jbrowse-plugin-mafviewer 1.2.4 → 1.3.1

package/dist/BigMafAdapter/BigMafAdapter.js

@@ -74,7 +74,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
                             srcSize: +ad[2],
                             strand: ad[3] === '+' ? 1 : -1,
                             unknown: +ad[4],
-                            data: alns[i],
+                            seq: alns[i],
                         };
                     }
                     observer.next(new SimpleFeature({

package/dist/BigMafAdapter/BigMafAdapter.js.map

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

@@ -0,0 +1,10 @@
+import React from 'react';
+interface CrosshairsProps {
+    width: number;
+    height: number;
+    scrollTop: number;
+    mouseX?: number;
+    mouseY: number;
+}
+declare const Crosshairs: ({ width, height, scrollTop, mouseX, mouseY, }: CrosshairsProps) => React.JSX.Element;
+export default Crosshairs;

package/dist/LinearMafDisplay/components/Crosshairs.js

@@ -0,0 +1,18 @@
+import React from 'react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    cursor: {
+        pointerEvents: 'none',
+    },
+});
+const Crosshairs = ({ width, height, scrollTop, mouseX, mouseY, }) => {
+    const { classes } = useStyles();
+    return (React.createElement("svg", { className: classes.cursor, width: width, height: height, style: {
+            position: 'absolute',
+            top: scrollTop,
+        } },
+        React.createElement("line", { x1: 0, x2: width, y1: mouseY - scrollTop, y2: mouseY - scrollTop, stroke: "black" }),
+        React.createElement("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })));
+};
+export default Crosshairs;
+//# sourceMappingURL=Crosshairs.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Crosshairs.js","sourceRoot":"","sources":["../../../src/LinearMafDisplay/components/Crosshairs.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,aAAa,EAAE,MAAM;KACtB;CACF,CAAC,CAAA;AAUF,MAAM,UAAU,GAAG,CAAC,EAClB,KAAK,EACL,MAAM,EACN,SAAS,EACT,MAAM,EACN,MAAM,GACU,EAAE,EAAE;IACpB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,OAAO,CACL,6BACE,SAAS,EAAE,OAAO,CAAC,MAAM,EACzB,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,SAAS;SACf;QAED,8BACE,EAAE,EAAE,CAAC,EACL,EAAE,EAAE,KAAK,EACT,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,EAAE,EAAE,MAAM,GAAG,SAAS,EACtB,MAAM,EAAC,OAAO,GACd;QACF,8BAAM,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAC,OAAO,GAAG,CAC9D,CACP,CAAA;AACH,CAAC,CAAA;AAED,eAAe,UAAU,CAAA"}

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

@@ -0,0 +1,11 @@
+import React from 'react';
+import type { LinearMafDisplayModel } from '../../stateModel';
+declare const GetSequenceDialog: ({ onClose, model, selectionCoords, }: {
+    onClose: () => void;
+    model: LinearMafDisplayModel;
+    selectionCoords?: {
+        dragStartX: number;
+        dragEndX: number;
+    };
+}) => React.JSX.Element;
+export default GetSequenceDialog;

