jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/dist/BigMafAdapter/BigMafAdapter.js

@@ -2,10 +2,11 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { SimpleFeature, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { getSnapshot } from 'mobx-state-tree';
+import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { firstValueFrom, toArray } from 'rxjs';
 import parseNewick from '../parseNewick';
 import { normalize } from '../util';
+import { parseAssemblyAndChrSimple } from '../util/parseAssemblyName';
 export default class BigMafAdapter extends BaseFeatureDataAdapter {
     setupP;
     async setup() {
@@ -72,10 +73,8 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
                             if (referenceSeq === undefined) {
                                 referenceSeq = sequence;
                             }
-                            // Parse organism and chromosome once
-                            const dotIndex = organismChr.indexOf('.');
-                            const org = organismChr.slice(0, Math.max(0, dotIndex));
-                            const chr = organismChr.slice(Math.max(0, dotIndex + 1));
+                            // Parse organism and chromosome
+                            const { assemblyName: org, chr } = parseAssemblyAndChrSimple(organismChr);
                             // Create alignment record directly
                             alignments[org] = {
                                 chr,

package/dist/BigMafAdapter/BigMafAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BigMafAdapter.js","sourceRoot":"","sources":["../../src/BigMafAdapter/BigMafAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAChE,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AACtD,OAAO,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9C,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,yBAAyB,EAAE,MAAM,2BAA2B,CAAA;AAarE,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IACxD,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,eAAe;aACtB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBAC9C,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACtC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAkB;QAC3C,MAAM,EAAE,cAAc,GAAG,GAAG,EAAE,GAAE,CAAC,EAAE,GAAG,IAAI,IAAI,EAAE,CAAA;QAChD,2CAA2C;QAC3C,MAAM,gBAAgB,GAAG,IAAI,CAAA;QAE7B,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACtC,MAAM,QAAQ,GAAG,MAAM,YAAY,CACjC,wBAAwB,EACxB,cAAc,EACd,GAAG,EAAE,CAAC,cAAc,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CACjE,CAAA;YACD,MAAM,YAAY,CAAC,uBAAuB,EAAE,cAAc,EAAE,GAAG,EAAE;gBAC/D,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;oBAC/B,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAW,CAAA;oBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;oBAE7B,iDAAiD;oBACjD,IAAI,kBAAkB,GAAG,CAAC,CAAA;oBAC1B,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;wBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;4BAC1B,kBAAkB,EAAE,CAAA;wBACtB,CAAC;oBACH,CAAC;oBAED,uDAAuD;oBACvD,MAAM,IAAI,GAAG,IAAI,KAAK,CAAS,kBAAkB,CAAC,CAAA;oBAClD,MAAM,UAAU,GAAG,EAAoC,CAAA;oBAEvD,IAAI,aAAa,GAAG,CAAC,CAAA;oBACrB,IAAI,YAAgC,CAAA;oBAEpC,6CAA6C;oBAC7C,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;wBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;4BAC1B,kCAAkC;4BAClC,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BAC3C,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;4BAC1B,MAAM,WAAW,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;4BAE7B,oCAAoC;4BACpC,IAAI,CAAC,aAAa,CAAC,GAAG,QAAQ,CAAA;4BAE9B,0CAA0C;4BAC1C,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;gCAC/B,YAAY,GAAG,QAAQ,CAAA;4BACzB,CAAC;4BAED,gCAAgC;4BAChC,MAAM,EAAE,YAAY,EAAE,GAAG,EAAE,GAAG,EAAE,GAC9B,yBAAyB,CAAC,WAAW,CAAC,CAAA;4BAExC,mCAAmC;4BACnC,UAAU,CAAC,GAAG,CAAC,GAAG;gCAChB,GAAG;gCACH,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACjB,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACnB,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gCACjC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACnB,GAAG,EAAE,QAAQ;6BACd,CAAA;4BAED,aAAa,EAAE,CAAA;wBACjB,CAAC;oBACH,CAAC;oBAED,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;wBAChB,EAAE,EAAE,OAAO,CAAC,EAAE,EAAE;wBAChB,IAAI,EAAE;4BACJ,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;4BAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;4BACvB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC;4BAC/B,GAAG,EAAE,YAAY;4BACjB,UAAU;yBACX;qBACF,CAAC,CACH,CAAA;gBACH,CAAC;YACH,CAAC,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACxC,MAAM,EAAE,GACN,KAAK,CAAC,GAAG,KAAK,gBAAgB;YAC5B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,MAAM,YAAY,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAEhD,2EAA2E;QAC3E,OAAO;QACP,OAAO;YACL,OAAO,EAAE,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YAC3C,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;SACvC,CAAA;IACH,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}

package/dist/BigMafAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
@@ -28,5 +28,5 @@ declare const configSchema: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js

