@jbrowse/plugin-alignments 2.2.0 → 2.2.1

package/src/PileupRenderer/{PileupRenderer.tsx → PileupRenderer.ts}

@@ -178,9 +178,9 @@ export default class PileupRenderer extends BoxRendererType {
 
     // Expand the start and end of feature when softclipping enabled
     if (showSoftClip) {
-      const mismatches = feature.get('mismatches') as Mismatch[]
+      const mismatches = feature.get('mismatches') as Mismatch[] | undefined
       const seq = feature.get('seq') as string
-      if (seq) {
+      if (seq && mismatches) {
         for (let i = 0; i < mismatches.length; i += 1) {
           const { type, start, cliplen = 0 } = mismatches[i]
           if (type === 'softclip') {
@@ -849,7 +849,7 @@ export default class PileupRenderer extends BoxRendererType {
 
     const pxPerBp = Math.min(1 / bpPerPx, 2)
     const w = Math.max(minSubfeatureWidth, pxPerBp)
-    const mismatches: Mismatch[] = feature.get('mismatches')
+    const mismatches = feature.get('mismatches') as Mismatch[] | undefined
     const heightLim = charHeight - 2
 
     // extraHorizontallyFlippedOffset is used to draw interbase items, which
@@ -858,6 +858,10 @@ export default class PileupRenderer extends BoxRendererType {
       ? 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) {
@@ -1052,7 +1056,7 @@ export default class PileupRenderer extends BoxRendererType {
     const { regions, bpPerPx } = renderArgs
     const [region] = regions
     const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')
-    const mismatches: Mismatch[] = feature.get('mismatches')
+    const mismatches = feature.get('mismatches') as Mismatch[] | undefined
     const seq = feature.get('seq')
     const { charWidth, charHeight } = this.getCharWidthHeight()
     const { bases } = theme.palette
@@ -1065,59 +1069,49 @@ export default class PileupRenderer extends BoxRendererType {
     }
 
     // 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] = bpSpanPx(
-              softClipStart + k,
-              softClipStart + k + 1,
-              region,
-              bpPerPx,
-            )
-            const softClipWidthPx = Math.max(
-              minFeatWidth,
-              Math.abs(softClipLeftPx - softClipRightPx),
-            )
+    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
+          }
 
-            // 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,
-            )
+          const [leftPx, rightPx] = bpSpanPx(
+            start + k,
+            start + k + 1,
+            region,
+            bpPerPx,
+          )
+          const widthPx = Math.max(minFeatWidth, rightPx - leftPx)
 
-            if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) {
-              ctx.fillStyle = theme.palette.getContrastText(baseColor)
-              ctx.fillText(
-                base,
-                softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1,
-                topPx + heightPx,
-              )
-            }
+          // 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({

package/src/PileupRenderer/index.ts

@@ -4,13 +4,12 @@ import ReactComponent from './components/PileupRendering'
 import configSchema from './configSchema'
 
 export default function register(pluginManager: PluginManager) {
-  pluginManager.addRendererType(
-    () =>
-      new PileupRenderer({
-        name: 'PileupRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-      }),
-  )
+  pluginManager.addRendererType(() => {
+    return new PileupRenderer({
+      name: 'PileupRenderer',
+      ReactComponent,
+      configSchema,
+      pluginManager,
+    })
+  })
 }

package/src/SNPCoverageAdapter/configSchema.ts

@@ -1,22 +1,23 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import PluginManager from '@jbrowse/core/PluginManager'
 
 /**
  * #config SNPCoverageAdapter
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
-const SNPCoverageAdapter = (pluginManager: PluginManager) =>
-  ConfigurationSchema(
-    'SNPCoverageAdapter',
-    {
-      /**
-       * #slot
-       * normally refers to a BAM or CRAM adapter
-       */
-      subadapter: pluginManager.pluggableConfigSchemaType('adapter'),
+const configSchema = ConfigurationSchema(
+  'SNPCoverageAdapter',
+  {
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+      type: 'frozen',
+      defaultValue: null,
     },
-    { explicitlyTyped: true },
-  )
+  },
+  { explicitlyTyped: true },
+)
 
-export default SNPCoverageAdapter
+export default configSchema

package/src/SNPCoverageAdapter/index.ts

@@ -1,23 +1,22 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchemaFactory from './configSchema'
+import configSchema from './configSchema'
 import { capabilities } from './SNPCoverageAdapter'
 
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'SNPCoverageAdapter',
-        adapterMetadata: {
-          category: null,
-          displayName: null,
-          hiddenFromGUI: true,
-          description: null,
-        },
-        getAdapterClass: () =>
-          import('./SNPCoverageAdapter').then(r => r.default),
-        configSchema: configSchemaFactory(pluginManager),
-        adapterCapabilities: capabilities,
-      }),
-  )
+export default function (pluginManager: PluginManager) {
+  pluginManager.addAdapterType(() => {
+    return new AdapterType({
+      name: 'SNPCoverageAdapter',
+      adapterMetadata: {
+        category: null,
+        displayName: null,
+        hiddenFromGUI: true,
+        description: null,
+      },
+      getAdapterClass: () =>
+        import('./SNPCoverageAdapter').then(r => r.default),
+      configSchema,
+      adapterCapabilities: capabilities,
+    })
+  })
 }

package/src/__snapshots__/index.test.ts.snap

@@ -1,3 +1,3 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`plugin in a stock JBrowse 1`] = `Object {}`;
+exports[`plugin in a stock JBrowse 1`] = `{}`;

package/src/index.ts

@@ -12,7 +12,10 @@ import SNPCoverageRendererF from './SNPCoverageRenderer'
 import PileupRendererF from './PileupRenderer'
 import LinearAlignmentsDisplayF from './LinearAlignmentsDisplay'
 import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay'
-import LinearPileupDisplayF from './LinearPileupDisplay'
+import LinearPileupDisplayF, {
+  linearPileupDisplayStateModelFactory,
+  linearPileupDisplayConfigSchemaFactory,
+} from './LinearPileupDisplay'
 import AlignmentsTrackF from './AlignmentsTrack'
 import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail'
 
@@ -28,9 +31,6 @@ import {
   TrackTypeGuesser,
 } from '@jbrowse/core/util/tracks'
 
-export { MismatchParser }
-export type { LinearPileupDisplayModel }
-
 export default class AlignmentsPlugin extends Plugin {
   name = 'AlignmentsPlugin'
 
@@ -125,3 +125,10 @@ export default class AlignmentsPlugin extends Plugin {
     )
   }
 }
+
+export {
+  linearPileupDisplayConfigSchemaFactory,
+  linearPileupDisplayStateModelFactory,
+  MismatchParser,
+}
+export type { LinearPileupDisplayModel }