@jbrowse/plugin-alignments 1.7.4 → 1.7.7

package/dist/LinearPileupDisplay/configSchema.js

@@ -12,18 +12,16 @@ var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
 var _mobxStateTree = require("mobx-state-tree");
 
 function PileupConfigFactory(pluginManager) {
-  var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema;
-  var SvgFeatureRendererConfigSchema = pluginManager.getRendererType('SvgFeatureRenderer').configSchema; // modify config schema to take in a sub coverage display
+  var PileupRendererConfigSchema = pluginManager.getRendererType('PileupRenderer').configSchema; // modify config schema to take in a sub coverage display
 
   return (0, _configuration.ConfigurationSchema)('LinearPileupDisplay', {
     defaultRendering: {
       type: 'stringEnum',
-      model: _mobxStateTree.types.enumeration('Rendering', ['pileup', 'svg']),
+      model: _mobxStateTree.types.enumeration('Rendering', ['pileup']),
       defaultValue: 'pileup'
     },
     renderers: (0, _configuration.ConfigurationSchema)('RenderersConfiguration', {
-      PileupRenderer: PileupRendererConfigSchema,
-      SvgFeatureRenderer: SvgFeatureRendererConfigSchema
+      PileupRenderer: PileupRendererConfigSchema
     }),
     renderer: '',
     maxFeatureScreenDensity: {

package/dist/LinearPileupDisplay/model.d.ts

@@ -1,7 +1,7 @@
 /// <reference types="react" />
+import { Feature } from '@jbrowse/core/util';
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import { Instance } from 'mobx-state-tree';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
 import { LinearPileupDisplayConfigModel } from './configSchema';
 declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel) => import("mobx-state-tree").IModelType<{
@@ -174,7 +174,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
         headers?: Record<string, string> | undefined;
         signal?: AbortSignal | undefined;
         filters?: string[] | undefined;
-    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    }): Promise<{}>;
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;

package/dist/LinearPileupDisplay/model.js

@@ -177,7 +177,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
     return {
       afterAttach: function afterAttach() {
         (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-          var _getSession, rpcManager, sortedBy, colorBy, view, uniqueTagSet, uniqueModificationsSet, pos, refName, assemblyName, region;
+          var _getSession, rpcManager, view, sortedBy, colorBy, parentTrack, adapterConfig, rendererType, staticBlocks, bpPerPx, uniqueTagSet, adapter, pos, refName, assemblyName;
 
           return _regenerator.default.wrap(function _callee$(_context) {
             while (1) {
@@ -185,84 +185,88 @@ var stateModelFactory = function stateModelFactory(configSchema) {
                 case 0:
                   _context.prev = 0;
                   _getSession = (0, _util.getSession)(self), rpcManager = _getSession.rpcManager;
-                  sortedBy = self.sortedBy, colorBy = self.colorBy;
-                  view = (0, _util.getContainingView)(self); // continually generate the vc pairing, set and rerender if any
+                  view = (0, _util.getContainingView)(self);
+                  sortedBy = self.sortedBy, colorBy = self.colorBy, parentTrack = self.parentTrack, adapterConfig = self.adapterConfig, rendererType = self.rendererType;
+                  staticBlocks = view.staticBlocks, bpPerPx = view.bpPerPx; // continually generate the vc pairing, set and rerender if any
                   // new values seen
 
                   if (!(colorBy !== null && colorBy !== void 0 && colorBy.tag)) {
-                    _context.next = 9;
+                    _context.next = 10;
                     break;
                   }
 
-                  _context.next = 7;
-                  return (0, _shared.getUniqueTagValues)(self, colorBy, view.staticBlocks);
+                  _context.next = 8;
+                  return (0, _shared.getUniqueTagValues)(self, colorBy, staticBlocks);
 
-                case 7:
+                case 8:
                   uniqueTagSet = _context.sent;
                   self.updateColorTagMap(uniqueTagSet);
 
-                case 9:
+                case 10:
                   if (!((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications')) {
-                    _context.next = 14;
+                    _context.next = 17;
                     break;
                   }
 
-                  _context.next = 12;
-                  return (0, _shared.getUniqueModificationValues)(self, (0, _configuration.getConf)(self.parentTrack, ['adapter']), colorBy, view.staticBlocks);
+                  adapter = (0, _configuration.getConf)(parentTrack, ['adapter']);
+                  _context.t0 = self;
+                  _context.next = 15;
+                  return (0, _shared.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks);
 
