jbrowse-plugin-mafviewer 1.2.3 → 1.3.0

package/src/util/useSequences.ts

@@ -0,0 +1,90 @@
+import { useEffect, useState } from 'react'
+
+import { getContainingView, getSession } from '@jbrowse/core/util'
+import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+
+import type { LinearMafDisplayModel } from '../LinearMafDisplay/stateModel'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
+interface SelectionCoords {
+  dragStartX: number
+  dragEndX: number
+}
+
+interface UseSequencesOptions {
+  model: LinearMafDisplayModel
+  selectionCoords?: SelectionCoords
+  showAllLetters: boolean
+}
+
+/**
+ * React hook to fetch sequences for the given selection coordinates
+ * @param options - The options for fetching sequences
+ * @returns An object containing the sequence, loading state, and error
+ */
+export function useSequences({
+  model,
+  selectionCoords,
+  showAllLetters,
+}: UseSequencesOptions) {
+  const [sequence, setSequence] = useState<string>('')
+  const [loading, setLoading] = useState(true)
+  const [error, setError] = useState<unknown>()
+
+  useEffect(() => {
+    // If no selection coordinates, no need to fetch
+    if (!selectionCoords) {
+      return
+    }
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        setLoading(true)
+        setError(undefined)
+
+        const { samples, adapterConfig } = model
+        const { rpcManager } = getSession(model)
+        const sessionId = getRpcSessionId(model)
+        const view = getContainingView(model) as LinearGenomeViewModel
+        const { refName, assemblyName } = view.displayedRegions[0]!
+        const { dragStartX, dragEndX } = selectionCoords
+        const [s, e] = [
+          Math.min(dragStartX, dragEndX),
+          Math.max(dragStartX, dragEndX),
+        ]
+
+        const fastaSequence = (await rpcManager.call(
+          sessionId,
+          'MafGetSequences',
+          {
+            sessionId,
+            adapterConfig,
+            samples,
+            showAllLetters,
+            regions: [
+              {
+                refName,
+                start: view.pxToBp(s).coord - 1,
+                end: view.pxToBp(e).coord,
+                assemblyName,
+              },
+            ],
+          },
+        )) as string[]
+
+        const formattedSequence = fastaSequence
+          .map((r, idx) => `>${samples![idx]!.label}\n${r}`)
+          .join('\n')
+
+        setSequence(formattedSequence)
+      } catch (e) {
+        console.error(e)
+        setError(e)
+      } finally {
+        setLoading(false)
+      }
+    })()
+  }, [model, selectionCoords, showAllLetters])
+
+  return { sequence, loading, error }
+}

package/src/util.ts

@@ -3,9 +3,13 @@ function isStrs(array: unknown[]): array is string[] {
 }
 
 export function normalize(
-  r: string[] | { id: string; label: string; color?: string }[],
+  r: string[] | { id: string; label?: string; color?: string }[],
 ) {
   return isStrs(r)
-    ? r.map(elt => ({ id: elt, label: elt, color: undefined }))
+    ? r.map(elt => ({
+        id: elt,
+        label: elt,
+        color: undefined,
+      }))
     : r
 }

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

@@ -1,8 +0,0 @@
-import React from 'react';
-import { LinearMafDisplayModel } from '../stateModel';
-declare const ColorLegend: ({ model, labelWidth, svgFontSize, }: {
-    model: LinearMafDisplayModel;
-    svgFontSize: number;
-    labelWidth: number;
-}) => React.JSX.Element;
-export default ColorLegend;

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

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

@@ -1,50 +0,0 @@
-import React, { useRef, useState } from 'react';
-import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
-import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
-import { getContainingView, getEnv } from '@jbrowse/core/util';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import YScaleBars from './YScaleBars';
-const useStyles = makeStyles()({
-    cursor: {
-        pointerEvents: 'none',
-    },
-});
-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 LinearGenomePlugin = pluginManager.getPlugin('LinearGenomeViewPlugin');
-    const { BaseLinearDisplayComponent } = LinearGenomePlugin.exports;
-    const [mouseY, setMouseY] = useState();
-    const [mouseX, setMouseX] = 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);
-        }, onMouseLeave: () => {
-            setMouseY(undefined);
-            setMouseX(undefined);
-        } },
-        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));
-});
-export default LinearMafDisplay;
-//# sourceMappingURL=ReactComponent.js.map

