +7 -0
- package/src/utils/massageTickSpacing.js +19 -0
- package/src/utils/onlyUpdateForKeysDeep.js +31 -0
- package/src/utils/prepareRowData.js +64 -0
- package/src/utils/proteinUtils.js +3 -0
- package/src/utils/pureNoFunc.js +18 -0
- package/src/utils/selectionLayer.js +25 -0
- package/src/utils/shouldRerender.js +27 -0
- package/src/utils/showFileDialog.js +26 -0
- package/src/utils/updateLabelsForInViewFeatures.js +55 -0
- package/src/utils/updateLabelsForInViewFeaturesCircView.js +41 -0
- package/src/utils/useAAColorType.js +8 -0
- package/src/utils/useAnnotationLimits.js +42 -0
- package/src/utils/useChromatogramPrefs.js +31 -0
- package/src/utils/useLadders.js +6 -0
- package/src/utils/useMeltingTemp.js +7 -0
- package/src/utils/useTmType.js +10 -0
- package/src/withEditorInteractions/Keyboard.js +86 -0
- package/src/withEditorInteractions/clickAndDragUtils.js +576 -0
- package/src/withEditorInteractions/createSequenceInputPopup.js +296 -0
- package/src/withEditorInteractions/createSequenceInputPopupStyle.css +85 -0
- package/src/withEditorInteractions/getBpsPerRow.js +19 -0
- package/src/withEditorInteractions/index.js +1252 -0
- package/src/withEditorInteractions/isElementInViewport.js +29 -0
- package/src/withEditorInteractions/moveCaret.js +58 -0
- package/src/withEditorProps/index.js +1010 -0
- package/index.mjs +0 -193201
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import { ZoomCircularViewSlider } from "./ZoomCircularViewSlider";
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+
getClientX,
|
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35
|
+
getClientY,
|
|
36
|
+
getParedDownWarning,
|
|
37
|
+
pareDownAnnotations
|
|
38
|
+
} from "../utils/editorUtils";
|
|
39
|
+
import { getAllSelectionLayers } from "../utils/selectionLayer";
|
|
40
|
+
import classNames from "classnames";
|
|
41
|
+
import calculateTickMarkPositionsForGivenRange from "../utils/calculateTickMarkPositionsForGivenRange";
|
|
42
|
+
import { RotateCircularViewSlider } from "./RotateCircularViewSlider";
|
|
43
|
+
import { AxisNumbers } from "./AxisNumbers";
|
|
44
|
+
import { positionCutsites } from "./positionCutsites";
|
|
45
|
+
import { usePinch } from "@use-gesture/react";
|
|
46
|
+
import { CircularZoomMinimap } from "./CircularZoomMinimap";
|
|
47
|
+
import { normalizeAngleRange } from "./normalizeAngleRange";
|
|
48
|
+
import { CircularDnaSequence } from "./CircularDnaSequence";
|
|
49
|
+
import { VeTopRightContainer } from "./VeTopRightContainer";
|
|
50
|
+
import { normalizeAngle } from "./normalizeAngle";
|
|
51
|
+
import {
|
|
52
|
+
editorDragged,
|
|
53
|
+
editorDragStarted,
|
|
54
|
+
editorDragStopped
|
|
55
|
+
} from "../withEditorInteractions/clickAndDragUtils";
|
|
56
|
+
// import { updateLabelsForInViewFeaturesCircView } from "../utils/updateLabelsForInViewFeaturesCircView";
|
|
57
|
+
|
|
58
|
+
const BASE_RADIUS = 70;
|
|
59
|
+
|
|
60
|
+
function getNearestCursorPositionToMouseEvent(
|
|
61
|
+
event,
|
|
62
|
+
{
|
|
63
|
+
updateSelectionOrCaret,
|
|
64
|
+
caretPosition,
|
|
65
|
+
selectionLayer,
|
|
66
|
+
caretPositionUpdate,
|
|
67
|
+
selectionLayerUpdate,
|
|
68
|
+
sequenceData,
|
|
69
|
+
sequenceLength,
|
|
70
|
+
circRef,
|
|
71
|
+
rotationRadians
|
|
72
|
+
},
|
|
73
|
+
callback
|
|
74
|
+
) {
|
|
75
|
+
const clientX = getClientX(event);
|
|
76
|
+
const clientY = getClientY(event);
|
|
77
|
+
if (!clientX) {
|
|
78
|
+
return;
|
|
79
|
+
}
|
|
80
|
+
const boundingRect = circRef.current.getBoundingClientRect();
|
|
81
|
+
//get relative click positions
|
|
82
|
+
const clickX = clientX - boundingRect.left - boundingRect.width / 2;
|
|
83
|
+
const clickY = clientY - boundingRect.top - boundingRect.height / 2;
|
|
84
|
+
|
|
85
|
+
//get angle
|
|
86
|
+
let angle = Math.atan2(clickY, clickX) + Math.PI / 2 - rotationRadians;
|
|
87
|
+
if (angle < 0) angle += Math.PI * 2; //normalize the angle if necessary
|
|
88
|
+
let nearestCaretPos =
|
|
89
|
+
sequenceLength === 0
|
|
90
|
+
? 0