-                case 12:
-                  uniqueModificationsSet = _context.sent;
-                  self.updateModificationColorMap(uniqueModificationsSet);
+                case 15:
+                  _context.t1 = _context.sent;
 
-                case 14:
+                  _context.t0.updateModificationColorMap.call(_context.t0, _context.t1);
+
+                case 17:
                   if (!sortedBy) {
-                    _context.next = 23;
+                    _context.next = 25;
                     break;
                   }
 
-                  pos = sortedBy.pos, refName = sortedBy.refName, assemblyName = sortedBy.assemblyName;
-                  region = {
-                    start: pos,
-                    end: pos + 1,
-                    refName: refName,
-                    assemblyName: assemblyName
-                  }; // render just the sorted region first
+                  pos = sortedBy.pos, refName = sortedBy.refName, assemblyName = sortedBy.assemblyName; // render just the sorted region first
 
-                  _context.next = 19;
+                  _context.next = 21;
                   return self.rendererType.renderInClient(rpcManager, _objectSpread({
                     assemblyName: assemblyName,
-                    regions: [region],
-                    adapterConfig: self.adapterConfig,
-                    rendererType: self.rendererType.name,
+                    regions: [{
+                      start: pos,
+                      end: pos + 1,
+                      refName: refName,
+                      assemblyName: assemblyName
+                    }],
+                    adapterConfig: adapterConfig,
+                    rendererType: rendererType.name,
                     sessionId: (0, _tracks.getRpcSessionId)(self),
+                    layoutId: view.id,
                     timeout: 1000000
                   }, self.renderProps()));
 
-                case 19:
+                case 21:
                   self.setReady(true);
-                  self.setCurrBpPerPx(view.bpPerPx);
-                  _context.next = 24;
+                  self.setCurrBpPerPx(bpPerPx);
+                  _context.next = 26;
                   break;
 
-                case 23:
+                case 25:
                   self.setReady(true);
 
-                case 24:
-                  _context.next = 30;
+                case 26:
+                  _context.next = 32;
                   break;
 
-                case 26:
-                  _context.prev = 26;
-                  _context.t0 = _context["catch"](0);
-                  console.error(_context.t0);
-                  self.setError(_context.t0);
+                case 28:
+                  _context.prev = 28;
+                  _context.t2 = _context["catch"](0);
+                  console.error(_context.t2);
+                  self.setError(_context.t2);
 
