@jbrowse/plugin-linear-genome-view 4.1.15 → 4.2.1

package/esm/BaseLinearDisplay/components/FloatingLabels.js

@@ -1,5 +1,4 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { memo } from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { getContainingView } from '@jbrowse/core/util';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { observer } from 'mobx-react';
@@ -25,12 +24,6 @@ const useStyles = makeStyles()({
         lineHeight: 1,
     },
 });
-const FixedLabel = memo(function FixedLabel({ text, color, isOverlay, featureLeftPx, featureId, subfeatureId, y, tooltip, labelClass, overlayClass, }) {
-    return (_jsx("div", { "data-feature-id": featureId, "data-subfeature-id": subfeatureId, "data-tooltip": tooltip, className: isOverlay ? `${labelClass} ${overlayClass}` : labelClass, style: {
-            color,
-            transform: `translate(calc(${featureLeftPx}px - var(--offset-px)), ${y}px)`,
-        }, children: text }));
-});
 function FloatingLabel({ text, color, isOverlay, featureLeftPx, featureRightPx, featureId, subfeatureId, labelWidth, y, offsetPx, tooltip, labelClass, overlayClass, }) {
     const x = calculateFloatingLabelPosition(featureLeftPx, featureRightPx, labelWidth, offsetPx);
     return (_jsx("div", { "data-feature-id": featureId, "data-subfeature-id": subfeatureId, "data-tooltip": tooltip, className: isOverlay ? `${labelClass} ${overlayClass}` : labelClass, style: { color, transform: `translate(${x}px,${y}px)` }, children: text }));
@@ -41,8 +34,7 @@ const FloatingLabels = observer(function FloatingLabels({ model, }) {
     const { offsetPx } = view;
     const featureLabels = model.floatingLabelData;
     const { onFeatureClick, onFeatureContextMenu, onMouseMove } = model.renderingProps();
-    const fixedLabels = [];
-    const floatingLabels = [];
+    const labels = [];
     for (const [key, { leftPx, topPx, totalFeatureHeight, floatingLabels: labelData, featureWidth, },] of featureLabels.entries()) {
         const featureVisualBottom = topPx + totalFeatureHeight;
         const featureRightPx = leftPx + featureWidth;
@@ -52,15 +44,10 @@ const FloatingLabels = observer(function FloatingLabels({ model, }) {
             const y = featureVisualBottom + relativeY;
             const labelKey = `${key}-${i}`;
             const featureId = parentFeatureId ?? key;
-            if (labelWidth > featureWidth) {
-                fixedLabels.push(_jsx(FixedLabel, { text: text, color: color, isOverlay: isOverlay ?? false, featureLeftPx: leftPx, featureId: featureId, subfeatureId: subfeatureId, y: y, tooltip: tooltip, labelClass: classes.label, overlayClass: classes.overlay }, labelKey));
-            }
-            else {
-                floatingLabels.push(_jsx(FloatingLabel, { text: text, color: color, isOverlay: isOverlay ?? false, featureLeftPx: leftPx, featureRightPx: featureRightPx, featureId: featureId, subfeatureId: subfeatureId, labelWidth: labelWidth, y: y, offsetPx: offsetPx, tooltip: tooltip, labelClass: classes.label, overlayClass: classes.overlay }, labelKey));
-            }
+            labels.push(_jsx(FloatingLabel, { text: text, color: color, isOverlay: isOverlay ?? false, featureLeftPx: leftPx, featureRightPx: featureRightPx, featureId: featureId, subfeatureId: subfeatureId, labelWidth: labelWidth, y: y, offsetPx: offsetPx, tooltip: tooltip, labelClass: classes.label, overlayClass: classes.overlay }, labelKey));
         }
     }
-    return (_jsxs("div", { className: classes.container, style: { '--offset-px': `${offsetPx}px` }, onClick: e => {
+    return (_jsx("div", { className: classes.container, onClick: e => {
             const target = e.target;
             const subfeatureId = target.dataset.subfeatureId;
             const featureId = subfeatureId ?? target.dataset.featureId;
@@ -83,6 +70,6 @@ const FloatingLabels = observer(function FloatingLabels({ model, }) {
                 onMouseMove?.(e, featureId, tooltip);
                 model.setSubfeatureIdUnderMouse(subfeatureId);
             }
-        }, children: [fixedLabels, floatingLabels] }));
+        }, children: labels }));
 });
 export default FloatingLabels;