|
|
91
|
+
: normalizePositionByRangeLength(
|
|
92
|
+
getPositionFromAngle(angle, sequenceLength, true),
|
|
93
|
+
sequenceLength
|
|
94
|
+
); //true because we're in between positions
|
|
95
|
+
if (sequenceData && sequenceData.isProtein) {
|
|
96
|
+
nearestCaretPos = Math.round(nearestCaretPos / 3) * 3;
|
|
97
|
+
}
|
|
98
|
+
|
|
99
|
+
callback({
|
|
100
|
+
updateSelectionOrCaret,
|
|
101
|
+
caretPosition,
|
|
102
|
+
selectionLayer,
|
|
103
|
+
caretPositionUpdate,
|
|
104
|
+
selectionLayerUpdate,
|
|
105
|
+
sequenceLength,
|
|
106
|
+
event,
|
|
107
|
+
doNotWrapOrigin: !(sequenceData && sequenceData.circular),
|
|
108
|
+
className: event.target.parentNode.className.animVal,
|
|
109
|
+
shiftHeld: event.shiftKey,
|
|
110
|
+
nearestCaretPos,
|
|
111
|
+
selectionStartGrabbed: event.target.parentNode.classList.contains(
|
|
112
|
+
draggableClassnames.selectionStart
|
|
113
|
+
),
|
|
114
|
+
selectionEndGrabbed: event.target.parentNode.classList.contains(
|
|
115
|
+
draggableClassnames.selectionEnd
|
|
116
|
+
)
|
|
117
|
+
});
|
|
118
|
+
}
|
|
119
|
+
|
|
120
|
+
export function CircularView(props) {
|
|
121
|
+
const [limits] = useAnnotationLimits();
|
|
122
|
+
let [rotationRadians, setRotationRadians] = useState(0);
|
|
123
|
+
let [_zoomLevel, setZoomLevel] = useState(1);
|
|
124
|
+
|
|
125
|
+
if (props.circ_zoomLevel !== undefined) {
|
|
126
|
+
//override from the editor to not lose the state when the Circular View component isn't rendered
|
|
127
|
+
rotationRadians = props.circ_rotationRadians;
|
|
128
|
+
setRotationRadians = props.circ_setRotationRadians;
|
|
129
|
+
_zoomLevel = props.circ_zoomLevel;
|
|
130
|
+
setZoomLevel = props.circ_setZoomLevel;
|
|
131
|
+
}
|
|
132
|
+
const { sequenceData = {}, smallSlider } = props;
|
|
133
|
+
const { sequence = "atgc", circular } = sequenceData;
|
|
134
|
+
|
|
135
|
+
const sequenceLength = sequenceData.noSequence
|
|
136
|
+
? sequenceData.size
|
|
137
|
+
: sequenceData.sequence.length;
|
|
138
|
+
|
|
139
|
+
const hasZoomableLength = sequenceLength >= 50;
|
|
140
|
+
const hasRotateableLength = sequenceLength >= 10;
|
|
141
|
+
if (!hasZoomableLength) _zoomLevel = 1;
|
|
142
|
+
if (!hasRotateableLength) rotationRadians = 0;
|
|
143
|
+
const circRef = useRef();
|
|
144
|
+
const rotateHelper = useRef({});
|
|
145
|
+
const zoomHelper = useRef({});
|
|
146
|
+
useEffect(() => {
|
|
147
|
+
rotateHelper.current.triggerChange &&
|
|
148
|
+
rotateHelper.current.triggerChange(({ changeValue }) => {
|
|
149
|
+
changeValue(
|
|
150
|
+
(normalizeAngle(Math.PI * 2 - rotationRadians) / Math.PI) * 180
|
|
151
|
+
);
|
|
152
|
+
});
|
|
153
|
+
// eslint-disable-next-line react-hooks/exhaustive-deps
|
|
154
|
+
}, []);
|
|
155
|
+
let zoomLevel = _zoomLevel;
|
|
156
|
+
|
|
157
|
+
let smallZoom = 1;
|
|
158
|
+
if (_zoomLevel < 1) {
|
|
159
|
+
smallZoom = _zoomLevel;
|
|
160
|
+
zoomLevel = 1;
|
|
161
|
+
}
|
|
162
|
+
|
|
163
|
+
const {
|
|
164
|
+
//set defaults for all of these vars
|
|
165
|
+
width = 400,
|
|
166
|
+
height = 400,
|
|
167
|
+
noRedux,
|
|
168
|
+
readOnly,
|
|
169
|
+
hideName = false,
|
|
170
|
+
editorName,
|
|
171
|
+
smartCircViewLabelRender,
|
|
172
|
+
showCicularViewInternalLabels,
|
|
173
|
+
withRotateCircularView: _withRotateCircularView,
|
|
174
|
+
withZoomCircularView,
|
|
175
|
+
selectionLayer = { start: -1, end: -1 },
|
|
176
|
+
annotationHeight = 15,
|
|
177
|
+
spaceBetweenAnnotations = 2,
|
|
178
|
+
annotationVisibility = {},
|
|
179
|
+
annotationLabelVisibility = {},
|
|
180
|
+
caretPosition = -1,
|
|
181
|
+
editorClicked = noop,
|
|
182
|
+
backgroundRightClicked = noop,
|
|
183
|
+
searchLayers = [],
|
|
184
|
+
additionalSelectionLayers = [],
|
|
185
|
+
maxAnnotationsToDisplay,
|
|
186
|
+
searchLayerRightClicked = noop,
|
|
187
|
+
selectionLayerRightClicked = noop,
|
|
188
|
+
searchLayerClicked = noop,
|
|
189
|
+
instantiated,
|
|
190
|
+
noWarnings,
|
|
191
|
+
labelLineIntensity,
|
|
192
|
+
fontHeightMultiplier,