package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js

@@ -0,0 +1,97 @@
+import React, { useState } from 'react';
+import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
+import { Button, DialogActions, DialogContent, TextField, ToggleButton, ToggleButtonGroup, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { useSequences } from '../../../util/useSequences';
+const useStyles = makeStyles()({
+    dialogContent: {
+        width: '80em',
+    },
+    textAreaInput: {
+        fontFamily: 'monospace',
+        whiteSpace: 'pre',
+        overflowX: 'auto',
+    },
+    ml: {
+        marginLeft: 10,
+    },
+});
+const GetSequenceDialog = observer(function ({ onClose, model, selectionCoords, }) {
+    const [showAllLetters, setShowAllLetters] = useState(true);
+    const { classes } = useStyles();
+    const { sequence, loading, error } = useSequences({
+        model,
+        selectionCoords,
+        showAllLetters,
+    });
+    const sequenceTooLarge = sequence ? sequence.length > 1_000_000 : false;
+    return (React.createElement(Dialog, { open: true, onClose: onClose, title: "Subsequence Data", maxWidth: "xl" },
+        React.createElement(DialogContent, null,
+            React.createElement("div", { style: {
+                    display: 'flex',
+                    alignItems: 'center',
+                    marginBottom: '16px',
+                } },
+                React.createElement(ToggleButtonGroup, { value: showAllLetters, exclusive: true, size: "small", onChange: (_event, newDisplayMode) => {
+                        if (newDisplayMode !== null) {
+                            setShowAllLetters(newDisplayMode);
+                        }
+                    } },
+                    React.createElement(ToggleButton, { value: true }, "Show All Letters"),
+                    React.createElement(ToggleButton, { value: false }, "Show Only Differences")),
+                React.createElement("div", { style: { flexGrow: 1 } }),
+                React.createElement(Button, { variant: "contained", color: "primary", disabled: loading || !sequence, onClick: () => {
+                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                        ;
+                        (async () => {
+                            try {
+                                await navigator.clipboard.writeText(sequence);
+                                getSession(model).notify('Sequence copied to clipboard', 'info');
+                            }
+                            catch (e) {
+                                console.error(e);
+                                getSession(model).notifyError(`${e}`, e);
+                            }
+                        })();
+                    } }, "Copy to Clipboard"),
+                React.createElement(Button, { variant: "contained", color: "secondary", disabled: loading || !sequence, onClick: () => {
+                        try {
+                            const url = URL.createObjectURL(new Blob([sequence], { type: 'text/plain' }));
+                            // Create a temporary anchor element
+                            const a = document.createElement('a');
+                            a.href = url;
+                            a.download = 'sequence.fasta';
+                            // Trigger the download
+                            document.body.append(a);
+                            a.click();
+                            // Clean up
+                            a.remove();
+                            URL.revokeObjectURL(url);
+                            getSession(model).notify('Sequence downloaded', 'info');
+                        }
+                        catch (e) {
+                            console.error(e);
+                            getSession(model).notifyError(`${e}`, e);
+                        }
+                    } }, "Download")),
+            error ? (React.createElement(ErrorMessage, { error: error })) : (React.createElement(React.Fragment, null,
+                loading ? React.createElement(LoadingEllipses, null) : null,
+                React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: loading
+                        ? 'Loading...'
+                        : sequenceTooLarge
+                            ? 'Reference sequence too large to display, use the download FASTA button'
+                            : sequence, slotProps: {
+                        input: {
+                            readOnly: true,
+                            classes: {
+                                input: classes.textAreaInput,
+                            },
+                        },
+                    } })))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { color: "primary", variant: "outlined", onClick: onClose }, "Close"))));
+});
+export default GetSequenceDialog;
+//# sourceMappingURL=GetSequenceDialog.js.map

