@teselagen/ove 0.8.7 → 0.8.9

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.8.7",
+  "version": "0.8.9",
   "main": "./src/index.js",
   "type": "module",
   "exports": {

package/selectors/annotationSearchSelector.d.ts

@@ -1,5 +1,5 @@
 export const searchableTypes: string[];
-declare const _default: ((state: any) => any[][]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, ...args: any[]) => any[][], {
+declare const _default: ((state: any) => any[]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, ...args: any[]) => any[], {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/cdsFeaturesSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => any[]) & import('reselect').OutputSelectorFields<(args_0: any) => any[], {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/cutsitesSelector.d.ts

@@ -1,11 +1,11 @@
 declare const _default: ((state: any) => {
     cutsitesByName: {};
     cutsitesById: {};
-    cutsitesArray: never[];
+    cutsitesArray: any;
 }) & import('reselect').OutputSelectorFields<(...args: any) => {
     cutsitesByName: {};
     cutsitesById: {};
-    cutsitesArray: never[];
+    cutsitesArray: any;
 }, {
     clearCache: () => void;
 }> & {

package/selectors/filteredFeaturesSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => Partial<any>) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any, args_4: any) => Partial<any>, {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any, args_4: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/filteredPartsSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => any[]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any, args_4: any) => any[], {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any, args_4: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/filteredPrimersSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => Partial<any>) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any) => Partial<any>, {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/searchLayersSelector.d.ts

@@ -1,4 +1,4 @@
-declare const _default: ((state: any) => any[]) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any, args_4: any, args_5: any, args_6: any, args_7: any, args_8: any) => any[], {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: any, args_2: any, args_3: any, args_4: any, args_5: any, args_6: any, args_7: any, args_8: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/selectors/translationsSelector.d.ts

@@ -1,14 +1,4 @@
-declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(args_0: any, args_1: unknown, args_2: any, args_3: {
-    start: number;
-    end: number;
-    length: number;
-    internalStartCodonIndices: never[];
-    frame: number;
-    forward: any;
-    annotationTypePlural: string;
-    isOrf: boolean;
-    id: any;
-}[], args_4: any, args_5: any, args_6: any[], args_7: any, args_8: any, args_9: any, args_10: any, args_11: any, args_12: any) => any, {
+declare const _default: ((state: any) => any) & import('reselect').OutputSelectorFields<(...args: any) => any, {
     clearCache: () => void;
 }> & {
     clearCache: () => void;

package/src/AlignmentView/index.js

@@ -74,7 +74,11 @@ import { coerceInitialValue } from "./coerceInitialValue";
 import { tabHeight } from "../constants";
 import LabileSitesLayer from "./LabileSitesLayer";
 import PropertySidePanel from "../PropertySidePanel";
-import { getAlignedAminoAcidSequenceProps } from "../utils/getAlignedAminoAcidSequenceProps";
+import {
+  getAlignedAminoAcidSequenceProps,
+  getLabileSites,
+  parseTracks
+} from "../utils/getAlignedAminoAcidSequenceProps";
 
 let charWidthInLinearViewDefault = 12;
 try {
@@ -244,6 +248,11 @@ export const AlignmentView = props => {
     }
   };
 
+  const aminoAcidAlignmentProperties = useMemo(() => {
+    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
+    return getAlignedAminoAcidSequenceProps(alignmentTracks);
+  }, [alignmentTracks, isPairwise]);
+
   useEffect(() => {
     window.scrollAlignmentToPercent = scrollAlignmentToPercent;
     if (window.Cypress)
@@ -684,11 +693,6 @@ export const AlignmentView = props => {
     });
   };
 
-  const aminoAcidAlignmentProperties = useMemo(() => {
-    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
-    return getAlignedAminoAcidSequenceProps(alignmentTracks);
-  }, [alignmentTracks, isPairwise]);
-
   const renderItem = (_i, _key, isTemplate, cloneProps) => {
     const isDragDisabled = !allowTrackRearrange || isPairwise;
     let i;
@@ -1966,6 +1970,9 @@ export default compose(
         }
       });
 