@@ -1,118 +1,39 @@
-import React, { useCallback, useEffect, useRef, useState } from 'react';
+import React, { useRef } from 'react';
 import { Menu } from '@jbrowse/core/ui';
-import { getContainingView, getEnv } from '@jbrowse/core/util';
+import { getContainingView, getEnv, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import Crosshairs from './Crosshairs';
-import SequenceDialog from './GetSequenceDialog/GetSequenceDialog';
 import MAFTooltip from './MAFTooltip';
+import MsaHighlightOverlay from './MsaHighlightOverlay';
 import YScaleBars from './Sidebar/YScaleBars';
+import { useDragSelection } from './useDragSelection';
 const LinearMafDisplay = observer(function (props) {
     const { model } = props;
     const { pluginManager } = getEnv(model);
-    const { rowHeight, height, scrollTop, samples: sources } = model;
+    const { height, scrollTop, samples: sources } = model;
     const ref = useRef(null);
     const theme = useTheme();
+    const session = getSession(model);
     const LinearGenomePlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
     const { BaseLinearDisplayComponent } = LinearGenomePlugin.exports;
-    const [mouseY, setMouseY] = useState();
-    const [mouseX, setMouseX] = useState();
-    const [isDragging, setIsDragging] = useState(false);
-    const [dragStartX, setDragStartX] = useState();
-    const [dragEndX, setDragEndX] = useState();
-    const [showSelectionBox, setShowSelectionBox] = useState(false);
-    const [contextCoord, setContextCoord] = useState();
-    const [showSequenceDialog, setShowSequenceDialog] = useState(false);
-    const [selectionCoords, setSelectionCoords] = useState();
-    const { width } = getContainingView(model);
-    const handleMouseDown = (event) => {
-        const rect = ref.current?.getBoundingClientRect();
-        const left = rect?.left || 0;
-        const clientX = event.clientX - left;
-        // Clear the previous selection box when starting a new drag
-        setShowSelectionBox(false);
-        setIsDragging(true);
-        setDragStartX(clientX);
-        setDragEndX(clientX);
-        event.stopPropagation();
-    };
-    const handleMouseMove = (event) => {
-        const rect = ref.current?.getBoundingClientRect();
-        const top = rect?.top || 0;
-        const left = rect?.left || 0;
-        const clientX = event.clientX - left;
-        const clientY = event.clientY - top;
-        setMouseY(clientY);
-        setMouseX(clientX);
-        if (isDragging) {
-            setDragEndX(clientX);
-        }
-    };
-    const handleMouseUp = (event) => {
-        if (isDragging && dragStartX !== undefined && dragEndX !== undefined) {
-            // Calculate the drag distance
-            const dragDistanceX = Math.abs(dragEndX - dragStartX);
-            // Only show context menu if the drag distance is at least 2 pixels in either direction
-            if (dragDistanceX >= 2) {
-                setContextCoord({
-                    coord: [event.clientX, event.clientY],
-                    dragEndX: event.clientX,
-                    dragStartX: dragStartX,
-                });
-                // Set showSelectionBox to true to keep the selection visible
-                setShowSelectionBox(true);
-            }
-            else {
-                // For very small drags (less than 2px), don't show selection box or context menu
-                clearSelectionBox();
-            }
-        }
-        // Only set isDragging to false, but keep the coordinates
-        setIsDragging(false);
-    };
-    // Function to clear the selection box
-    const clearSelectionBox = useCallback(() => {
-        setShowSelectionBox(false);
-        setDragStartX(undefined);
-        setDragEndX(undefined);
-    }, []);
-    // Add keydown event handler to clear selection box when Escape key is pressed
-    useEffect(() => {
-        const handleKeyDown = (event) => {
-            if (event.key === 'Escape' && showSelectionBox) {
-                clearSelectionBox();
-            }
-        };
-        // Add click handler to clear selection box when clicking outside of it
-        const handleClickOutside = (event) => {
-            if (ref.current &&
-                !ref.current.contains(event.target) &&
-                showSelectionBox) {
-                clearSelectionBox();
-            }
-        };
-        document.addEventListener('keydown', handleKeyDown);
-        document.addEventListener('click', handleClickOutside);
-        return () => {