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

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

@@ -1,50 +1,168 @@
-import React, { useRef, useState } from 'react';
-import { SanitizedHTML } from '@jbrowse/core/ui';
-import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
+import React, { useEffect, useRef, useState } from 'react';
+import { Menu } from '@jbrowse/core/ui';
 import { getContainingView, getEnv } from '@jbrowse/core/util';
+import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import YScaleBars from './YScaleBars';
-const useStyles = makeStyles()({
-    cursor: {
-        pointerEvents: 'none',
-    },
-});
+import Crosshairs from './Crosshairs';
+import SequenceDialog from './GetSequenceDialog/GetSequenceDialog';
+import MAFTooltip from './MAFTooltip';
+import YScaleBars from './Sidebar/YScaleBars';
 const LinearMafDisplay = observer(function (props) {
     const { model } = props;
-    const { classes } = useStyles();
     const { pluginManager } = getEnv(model);
     const { rowHeight, height, scrollTop, samples: sources } = model;
     const ref = useRef(null);
+    const theme = useTheme();
     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);
-    return (React.createElement("div", { ref: ref, onMouseMove: event => {
-            const rect = ref.current?.getBoundingClientRect();
-            const top = rect?.top || 0;
-            const left = rect?.left || 0;
-            setMouseY(event.clientY - top);
-            setMouseX(event.clientX - left);
+    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 = () => {
+        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]);
+    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);
         } },
         React.createElement(BaseLinearDisplayComponent, { ...props }),
         React.createElement(YScaleBars, { model: model }),
-        mouseY && sources ? (React.createElement("div", { style: { position: 'relative' } },
-            React.createElement("svg", { className: classes.cursor, width: width, height: height, style: {
-                    position: 'absolute',
-                    top: scrollTop,
-                } },
-                React.createElement("line", { x1: 0, x2: width, y1: mouseY - scrollTop, y2: mouseY - scrollTop, stroke: "black" }),
-                React.createElement("line", { x1: mouseX, x2: mouseX, y1: 0, y2: height, stroke: "black" })),
-            React.createElement(BaseTooltip, null,
-                React.createElement(SanitizedHTML, { html: Object.entries(sources[Math.floor(mouseY / rowHeight)] || {})
-                        .filter(([key]) => key !== 'color' && key !== 'id')
-                        .map(([key, value]) => `${key}:${value}`)
-                        .join('\n') })))) : null));
+        mouseY && mouseX && sources && !contextCoord && !showSequenceDialog ? (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,
+        (isDragging || showSelectionBox) &&
+            dragStartX !== undefined &&
+            dragEndX !== undefined ? (React.createElement("div", { style: {
+                position: 'absolute',
+                left: Math.min(dragStartX, dragEndX),
+                top: 0,
+                width: Math.abs(dragEndX - dragStartX),
+                height,
+                backgroundColor: 'rgba(0, 0, 255, 0.2)',
+                border: '1px solid rgba(0, 0, 255, 0.5)',
+                pointerEvents: 'none',
+            } })) : null,
+        React.createElement(Menu, { open: Boolean(contextCoord), onMenuItemClick: (_, callback) => {
+                callback();
+                setContextCoord(undefined);
+            }, onClose: () => {
+                setContextCoord(undefined);
+            }, slotProps: {
+                transition: {
+                    onExit: () => {
+                        setContextCoord(undefined);
+                    },
+                },
+            }, anchorReference: "anchorPosition", anchorPosition: contextCoord
+                ? { top: contextCoord.coord[1], left: contextCoord.coord[0] }
+                : undefined, style: {
+                zIndex: theme.zIndex.tooltip,
+            }, menuItems: [
+                {
+                    label: 'View subsequence',
+                    onClick: () => {
+                        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
+                        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

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

@@ -0,0 +1,12 @@
+import React from 'react';
+import type { LinearMafDisplayModel } from '../stateModel';
+interface MAFTooltipProps {
+    mouseY: number;
+    mouseX: number;
+    rowHeight: number;
+    sources: Record<string, any>[];
+    model: LinearMafDisplayModel;
+    origMouseX?: number;
+}
+declare const MAFTooltip: ({ model, mouseY, mouseX, origMouseX, rowHeight, sources, }: MAFTooltipProps) => React.JSX.Element | null;
+export default MAFTooltip;

package/dist/LinearMafDisplay/components/MAFTooltip.js

@@ -0,0 +1,29 @@
+import React from 'react';
+import { SanitizedHTML } from '@jbrowse/core/ui';
+import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
+import { getBpDisplayStr, getContainingView, toLocale, } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+const MAFTooltip = observer(function ({ model, mouseY, mouseX, origMouseX, rowHeight, sources, }) {
+    const view = getContainingView(model);
+    const ret = Object.entries(sources[Math.floor(mouseY / rowHeight)] || {})
+        .filter(([key]) => key !== 'color' && key !== 'id')
+        .map(([key, value]) => `${key}:${value}`)
+        .join('\n');
+    const p1 = origMouseX ? view.pxToBp(origMouseX) : undefined;
+    const p2 = view.pxToBp(mouseX);
+    return ret ? (React.createElement(BaseTooltip, null,
+        React.createElement(SanitizedHTML, { html: [
+                ret,
+                ...(p1
+                    ? [
+                        `Start: ${p1.refName}:${toLocale(p1.coord)}`,
+                        `End: ${p2.refName}:${toLocale(p2.coord)}`,
+                        `Length: ${getBpDisplayStr(Math.abs(p1.coord - p2.coord))}`,
+                    ]
+                    : [`${p2.refName}:${toLocale(p2.coord)}`]),
+            ]
+                .filter(f => !!f)
+                .join('<br/>') }))) : null;
+});
+export default MAFTooltip;
+//# sourceMappingURL=MAFTooltip.js.map