|
|
193
|
+
hoveredId,
|
|
194
|
+
labelSize,
|
|
195
|
+
nameFontSizeCircularView = 14,
|
|
196
|
+
fullScreen
|
|
197
|
+
} = props;
|
|
198
|
+
const withRotateCircularView =
|
|
199
|
+
_withRotateCircularView || withZoomCircularView; //if we're showing zoom then we MUST show rotation as well
|
|
200
|
+
|
|
201
|
+
const sequenceName = hideName ? "" : sequenceData.name || "";
|
|
202
|
+
let annotationsSvgs = [];
|
|
203
|
+
let labels = {};
|
|
204
|
+
|
|
205
|
+
const { isProtein } = sequenceData;
|
|
206
|
+
const maxZoomLevel = Math.max(5, Math.floor(sequenceLength / 100));
|
|
207
|
+
|
|
208
|
+
const svgWidth = Math.max(Number(width) || 300);
|
|
209
|
+
const svgHeight = Math.max(Number(height) || 300);
|
|
210
|
+
const percentOfCircle = ((1 / zoomLevel) * Math.min(svgWidth, 800)) / 800;
|
|
211
|
+
const isZoomedIn = zoomLevel !== 1;
|
|
212
|
+
let radius = BASE_RADIUS;
|
|
213
|
+
const rotation = 2 * Math.PI - rotationRadians; //get radians
|
|
214
|
+
|
|
215
|
+
let rangeToShowLength = sequenceLength;
|
|
216
|
+
let rangeToShow = { start: 0, end: Math.max(sequenceLength - 1, 0) };
|
|
217
|
+
let visibleAngleRange;
|
|
218
|
+
if (isZoomedIn) {
|
|
219
|
+
const visibleAngle = Math.PI * percentOfCircle;
|
|
220
|
+
radius = Math.max(BASE_RADIUS, svgWidth / Math.sin(visibleAngle / 2) / 2);
|
|
221
|
+
|
|
222
|
+
visibleAngleRange = normalizeAngleRange({
|
|
223
|
+
start: rotation - visibleAngle / 2,
|
|
224
|
+
end: rotation + visibleAngle / 2
|
|
225
|
+
});
|
|
226
|
+
const rangeToShowStart = getPositionFromAngle(
|
|
227
|
+
visibleAngleRange.start,
|
|
228
|
+
sequenceLength
|
|
229
|
+
);
|
|
230
|
+
const rangeToShowEnd = getPositionFromAngle(
|
|
231
|
+
visibleAngleRange.end,
|
|
232
|
+
sequenceLength
|
|
233
|
+
);
|
|
234
|
+
rangeToShow = {
|
|
235
|
+
start: normalizePositionByRangeLength(rangeToShowStart, sequenceLength),
|
|
236
|
+
end: normalizePositionByRangeLength(rangeToShowEnd, sequenceLength)
|
|
237
|
+
};
|
|
238
|
+
|
|
239
|
+
rangeToShowLength = getRangeLength(rangeToShow, sequenceLength);
|
|
240
|
+
}
|
|
241
|
+
const innerRadius = radius - 10;
|
|
242
|
+
const initialRadius = radius;
|
|
243
|
+
const showSeq = isZoomedIn && rangeToShowLength < 140;
|
|
244
|
+
const showSeqText = rangeToShowLength < 80;
|
|
245
|
+
|
|
246
|
+
//RENDERING CONCEPTS:
|
|
247
|
+
//-"Circular" annotations get a radius, and a curvature based on their radius:
|
|
248
|
+
//<CircularFeature>
|
|
249
|
+
//-Then we rotate the annotations as necessary (and optionally flip them):
|
|
250
|
+
//<PositionAnnotationOnCircle>
|
|
251
|
+
|
|
252
|
+
const layersToDraw = [
|
|
253
|
+
{ zIndex: 10, layerName: "sequenceChars" },
|
|
254
|
+
{
|
|
255
|
+
zIndex: 20,
|
|
256
|
+
layerName: "features",
|
|
257
|
+
isAnnotation: true,
|
|
258
|
+
// spaceBefore: 10,
|
|
259
|
+
spaceAfter: 5
|
|
260
|
+
},
|
|
261
|
+
|
|
262
|
+
...(annotationVisibility.axis
|
|
263
|
+
? [
|
|
264
|
+
{
|
|
265
|
+
layerName: "axisNumbers",
|
|
266
|
+
annotationType: "axisNumbers",
|
|
267
|
+
Annotation: AxisNumbers,
|
|
268
|
+
isAnnotation: true,
|
|
269
|
+
noTitle: true,
|
|
270
|
+
noHover: true,
|
|
271
|
+
annotations: calculateTickMarkPositionsForGivenRange({
|
|
272
|
+
increaseOffset: true,
|
|
273
|
+
range: rangeToShow,
|
|
274
|
+
tickSpacing:
|
|
275
|
+
rangeToShowLength < 10
|
|
276
|
+
? 2
|
|
277
|
+
: rangeToShowLength < 50
|
|
278
|
+
? Math.ceil(rangeToShowLength / 25) * 5
|
|
279
|
+
: Math.ceil(rangeToShowLength / 100) * 10,
|
|
280
|
+
sequenceLength,
|
|
281
|
+
isProtein
|
|
282
|
+
}).map((pos) => {
|
|
283
|
+
return {
|
|
284
|
+
name: "Tick Mark",
|
|
285
|
+
tickPosition: pos,
|
|
286
|
+
start: pos,
|
|
287
|
+
end: pos
|
|
288
|
+
};
|
|
289
|
+
}),
|
|
290
|
+
annotationProps: {
|
|
291
|
+
hideTicks: !annotationVisibility.axis,
|
|
292
|
+
hideNumbers: !annotationVisibility.axisNumbers
|
|
293
|
+
},
|
|
294
|
+
useCenter: true,
|
|
295
|
+
|
|
296
|
+
passAnnotation: true,
|
|
297
|
+