-            document.removeEventListener('keydown', handleKeyDown);
-            document.removeEventListener('click', handleClickOutside);
-        };
-    }, [showSelectionBox, clearSelectionBox]);
+    const { isDragging, dragStartX, dragEndX, showSelectionBox, mouseX, mouseY, contextCoord, setContextCoord, handleMouseDown, handleMouseMove, handleMouseUp, handleMouseLeave, clearSelectionBox, } = useDragSelection(ref);
+    const view = getContainingView(model);
+    const { width } = view;
     return (React.createElement("div", { ref: ref, onMouseDown: handleMouseDown, onMouseMove: handleMouseMove, onMouseUp: handleMouseUp, onDoubleClick: () => {
-            // Clear selection box on double click
             if (showSelectionBox) {
                 clearSelectionBox();
             }
-        }, onMouseLeave: () => {
-            setMouseY(undefined);
-            setMouseX(undefined);
-            setIsDragging(false);
-        } },
+        }, onMouseLeave: handleMouseLeave },
         React.createElement(BaseLinearDisplayComponent, { ...props }),
         model.showSidebar ? React.createElement(YScaleBars, { model: model }) : null,
-        mouseY && mouseX && sources && !contextCoord && !showSequenceDialog ? (React.createElement("div", { style: { position: 'relative' } },
+        React.createElement(MsaHighlightOverlay, { model: model, view: view, height: height }),
+        mouseY !== undefined &&
+            mouseX !== undefined &&
+            sources &&
+            !contextCoord ? (React.createElement("div", { style: { position: 'relative' } },
             React.createElement(Crosshairs, { width: width, height: height, scrollTop: scrollTop, mouseX: mouseX, mouseY: mouseY }),
-            React.createElement(MAFTooltip, { model: model, mouseX: mouseX, mouseY: mouseY, origMouseX: dragStartX, rowHeight: rowHeight, sources: sources }))) : null,
+            React.createElement(MAFTooltip, { model: model, mouseX: mouseX, origMouseX: isDragging ? dragStartX : undefined }))) : null,
         (isDragging || showSelectionBox) &&
             dragStartX !== undefined &&
             dragEndX !== undefined ? (React.createElement("div", { style: {
@@ -147,22 +68,31 @@ const LinearMafDisplay = observer(function (props) {
                         if (!contextCoord) {
                             return;
                         }
-                        // Store the selection coordinates for the SequenceDialog to use
-                        setSelectionCoords({
-                            dragStartX: contextCoord.dragStartX,
-                            dragEndX: contextCoord.dragEndX,
-                        });
-                        // Show the dialog
-                        setShowSequenceDialog(true);
-                        // Close the context menu
+                        const { refName, assemblyName } = view.displayedRegions[0];
+                        const [s, e] = [
+                            Math.min(contextCoord.dragStartX, contextCoord.dragEndX),
+                            Math.max(contextCoord.dragStartX, contextCoord.dragEndX),
+                        ];
+                        if (isSessionModelWithWidgets(session)) {
+                            const widget = session.addWidget('MafSequenceWidget', 'mafSequence', {
+                                adapterConfig: model.adapterConfig,
+                                samples: model.samples,
+                                regions: [
+                                    {
+                                        refName,
+                                        start: view.pxToBp(s).coord - 1,
+                                        end: view.pxToBp(e).coord,
+                                        assemblyName,
+                                    },
+                                ],
+                                connectedViewId: view.id,
+                            });
+                            session.showWidget(widget);
+                        }
                         setContextCoord(undefined);
                     },
                 },
-            ] }),
-        showSequenceDialog ? (React.createElement(SequenceDialog, { model: model, selectionCoords: selectionCoords, onClose: () => {
-                setShowSequenceDialog(false);
-                setSelectionCoords(undefined);
-            } })) : null));
+            ] })));
 });
 export default LinearMafDisplay;
 //# sourceMappingURL=LinearMafDisplayComponent.js.map