+      const tracks = parseTracks(alignmentTracks);
+      const labileSites = getLabileSites(tracks, 0.5);
+
       const annotationsWithCounts = [];
       if (alignmentTracks) {
         let totalNumOfFeatures = 0;
@@ -1980,7 +1987,8 @@ export default compose(
         });
         annotationsWithCounts.push({
           features: totalNumOfFeatures,
-          parts: totalNumOfParts
+          parts: totalNumOfParts,
+          labileSites: labileSites.sites?.length ?? 0
         });
       } else if (pairwiseAlignments) {
         pairwiseAlignments.forEach(pairwise => {

package/src/BarPlot/index.js

@@ -6,7 +6,7 @@
  * @param {number} [props.height=150]
  * @param {string[]} [props.barColors]
  */
-import React from 'react'
+import React from "react";
 export function BarPlot({
   data,
   width = 300,

package/src/Editor/index.js

@@ -41,7 +41,7 @@ import LinearView from "../LinearView";
 import RowView from "../RowView";
 import StatusBar from "../StatusBar";
 import DropHandler from "./DropHandler";
-import Properties from "../helperComponents/PropertiesDialog";
+import PropertiesDialog from "../helperComponents/PropertiesDialog";
 import "./style.css";
 import { DragDropContext, Droppable, Draggable } from "@hello-pangea/dnd";
 import DigestTool from "../DigestTool/DigestTool";
@@ -76,7 +76,7 @@ const _panelMap = {
   digestTool: DigestTool,
   pcrTool: PCRTool,
   properties: {
-    comp: Properties,
+    comp: PropertiesDialog,
     panelSpecificProps: ["PropertiesProps"]
   },
   mismatches: Mismatches

package/src/Editor/userDefinedHandlersAndOpts.js

@@ -11,6 +11,8 @@ export const userDefinedHandlersAndOpts = [
   "allowPrimerBasesToBeEdited",
   "truncateLabelsThatDoNotFit",
   "smartCircViewLabelRender",
+  "on_setPanelAsActive",
+  "on_propertiesViewTabUpdate",
   "onConfigureFeatureTypesClick",
   "allPartTags",
   "bpLimit",

package/src/PropertySidePanel/index.js

@@ -187,6 +187,7 @@ export default ({ properties, setProperties, style }) => {
     <div
       ref={sidebarRef}
       style={{
+        position: "relative",
         width: isOpen ? 350 : 0,
         minWidth: isOpen ? 350 : 0,
         maxWidth: isOpen ? 350 : 0,
@@ -205,7 +206,7 @@ export default ({ properties, setProperties, style }) => {
       <Button
         style={{
           position: "absolute",
-          top: 5,
+          top: 0,
           right: 10,
           zIndex: 1,
           cursor: "pointer"

package/src/redux/panelsShown.js

@@ -17,7 +17,7 @@ export const togglePanelFullScreen = createAction("togglePanelFullScreen");
 export const collapsePanel = createAction("collapsePanel");
 export const closePanel = createAction("closePanel");
 export const _collapseSplitScreen = createAction("_collapseSplitScreen");
-export const setPanelAsActive = createAction("setPanelAsActive");
+export const setPanelAsActive = createAction("SET_PANEL_AS_ACTIVE");
 export const flipActiveTabFromLinearOrCircularIfNecessary = createAction(
   "flipActiveTabFromLinearOrCircularIfNecessary"
 );

package/src/utils/getAlignedAminoAcidSequenceProps.js

@@ -214,7 +214,7 @@ function getIdentityAndFrequencies(alignedSequences) {
   };
 }
 
-function getLabileSites(alignedSequences, threshold = 0.5) {
+export function getLabileSites(alignedSequences, threshold = 0.5) {
   const sequences = Object.values(alignedSequences);
   const alignmentLength = sequences[0].length;
 
@@ -261,7 +261,7 @@ function getLabileSites(alignedSequences, threshold = 0.5) {
   };
 }
 
-export const getAlignedAminoAcidSequenceProps = tracks => {
+export function parseTracks(tracks) {
   let sequences = {};
 
   tracks.forEach(at => {
@@ -271,6 +271,12 @@ export const getAlignedAminoAcidSequenceProps = tracks => {
     };
   });
 