allOnSameLevel: true,
|
|
298
|
+
addHeight: true,
|
|
299
|
+
alwaysShow: true,
|
|
300
|
+
showLabels: false,
|
|
301
|
+
spaceBefore: 0,
|
|
302
|
+
spaceAfter: 0
|
|
303
|
+
},
|
|
304
|
+
{
|
|
305
|
+
zIndex: 0,
|
|
306
|
+
layerName: "axis",
|
|
307
|
+
Annotation: Axis,
|
|
308
|
+
spaceBefore: 10,
|
|
309
|
+
spaceAfter: 5
|
|
310
|
+
}
|
|
311
|
+
]
|
|
312
|
+
: []),
|
|
313
|
+
{
|
|
314
|
+
zIndex: 10,
|
|
315
|
+
layerName: "cutsites",
|
|
316
|
+
fontStyle: "italic",
|
|
317
|
+
Annotation: Cutsite,
|
|
318
|
+
hideAnnotation: showSeqText,
|
|
319
|
+
useStartAngle: true,
|
|
320
|
+
allOnSameLevel: true,
|
|
321
|
+
noHeight: true,
|
|
322
|
+
addHeight: false,
|
|
323
|
+
positionBy: positionCutsites,
|
|
324
|
+
isAnnotation: true
|
|
325
|
+
},
|
|
326
|
+
...(showSeq && annotationVisibility.sequence
|
|
327
|
+
? [
|
|
328
|
+
{
|
|
329
|
+
layerName: "dnaSequences",
|
|
330
|
+
annotationType: "dnaSequences",
|
|
331
|
+
noTitle: true,
|
|
332
|
+
Annotation: CircularDnaSequence,
|
|
333
|
+
isAnnotation: true,
|
|
334
|
+
annotationProps: {
|
|
335
|
+
showReverseSequence: annotationVisibility.reverseSequence,
|
|
336
|
+
showDnaColors: annotationVisibility.dnaColors,
|
|
337
|
+
showSeqText
|
|
338
|
+
},
|
|
339
|
+
noHover: true,
|
|
340
|
+
annotations: getSequenceWithinRange(rangeToShow, sequence)
|
|
341
|
+
.split("")
|
|
342
|
+
.map((letter, i) => {
|
|
343
|
+
const pos = rangeToShow.start + i;
|
|
344
|
+
return {
|
|
345
|
+
className: `ve-dna-letter-${pos}`,
|
|
346
|
+
start: pos,
|
|
347
|
+
end: pos,
|
|
348
|
+
letter
|
|
349
|
+
};
|
|
350
|
+
}),
|
|
351
|
+
useCenter: true,
|
|
352
|
+
passAnnotation: true,
|
|
353
|
+
allOnSameLevel: true,
|
|
354
|
+
addHeight: true,
|
|
355
|
+
alwaysShow: true,
|
|
356
|
+
showLabels: false,
|
|
357
|
+
spaceBefore: 5,
|
|
358
|
+
spaceAfter: annotationVisibility.reverseSequence ? 20 : 5
|
|
359
|
+
}
|
|
360
|
+
]
|
|
361
|
+
: []),
|
|
362
|
+
{
|
|
363
|
+
zIndex: 15,
|
|
364
|
+
alwaysShow: true,
|
|
365
|
+
layerName: "caret",
|
|
366
|
+
Annotation: drawCaret
|
|
367
|
+
},
|
|
368
|
+
|
|
369
|
+
{
|
|
370
|
+
zIndex: 10,
|
|
371
|
+
alwaysShow: true,
|
|
372
|
+
layerName: "selectionLayer",
|
|
373
|
+
Annotation: drawSelectionLayer,
|
|
374
|
+
spaceAfter: 10
|
|
375
|
+
},
|
|
376
|
+
{
|
|
377
|
+
zIndex: 20,
|
|
378
|
+
layerName: "replacementLayers",
|
|
379
|
+
isAnnotation: true,
|
|
380
|
+
spaceAfter: 20
|
|
381
|
+
},
|
|
382
|
+
{
|
|
383
|
+
zIndex: 20,
|
|
384
|
+
layerName: "deletionLayers",
|
|
385
|
+
isAnnotation: true,
|
|
386
|
+
spaceAfter: 20
|
|
387
|
+
},
|
|
388
|
+
|
|
389
|
+
{
|
|
390
|
+
zIndex: 20,
|
|
391
|
+
Annotation: Orf,
|
|
392
|
+
showLabels: false,
|
|
393
|
+
getColor: getOrfColor,
|
|
394
|
+
layerName: "orfs",
|
|
395
|
+
isAnnotation: true,
|
|
396
|
+
spaceBefore: 10
|
|
397
|
+
},
|
|
398
|
+
{
|
|
399
|
+
spaceBefore: 10,
|
|
400
|
+
spaceAfter: 5,
|
|
401
|
+
zIndex: 20,
|
|
402
|
+
Annotation: Primer,
|
|
403
|
+
isAnnotation: true,
|
|
404
|
+
layerName: "primers"
|
|
405
|
+
},
|
|
406
|
+
{
|
|
407
|
+
zIndex: 20,
|
|
408
|
+
layerName: "parts",
|
|
409
|
+
isAnnotation: true,
|
|
410
|
+
spaceBefore: 10,
|
|
411
|
+
spaceAfter: 5
|
|
412
|
+
},
|
|
413
|
+
{
|
|
414
|
+
zIndex: 20,
|
|
415
|
+
layerName: "lineageAnnotations",
|
|
416
|
+
isAnnotation: true,
|
|
417
|
+
spaceBefore: 10,
|
|
418
|
+
spaceAfter: 5
|
|
419
|
+
},
|
|
420
|
+
{
|
|
421
|
+
zIndex: 20,
|
|
422
|
+
layerName: "assemblyPieces",
|
|
423
|
+
isAnnotation: true,
|
|
424
|
+
spaceBefore: 10,
|
|
425
|
+
spaceAfter: 5
|
|
426
|
+
},
|
|
427
|
+
{
|
|
428
|
+
zIndex: 20,
|
|
429
|
+
layerName: "warnings",
|
|
430
|
+
isAnnotation: true,
|
|
431
|
+
spaceBefore: 10,
|
|
432
|
+
spaceAfter: 5
|
|
433
|
+
},
|
|
434
|
+
{
|
|
435
|
+
zIndex: 30,
|
|
436
|
+
alwaysShow: true,
|
|
437
|
+
layerName: "labels",
|
|
438
|
+
Annotation: Labels,
|
|
439
|
+
circularViewWidthVsHeightRatio: width / height,
|
|
440
|
+
passLabels: true,
|
|
441
|
+