package/dist/LinearMafDisplay/components/LinearMafDisplayComponent.js.map

@@ -1 +1 @@
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package/dist/LinearMafDisplay/components/MAFTooltip.d.ts

@@ -1,10 +1,7 @@
 import React from 'react';
 import type { LinearMafDisplayModel } from '../stateModel';
 declare const MAFTooltip: ({ model, mouseX, origMouseX, }: {
-    mouseY: number;
     mouseX: number;
-    rowHeight: number;
-    sources: Record<string, any>[];
     model: LinearMafDisplayModel;
     origMouseX?: number;
 }) => React.JSX.Element | null;

package/dist/LinearMafDisplay/components/MAFTooltip.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MAFTooltip.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/MAFTooltip.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAA;AAChD,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,sBAAsB,EAAE,MAAM,SAAS,CAAA;AAMhD,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EACpC,KAAK,EACL,MAAM,EACN,UAAU,GAKX;IACC,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAC9D,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC3D,MAAM,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAE9B,OAAO,WAAW,CAAC,CAAC,CAAC,CACnB,oBAAC,WAAW;QACV,oBAAC,aAAa,IACZ,IAAI,EAAE,sBAAsB,CAAC,WAA0B,EAAE,EAAE,EAAE,EAAE,CAAC,GAChE,CACU,CACf,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/components/MsaHighlightOverlay.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import type { LinearMafDisplayModel } from '../stateModel';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+declare const MsaHighlightOverlay: ({ model, view, height, }: {
+    model: LinearMafDisplayModel;
+    view: LinearGenomeViewModel;
+    height: number;
+}) => React.JSX.Element | null;
+export default MsaHighlightOverlay;

package/dist/LinearMafDisplay/components/MsaHighlightOverlay.js

@@ -0,0 +1,34 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+const MsaHighlightOverlay = observer(function MsaHighlightOverlay({ model, view, height, }) {
+    const { msaHighlights } = model;
+    if (msaHighlights.length === 0) {
+        return null;
+    }
+    const { offsetPx } = view;
+    const displayedRegion = view.displayedRegions[0];
+    if (!displayedRegion) {
+        return null;
+    }
+    return (React.createElement(React.Fragment, null, msaHighlights.map((highlight, idx) => {
+        // Check if highlight is on the displayed refName
+        if (highlight.refName !== displayedRegion.refName) {
+            return null;
+        }
+        const startPx = (highlight.start - displayedRegion.start) / view.bpPerPx - offsetPx;
+        const endPx = (highlight.end - displayedRegion.start) / view.bpPerPx - offsetPx;
+        const widthPx = Math.max(endPx - startPx, 2);
+        return (React.createElement("div", { key: idx, style: {
+                position: 'absolute',
+                left: startPx,
+                top: 0,
+                width: widthPx,
+                height,
+                backgroundColor: 'rgba(255, 165, 0, 0.4)',
+                border: '1px solid rgba(255, 165, 0, 0.8)',
+                pointerEvents: 'none',
+            } }));
+    })));
+});
+export default MsaHighlightOverlay;
+//# sourceMappingURL=MsaHighlightOverlay.js.map

package/dist/LinearMafDisplay/components/MsaHighlightOverlay.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/components/Sidebar/SvgWrapper.js

@@ -1,9 +1,9 @@
 import React, { useEffect, useRef } from 'react';
 import { ResizeHandle } from '@jbrowse/core/ui';
 import { getContainingView } from '@jbrowse/core/util';
+import { isAlive } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
-import { isAlive } from 'mobx-state-tree';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     resizeHandle: {

package/dist/LinearMafDisplay/components/Sidebar/SvgWrapper.js.map

@@ -1 +1 @@
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package/dist/LinearMafDisplay/components/useDragSelection.d.ts

@@ -0,0 +1,25 @@
+interface DragSelectionState {
+    isDragging: boolean;
+    dragStartX: number | undefined;
+    dragEndX: number | undefined;
+    showSelectionBox: boolean;
+    mouseX: number | undefined;
+    mouseY: number | undefined;
+}
+interface DragSelectionHandlers {
+    handleMouseDown: (event: React.MouseEvent) => void;
+    handleMouseMove: (event: React.MouseEvent) => void;
+    handleMouseUp: (event: React.MouseEvent) => void;
+    handleMouseLeave: () => void;
+    clearSelectionBox: () => void;
+}
+interface ContextCoord {
+    coord: [number, number];
+    dragStartX: number;
+    dragEndX: number;
+}
+export declare function useDragSelection(ref: React.RefObject<HTMLDivElement | null>): DragSelectionState & DragSelectionHandlers & {
+    contextCoord: ContextCoord | undefined;
+    setContextCoord: (coord: ContextCoord | undefined) => void;
+};
+export {};

