jbrowse-plugin-mafviewer 1.2.3 → 1.2.4

package/src/LinearMafRenderer/makeImageData.ts

@@ -74,11 +74,12 @@ export function makeImageData({
       }
 
       const t = rowHeight * row
+      const t2 = offset + t
 
       // gaps
       ctx.beginPath()
       ctx.fillStyle = 'black'
-      for (let i = 0, o = 0; i < alignment.length; i++) {
+      for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
         if (seq[i] !== '-') {
           if (alignment[i] === '-') {
             const l = leftPx + scale * o
@@ -93,12 +94,12 @@ export function makeImageData({
       if (!showAllLetters) {
         // matches
         ctx.fillStyle = 'lightgrey'
-        for (let i = 0, o = 0; i < alignment.length; i++) {
+        for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
           if (seq[i] !== '-') {
             const c = alignment[i]
             const l = leftPx + scale * o
             if (seq[i] === c && c !== '-' && c !== ' ') {
-              fillRect(ctx, l, offset + t, scale + f, h, canvasWidth)
+              fillRect(ctx, l, t2, scale + f, h, canvasWidth)
             }
             o++
           }
@@ -106,7 +107,7 @@ export function makeImageData({
       }
 
       // mismatches
-      for (let i = 0, o = 0; i < alignment.length; i++) {
+      for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
         const c = alignment[i]
         if (seq[i] !== '-') {
           if (c !== '-') {
@@ -115,7 +116,7 @@ export function makeImageData({
               fillRect(
                 ctx,
                 l,
-                offset + t,
+                t2,
                 scale + f,
                 h,
                 canvasWidth,
@@ -128,7 +129,7 @@ export function makeImageData({
               fillRect(
                 ctx,
                 l,
-                offset + t,
+                t2,
                 scale + f,
                 h,
                 canvasWidth,
@@ -146,7 +147,7 @@ export function makeImageData({
       // font
       const charSizeW = 10
       if (scale >= charSizeW) {
-        for (let i = 0, o = 0; i < alignment.length; i++) {
+        for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
           if (seq[i] !== '-') {
             const l = leftPx + scale * o
             const offset = (scale - charSizeW) / 2 + 1
@@ -182,8 +183,8 @@ export function makeImageData({
       }
 
       const t = rowHeight * row
-
-      for (let i = 0, o = 0; i < alignment.length; i++) {
+      const t2 = offset + t
+      for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
         let ins = ''
         while (seq[i] === '-') {
           if (alignment[i] !== '-' && alignment[i] !== ' ') {
@@ -197,14 +198,14 @@ export function makeImageData({
           if (ins.length > 10) {
             const txt = `${ins.length}`
             if (bpPerPx > 10) {
-              fillRect(ctx, l - 1, t, 2, h, canvasWidth, 'purple')
+              fillRect(ctx, l - 1, t2, 2, h, canvasWidth, 'purple')
             } else if (h > charHeight) {
-              const rwidth = measureText(txt)
-              const padding = 5
+              const rwidth = measureText(txt, 10)
+              const padding = 2
               fillRect(
                 ctx,
                 l - rwidth / 2 - padding,
-                t,
+                t2,
                 rwidth + 2 * padding,
                 h,
                 canvasWidth,
@@ -217,7 +218,7 @@ export function makeImageData({
               fillRect(
                 ctx,
                 l - padding,
-                t,
+                t2,
                 2 * padding,
                 h,
                 canvasWidth,
@@ -225,10 +226,10 @@ export function makeImageData({
               )
             }
           } else {
-            fillRect(ctx, l, offset + t, 1, h, canvasWidth, 'purple')
+            fillRect(ctx, l, t2, 1, h, canvasWidth, 'purple')
             if (bpPerPx < 0.2 && rowHeight > 5) {
-              fillRect(ctx, l - 2, offset + t, 5, 1, canvasWidth)
-              fillRect(ctx, l - 2, offset + t + h - 1, 5, 1, canvasWidth)
+              fillRect(ctx, l - 2, t2, 5, 1, canvasWidth)
+              fillRect(ctx, l - 2, t2 + h - 1, 5, 1, canvasWidth)
             }
           }
         }

package/src/MafAddTrackWorkflow/index.ts

@@ -2,7 +2,6 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes'
 import { types } from 'mobx-state-tree'
 
-// locals
 import MultiMAFWidget from './AddTrackWorkflow'
 
 export default function MafAddTrackWorkflowF(pluginManager: PluginManager) {

package/src/MafTabixAdapter/MafTabixAdapter.ts

@@ -29,16 +29,16 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
   public setupP?: Promise<{ adapter: BaseFeatureDataAdapter }>
 
   async setupPre() {
-    const config = this.config
     if (!this.getSubAdapter) {
       throw new Error('no getSubAdapter available')
     }
-    const adapter = await this.getSubAdapter({
-      ...getSnapshot(config),
-      type: 'BedTabixAdapter',
-    })
     return {
-      adapter: adapter.dataAdapter as BaseFeatureDataAdapter,
+      adapter: (
+        await this.getSubAdapter({
+          ...getSnapshot(this.config),
+          type: 'BedTabixAdapter',
+        })
+      ).dataAdapter as BaseFeatureDataAdapter,
     }
   }
   async setupPre2() {
@@ -86,7 +86,8 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
           const alignments = {} as Record<string, OrganismRecord>
 
           // eslint-disable-next-line @typescript-eslint/prefer-for-of
-          for (let j = 0; j < data.length; j++) {
+          const len = data.length
+          for (let j = 0; j < len; j++) {
             const elt = data[j]!
             const seq = elt.split(':')[5]!
             const ad = elt.split(':')
@@ -106,6 +107,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
             }
             if (assemblyName) {
               firstAssemblyNameFound = firstAssemblyNameFound || assemblyName
+
               alignments[assemblyName] = {
                 chr: last,
                 start: +ad[1]!,

package/src/MafTabixAdapter/configSchema.ts

@@ -63,7 +63,35 @@ const configSchema = ConfigurationSchema(
       },
     },
   },
-  { explicitlyTyped: true },
+  {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+      // populate from just snap.uri
+      return snap.uri
+        ? {
+            ...snap,
+            ...(snap.nhUri
+              ? {
+                  nhLocation: {
+                    uri: snap.nhUri,
+                    baseUri: snap.baseUri,
+                  },
+                }
+              : {}),
+            bedGzLocation: {
+              uri: snap.uri,
+              baseUri: snap.baseUri,
+            },
+            index: {
+              location: {
+                uri: `${snap.uri}.tbi`,
+                baseUri: snap.baseUri,
+              },
+            },
+          }
+        : snap
+    },
+  },
 )
 
 export default configSchema

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/ReactComponent.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/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