labelLineIntensity: labelLineIntensity,
|
|
442
|
+
labelSize: labelSize,
|
|
443
|
+
fontHeightMultiplier: fontHeightMultiplier,
|
|
444
|
+
textScalingFactor: 700 / Math.min(width, height)
|
|
445
|
+
}
|
|
446
|
+
];
|
|
447
|
+
const paredDownMessages = [];
|
|
448
|
+
const output = layersToDraw
|
|
449
|
+
.map((layer) => {
|
|
450
|
+
const {
|
|
451
|
+
layerName,
|
|
452
|
+
maxToDisplay,
|
|
453
|
+
Comp,
|
|
454
|
+
Annotation,
|
|
455
|
+
fontStyle,
|
|
456
|
+
alwaysShow,
|
|
457
|
+
isAnnotation,
|
|
458
|
+
spaceBefore = 0,
|
|
459
|
+
spaceAfter = 0,
|
|
460
|
+
zIndex,
|
|
461
|
+
passLabels,
|
|
462
|
+
noTitle,
|
|
463
|
+
...rest
|
|
464
|
+
} = layer;
|
|
465
|
+
if (!(alwaysShow || annotationVisibility[layerName])) {
|
|
466
|
+
return null;
|
|
467
|
+
}
|
|
468
|
+
//DRAW FEATURES
|
|
469
|
+
let comp;
|
|
470
|
+
let results;
|
|
471
|
+
|
|
472
|
+
const singularName = getSingular(layerName);
|
|
473
|
+
const nameUpper = upperFirst(layerName);
|
|
474
|
+
radius += spaceBefore;
|
|
475
|
+
|
|
476
|
+
const sharedProps = {
|
|
477
|
+
radius,
|
|
478
|
+
innerRadius: BASE_RADIUS,
|
|
479
|
+
outerRadius: radius,
|
|
480
|
+
noRedux,
|
|
481
|
+
isProtein,
|
|
482
|
+
smartCircViewLabelRender,
|
|
483
|
+
extraSideSpace: Math.max(0, width - height),
|
|
484
|
+
onClick: props[singularName + "Clicked"],
|
|
485
|
+
onDoubleClick: props[singularName + "DoubleClicked"],
|
|
486
|
+
onRightClicked: props[singularName + "RightClicked"],
|
|
487
|
+
sequenceLength,
|
|
488
|
+
editorName,
|
|
489
|
+
showCicularViewInternalLabels,
|
|
490
|
+
...rest
|
|
491
|
+
};
|
|
492
|
+
if (isAnnotation) {
|
|
493
|
+
//we're drawing features/cutsites/primers/orfs/etc (something that lives on the seqData)
|
|
494
|
+
if (!map(sequenceData[layerName]).length && !alwaysShow) {
|
|
495
|
+
radius -= spaceBefore;
|
|
496
|
+
return null;
|
|
497
|
+
}
|
|
498
|
+
|
|
499
|
+
const trimmedAnnotations = flatMap(
|
|
500
|
+
layer.annotations ||
|
|
501
|
+
sequenceData["filtered" + nameUpper] ||
|
|
502
|
+
sequenceData[layerName] ||
|
|
503
|
+
[],
|
|
504
|
+
(range) => {
|
|
505
|
+
const overlapOfRanges = getOverlapsOfPotentiallyCircularRanges(
|
|
506
|
+
range,
|
|
507
|
+
rangeToShow,
|
|
508
|
+
sequenceLength,
|
|
509
|
+
true
|
|
510
|
+
);
|
|
511
|
+
if (!overlapOfRanges || !overlapOfRanges.length) return [];
|
|
512
|
+
return { ...range };
|
|
513
|
+
}
|
|
514
|
+
);
|
|
515
|
+
|
|
516
|
+
const maxToShow =
|
|
517
|
+
!isZoomedIn &&
|
|
518
|
+
((maxAnnotationsToDisplay
|
|
519
|
+
? maxAnnotationsToDisplay[layerName]
|
|
520
|
+
: limits[layerName]) ||
|
|
521
|
+
50);
|
|
522
|
+
const [trimmedAndParedAnns, paredDown] = maxToShow
|
|
523
|
+
? pareDownAnnotations(trimmedAnnotations, maxToShow)
|
|
524
|
+
: [trimmedAnnotations];
|
|
525
|
+
|
|
526
|
+
if (paredDown) {
|
|
527
|
+
paredDownMessages.push(
|
|
528
|
+
getParedDownWarning({
|
|
529
|
+
nameUpper,
|
|
530
|
+
maxToShow,
|
|
531
|
+
isAdjustable: !maxAnnotationsToDisplay
|
|
532
|
+
})
|
|
533
|
+
);
|
|
534
|
+
}
|
|
535
|
+
|
|
536
|
+
results = drawAnnotations({
|
|
537
|
+
readOnly,
|
|
538
|
+
noTitle,
|
|
539
|
+
rotationRadians,
|
|
540
|
+
visibleAngleRange,
|
|
541
|
+
isZoomedIn,
|
|
542
|
+
Annotation: Annotation || Comp || Feature,
|
|
543
|
+
fontStyle: fontStyle,
|
|
544
|
+
hoveredId: hoveredId,
|
|
545
|
+
annotationType: singularName,
|
|
546
|
+
type: singularName,
|
|
547
|
+
reverseAnnotations: true,
|
|
548
|
+
showLabels: !(annotationLabelVisibility[layerName] === false),
|
|
549
|
+
annotations: trimmedAndParedAnns,
|
|
550
|
+
annotationHeight,
|
|
551
|
+
spaceBetweenAnnotations,
|
|
552
|
+
...sharedProps,
|
|
553
|
+
...props[singularName + "Options"]
|
|
554
|
+
});
|
|
555
|
+
} else {
|
|
556
|
+
//we're drawing axis/selectionLayer/labels/caret/etc (something that doesn't live on the seqData)
|
|
557
|
+
results = Annotation({
|
|
558
|
+
rotationRadians: rotationRadians,
|
|
559
|
+
...(passLabels && { labels }),
|
|
560
|
+
...sharedProps