package/esm/BaseLinearDisplay/components/util.js

@@ -80,10 +80,11 @@ export function deduplicateFeatureLabels(layoutFeatures, view, assembly, bpPerPx
         if (leftPx === undefined) {
             continue;
         }
+        const floorLeftPx = Math.floor(leftPx);
         const existing = featureLabels.get(key);
-        if (!existing || leftPx < existing.leftPx) {
+        if (!existing || floorLeftPx < existing.leftPx) {
             featureLabels.set(key, {
-                leftPx,
+                leftPx: floorLeftPx,
                 topPx: effectiveTopPx,
                 totalFeatureHeight,
                 floatingLabels,
@@ -96,11 +97,11 @@ export function deduplicateFeatureLabels(layoutFeatures, view, assembly, bpPerPx
 export function calculateFloatingLabelPosition(featureLeftPx, featureRightPx, labelWidth, offsetPx) {
     const featureWidth = featureRightPx - featureLeftPx;
     if (labelWidth > featureWidth) {
-        return featureLeftPx - offsetPx;
+        return Math.round(featureLeftPx - offsetPx);
     }
     const viewportLeft = Math.max(0, offsetPx);
     const leftPx = Math.max(featureLeftPx, viewportLeft);
     const naturalX = leftPx - offsetPx;
     const maxX = featureRightPx - offsetPx - labelWidth;
-    return clamp(naturalX, 0, maxX);
+    return Math.round(clamp(naturalX, 0, maxX));
 }

package/esm/LinearGenomeView/afterAttach.js

@@ -20,7 +20,14 @@ export function setupInitAutorun(self) {
             }
             try {
                 if (init.loc) {
-                    await self.navToLocString(init.loc, init.assembly);
+                    const asm = await assemblyManager.waitForAssembly(init.assembly);
+                    if (!asm) {
+                        throw new Error('Assembly not found');
+                    }
+                    await self.navToSearchString({
+                        input: init.loc,
+                        assembly: asm,
+                    });
                 }
                 else {
                     self.showAllRegionsInAssembly(init.assembly);

package/esm/LinearGenomeView/components/ImportForm.js

@@ -23,7 +23,7 @@ const LinearGenomeViewImportForm = observer(function LinearGenomeViewImportForm(
     const { classes } = useStyles();
     const session = getSession(model);
     const { assemblyNames, assemblyManager } = session;
-    const { error } = model;
+    const { initialized, error } = model;
     const [selectedAsm, setSelectedAsm] = useState(assemblyNames[0]);
     const [option, setOption] = useState();
     const assembly = assemblyManager.get(selectedAsm);
@@ -38,7 +38,7 @@ const LinearGenomeViewImportForm = observer(function LinearGenomeViewImportForm(
     useEffect(() => {
         setValue(r0);
     }, [r0, selectedAsm]);
-    return (_jsxs("div", { className: classes.container, children: [displayError ? _jsx(ErrorMessage, { error: displayError }) : null, _jsx(Container, { className: classes.importFormContainer, children: _jsx("form", { onSubmit: async (event) => {
+    return (_jsxs("div", { className: classes.container, children: [displayError ? _jsx(ErrorMessage, { error: displayError }) : null, initialized ? (_jsx(Container, { className: classes.importFormContainer, children: _jsx("form", { onSubmit: async (event) => {
                         event.preventDefault();
                         model.setError(undefined);
                         if (value) {
@@ -72,6 +72,6 @@ const LinearGenomeViewImportForm = observer(function LinearGenomeViewImportForm(
                                     }, localStorageKey: "lgv", session: session, selected: selectedAsm }) }), selectedAsm ? (assemblyError ? (_jsx(CloseIcon, { style: { color: 'red' } })) : assemblyLoaded ? (_jsx(FormControl, { children: _jsx(ImportFormRefNameAutocomplete, { value: value, setValue: setValue, selectedAsm: selectedAsm, setOption: setOption, model: model }) })) : (_jsx(CircularProgress, { size: 20, disableShrink: true }))) : null, _jsx(FormControl, { children: _jsx(Button, { type: "submit", disabled: !value, className: classes.button, variant: "contained", color: "primary", children: "Open" }) }), _jsx(FormControl, { children: _jsx(Button, { disabled: !value, className: classes.button, onClick: () => {
                                         model.setError(undefined);
                                         model.showAllRegionsInAssembly(selectedAsm);
-                                    }, variant: "contained", color: "secondary", children: "Show all regions in assembly" }) })] }) }) })] }));
+                                    }, variant: "contained", color: "secondary", children: "Show all regions in assembly" }) })] }) }) })) : null] }));
 });
 export default LinearGenomeViewImportForm;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "4.1.15",
+  "version": "4.2.1",
   "type": "module",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
@@ -22,15 +22,15 @@
   ],
   "dependencies": {
     "@jbrowse/mobx-state-tree": "^5.6.0",
-    "@mui/icons-material": "^7.3.9",
-    "@mui/material": "^7.3.9",
+    "@mui/icons-material": "^7.3.10",
+    "@mui/material": "^7.3.10",
     "@types/file-saver-es": "^2.0.3",
     "copy-to-clipboard": "^3.3.3",
     "file-saver-es": "^2.0.5",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
-    "@jbrowse/core": "^4.1.15",
-    "@jbrowse/product-core": "^4.1.15"
+    "@jbrowse/core": "^4.2.1",
+    "@jbrowse/product-core": "^4.2.1"
   },
   "peerDependencies": {
     "react": ">=18.0.0",