@jbrowse/plugin-alignments 2.2.0 → 2.2.1

package/dist/LinearPileupDisplay/model.js

@@ -57,6 +57,7 @@ const rendererTypes = new Map([
 ]);
 /**
  * #stateModel LinearPileupDisplay
+ * extends `BaseLinearDisplay`
  */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
@@ -111,6 +112,9 @@ function stateModelFactory(configSchema) {
             tag: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
             extra: mobx_state_tree_1.types.frozen(),
         })),
+        /**
+         * #property
+         */
         filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.model({
             flagInclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
             flagExclude: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1540),
@@ -122,6 +126,7 @@ function stateModelFactory(configSchema) {
         colorTagMap: mobx_1.observable.map({}),
         modificationTagMap: mobx_1.observable.map({}),
         featureUnderMouseVolatile: undefined,
+        currSortBpPerPx: 0,
         ready: false,
     }))
         .actions(self => ({
@@ -131,6 +136,12 @@ function stateModelFactory(configSchema) {
         setReady(flag) {
             self.ready = flag;
         },
+        /**
+         * #action
+         */
+        setCurrSortBpPerPx(n) {
+            self.currSortBpPerPx = n;
+        },
         /**
          * #action
          */
@@ -248,7 +259,7 @@ function stateModelFactory(configSchema) {
                             ...self.renderProps(),
                         });
                         self.setReady(true);
-                        self.setCurrBpPerPx(bpPerPx);
+                        self.setCurrSortBpPerPx(bpPerPx);
                     }
                     else {
                         self.setReady(true);
@@ -260,6 +271,8 @@ function stateModelFactory(configSchema) {
                 }
             }, { delay: 1000 }));
             // autorun synchronizes featureUnderMouse with featureIdUnderMouse
+            // asynchronously. this is needed due to how we do not serialize all
+            // features from the BAM/CRAM over the rpc
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
                 var _a;
                 const session = (0, util_1.getSession)(self);
@@ -479,13 +492,13 @@ function stateModelFactory(configSchema) {
              */
             renderProps() {
                 const view = (0, util_1.getContainingView)(self);
-                const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currBpPerPx, ready, } = self;
+                const { colorTagMap, modificationTagMap, sortedBy, colorBy, filterBy, rpcDriverName, currSortBpPerPx, ready, } = self;
                 const superProps = superRenderProps();
                 return {
                     ...superProps,
                     notReady: superProps.notReady ||
                         !ready ||
-                        (sortedBy && currBpPerPx !== view.bpPerPx),
+                        (sortedBy && currSortBpPerPx !== view.bpPerPx),
                     rpcDriverName,
                     displayModel: self,
                     sortedBy,
@@ -604,39 +617,27 @@ function stateModelFactory(configSchema) {
                         subMenu: [
                             {
                                 label: 'Normal',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'normal' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'normal' }),
                             },
                             {
                                 label: 'Mapping quality',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'mappingQuality' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'mappingQuality' }),
                             },
                             {
                                 label: 'Strand',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'strand' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'strand' }),
                             },
                             {
                                 label: 'Pair orientation',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'pairOrientation' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'pairOrientation' }),
                             },
                             {
                                 label: 'Per-base quality',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'perBaseQuality' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'perBaseQuality' }),
                             },
                             {
                                 label: 'Per-base lettering',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'perBaseLettering' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'perBaseLettering' }),
                             },
                             {
                                 label: 'Modifications or methylation',
@@ -649,15 +650,11 @@ function stateModelFactory(configSchema) {
                             },
                             {
                                 label: 'Insert size',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'insertSize' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'insertSize' }),
                             },
                             {
                                 label: 'Stranded paired-end',
-                                onClick: () => {
-                                    self.setColorScheme({ type: 'reverseTemplate' });
-                                },
+                                onClick: () => self.setColorScheme({ type: 'reverseTemplate' }),
                             },
                             {
                                 label: 'Color by tag...',
@@ -702,9 +699,7 @@ function stateModelFactory(configSchema) {
                         label: 'Fade mismatches by quality',
                         type: 'checkbox',
                         checked: self.mismatchAlphaSetting,
-                        onClick: () => {
-                            self.toggleMismatchAlpha();
-                        },
+                        onClick: () => self.toggleMismatchAlpha(),
                     },
                 ];
             },

package/dist/LinearPileupDisplay/model.js.map

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package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { Feature } from '@jbrowse/core/util/simpleFeature';
-declare type Coord = [number, number];
+type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
     model: {
         featureUnderMouse: Feature;