|
|
561
|
+
});
|
|
562
|
+
}
|
|
563
|
+
if (results) {
|
|
564
|
+
// //update the radius, labels, and svg
|
|
565
|
+
radius += results.height || 0;
|
|
566
|
+
//tnr: we had been storing labels as a keyed-by-id object but that caused parts and features with the same id to override eachother
|
|
567
|
+
labels = [...map(labels), ...map(results.labels || {})];
|
|
568
|
+
comp = results.component === undefined ? results : results.component;
|
|
569
|
+
}
|
|
570
|
+
radius += spaceAfter;
|
|
571
|
+
// console.warn('radius after draw:',JSON.stringify(radius,null,4))
|
|
572
|
+
return {
|
|
573
|
+
result: comp,
|
|
574
|
+
zIndex
|
|
575
|
+
};
|
|
576
|
+
})
|
|
577
|
+
.filter(function (i) {
|
|
578
|
+
return !!i;
|
|
579
|
+
});
|
|
580
|
+
|
|
581
|
+
annotationsSvgs = sortBy(output, "zIndex").reduce(function (arr, { result }) {
|
|
582
|
+
return arr.concat(result);
|
|
583
|
+
}, []);
|
|
584
|
+
|
|
585
|
+
function drawSelectionLayer() {
|
|
586
|
+
//DRAW SELECTION LAYER
|
|
587
|
+
return getAllSelectionLayers({
|
|
588
|
+
additionalSelectionLayers,
|
|
589
|
+
searchLayers,
|
|
590
|
+
selectionLayer
|
|
591
|
+
})
|
|
592
|
+
.map(function (selectionLayer, index) {
|
|
593
|
+
if (
|
|
594
|
+
selectionLayer.start >= 0 &&
|
|
595
|
+
selectionLayer.end >= 0 &&
|
|
596
|
+
sequenceLength > 0
|
|
597
|
+
) {
|
|
598
|
+
return (
|
|
599
|
+
<SelectionLayer
|
|
600
|
+
key={index}
|
|
601
|
+
{...{
|
|
602
|
+
index,
|
|
603
|
+
isDraggable: true,
|
|
604
|
+
isProtein,
|
|
605
|
+
key: "veCircularViewSelectionLayer" + index,
|
|
606
|
+
selectionLayer,
|
|
607
|
+
onRightClicked: selectionLayer.isSearchLayer
|
|
608
|
+
? searchLayerRightClicked
|
|
609
|
+
: selectionLayerRightClicked,
|
|
610
|
+
onClick: selectionLayer.isSearchLayer
|
|
611
|
+
? searchLayerClicked
|
|
612
|
+
: undefined,
|
|
613
|
+
sequenceLength,
|
|
614
|
+
radius,
|
|
615
|
+
innerRadius
|
|
616
|
+
}}
|
|
617
|
+
/>
|
|
618
|
+
);
|
|
619
|
+
} else {
|
|
620
|
+
return null;
|
|
621
|
+
}
|
|
622
|
+
})
|
|
623
|
+
.filter((el) => {
|
|
624
|
+
return !!el;
|
|
625
|
+
});
|
|
626
|
+
}
|
|
627
|
+
|
|
628
|
+
function drawCaret() {
|
|
629
|
+
//DRAW CARET
|
|
630
|
+
if (
|
|
631
|
+
caretPosition !== -1 &&
|
|
632
|
+
selectionLayer.start < 0 &&
|
|
633
|
+
sequenceLength >= 0
|
|
634
|
+
) {
|
|
635
|
+
//only render if there is no selection layer
|
|
636
|
+
return (
|
|
637
|
+
<Caret
|
|
638
|
+
{...{
|
|
639
|
+
caretPosition,
|
|
640
|
+
sequenceLength,
|
|
641
|
+
isProtein,
|
|
642
|
+
innerRadius,
|
|
643
|
+
outerRadius: radius,
|
|
644
|
+
key: "veCircularViewCaret"
|
|
645
|
+
}}
|
|
646
|
+
/>
|
|
647
|
+
);
|
|
648
|
+
}
|
|
649
|
+
}
|
|
650
|
+
|
|
651
|
+
//tnr: Make the radius have a minimum so the empty yellow axis circle doesn't take up the entire screen
|
|
652
|
+
if (radius < 150) radius = 150;
|
|
653
|
+
const widthToUse = Math.max(Number(width) || 300);
|
|
654
|
+
const heightToUse = Math.max(Number(height) || 300);
|
|
655
|
+
const bpTitle = isProtein
|
|
656
|
+
? `${Math.floor(sequenceLength / 3)} AAs`
|
|
657
|
+
: `${sequenceLength} bps`;
|
|
658
|
+
const nameEl = (
|
|
659
|
+
<div
|
|
660
|
+
className="veSequenceName"
|
|
661
|
+
style={{
|
|
662
|
+
position: "absolute",
|
|
663
|
+
width: "100%",
|
|
664
|
+
height: "100%",
|
|
665
|
+
pointerEvents: "none",
|
|
666
|
+
display: "flex",
|
|
667
|
+
justifyContent: "center",
|
|
668
|
+
alignItems: isZoomedIn || smallZoom < 1 ? "end" : "center",
|
|
669
|
+
paddingLeft: isZoomedIn || smallZoom < 1 ? 20 : 0,
|
|
670
|
+
paddingRight: isZoomedIn || smallZoom < 1 ? 20 : 0,
|
|
671
|
+
textAlign: "center",
|
|
672
|
+
|
|
673
|
+
zIndex: 1
|
|
674
|
+
}}
|
|
675
|
+
>
|
|
676
|
+
<div style={{ marginBottom: isZoomedIn || smallZoom < 1 ? 80 : 0 }}>
|
|
677
|
+
<div
|
|
678
|
+
title={sequenceName}
|
|
679
|
+
className="veCircularViewTextWrapper"
|
|
680
|
+
style={{
|
|
681
|
+
textAlign: "center",
|
|
682
|
+
display: "-webkit-box",
|
|
683
|
+
WebkitLineClamp: "3",