-                case 30:
+                case 32:
                 case "end":
                   return _context.stop();
               }
             }
-          }, _callee, null, [[0, 26]]);
+          }, _callee, null, [[0, 28]]);
         })), {
           delay: 1000
         }));
@@ -430,7 +434,129 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           colorTagMap: JSON.parse(JSON.stringify(colorTagMap)),
           modificationTagMap: JSON.parse(JSON.stringify(modificationTagMap)),
           showSoftClip: self.showSoftClipping,
-          config: self.rendererConfig
+          config: self.rendererConfig,
+          onFeatureClick: function onFeatureClick(_, featureId) {
+            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+              var session, rpcManager, f, sessionId, _ref3, feature;
+
+              return _regenerator.default.wrap(function _callee2$(_context2) {
+                while (1) {
+                  switch (_context2.prev = _context2.next) {
+                    case 0:
+                      session = (0, _util.getSession)(self);
+                      rpcManager = session.rpcManager;
+                      _context2.prev = 2;
+                      f = featureId || self.featureIdUnderMouse;
+
+                      if (f) {
+                        _context2.next = 8;
+                        break;
+                      }
+
+                      self.clearFeatureSelection();
+                      _context2.next = 14;
+                      break;
+
+                    case 8:
+                      sessionId = (0, _tracks.getRpcSessionId)(self);
+                      _context2.next = 11;
+                      return rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                        featureId: f,
+                        sessionId: sessionId,
+                        layoutId: (0, _util.getContainingView)(self).id,
+                        rendererType: 'PileupRenderer'
+                      });
+
+                    case 11:
+                      _ref3 = _context2.sent;
+                      feature = _ref3.feature;
+
+                      if (feature) {
+                        // @ts-ignore
+                        self.selectFeature(new _util.SimpleFeature(feature));
+                      }
+
+                    case 14:
+                      _context2.next = 20;
+                      break;
+
+                    case 16:
+                      _context2.prev = 16;
+                      _context2.t0 = _context2["catch"](2);
+                      console.error(_context2.t0);
+                      session.notify("".concat(_context2.t0));
+
+                    case 20:
+                    case "end":
+                      return _context2.stop();
+                  }
+                }
+              }, _callee2, null, [[2, 16]]);
+            }))();
+          },
+          onClick: function onClick() {
+            self.clearFeatureSelection();
+          },
+          // similar to click but opens a menu with further options
+          onFeatureContextMenu: function onFeatureContextMenu(_, featureId) {
+            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+              var session, rpcManager, f, sessionId, _ref4, feature;
+
+              return _regenerator.default.wrap(function _callee3$(_context3) {
+                while (1) {
+                  switch (_context3.prev = _context3.next) {
+                    case 0:
+                      session = (0, _util.getSession)(self);
+                      rpcManager = session.rpcManager;
+                      _context3.prev = 2;
+                      f = featureId || self.featureIdUnderMouse;
+
+                      if (f) {
+                        _context3.next = 8;
+                        break;
+                      }
+
+                      self.clearFeatureSelection();
+                      _context3.next = 14;
+                      break;
+
+                    case 8:
+                      sessionId = (0, _tracks.getRpcSessionId)(self);
+                      _context3.next = 11;
+                      return rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                        featureId: f,
+                        sessionId: sessionId,
+                        layoutId: (0, _util.getContainingView)(self).id,
+                        rendererType: 'PileupRenderer'
+                      });
+
+                    case 11:
+                      _ref4 = _context3.sent;
+                      feature = _ref4.feature;
+
+                      if (feature) {
+                        // @ts-ignore
+                        self.setContextMenuFeature(new _util.SimpleFeature(feature));
+                      }
+
+                    case 14:
+                      _context3.next = 20;
+                      break;
+
+                    case 16:
+                      _context3.prev = 16;
+                      _context3.t0 = _context3["catch"](2);
+                      console.error(_context3.t0);
+                      session.notify("".concat(_context3.t0));
+
+                    case 20:
+                    case "end":
+                      return _context3.stop();
+                  }
+                }
+              }, _callee3, null, [[2, 16]]);
+            }))();
+          }
         });
       },
       trackMenuItems: function trackMenuItems() {

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -177,7 +177,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         headers?: Record<string, string> | undefined;
         signal?: AbortSignal | undefined;
         filters?: string[] | undefined;
-    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    }): Promise<{}>;
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -102,7 +102,7 @@ export default class PileupRenderer extends BoxRendererType {
     layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
     fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
     render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<string, Feature>;
+        features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;
@@ -111,7 +111,7 @@ export default class PileupRenderer extends BoxRendererType {
         imageData?: undefined;
         html?: string | undefined;
     } | {
-        features: Map<string, Feature>;
+        features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;

package/dist/PileupRenderer/PileupRenderer.js

@@ -185,7 +185,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
         throw new Error("feature ".concat(feature.id(), " is not on the current region's reference sequence ").concat(region.refName));
       }
 
-      var topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx);
+      var topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx, feature);
 
       if (topPx === null) {
         return null;
@@ -809,7 +809,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           ctx.fillStyle = 'purple';
           var pos = leftPx + extraHorizontallyFlippedOffset;
           var len = +mismatch.base || mismatch.length;
-          var insW = Math.max(minSubfeatureWidth, Math.min(1.2, 1 / bpPerPx));
+          var insW = Math.max(minSubfeatureWidth / 2, Math.min(1.2, 1 / bpPerPx));
 
           if (len < 10) {
             ctx.fillRect(pos, topPx, insW, heightPx);
@@ -1187,7 +1187,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               case 23:
                 results = _context3.sent;
                 return _context3.abrupt("return", _objectSpread(_objectSpread(_objectSpread({}, results), res), {}, {
-                  features: features,
+                  features: new Map(),
                   layout: layout,
                   height: height,
                   width: width,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "1.7.4",
+  "version": "1.7.7",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -57,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "0a3e0c58055bbab8e3ab0270c139291b96eff403"
+  "gitHead": "2c26e04ae942c380bf2f5b79ef7a49cc32b7bfed"
 }

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,