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

@@ -457,5 +457,5 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         onClick: () => void;
     })[];
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
+export type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
 export default stateModelFactory;

package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,6 +1,6 @@
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { Region } from '@jbrowse/core/util';
 import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { Region } from '@jbrowse/core/util/types';
 import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
 export declare class PileupGetGlobalValueForTag extends RpcMethodType {
     name: string;

package/dist/PileupRPC/rpcMethods.js

@@ -4,10 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PileupGetVisibleModifications = exports.PileupGetGlobalValueForTag = void 0;
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 const util_1 = require("@jbrowse/core/util");
 const operators_1 = require("rxjs/operators");
+// locals
 const util_2 = require("../util");
 const MismatchParser_1 = require("../BamAdapter/MismatchParser");
 class PileupGetGlobalValueForTag extends RpcMethodType_1.default {
@@ -26,9 +27,11 @@ class PileupGetGlobalValueForTag extends RpcMethodType_1.default {
         return super.serializeArguments(renamedArgs, rpcDriverClassName);
     }
     async execute(args, rpcDriverClassName) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions, tag } = deserializedArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const pm = this.pluginManager;
+        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions, tag } = deArgs;
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig))
+            .dataAdapter;
         const features = dataAdapter.getFeaturesInMultipleRegions(regions);
         const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
         const uniqueValues = new Set();
@@ -59,9 +62,11 @@ class PileupGetVisibleModifications extends RpcMethodType_1.default {
         return super.serializeArguments(renamedArgs, rpcDriverClassName);
     }
     async execute(args, rpcDriverClassName) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions } = deserializedArgs;
-        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
+        const pm = this.pluginManager;
+        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { adapterConfig, sessionId, regions } = deArgs;
+        const dataAdapter = (await (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig))
+            .dataAdapter;
         const features = dataAdapter.getFeaturesInMultipleRegions(regions);
         const featuresArray = await features.pipe((0, operators_1.toArray)()).toPromise();
         const uniqueValues = new Set();

package/dist/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -11,7 +11,7 @@ export interface PileupLayoutSessionProps {
     sortedBy: unknown;
     showSoftClip: unknown;
 }
-declare type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
+type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
 interface CachedPileupLayout {
     layout: MyMultiLayout;
     config: AnyConfigurationModel;

package/dist/PileupRenderer/PileupRenderer.js

@@ -107,7 +107,7 @@ class PileupRenderer extends BoxRendererType_1.default {
         if (showSoftClip) {
             const mismatches = feature.get('mismatches');
             const seq = feature.get('seq');
-            if (seq) {
+            if (seq && mismatches) {
                 for (let i = 0; i < mismatches.length; i += 1) {
                     const { type, start, cliplen = 0 } = mismatches[i];
                     if (type === 'softclip') {
@@ -543,6 +543,9 @@ class PileupRenderer extends BoxRendererType_1.default {
         const extraHorizontallyFlippedOffset = region.reversed
             ? 1 / bpPerPx + 1
             : -1;
+        if (!mismatches) {
+            return;
+        }
         // two pass rendering: first pass, draw all the mismatches except wide
         // insertion markers
         for (let i = 0; i < mismatches.length; i += 1) {
@@ -671,34 +674,35 @@ class PileupRenderer extends BoxRendererType_1.default {
             deletion: '#808080', // gray
         };
         // Display all bases softclipped off in lightened colors
-        if (seq) {
-            mismatches
-                .filter(mismatch => mismatch.type === 'softclip')
-                .forEach(mismatch => {
-                const softClipLength = mismatch.cliplen || 0;
-                const s = feature.get('start');
-                const softClipStart = mismatch.start === 0 ? s - softClipLength : s + mismatch.start;
-                for (let k = 0; k < softClipLength; k += 1) {
-                    const base = seq.charAt(k + mismatch.start);
-                    // If softclip length+start is longer than sequence, no need to
-                    // continue showing base
-                    if (!base) {
-                        return;
-                    }
-                    const [softClipLeftPx, softClipRightPx] = (0, util_1.bpSpanPx)(softClipStart + k, softClipStart + k + 1, region, bpPerPx);
-                    const softClipWidthPx = Math.max(minFeatWidth, Math.abs(softClipLeftPx - softClipRightPx));
-                    // Black accounts for IUPAC ambiguity code bases such as N that
-                    // show in soft clipping
-                    const baseColor = colorForBase[base] || '#000000';
-                    ctx.fillStyle = baseColor;
-                    fillRect(ctx, softClipLeftPx, topPx, softClipWidthPx, heightPx, canvasWidth);
-                    if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) {
-                        ctx.fillStyle = theme.palette.getContrastText(baseColor);
-                        ctx.fillText(base, softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1, topPx + heightPx);
-                    }
-                }
-            });
+        if (!(seq && mismatches)) {
+            return;
         }
+        mismatches
+            .filter(mismatch => mismatch.type === 'softclip')
+            .forEach(mismatch => {
+            const len = mismatch.cliplen || 0;
+            const s = feature.get('start');
+            const start = mismatch.start === 0 ? s - len : s + mismatch.start;
+            for (let k = 0; k < len; k += 1) {
+                const base = seq.charAt(k + mismatch.start);
+                // If softclip length+start is longer than sequence, no need to
+                // continue showing base
+                if (!base) {
+                    return;
+                }
+                const [leftPx, rightPx] = (0, util_1.bpSpanPx)(start + k, start + k + 1, region, bpPerPx);
+                const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
+                // Black accounts for IUPAC ambiguity code bases such as N that
+                // show in soft clipping
+                const baseColor = colorForBase[base] || '#000000';
+                ctx.fillStyle = baseColor;
+                fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
+                if (widthPx >= charWidth && heightPx >= charHeight - 5) {
+                    ctx.fillStyle = theme.palette.getContrastText(baseColor);
+                    ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
+                }
+            }
+        });
     }
     makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
         const { layout, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;

