@jbrowse/plugin-alignments 1.7.3 → 1.7.6

package/dist/util.d.ts

@@ -14,6 +14,6 @@ export declare const orientationTypes: {
         [key: string]: string;
     };
 };
-export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
+export declare function getColorWGBS(strand: number, base: string): "#888" | "#f00" | "#00f";
 export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
 export declare function shouldFetchReferenceSequence(type?: string): boolean;

package/dist/util.js

@@ -22,7 +22,7 @@ var _operators = require("rxjs/operators");
 
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
 // BAM does not
@@ -101,11 +101,11 @@ function fetchSequence(_x, _x2) {
 
 
 function _fetchSequence() {
-  _fetchSequence = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(region, adapter) {
+  _fetchSequence = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(region, adapter) {
     var _feats$;
 
     var end, originalRefName, refName, feats;
-    return _regenerator["default"].wrap(function _callee$(_context) {
+    return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.7.3",
+  "version": "1.7.6",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -33,15 +33,14 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
+    "@babel/runtime": "^7.17.9",
     "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.6.1",
     "@material-ui/icons": "^4.9.1",
-    "abortable-promise-cache": "^1.5.0",
     "color": "^3.1.2",
     "copy-to-clipboard": "^3.3.1",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle": "^2.2.2",
-    "json-stable-stringify": "^1.0.1"
+    "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -58,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
+  "gitHead": "dbd73f99714e395cf20877d5e05d26855857a0e3"
 }

package/src/LinearPileupDisplay/configSchema.ts

@@ -6,8 +6,6 @@ import PluginManager from '@jbrowse/core/PluginManager'
 function PileupConfigFactory(pluginManager: PluginManager) {
   const PileupRendererConfigSchema =
     pluginManager.getRendererType('PileupRenderer').configSchema
-  const SvgFeatureRendererConfigSchema =
-    pluginManager.getRendererType('SvgFeatureRenderer').configSchema
 
   // modify config schema to take in a sub coverage display
   return ConfigurationSchema(
@@ -15,12 +13,11 @@ function PileupConfigFactory(pluginManager: PluginManager) {
     {
       defaultRendering: {
         type: 'stringEnum',
-        model: types.enumeration('Rendering', ['pileup', 'svg']),
+        model: types.enumeration('Rendering', ['pileup']),
         defaultValue: 'pileup',
       },
       renderers: ConfigurationSchema('RenderersConfiguration', {
         PileupRenderer: PileupRendererConfigSchema,
-        SvgFeatureRenderer: SvgFeatureRendererConfigSchema,
       }),
       renderer: '',
       maxFeatureScreenDensity: {

package/src/LinearPileupDisplay/model.ts

@@ -9,6 +9,8 @@ import {
   getSession,
   isSessionModelWithWidgets,
   getContainingView,
+  SimpleFeature,
+  Feature,
 } from '@jbrowse/core/util'
 
 import VisibilityIcon from '@material-ui/icons/Visibility'
@@ -19,7 +21,6 @@ import {
 } from '@jbrowse/plugin-linear-genome-view'
 import { cast, types, addDisposer, getEnv, Instance } from 'mobx-state-tree'
 import copy from 'copy-to-clipboard'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
 import MenuOpenIcon from '@material-ui/icons/MenuOpen'
 import SortIcon from '@material-ui/icons/Sort'
 import PaletteIcon from '@material-ui/icons/Palette'
@@ -158,8 +159,15 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
             async () => {
               try {
                 const { rpcManager } = getSession(self)
-                const { sortedBy, colorBy } = self
                 const view = getContainingView(self) as LGV
+                const {
+                  sortedBy,
+                  colorBy,
+                  parentTrack,
+                  adapterConfig,
+                  rendererType,
+                } = self
+                const { staticBlocks, bpPerPx } = view
 
                 // continually generate the vc pairing, set and rerender if any
                 // new values seen
@@ -167,44 +175,46 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
                   const uniqueTagSet = await getUniqueTagValues(
                     self,
                     colorBy,
-                    view.staticBlocks,
+                    staticBlocks,
                   )
                   self.updateColorTagMap(uniqueTagSet)
                 }
 
                 if (colorBy?.type === 'modifications') {
-                  const uniqueModificationsSet =
+                  const adapter = getConf(parentTrack, ['adapter'])
+                  self.updateModificationColorMap(
                     await getUniqueModificationValues(
                       self,
-                      getConf(self.parentTrack, ['adapter']),
+                      adapter,
                       colorBy,
-                      view.staticBlocks,
-                    )
-                  self.updateModificationColorMap(uniqueModificationsSet)
+                      staticBlocks,
+                    ),
+                  )
                 }
 
                 if (sortedBy) {
                   const { pos, refName, assemblyName } = sortedBy
 
