@teselagen/ove 0.8.8 → 0.8.10

package/index.cjs.js

@@ -19741,6 +19741,9 @@ function tableQueryParamsToHasuraClauses({
       } else {
         if (path2) {
           const allPaths = [path2, ...additionalSearchPaths];
+          if (allPaths.length > 1) {
+            return { _or: allPaths.map((p2) => addColumnFilters(p2)) };
+          }
           return allPaths.map((p2) => addColumnFilters(p2));
         } else {
           return addColumnFilters(filterOn);
@@ -116627,7 +116630,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.7";
+const version = "0.8.9";
 const packageJson = {
   version
 };
@@ -138107,6 +138110,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
     {
       ref: sidebarRef,
       style: __spreadValues({
+        position: "relative",
         width: isOpen ? 350 : 0,
         minWidth: isOpen ? 350 : 0,
         maxWidth: isOpen ? 350 : 0,
@@ -138126,7 +138130,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
       {
         style: {
           position: "absolute",
-          top: 5,
+          top: 0,
           right: 10,
           zIndex: 1,
           cursor: "pointer"
@@ -138351,13 +138355,18 @@ function getLabileSites(alignedSequences, threshold = 0.5) {
   };
 }
 __name(getLabileSites, "getLabileSites");
-const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+function parseTracks(tracks) {
   let sequences = {};
   tracks.forEach((at) => {
     sequences = __spreadProps(__spreadValues({}, sequences), {
       [at.alignmentData.name]: at.alignmentData.sequence
     });
   });
+  return sequences;
+}
+__name(parseTracks, "parseTracks");
+const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+  const sequences = parseTracks(tracks);
   const identity4 = calculateIdentityMatrix(sequences);
   const { overallIdentity, frequencies } = getIdentityAndFrequencies(sequences);
   const labileSites = getLabileSites(sequences, 0.5);
@@ -138609,6 +138618,10 @@ ${seqDataToCopy}\r
       alignmentHolderTop.current.scrollLeft = scrollPercentageToUse * (alignmentHolderTop.current.scrollWidth - alignmentHolderTop.current.clientWidth);
     }
   }, "scrollAlignmentToPercent");
+  const aminoAcidAlignmentProperties = React.useMemo(() => {
+    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
+    return getAlignedAminoAcidSequenceProps(alignmentTracks);
+  }, [alignmentTracks, isPairwise]);
   React.useEffect(() => {
     window.scrollAlignmentToPercent = scrollAlignmentToPercent;
     if (window.Cypress)
@@ -138975,10 +138988,6 @@ ${seqDataToCopy}\r
       annotationLabelVisibility: alignmentVisibilityToolOptions.alignmentAnnotationLabelVisibility
     });
   }, "estimateRowHeight");
-  const aminoAcidAlignmentProperties = React.useMemo(() => {
-    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
-    return getAlignedAminoAcidSequenceProps(alignmentTracks);
-  }, [alignmentTracks, isPairwise]);
   const renderItem = /* @__PURE__ */ __name((_i, _key, isTemplate, cloneProps) => {
     var _a3, _b2, _c, _d, _e;
     const isDragDisabled = !allowTrackRearrange || isPairwise;
@@ -140041,6 +140050,7 @@ const AlignmentView$1 = compose(
   withEditorProps,
   reactRedux.connect(
     (state2, ownProps) => {
+      var _a2, _b2;
       const {
         VectorEditor: {
           __allEditorsOptions: { alignments: alignments2 }
@@ -140105,6 +140115,8 @@ const AlignmentView$1 = compose(
           togglableAlignmentAnnotationSettings[annotation] = alignmentAnnotationVisibility[annotation];
         }
       });
+      const tracks = parseTracks(alignmentTracks);
+      const labileSites = getLabileSites(tracks, 0.5);
       const annotationsWithCounts = [];
       if (alignmentTracks) {
         let totalNumOfFeatures = 0;
@@ -140119,7 +140131,8 @@ const AlignmentView$1 = compose(
         });
         annotationsWithCounts.push({
           features: totalNumOfFeatures,
-          parts: totalNumOfParts
+          parts: totalNumOfParts,
+          labileSites: (_b2 = (_a2 = labileSites.sites) == null ? void 0 : _a2.length) != null ? _b2 : 0
         });
       } else if (pairwiseAlignments) {
         pairwiseAlignments.forEach((pairwise) => {
@@ -143823,6 +143836,7 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
           isProtein: isProtein2,
           compact: true,
           isInfinite: true,
+          withDisplayOptions: true,
           schema: this.schema,
           entities: annotationsToUse
         }

