jbrowse-plugin-mafviewer 1.2.0 → 1.2.2

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.2.0",
+  "version": "1.2.2",
   "license": "MIT",
   "name": "jbrowse-plugin-mafviewer",
   "keywords": [
@@ -66,6 +66,7 @@
     "buffer": "^6.0.3",
     "d3-array": "^3.2.4",
     "d3-hierarchy": "^3.1.2",
+    "fast-deep-equal": "^3.1.3",
     "generic-filehandle2": "^1.0.0",
     "long": "^5.2.3"
   }

package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts

@@ -17,9 +17,9 @@ import VirtualOffset from './virtualOffset'
 import parseNewick from '../parseNewick'
 import { normalize } from '../util'
 import { parseRowInstructions } from './rowInstructions'
+import { parseLineByLine } from './util'
 
 import type { IndexData, OrganismRecord } from './types'
-import { parseLineByLine } from './util'
 interface Entry {
   type: string
   row: number
@@ -101,7 +101,6 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
 
   getFeatures(query: Region, opts?: BaseOptions) {
     const { statusCallback = () => {} } = opts || {}
-    console.log(query.start, query.end, 'wtf')
     return ObservableCreate<Feature>(async observer => {
       try {
         const byteRanges = await this.setup()

package/src/LinearMafDisplay/components/ColorLegend.tsx

@@ -43,10 +43,10 @@ const ColorLegend = observer(function ({
           ? samples.map((sample, idx) => (
               <text
                 key={`${sample.id}-${idx}`}
-                y={idx * rowHeight + rowHeight / 2}
                 dominantBaseline="middle"
-                x={2}
                 fontSize={svgFontSize}
+                x={2}
+                y={idx * rowHeight + rowHeight / 2}
               >
                 {sample.label}
               </text>

package/src/LinearMafDisplay/components/RectBg.tsx

@@ -7,7 +7,7 @@ const RectBg = (props: {
   height: number
   color?: string
 }) => {
-  const { color = 'rgb(255,255,255,0.8)' } = props
+  const { color = 'rgb(255,255,255,0.5)' } = props
   return <rect {...props} fill={color} />
 }
 

package/src/LinearMafDisplay/stateModel.ts

@@ -3,9 +3,9 @@ import { getEnv, getSession } from '@jbrowse/core/util'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
 import { ascending } from 'd3-array'
 import { cluster, hierarchy } from 'd3-hierarchy'
+import deepEqual from 'fast-deep-equal'
 import { autorun } from 'mobx'
 import { addDisposer, isAlive, types } from 'mobx-state-tree'
-import deepEqual from 'fast-deep-equal'
 
 import SetRowHeightDialog from './components/SetRowHeight'
 import { maxLength, setBrLength } from './types'
@@ -244,7 +244,7 @@ export default function stateModelFactory(
           return {
             ...s,
             notReady:
-              !self.volatileSamples || !self.volatileTree || super.notReady,
+              (!self.volatileSamples && !self.volatileTree) || super.notReady,
             config: rendererConfig,
             samples,
             rowHeight,
@@ -260,16 +260,36 @@ export default function stateModelFactory(
           return [
             ...superTrackMenuItems(),
             {
-              label: 'Set row height',
-              onClick: () => {
-                getSession(self).queueDialog(handleClose => [
-                  SetRowHeightDialog,
-                  {
-                    model: self,
-                    handleClose,
+              label: 'Set feature height',
+              type: 'subMenu',
+              subMenu: [
+                {
+                  label: 'Normal',
+                  onClick: () => {
+                    self.setRowHeight(15)
+                    self.setRowProportion(0.8)
                   },
-                ])
-              },
+                },
+                {
+                  label: 'Compact',
+                  onClick: () => {
+                    self.setRowHeight(8)
+                    self.setRowProportion(0.9)
+                  },
+                },
+                {
+                  label: 'Manually set height',
+                  onClick: () => {
+                    getSession(self).queueDialog(handleClose => [
+                      SetRowHeightDialog,
+                      {
+                        model: self,
+                        handleClose,
+                      },
+                    ])
+                  },
+                },
+              ],
             },
             {
               label: 'Show all letters',

package/src/LinearMafRenderer/makeImageData.ts

@@ -40,7 +40,6 @@ export function makeImageData({
     samples,
     rowProportion,
     features,
-    statusCallback,
   } = renderArgs
   const region = regions[0]!
   const canvasWidth = (region.end - region.start) / bpPerPx

package/src/LinearMafRenderer/util.ts

@@ -1,4 +1,5 @@
 import { measureText } from '@jbrowse/core/util'
+
 import type { Theme } from '@mui/material'
 
 export function getContrastBaseMap(theme: Theme) {

package/src/MafTabixAdapter/MafTabixAdapter.ts

@@ -85,6 +85,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
           const data = (feature.get('field5') as string).split(',')
           const alignments = {} as Record<string, OrganismRecord>
 
+          // eslint-disable-next-line @typescript-eslint/prefer-for-of
           for (let j = 0; j < data.length; j++) {
             const elt = data[j]!
             const seq = elt.split(':')[5]!
@@ -116,17 +117,6 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
             }
           }
 
-          console.log(
-            {
-              alignments,
-              firstAssemblyNameFound,
-              refAssemblyName,
-              q: query.assemblyName,
-            },
-            alignments[refAssemblyName],
-            alignments[query.assemblyName],
-            alignments[firstAssemblyNameFound],
-          )
           observer.next(
             new SimpleFeature({
               id: feature.id(),