|
|
684
|
+
WebkitBoxOrient: "vertical",
|
|
685
|
+
overflow: "hidden",
|
|
686
|
+
wordBreak: "break-all",
|
|
687
|
+
textOverflow: "ellipsis",
|
|
688
|
+
width: isZoomedIn || smallZoom < 1 ? undefined : innerRadius,
|
|
689
|
+
maxHeight: innerRadius - 15,
|
|
690
|
+
fontSize: nameFontSizeCircularView
|
|
691
|
+
}}
|
|
692
|
+
>
|
|
693
|
+
{sequenceName}
|
|
694
|
+
</div>
|
|
695
|
+
<span title={bpTitle} style={{ fontSize: 10 }}>
|
|
696
|
+
{bpTitle}
|
|
697
|
+
</span>
|
|
698
|
+
</div>
|
|
699
|
+
</div>
|
|
700
|
+
);
|
|
701
|
+
|
|
702
|
+
const target = React.useRef();
|
|
703
|
+
|
|
704
|
+
usePinch(
|
|
705
|
+
({ delta: [d], event }) => {
|
|
706
|
+
if (d === 0) return;
|
|
707
|
+
event.stopPropagation();
|
|
708
|
+
zoomHelper.current.triggerChange &&
|
|
709
|
+
zoomHelper.current.triggerChange(({ changeValue, value }) => {
|
|
710
|
+
changeValue(value + d * 5);
|
|
711
|
+
});
|
|
712
|
+
},
|
|
713
|
+
{
|
|
714
|
+
target,
|
|
715
|
+
from: [zoomLevel]
|
|
716
|
+
}
|
|
717
|
+
);
|
|
718
|
+
const toPass = { ...props, sequenceLength, circRef, rotationRadians };
|
|
719
|
+
|
|
720
|
+
return (
|
|
721
|
+
<div
|
|
722
|
+
style={{
|
|
723
|
+
width: widthToUse,
|
|
724
|
+
height: heightToUse,
|
|
725
|
+
position: "relative",
|
|
726
|
+
overflow: "hidden"
|
|
727
|
+
}}
|
|
728
|
+
onWheel={
|
|
729
|
+
withZoomCircularView && hasRotateableLength
|
|
730
|
+
? (e) => {
|
|
731
|
+
let delta = e.deltaY;
|
|
732
|
+
if (Math.abs(e.deltaY) < Math.abs(e.deltaX)) {
|
|
733
|
+
delta = e.deltaX;
|
|
734
|
+
}
|
|
735
|
+
rotateHelper.current.triggerChange &&
|
|
736
|
+
rotateHelper.current.triggerChange(({ changeValue, value }) => {
|
|
737
|
+
changeValue(
|
|
738
|
+
(normalizeAngle(((value + delta / 4) * Math.PI) / 180) /
|
|
739
|
+
Math.PI) *
|
|
740
|
+
180
|
|
741
|
+
);
|
|
742
|
+
});
|
|
743
|
+
|
|
744
|
+
e.stopPropagation();
|
|
745
|
+
}
|
|
746
|
+
: undefined
|
|
747
|
+
}
|
|
748
|
+
className={classNames("veCircularView", props.className)}
|
|
749
|
+
>
|
|
750
|
+
{!hideName && isZoomedIn && nameEl}
|
|
751
|
+
|
|
752
|
+
{withRotateCircularView && hasRotateableLength && (
|
|
753
|
+
<RotateCircularViewSlider
|
|
754
|
+
bindOutsideChangeHelper={rotateHelper.current}
|
|
755
|
+
zoomLevel={zoomLevel}
|
|
756
|
+
smallSlider={smallSlider}
|
|
757
|
+
maxZoomLevel={maxZoomLevel}
|
|
758
|
+
setRotationRadians={setRotationRadians}
|
|
759
|
+
></RotateCircularViewSlider>
|
|
760
|
+
)}
|
|
761
|
+
{withZoomCircularView && hasZoomableLength && (
|
|
762
|
+
<ZoomCircularViewSlider
|
|
763
|
+
zoomHelper={zoomHelper}
|
|
764
|
+
smallSlider={smallSlider}
|
|
765
|
+
onZoom={() => {
|
|
766
|
+
const caret =
|
|
767
|
+
caretPosition > -1
|
|
768
|
+
? caretPosition
|
|
769
|
+
: selectionLayer.start > -1
|
|
770
|
+
? getMiddleOfRange(selectionLayer, sequenceLength)
|
|
771
|
+
: undefined;
|
|
772
|
+
if (caret !== undefined) {
|
|
773
|
+
const radToRotateTo = (caret / sequenceLength) * Math.PI * 2;
|
|
774
|
+
rotateHelper.current.triggerChange &&
|
|
775
|
+
rotateHelper.current.triggerChange(({ changeValue }) => {
|
|
776
|
+
const isInView = isRangeOrPositionWithinRange(
|
|
777
|
+
caret,
|
|
778
|
+
rangeToShow,
|
|
779
|
+
sequenceLength
|
|
780
|
+
);
|
|
781
|
+
if (!isInView) {
|
|
782
|
+
if (selectionLayer.start > -1) {
|
|
783
|
+
const trimmed = trimRangeByAnotherRange(
|
|
784
|
+
selectionLayer,
|
|
785
|
+
rangeToShow,
|
|
786
|
+
sequenceLength
|
|
787
|
+
);
|
|
788
|
+
if (
|
|
789
|
+
trimmed.start !== selectionLayer.start ||
|
|
790
|
+
trimmed.end !== selectionLayer.end
|
|
791
|
+
)
|
|
792
|
+
return;
|
|
793
|
+
}
|
|
794
|
+
changeValue((radToRotateTo / Math.PI) * 180);
|
|
795
|
+
}
|
|
796
|
+
});
|
|
797
|
+
}
|
|
798
|
+
// updateLabelsForInViewFeaturesCircView({ radius });
|
|
799
|
+
}}
|
|
800
|
+
zoomLevel={_zoomLevel}
|
|
801
|
+
maxZoomLevel={maxZoomLevel}
|
|
802
|
+
setZoomLevel={setZoomLevel}
|
|
803
|
+
/>
|
|
804
|
+
)}
|
|
805
|
+
<Draggable
|
|