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

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

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

@@ -1,36 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { Button, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()({
-    root: {
-        width: 500,
-    },
-});
-const SetRowHeightDialog = observer(function (props) {
-    const { model, handleClose } = props;
-    const { classes } = useStyles();
-    const [rowHeight, setRowHeight] = useState(`${model.rowHeight}`);
-    const [rowProportion, setRowProportion] = useState(`${model.rowProportion}`);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Set row height" },
-        React.createElement(DialogContent, { className: classes.root },
-            React.createElement(Typography, null, "Set row height and the proportion of the row height to use for drawing each row"),
-            React.createElement(TextField, { value: rowHeight, helperText: "Enter row height", onChange: event => {
-                    setRowHeight(event.target.value);
-                } }),
-            React.createElement(TextField, { value: rowProportion, helperText: "Enter row proportion", onChange: event => {
-                    setRowProportion(event.target.value);
-                } }),
-            React.createElement(DialogActions, null,
-                React.createElement(Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
-                        model.setRowProportion(+rowProportion);
-                        model.setRowHeight(+rowHeight);
-                        handleClose();
-                    } }, "Submit"),
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        handleClose();
-                    } }, "Cancel")))));
-});
-export default SetRowHeightDialog;
-//# sourceMappingURL=SetRowHeight.js.map

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

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

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

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

@@ -1,20 +0,0 @@
-import React from 'react';
-import { measureText } from '@jbrowse/core/util';
-import { observer } from 'mobx-react';
-import ColorLegend from './ColorLegend';
-import SvgWrapper from './SvgWrapper';
-import { max } from './util';
-export const YScaleBars = observer(function (props) {
-    const { model } = props;
-    const { rowHeight, samples } = model;
-    const svgFontSize = Math.min(Math.max(rowHeight, 8), 14);
-    const canDisplayLabel = rowHeight >= 8;
-    const minWidth = 20;
-    const labelWidth = max(samples
-        ?.map(s => measureText(s.label, svgFontSize))
-        .map(width => (canDisplayLabel ? width : minWidth)) || [], 0);
-    return (React.createElement(SvgWrapper, { ...props },
-        React.createElement(ColorLegend, { model: model, labelWidth: labelWidth, svgFontSize: svgFontSize })));
-});
-export default YScaleBars;
-//# sourceMappingURL=YScaleBars.js.map

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

@@ -1 +0,0 @@
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package/dist/MafRPC/index.js.map

@@ -1 +0,0 @@
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package/src/LinearMafDisplay/components/ReactComponent.tsx

@@ -1,91 +0,0 @@
-import React, { useRef, useState } from 'react'
-
-import BaseTooltip from '@jbrowse/core/ui/BaseTooltip'
-import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML'
-import { getContainingView, getEnv } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-import YScaleBars from './YScaleBars'
-import { LinearMafDisplayModel } from '../stateModel'
-
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-
-const useStyles = makeStyles()({
-  cursor: {
-    pointerEvents: 'none',
-  },
-})
-
-const LinearMafDisplay = observer(function (props: {
-  model: LinearMafDisplayModel
-}) {
-  const { model } = props
-  const { classes } = useStyles()
-  const { pluginManager } = getEnv(model)
-  const { rowHeight, height, scrollTop, samples: sources } = model
-  const ref = useRef<HTMLDivElement>(null)
-
-  const LinearGenomePlugin = pluginManager.getPlugin(
-    'LinearGenomeViewPlugin',
-  ) as import('@jbrowse/plugin-linear-genome-view').default
-  const { BaseLinearDisplayComponent } = LinearGenomePlugin.exports
-
-  const [mouseY, setMouseY] = useState<number>()
-  const [mouseX, setMouseX] = useState<number>()
-  const { width } = getContainingView(model) as LinearGenomeViewModel
-
-  return (
-    <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)
-      }}
-      onMouseLeave={() => {
-        setMouseY(undefined)
-        setMouseX(undefined)
-      }}
-    >
-      <BaseLinearDisplayComponent {...props} />
-      <YScaleBars model={model} />
-      {mouseY && sources ? (
-        <div style={{ position: 'relative' }}>
-          <svg
-            className={classes.cursor}
-            width={width}
-            height={height}
-            style={{
-              position: 'absolute',
-              top: scrollTop,
-            }}
-          >
-            <line
-              x1={0}
-              x2={width}
-              y1={mouseY - scrollTop}
-              y2={mouseY - scrollTop}
-              stroke="black"
-            />
-            <line x1={mouseX} x2={mouseX} y1={0} y2={height} stroke="black" />
-          </svg>
-          <BaseTooltip>
-            <SanitizedHTML
-              html={Object.entries(
-                sources[Math.floor(mouseY / rowHeight)] || {},
-              )
-                .filter(([key]) => key !== 'color' && key !== 'id')
-                .map(([key, value]) => `${key}:${value}`)
-                .join('\n')}
-            />
-          </BaseTooltip>
-        </div>
-      ) : null}
-    </div>
-  )
-})
-
-export default LinearMafDisplay