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

@@ -0,0 +1 @@
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package/dist/LinearMafDisplay/components/SetRowHeightDialog/SetRowHeightDialog.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SetRowHeightDialog.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/SetRowHeightDialog/SetRowHeightDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,aAAa,EACb,aAAa,EACb,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,KAAK,EAAE,GAAG;KACX;CACF,CAAC,CAAA;AAEF,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAQ7C;IACC,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,GAAG,KAAK,CAAC,SAAS,EAAE,CAAC,CAAA;IAChE,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,GAAG,KAAK,CAAC,aAAa,EAAE,CAAC,CAAA;IAE5E,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,gBAAgB;QACvD,8BACE,QAAQ,EAAE,KAAK,CAAC,EAAE;gBAChB,KAAK,CAAC,cAAc,EAAE,CAAA;gBACtB,KAAK,CAAC,gBAAgB,CAAC,CAAC,aAAa,CAAC,CAAA;gBACtC,KAAK,CAAC,YAAY,CAAC,CAAC,SAAS,CAAC,CAAA;gBAC9B,WAAW,EAAE,CAAA;YACf,CAAC;YAED,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI;gBACpC,oBAAC,UAAU,0FAGE;gBACb,oBAAC,SAAS,IACR,KAAK,EAAE,SAAS,EAChB,UAAU,EAAC,kBAAkB,EAC7B,SAAS,QACT,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBAClC,CAAC,GACD;gBACF,oBAAC,SAAS,IACR,KAAK,EAAE,aAAa,EACpB,UAAU,EAAC,sBAAsB,EACjC,QAAQ,EAAE,KAAK,CAAC,EAAE;wBAChB,gBAAgB,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;oBACtC,CAAC,GACD;gBACF,oBAAC,aAAa;oBACZ,oBAAC,MAAM,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,SAAS,EAAC,IAAI,EAAC,QAAQ,aAEhD;oBACT,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,WAAW,EAAE,CAAA;wBACf,CAAC,aAGM,CACK,CACF,CACX,CACA,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,kBAAkB,CAAA"}

package/dist/LinearMafDisplay/components/{ColorLegend.d.ts → Sidebar/ColorLegend.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import type { LinearMafDisplayModel } from '../stateModel';
+import type { LinearMafDisplayModel } from '../../stateModel';
 declare const ColorLegend: ({ model, }: {
     model: LinearMafDisplayModel;
 }) => React.JSX.Element;

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

@@ -0,0 +1 @@
+{"version":3,"file":"ColorLegend.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/ColorLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,IAAI,MAAM,QAAQ,CAAA;AAIzB,MAAM,WAAW,GAAG,QAAQ,CAAC,UAAU,EACrC,KAAK,GAGN;IACC,MAAM,EACJ,UAAU,EACV,eAAe,EACf,WAAW,EACX,SAAS,EACT,OAAO,GAAG,EAAE,EACZ,SAAS,EACT,WAAW,GACZ,GAAG,KAAK,CAAA;IACT,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,SAAS,CAAC,CAAA;IAEzC,OAAO,CACL;QACE,oBAAC,MAAM,IACL,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,GAAG,SAAS,EACjC,MAAM,EAAE,WAAW,GACnB;QACF,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI;QACtB,2BAAG,SAAS,EAAE,aAAa,SAAS,GAAG,CAAC,KAAK;YAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC5B,oBAAC,MAAM,IACL,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,CAAC,EAAE,GAAG,GAAG,SAAS,EAClB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,UAAU,GAAG,CAAC,EACrB,MAAM,EAAE,SAAS,EACjB,KAAK,EAAE,MAAM,CAAC,KAAK,GACnB,CACH,CAAC;YACD,eAAe;gBACd,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC,CAC3B,8BACE,GAAG,EAAE,GAAG,MAAM,CAAC,EAAE,IAAI,GAAG,EAAE,EAC1B,gBAAgB,EAAC,QAAQ,EACzB,QAAQ,EAAE,WAAW,EACrB,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,GAAG,GAAG,SAAS,GAAG,SAAS,GAAG,CAAC,IAEjC,MAAM,CAAC,KAAK,CACR,CACR,CAAC;gBACJ,CAAC,CAAC,IAAI,CACN,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,WAAW,CAAA"}