package/index.es.js

@@ -19723,6 +19723,9 @@ function tableQueryParamsToHasuraClauses({
       } else {
         if (path2) {
           const allPaths = [path2, ...additionalSearchPaths];
+          if (allPaths.length > 1) {
+            return { _or: allPaths.map((p2) => addColumnFilters(p2)) };
+          }
           return allPaths.map((p2) => addColumnFilters(p2));
         } else {
           return addColumnFilters(filterOn);
@@ -116609,7 +116612,7 @@ function showFileDialog({ multiple = false, onSelect }) {
   input.click();
 }
 __name(showFileDialog, "showFileDialog");
-const version = "0.8.7";
+const version = "0.8.9";
 const packageJson = {
   version
 };
@@ -138089,6 +138092,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
     {
       ref: sidebarRef,
       style: __spreadValues({
+        position: "relative",
         width: isOpen ? 350 : 0,
         minWidth: isOpen ? 350 : 0,
         maxWidth: isOpen ? 350 : 0,
@@ -138108,7 +138112,7 @@ const PropertySidePanel = /* @__PURE__ */ __name(({ properties: properties2, set
       {
         style: {
           position: "absolute",
-          top: 5,
+          top: 0,
           right: 10,
           zIndex: 1,
           cursor: "pointer"
@@ -138333,13 +138337,18 @@ function getLabileSites(alignedSequences, threshold = 0.5) {
   };
 }
 __name(getLabileSites, "getLabileSites");
-const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+function parseTracks(tracks) {
   let sequences = {};
   tracks.forEach((at) => {
     sequences = __spreadProps(__spreadValues({}, sequences), {
       [at.alignmentData.name]: at.alignmentData.sequence
     });
   });
+  return sequences;
+}
+__name(parseTracks, "parseTracks");
+const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+  const sequences = parseTracks(tracks);
   const identity4 = calculateIdentityMatrix(sequences);
   const { overallIdentity, frequencies } = getIdentityAndFrequencies(sequences);
   const labileSites = getLabileSites(sequences, 0.5);
@@ -138591,6 +138600,10 @@ ${seqDataToCopy}\r
       alignmentHolderTop.current.scrollLeft = scrollPercentageToUse * (alignmentHolderTop.current.scrollWidth - alignmentHolderTop.current.clientWidth);
     }
   }, "scrollAlignmentToPercent");
+  const aminoAcidAlignmentProperties = useMemo$1(() => {
+    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
+    return getAlignedAminoAcidSequenceProps(alignmentTracks);
+  }, [alignmentTracks, isPairwise]);
   useEffect(() => {
     window.scrollAlignmentToPercent = scrollAlignmentToPercent;
     if (window.Cypress)
@@ -138957,10 +138970,6 @@ ${seqDataToCopy}\r
       annotationLabelVisibility: alignmentVisibilityToolOptions.alignmentAnnotationLabelVisibility
     });
   }, "estimateRowHeight");
-  const aminoAcidAlignmentProperties = useMemo$1(() => {
-    if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
-    return getAlignedAminoAcidSequenceProps(alignmentTracks);
-  }, [alignmentTracks, isPairwise]);
   const renderItem = /* @__PURE__ */ __name((_i, _key, isTemplate, cloneProps) => {
     var _a3, _b2, _c, _d, _e;
     const isDragDisabled = !allowTrackRearrange || isPairwise;
@@ -140023,6 +140032,7 @@ const AlignmentView$1 = compose(
   withEditorProps,
   connect(
     (state2, ownProps) => {
+      var _a2, _b2;
       const {
         VectorEditor: {
           __allEditorsOptions: { alignments: alignments2 }
@@ -140087,6 +140097,8 @@ const AlignmentView$1 = compose(
           togglableAlignmentAnnotationSettings[annotation] = alignmentAnnotationVisibility[annotation];
         }
       });
+      const tracks = parseTracks(alignmentTracks);
+      const labileSites = getLabileSites(tracks, 0.5);
       const annotationsWithCounts = [];
       if (alignmentTracks) {
         let totalNumOfFeatures = 0;
@@ -140101,7 +140113,8 @@ const AlignmentView$1 = compose(
         });
         annotationsWithCounts.push({
           features: totalNumOfFeatures,
-          parts: totalNumOfParts
+          parts: totalNumOfParts,
+          labileSites: (_b2 = (_a2 = labileSites.sites) == null ? void 0 : _a2.length) != null ? _b2 : 0
         });
       } else if (pairwiseAlignments) {
         pairwiseAlignments.forEach((pairwise) => {
@@ -143805,6 +143818,7 @@ const genericAnnotationProperties = /* @__PURE__ */ __name(({
           isProtein: isProtein2,
           compact: true,
           isInfinite: true,
+          withDisplayOptions: true,
           schema: this.schema,
           entities: annotationsToUse
         }