package/src/LinearMafDisplay/components/SetRowHeight.tsx

@@ -1,83 +0,0 @@
-import React, { useState } from 'react'
-
-import { Dialog } from '@jbrowse/core/ui'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-const useStyles = makeStyles()({
-  root: {
-    width: 500,
-  },
-})
-
-const SetRowHeightDialog = observer(function (props: {
-  model: {
-    rowHeight?: number
-    rowProportion?: number
-    setRowHeight: (arg: number) => void
-    setRowProportion: (arg: number) => void
-  }
-  handleClose: () => void
-}) {
-  const { model, handleClose } = props
-  const { classes } = useStyles()
-  const [rowHeight, setRowHeight] = useState(`${model.rowHeight}`)
-  const [rowProportion, setRowProportion] = useState(`${model.rowProportion}`)
-
-  return (
-    <Dialog open onClose={handleClose} title="Set row height">
-      <DialogContent className={classes.root}>
-        <Typography>
-          Set row height and the proportion of the row height to use for drawing
-          each row
-        </Typography>
-        <TextField
-          value={rowHeight}
-          helperText="Enter row height"
-          onChange={event => {
-            setRowHeight(event.target.value)
-          }}
-        />
-        <TextField
-          value={rowProportion}
-          helperText="Enter row proportion"
-          onChange={event => {
-            setRowProportion(event.target.value)
-          }}
-        />
-        <DialogActions>
-          <Button
-            variant="contained"
-            color="primary"
-            type="submit"
-            autoFocus
-            onClick={() => {
-              model.setRowProportion(+rowProportion)
-              model.setRowHeight(+rowHeight)
-              handleClose()
-            }}
-          >
-            Submit
-          </Button>
-          <Button
-            variant="contained"
-            color="secondary"
-            onClick={() => {
-              handleClose()
-            }}
-          >
-            Cancel
-          </Button>
-        </DialogActions>
-      </DialogContent>
-    </Dialog>
-  )
-})
-export default SetRowHeightDialog

package/src/LinearMafDisplay/components/YScaleBars.tsx

@@ -1,41 +0,0 @@
-import React from 'react'
-
-import { measureText } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-
-// locals
-import { LinearMafDisplayModel } from '../stateModel'
-import ColorLegend from './ColorLegend'
-import SvgWrapper from './SvgWrapper'
-import { max } from './util'
-
-export const YScaleBars = observer(function (props: {
-  model: LinearMafDisplayModel
-  orientation?: string
-  exportSVG?: boolean
-}) {
-  const { model } = props
-  const { rowHeight, samples } = model
-  const svgFontSize = Math.min(Math.max(rowHeight, 8), 14)
-  const canDisplayLabel = rowHeight >= 8
-  const minWidth = 20
-
-  const labelWidth = max(
-    samples
-      ?.map(s => measureText(s.label, svgFontSize))
-      .map(width => (canDisplayLabel ? width : minWidth)) || [],
-    0,
-  )
-
-  return (
-    <SvgWrapper {...props}>
-      <ColorLegend
-        model={model}
-        labelWidth={labelWidth}
-        svgFontSize={svgFontSize}
-      />
-    </SvgWrapper>
-  )
-})
-
-export default YScaleBars