-                  const region = {
-                    start: pos,
-                    end: pos + 1,
-                    refName,
-                    assemblyName,
-                  }
-
                   // render just the sorted region first
                   await self.rendererType.renderInClient(rpcManager, {
                     assemblyName,
-                    regions: [region],
-                    adapterConfig: self.adapterConfig,
-                    rendererType: self.rendererType.name,
+                    regions: [
+                      {
+                        start: pos,
+                        end: pos + 1,
+                        refName,
+                        assemblyName,
+                      },
+                    ],
+                    adapterConfig: adapterConfig,
+                    rendererType: rendererType.name,
                     sessionId: getRpcSessionId(self),
+                    layoutId: view.id,
                     timeout: 1000000,
                     ...self.renderProps(),
                   })
                   self.setReady(true)
-                  self.setCurrBpPerPx(view.bpPerPx)
+                  self.setCurrBpPerPx(bpPerPx)
                 } else {
                   self.setReady(true)
                 }
@@ -404,6 +414,73 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
             modificationTagMap: JSON.parse(JSON.stringify(modificationTagMap)),
             showSoftClip: self.showSoftClipping,
             config: self.rendererConfig,
+            async onFeatureClick(_: unknown, featureId: string | undefined) {
+              const session = getSession(self)
+              const { rpcManager } = session
+              try {
+                const f = featureId || self.featureIdUnderMouse
+                if (!f) {
+                  self.clearFeatureSelection()
+                } else {
+                  const sessionId = getRpcSessionId(self)
+                  const { feature } = (await rpcManager.call(
+                    sessionId,
+                    'CoreGetFeatureDetails',
+                    {
+                      featureId: f,
+                      sessionId,
+                      layoutId: getContainingView(self).id,
+                      rendererType: 'PileupRenderer',
+                    },
+                  )) as { feature: unknown }
+
+                  if (feature) {
+                    // @ts-ignore
+                    self.selectFeature(new SimpleFeature(feature))
+                  }
+                }
+              } catch (e) {
+                console.error(e)
+                session.notify(`${e}`)
+              }
+            },
+            onClick() {
+              self.clearFeatureSelection()
+            },
+            // similar to click but opens a menu with further options
+            async onFeatureContextMenu(
+              _: unknown,
+              featureId: string | undefined,
+            ) {
+              const session = getSession(self)
+              const { rpcManager } = session
+              try {
+                const f = featureId || self.featureIdUnderMouse
+                if (!f) {
+                  self.clearFeatureSelection()
+                } else {
+                  const sessionId = getRpcSessionId(self)
+                  const { feature } = (await rpcManager.call(
+                    sessionId,
+                    'CoreGetFeatureDetails',
+                    {
+                      featureId: f,
+                      sessionId,
+                      layoutId: getContainingView(self).id,
+                      rendererType: 'PileupRenderer',
+                    },
+                  )) as { feature: unknown }
+
+                  if (feature) {
+                    // @ts-ignore
+                    self.setContextMenuFeature(new SimpleFeature(feature))
+                  }
+                }
+              } catch (e) {
+                console.error(e)
+                session.notify(`${e}`)
+              }
+            },
           }
         },
 

package/src/PileupRenderer/PileupRenderer.tsx

@@ -191,6 +191,7 @@ export default class PileupRenderer extends BoxRendererType {
       feature.get('start') - expansionBefore,
       feature.get('end') + expansionAfter,
       heightPx,
+      feature,
     )
     if (topPx === null) {
       return null
@@ -814,7 +815,10 @@ export default class PileupRenderer extends BoxRendererType {
         ctx.fillStyle = 'purple'
         const pos = leftPx + extraHorizontallyFlippedOffset
         const len = +mismatch.base || mismatch.length
-        const insW = Math.max(minSubfeatureWidth, Math.min(1.2, 1 / bpPerPx))
+        const insW = Math.max(
+          minSubfeatureWidth / 2,
+          Math.min(1.2, 1 / bpPerPx),
+        )
         if (len < 10) {
           ctx.fillRect(pos, topPx, insW, heightPx)
           if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
@@ -1117,7 +1121,7 @@ export default class PileupRenderer extends BoxRendererType {
     return {
       ...results,
       ...res,
-      features,
+      features: new Map(),
       layout,
       height,
       width,