@teselagen/ove 0.8.8 → 0.8.9

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/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/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/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;