806
|
+
// enableUserSelectHack={false} //needed to prevent the input bubble from losing focus post user drag
|
|
807
|
+
bounds={{ top: 0, left: 0, right: 0, bottom: 0 }}
|
|
808
|
+
onDrag={(event) => {
|
|
809
|
+
getNearestCursorPositionToMouseEvent(event, toPass, editorDragged);
|
|
810
|
+
}}
|
|
811
|
+
onStart={(event) => {
|
|
812
|
+
getNearestCursorPositionToMouseEvent(
|
|
813
|
+
event,
|
|
814
|
+
toPass,
|
|
815
|
+
editorDragStarted
|
|
816
|
+
);
|
|
817
|
+
}}
|
|
818
|
+
onStop={editorDragStopped}
|
|
819
|
+
>
|
|
820
|
+
<div
|
|
821
|
+
ref={withZoomCircularView && hasZoomableLength ? target : undefined}
|
|
822
|
+
>
|
|
823
|
+
<svg
|
|
824
|
+
key="circViewSvg"
|
|
825
|
+
onClick={(event) => {
|
|
826
|
+
instantiated &&
|
|
827
|
+
getNearestCursorPositionToMouseEvent(
|
|
828
|
+
event,
|
|
829
|
+
toPass,
|
|
830
|
+
editorClicked
|
|
831
|
+
);
|
|
832
|
+
}}
|
|
833
|
+
onContextMenu={(e) => {
|
|
834
|
+
getNearestCursorPositionToMouseEvent(
|
|
835
|
+
e,
|
|
836
|
+
toPass,
|
|
837
|
+
backgroundRightClicked
|
|
838
|
+
);
|
|
839
|
+
}}
|
|
840
|
+
style={{
|
|
841
|
+
overflow: "visible",
|
|
842
|
+
display: "block"
|
|
843
|
+
}}
|
|
844
|
+
className="circularViewSvg"
|
|
845
|
+
viewBox={
|
|
846
|
+
isZoomedIn
|
|
847
|
+
? `${-svgWidth / 2 / smallZoom},${
|
|
848
|
+
-svgHeight / 2 / smallZoom -
|
|
849
|
+
(!isZoomedIn ? 0 : initialRadius + BASE_RADIUS * 2 - 100)
|
|
850
|
+
},${svgWidth / smallZoom},${svgHeight / smallZoom}`
|
|
851
|
+
: `-${radius} -${radius} ${radius * 2} ${radius * 2}`
|
|
852
|
+
}
|
|
853
|
+
width={svgWidth}
|
|
854
|
+
height={svgHeight}
|
|
855
|
+
>
|
|
856
|
+
<g>
|
|
857
|
+
{/* {isZoomedIn && (
|
|
858
|
+
|
|
859
|
+
)} */}
|
|
860
|
+
<circle
|
|
861
|
+
ref={circRef}
|
|
862
|
+
r={radius}
|
|
863
|
+
style={{ opacity: 0, zIndex: -1 }}
|
|
864
|
+
className="veHiddenAxis"
|
|
865
|
+
></circle>
|
|
866
|
+
{annotationsSvgs}
|
|
867
|
+
{!hideName && !isZoomedIn && (
|
|
868
|
+
<foreignObject
|
|
869
|
+
x={-72.5 / 2}
|
|
870
|
+
y={-72.5 / 2}
|
|
871
|
+
width={72.5}
|
|
872
|
+
height={72.5}
|
|
873
|
+
transform={`rotate(${(-rotationRadians * 180) / Math.PI})`}
|
|
874
|
+
>
|
|
875
|
+
<div
|
|
876
|
+
xmlns="http://www.w3.org/1999/xhtml"
|
|
877
|
+
key="circViewSvgCenterText"
|
|
878
|
+
className="veCircularViewMiddleOfVectorText"
|
|
879
|
+
>
|
|
880
|
+
<div
|
|
881
|
+
title={sequenceName}
|
|
882
|
+
className="veCircularViewTextWrapper"
|
|
883
|
+
style={{
|
|
884
|
+
display: "-webkit-box",
|
|
885
|
+
WebkitLineClamp: "3",
|
|
886
|
+
WebkitBoxOrient: "vertical",
|
|
887
|
+
overflow: "hidden",
|
|
888
|
+
wordBreak: "break-all",
|
|
889
|
+
textOverflow: "ellipsis",
|
|
890
|
+
width: 72.5,
|
|
891
|
+
maxHeight: 72.5 - 15,
|
|
892
|
+
fontSize: nameFontSizeCircularView
|
|
893
|
+
}}
|
|
894
|
+
>
|
|
895
|
+
{sequenceName}
|
|
896
|
+
</div>
|
|
897
|
+
<span title={bpTitle} style={{ fontSize: 10 }}>
|
|
898
|
+
{bpTitle}
|
|
899
|
+
</span>
|
|
900
|
+
</div>
|
|
901
|
+
</foreignObject>
|
|
902
|
+
)}
|
|
903
|
+
</g>
|
|
904
|
+
</svg>
|
|
905
|
+
<VeTopRightContainer {...{ fullScreen }}>
|
|
906
|
+
{!circular && !noWarnings && (
|
|
907
|
+
<VeWarning
|
|
908
|
+
key="ve-warning-circular-to-linear"
|
|
909
|
+
data-test="ve-warning-circular-to-linear"
|
|
910
|
+
intent="warning"
|
|
911
|
+
tooltip={
|
|
912
|
+
"Warning! You're viewing a linear sequence in the Circular Map. Click on 'Linear Map' to view the linear sequence in a more intuitive way."
|
|
913
|
+
}
|
|
914
|
+
/>
|
|
915
|
+
)}
|
|
916
|
+
{!noWarnings && paredDownMessages}
|
|
917
|
+
{isZoomedIn && (
|
|
918
|
+
<CircularZoomMinimap
|
|
919
|
+
rotationRadians={rotationRadians}
|
|
920
|
+
percentOfCircle={percentOfCircle}
|
|
921
|
+
></CircularZoomMinimap>
|
|
922
|
+
)}
|
|
923
|
+
</VeTopRightContainer>
|
|
924
|
+
</div>
|
|
925
|
+
</Draggable>
|
|
926
|
+
</div>
|
|
927
|
+
);
|
|
928
|
+
}
|
|
929
|
+
|
|
930
|
+
export default withEditorInteractions(CircularView);
|