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

@@ -0,0 +1 @@
+{"version":3,"file":"RectBg.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/RectBg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,MAAM,GAAG,CAAC,KAMf,EAAE,EAAE;IACH,MAAM,EAAE,KAAK,GAAG,sBAAsB,EAAE,GAAG,KAAK,CAAA;IAChD,OAAO,iCAAU,KAAK,EAAE,IAAI,EAAE,KAAK,GAAI,CAAA;AACzC,CAAC,CAAA;AAED,eAAe,MAAM,CAAA"}

package/dist/LinearMafDisplay/components/{SvgWrapper.d.ts → Sidebar/SvgWrapper.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import type { LinearMafDisplayModel } from '../stateModel';
+import type { LinearMafDisplayModel } from '../../stateModel';
 declare const SvgWrapper: ({ children, model, exportSVG, }: {
     model: LinearMafDisplayModel;
     children: React.ReactNode;

package/dist/LinearMafDisplay/components/{SvgWrapper.js → Sidebar/SvgWrapper.js}

@@ -7,13 +7,15 @@ const SvgWrapper = observer(function ({ children, model, exportSVG, }) {
     }
     else {
         const { totalHeight } = model;
+        const { width } = getContainingView(model);
         return (React.createElement("svg", { style: {
                 position: 'absolute',
+                userSelect: 'none',
                 top: 0,
                 left: 0,
                 pointerEvents: 'none',
                 height: totalHeight,
-                width: getContainingView(model).width,
+                width,
             } }, children));
     }
 });

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

@@ -0,0 +1 @@
+{"version":3,"file":"SvgWrapper.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/SvgWrapper.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EACpC,QAAQ,EACR,KAAK,EACL,SAAS,GAKV;IACC,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,0CAAG,QAAQ,CAAI,CAAA;IACxB,CAAC;SAAM,CAAC;QACN,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;QAC7B,MAAM,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;QACnE,OAAO,CACL,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,UAAU,EAAE,MAAM;gBAClB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,aAAa,EAAE,MAAM;gBACrB,MAAM,EAAE,WAAW;gBACnB,KAAK;aACN,IAEA,QAAQ,CACL,CACP,CAAA;IACH,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/components/{Tree.d.ts → Sidebar/Tree.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import type { LinearMafDisplayModel } from '../stateModel';
+import type { LinearMafDisplayModel } from '../../stateModel';
 declare const Tree: ({ model }: {
     model: LinearMafDisplayModel;
 }) => React.JSX.Element;

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

@@ -0,0 +1 @@
+{"version":3,"file":"Tree.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/Tree.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAAoC;IACzE,MAAM;IACJ,2EAA2E;IAC3E,mBAAmB;IACnB,8DAA8D;IAC9D,SAAS,EAAE,UAAU,EAErB,SAAS,EACT,aAAa,GACd,GAAG,KAAK,CAAA;IAET,OAAO,CACL,0CACG,SAAS;QACR,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YAChC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;YAC/B,MAAM,EAAE,GAAG,MAAM,CAAC,CAAE,CAAA;YACpB,MAAM,EAAE,GAAG,MAAM,CAAC,CAAE,CAAA;YACpB,mBAAmB;YACnB,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;YAChD,mBAAmB;YACnB,MAAM,EAAE,GAAG,aAAa,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAA;YAEhD,sEAAsE;YACtE,iEAAiE;YACjE,oBAAoB;YACpB,OAAO,CACL,oBAAC,KAAK,CAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;gBAC7C,8BAAM,MAAM,EAAC,OAAO,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,GAAI;gBACvD,8BAAM,MAAM,EAAC,OAAO,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,GAAI,CACxC,CAClB,CAAA;QACH,CAAC,CAAC;QACJ,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,IAAI,CAAA"}

package/dist/LinearMafDisplay/components/{YScaleBars.d.ts → Sidebar/YScaleBars.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import type { LinearMafDisplayModel } from '../stateModel';
+import type { LinearMafDisplayModel } from '../../stateModel';
 export declare const YScaleBars: (props: {
     model: LinearMafDisplayModel;
     orientation?: string;