+  return sequences;
+}
+
+export const getAlignedAminoAcidSequenceProps = tracks => {
+  const sequences = parseTracks(tracks);
+
   const identity = calculateIdentityMatrix(sequences);
   const { overallIdentity, frequencies } = getIdentityAndFrequencies(sequences);
   const labileSites = getLabileSites(sequences, 0.5);

package/src/withEditorProps/index.js

@@ -677,7 +677,8 @@ export function mapDispatchToActions(dispatch, ownProps) {
     editorName,
     actions,
     actionOverrides,
-    dispatch
+    dispatch,
+    ownProps
   );
   const updateSel =
     ownProps.selectionLayerUpdate || actionsToPass.selectionLayerUpdate;
@@ -717,7 +718,8 @@ export function getCombinedActions(
   editorName,
   actions,
   actionOverrides,
-  dispatch
+  dispatch,
+  ownProps
 ) {
   const meta = { editorName };
 
@@ -758,6 +760,21 @@ export function getCombinedActions(
     ...metaActions
     // ...metaOverrides
   };
+  function addGenericHook(hookName) {
+    const oldHook = actionsToPass[hookName];
+    actionsToPass[hookName] = (...args) => {
+      const toRet = oldHook(...args);
+      const newHookName = `on_${hookName}`;
+      if (ownProps[newHookName]) {
+        setTimeout(() => {
+          ownProps[newHookName](...args);
+        }, 0);
+      }
+      return toRet;
+    };
+  }
+  ["setPanelAsActive", "propertiesViewTabUpdate"].forEach(addGenericHook);
+
   return bindActionCreators(actionsToPass, dispatch);
 }
 

package/utils/addWrappedAddons.d.ts

@@ -1 +1 @@
-export function addWrappedAddons(anns: any, seqLen: any): any[];
+export function addWrappedAddons(anns: any, seqLen: any): any;

package/utils/editorUtils.d.ts

@@ -35,4 +35,4 @@ export function getStripedPattern({ color, id }: {
     color: any;
     id: any;
 }): import("react/jsx-runtime").JSX.Element;
-export function getEnzymeAliases(enzyme: any): any[];
+export function getEnzymeAliases(enzyme: any): any;

package/utils/getAlignedAminoAcidSequenceProps.d.ts

@@ -1,3 +1,15 @@
+export function getLabileSites(alignedSequences: any, threshold?: number): {
+    sites: {
+        position: number;
+        conservationScore: number;
+        residueVariation: string[];
+        frequencies: {};
+    }[];
+    conservationScores: (number | null)[];
+    totalLabileSites: number;
+    percentageLabile: number;
+};
+export function parseTracks(tracks: any): {};
 export function getAlignedAminoAcidSequenceProps(tracks: any): {
     overallIdentity: number;
     frequencies: number[];

package/withEditorInteractions/clickAndDragUtils.d.ts

@@ -41,17 +41,17 @@ export function updateSelectionOrCaret({ shiftHeld, sequenceLength, newRangeOrCa
     newRangeOrCaret: any;
     caretPosition: any;
     selectionLayer: any;
-    selectionLayerUpdate?: ((...args: any[]) => void) | undefined;
-    caretPositionUpdate?: ((...args: any[]) => void) | undefined;
+    selectionLayerUpdate?: any;
+    caretPositionUpdate?: any;
     doNotWrapOrigin: any;
-}): void;
+}): any;
 export function editorDragged({ nearestCaretPos, doNotWrapOrigin, caretPosition, easyStore, caretPositionUpdate, selectionLayerUpdate, selectionLayer, sequenceLength }: {
     nearestCaretPos: any;
     doNotWrapOrigin: any;
     caretPosition?: number | undefined;
     easyStore: any;
-    caretPositionUpdate?: ((...args: any[]) => void) | undefined;
-    selectionLayerUpdate?: ((...args: any[]) => void) | undefined;
+    caretPositionUpdate?: any;
+    selectionLayerUpdate?: any;
     selectionLayer?: {
         start: number;
         end: number;

package/withEditorProps/index.d.ts

@@ -4,7 +4,7 @@ export function mapDispatchToActions(dispatch: any, ownProps: any): {
     dispatch: any;
 };
 export function fakeActionOverrides(): {};
-export function getCombinedActions(editorName: any, actions: any, actionOverrides: any, dispatch: any): {};
+export function getCombinedActions(editorName: any, actions: any, actionOverrides: any, dispatch: any, ownProps: any): {};
 export function getShowGCContent(state: any, ownProps: any): any;
 export function handleSave(props: any): (opts?: {}) => Promise<any>;
 export function handleInverse(props: any): () => false | undefined;