package/dist/PileupRenderer/PileupRenderer.js.map

@@ -1 +1 @@
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package/dist/PileupRenderer/index.js

@@ -7,12 +7,14 @@ const PileupRenderer_1 = __importDefault(require("./PileupRenderer"));
 const PileupRendering_1 = __importDefault(require("./components/PileupRendering"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 function register(pluginManager) {
-    pluginManager.addRendererType(() => new PileupRenderer_1.default({
-        name: 'PileupRenderer',
-        ReactComponent: PileupRendering_1.default,
-        configSchema: configSchema_1.default,
-        pluginManager,
-    }));
+    pluginManager.addRendererType(() => {
+        return new PileupRenderer_1.default({
+            name: 'PileupRenderer',
+            ReactComponent: PileupRendering_1.default,
+            configSchema: configSchema_1.default,
+            pluginManager,
+        });
+    });
 }
 exports.default = register;
 //# sourceMappingURL=index.js.map

package/dist/PileupRenderer/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":";;;;;AACA,sEAA6C;AAC7C,mFAAyD;AACzD,kEAAyC;AAEzC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,wBAAc,CAAC;QACjB,IAAI,EAAE,gBAAgB;QACtB,cAAc,EAAd,yBAAc;QACd,YAAY,EAAZ,sBAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC;AAVD,2BAUC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":";;;;;AACA,sEAA6C;AAC7C,mFAAyD;AACzD,kEAAyC;AAEzC,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE;QACjC,OAAO,IAAI,wBAAc,CAAC;YACxB,IAAI,EAAE,gBAAgB;YACtB,cAAc,EAAd,yBAAc;YACd,YAAY,EAAZ,sBAAY;YACZ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AATD,2BASC"}

package/dist/SNPCoverageAdapter/configSchema.d.ts

@@ -1,3 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const SNPCoverageAdapter: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default SNPCoverageAdapter;
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/dist/SNPCoverageAdapter/configSchema.js

@@ -5,12 +5,15 @@ const configuration_1 = require("@jbrowse/core/configuration");
  * #config SNPCoverageAdapter
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const SNPCoverageAdapter = (pluginManager) => (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
+const configSchema = (0, configuration_1.ConfigurationSchema)('SNPCoverageAdapter', {
     /**
      * #slot
      * normally refers to a BAM or CRAM adapter
      */
-    subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
+    subadapter: {
+        type: 'frozen',
+        defaultValue: null,
+    },
 }, { explicitlyTyped: true });
-exports.default = SNPCoverageAdapter;
+exports.default = configSchema;
 //# sourceMappingURL=configSchema.js.map

package/dist/SNPCoverageAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,oBAAoB,EACpB;IACE;;;OAGG;IACH,UAAU,EAAE;QACV,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,IAAI;KACnB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AAED,kBAAe,YAAY,CAAA"}