package/dist/LinearMafDisplay/components/useDragSelection.js

@@ -0,0 +1,103 @@
+import { useCallback, useEffect, useState } from 'react';
+const MIN_DRAG_DISTANCE = 3;
+export function useDragSelection(ref) {
+    const [isDragging, setIsDragging] = useState(false);
+    const [dragStartX, setDragStartX] = useState();
+    const [dragEndX, setDragEndX] = useState();
+    const [showSelectionBox, setShowSelectionBox] = useState(false);
+    const [mouseX, setMouseX] = useState();
+    const [mouseY, setMouseY] = useState();
+    const [contextCoord, setContextCoord] = useState();
+    const clearSelectionBox = useCallback(() => {
+        setShowSelectionBox(false);
+        setDragStartX(undefined);
+        setDragEndX(undefined);
+    }, []);
+    const handleMouseDown = useCallback((event) => {
+        if (event.shiftKey) {
+            return;
+        }
+        const rect = ref.current?.getBoundingClientRect();
+        const left = rect?.left || 0;
+        const clientX = event.clientX - left;
+        setShowSelectionBox(false);
+        setIsDragging(true);
+        setDragStartX(clientX);
+        setDragEndX(clientX);
+        event.stopPropagation();
+    }, [ref]);
+    const handleMouseMove = useCallback((event) => {
+        const rect = ref.current?.getBoundingClientRect();
+        const top = rect?.top || 0;
+        const left = rect?.left || 0;
+        const clientX = event.clientX - left;
+        const clientY = event.clientY - top;
+        setMouseY(clientY);
+        setMouseX(clientX);
+        if (isDragging) {
+            setDragEndX(clientX);
+        }
+    }, [ref, isDragging]);
+    const handleMouseUp = useCallback((event) => {
+        if (isDragging && dragStartX !== undefined && dragEndX !== undefined) {
+            const dragDistanceX = Math.abs(dragEndX - dragStartX);
+            if (dragDistanceX > MIN_DRAG_DISTANCE) {
+                setContextCoord({
+                    coord: [event.clientX, event.clientY],
+                    dragEndX: event.clientX,
+                    dragStartX: dragStartX,
+                });
+                setShowSelectionBox(true);
+            }
+            else {
+                clearSelectionBox();
+            }
+        }
+        setIsDragging(false);
+    }, [isDragging, dragStartX, dragEndX, clearSelectionBox]);
+    const handleMouseLeave = useCallback(() => {
+        setMouseY(undefined);
+        setMouseX(undefined);
+        setIsDragging(false);
+    }, []);
+    useEffect(() => {
+        const handleKeyDown = (event) => {
+            if (event.key === 'Escape' && showSelectionBox) {
+                clearSelectionBox();
+            }
+        };
+        const handleClickOutside = (event) => {
+            if (ref.current &&
+                !ref.current.contains(event.target) &&
+                showSelectionBox) {
+                clearSelectionBox();
+            }
+        };
+        document.addEventListener('keydown', handleKeyDown);
+        document.addEventListener('click', handleClickOutside);
+        return () => {
+            document.removeEventListener('keydown', handleKeyDown);
+            document.removeEventListener('click', handleClickOutside);
+        };
+    }, [ref, showSelectionBox, clearSelectionBox]);
+    const dragDistance = dragStartX !== undefined && dragEndX !== undefined
+        ? Math.abs(dragEndX - dragStartX)
+        : 0;
+    const hasDraggedEnough = dragDistance > MIN_DRAG_DISTANCE;
+    return {
+        isDragging: isDragging && hasDraggedEnough,
+        dragStartX,
+        dragEndX,
+        showSelectionBox,
+        mouseX,
+        mouseY,
+        contextCoord,
+        setContextCoord,
+        handleMouseDown,
+        handleMouseMove,
+        handleMouseUp,
+        handleMouseLeave,
+        clearSelectionBox,
+    };
+}
+//# sourceMappingURL=useDragSelection.js.map

package/dist/LinearMafDisplay/components/useDragSelection.js.map

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/configSchema.d.ts

@@ -1,34 +1,7 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaType<{
     /**
      * #slot
      */
-    renderer: import("mobx-state-tree").IAnyModelType;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
+    renderer: import("@jbrowse/mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/esm/configuration/configurationSchema").ConfigurationSchemaOptions<any, undefined>>;