package/index.umd.js

@@ -45994,6 +45994,9 @@ ${latestSubscriptionCallbackError.current.stack}
         } else {
           if (path2) {
             const allPaths = [path2, ...additionalSearchPaths];
+            if (allPaths.length > 1) {
+              return { _or: allPaths.map((p2) => addColumnFilters(p2)) };
+            }
             return allPaths.map((p2) => addColumnFilters(p2));
           } else {
             return addColumnFilters(filterOn);
@@ -144725,7 +144728,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     input.click();
   }
   __name(showFileDialog, "showFileDialog");
-  const version = "0.8.7";
+  const version = "0.8.9";
   const packageJson = {
     version
   };
@@ -164603,6 +164606,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
       {
         ref: sidebarRef,
         style: __spreadValues({
+          position: "relative",
           width: isOpen2 ? 350 : 0,
           minWidth: isOpen2 ? 350 : 0,
           maxWidth: isOpen2 ? 350 : 0,
@@ -164622,7 +164626,7 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
         {
           style: {
             position: "absolute",
-            top: 5,
+            top: 0,
             right: 10,
             zIndex: 1,
             cursor: "pointer"
@@ -164847,13 +164851,18 @@ Part of ${annotation.translationType} Translation from BPs ${annotation.start +
     };
   }
   __name(getLabileSites, "getLabileSites");
-  const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+  function parseTracks(tracks) {
     let sequences = {};
     tracks.forEach((at) => {
       sequences = __spreadProps(__spreadValues({}, sequences), {
         [at.alignmentData.name]: at.alignmentData.sequence
       });
     });
+    return sequences;
+  }
+  __name(parseTracks, "parseTracks");
+  const getAlignedAminoAcidSequenceProps = /* @__PURE__ */ __name((tracks) => {
+    const sequences = parseTracks(tracks);
     const identity2 = calculateIdentityMatrix(sequences);
     const { overallIdentity, frequencies } = getIdentityAndFrequencies(sequences);
     const labileSites = getLabileSites(sequences, 0.5);
@@ -165105,6 +165114,10 @@ ${seqDataToCopy}\r
         alignmentHolderTop.current.scrollLeft = scrollPercentageToUse * (alignmentHolderTop.current.scrollWidth - alignmentHolderTop.current.clientWidth);
       }
     }, "scrollAlignmentToPercent");
+    const aminoAcidAlignmentProperties = reactExports.useMemo(() => {
+      if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
+      return getAlignedAminoAcidSequenceProps(alignmentTracks);
+    }, [alignmentTracks, isPairwise]);
     reactExports.useEffect(() => {
       window.scrollAlignmentToPercent = scrollAlignmentToPercent;
       if (window.Cypress)
@@ -165471,10 +165484,6 @@ ${seqDataToCopy}\r
         annotationLabelVisibility: alignmentVisibilityToolOptions.alignmentAnnotationLabelVisibility
       });
     }, "estimateRowHeight");
-    const aminoAcidAlignmentProperties = reactExports.useMemo(() => {
-      if (isPairwise || !alignmentTracks[0].sequenceData.isProtein) return;
-      return getAlignedAminoAcidSequenceProps(alignmentTracks);
-    }, [alignmentTracks, isPairwise]);
     const renderItem = /* @__PURE__ */ __name((_i, _key, isTemplate, cloneProps) => {
       var _a3, _b2, _c2, _d2, _e;
       const isDragDisabled = !allowTrackRearrange || isPairwise;
@@ -166537,6 +166546,7 @@ ${seqDataToCopy}\r
     withEditorProps,
     connect(
       (state2, ownProps) => {
+        var _a2, _b2;
         const {
           VectorEditor: {
             __allEditorsOptions: { alignments: alignments2 }
@@ -166601,6 +166611,8 @@ ${seqDataToCopy}\r
             togglableAlignmentAnnotationSettings[annotation] = alignmentAnnotationVisibility[annotation];
           }
         });
+        const tracks = parseTracks(alignmentTracks);
+        const labileSites = getLabileSites(tracks, 0.5);
         const annotationsWithCounts = [];
         if (alignmentTracks) {
           let totalNumOfFeatures = 0;
@@ -166615,7 +166627,8 @@ ${seqDataToCopy}\r
           });
           annotationsWithCounts.push({
             features: totalNumOfFeatures,
-            parts: totalNumOfParts
+            parts: totalNumOfParts,
+            labileSites: (_b2 = (_a2 = labileSites.sites) == null ? void 0 : _a2.length) != null ? _b2 : 0
           });
         } else if (pairwiseAlignments) {
           pairwiseAlignments.forEach((pairwise) => {
@@ -170319,6 +170332,7 @@ ${seqDataToCopy}\r
             isProtein: isProtein2,
             compact: true,
             isInfinite: true,
+            withDisplayOptions: true,
             schema: this.schema,
             entities: annotationsToUse
           }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@teselagen/ove",
-  "version": "0.8.8",
+  "version": "0.8.10",
   "main": "./src/index.js",
   "type": "module",
   "exports": {
@@ -19,7 +19,7 @@
     "@teselagen/range-utils": "0.3.13",
     "@teselagen/react-list": "0.8.18",
     "@teselagen/sequence-utils": "0.3.35",
-    "@teselagen/ui": "0.10.8",
+    "@teselagen/ui": "0.10.9",
     "@use-gesture/react": "10.3.0",
     "biomsa": "^0.2.4",
     "classnames": "^2.3.2",

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/helperComponents/PropertiesDialog/GenericAnnotationProperties.js

@@ -347,6 +347,7 @@ const genericAnnotationProperties = ({
           isProtein={isProtein}
           compact
           isInfinite
+          withDisplayOptions
           schema={this.schema}
           entities={annotationsToUse}
         />

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/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[];