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

@@ -0,0 +1 @@
+{"version":3,"file":"YScaleBars.js","sourceRoot":"","sources":["../../../../src/LinearMafDisplay/components/Sidebar/YScaleBars.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,WAAW,MAAM,eAAe,CAAA;AACvC,OAAO,UAAU,MAAM,cAAc,CAAA;AAIrC,MAAM,CAAC,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,KAI5C;IACC,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,OAAO,CACL,oBAAC,UAAU,OAAK,KAAK;QACnB,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB,CACd,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/LinearMafDisplay/renderSvg.js

@@ -1,6 +1,6 @@
 import React from 'react';
 import { getContainingView } from '@jbrowse/core/util';
-import YScaleBars from './components/YScaleBars';
+import YScaleBars from './components/Sidebar/YScaleBars';
 export async function renderSvg(self, opts, superRenderSvg) {
     const { height, id } = self;
     const { offsetPx, width } = getContainingView(self);

package/dist/LinearMafDisplay/renderSvg.js.map

@@ -1 +1 @@
-{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAEtD,OAAO,UAAU,MAAM,yBAAyB,CAAA;AAQhD,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAA2B,EAC3B,IAA6B,EAC7B,cAA2E;IAE3E,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IAC3B,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IAC5E,MAAM,MAAM,GAAG,WAAW,EAAE,EAAE,CAAA;IAC9B,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;QACP,2BAAG,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC5B,2BAAG,EAAE,EAAC,QAAQ,IAAE,MAAM,cAAc,CAAC,IAAI,CAAC,CAAK;YAC/C,2BAAG,SAAS,EAAE,aAAa,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG;gBAClD,oBAAC,UAAU,IAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAC,MAAM,EAAC,SAAS,SAAG,CACtD,CACF,CACH,CACJ,CAAA;AACH,CAAC"}
+{"version":3,"file":"renderSvg.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/renderSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AAEtD,OAAO,UAAU,MAAM,iCAAiC,CAAA;AAQxD,MAAM,CAAC,KAAK,UAAU,SAAS,CAC7B,IAA2B,EAC3B,IAA6B,EAC7B,cAA2E;IAE3E,MAAM,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IAC3B,MAAM,EAAE,QAAQ,EAAE,KAAK,EAAE,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;IAC5E,MAAM,MAAM,GAAG,WAAW,EAAE,EAAE,CAAA;IAC9B,OAAO,CACL;QACE;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,GAAI,CACzC,CACN;QACP,2BAAG,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC5B,2BAAG,EAAE,EAAC,QAAQ,IAAE,MAAM,cAAc,CAAC,IAAI,CAAC,CAAK;YAC/C,2BAAG,SAAS,EAAE,aAAa,IAAI,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,GAAG;gBAClD,oBAAC,UAAU,IAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAC,MAAM,EAAC,SAAS,SAAG,CACtD,CACF,CACH,CACJ,CAAA;AACH,CAAC"}

package/dist/LinearMafDisplay/stateModel.d.ts

@@ -93,6 +93,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     mismatchRendering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
+    showAsUpperCase: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -196,6 +197,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -205,7 +207,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -256,6 +258,10 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         samples: Sample[];
         tree: unknown;
     }): void;
+    /**
+     * #action
+     */
+    setShowAsUpperCase(arg: boolean): void;
 } & {
     /**
      * #getter
@@ -279,11 +285,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     /**
      * #getter
      */
-    readonly samples: Sample[] | {
-        label: string | undefined;
-        color: string | undefined;
-        id: string;
-    }[] | undefined;
+    readonly samples: Sample[] | undefined;
     /**
      * #getter
      */