@jbrowse/plugin-variants 2.1.6 → 2.2.0

package/src/StructuralVariantChordRenderer/configSchema.ts

@@ -0,0 +1,42 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+/**
+ * #config StructuralVariantChordRenderer
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'StructuralVariantChordRenderer',
+  {
+    /**
+     * #slot
+     */
+    strokeColor: {
+      type: 'color',
+      description: 'the line color of each arc',
+      defaultValue: 'rgba(255,133,0,0.32)',
+      contextVariable: ['feature'],
+    },
+    /**
+     * #slot
+     */
+    strokeColorSelected: {
+      type: 'color',
+      description: 'the line color of an arc that has been selected',
+      defaultValue: 'black',
+      contextVariable: ['feature'],
+    },
+    /**
+     * #slot
+     */
+    strokeColorHover: {
+      type: 'color',
+      description:
+        'the line color of an arc that is being hovered over with the mouse',
+      defaultValue: '#555',
+      contextVariable: ['feature'],
+    },
+  },
+  { explicitlyTyped: true },
+)
+
+export default configSchema

package/src/StructuralVariantChordRenderer/index.ts

@@ -1,41 +1,18 @@
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import PluginManager from '@jbrowse/core/PluginManager'
-
+import configSchema from './configSchema'
 import ReactComponent from './ReactComponent'
 
 const ChordRendererConfigF = (pluginManager: PluginManager) => {
-  const configSchema = ConfigurationSchema(
-    'StructuralVariantChordRenderer',
-    {
-      strokeColor: {
-        type: 'color',
-        description: 'the line color of each arc',
-        defaultValue: 'rgba(255,133,0,0.32)',
-        contextVariable: ['feature'],
-      },
-      strokeColorSelected: {
-        type: 'color',
-        description: 'the line color of an arc that has been selected',
-        defaultValue: 'black',
-        contextVariable: ['feature'],
-      },
-      strokeColorHover: {
-        type: 'color',
-        description:
-          'the line color of an arc that is being hovered over with the mouse',
-        defaultValue: '#555',
-        contextVariable: ['feature'],
-      },
-    },
-    { explicitlyTyped: true },
+  pluginManager.addRendererType(
+    () =>
+      new ChordRendererType({
+        name: 'StructuralVariantChordRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+      }),
   )
-  return new ChordRendererType({
-    name: 'StructuralVariantChordRenderer',
-    ReactComponent,
-    configSchema,
-    pluginManager,
-  })
 }
 
 export default ChordRendererConfigF

package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap

@@ -29,7 +29,7 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
       >
         <svg
           aria-hidden="true"
-          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium tss-rb1zhf-expandIcon css-i4bv87-MuiSvgIcon-root"
+          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-125qixp-MuiSvgIcon-root-expandIcon"
           data-testid="ExpandMoreIcon"
           focusable="false"
           viewBox="0 0 24 24"
@@ -55,7 +55,7 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
             role="region"
           >
             <div
-              class="MuiAccordionDetails-root tss-1g973hk-expansionPanelDetails css-15v22id-MuiAccordionDetails-root"
+              class="MuiAccordionDetails-root css-rqrb7m-MuiAccordionDetails-root-expansionPanelDetails"
             >
               <p
                 class="MuiTypography-root MuiTypography-body1 css-ahj2mt-MuiTypography-root"
@@ -63,15 +63,15 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 Core details
               </p>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                 >
                   Position
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     ctgA:177..177 
@@ -79,15 +79,15 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                 >
                   Name
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     rs123
@@ -95,15 +95,15 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                 >
                   Length
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     1
@@ -119,17 +119,17 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 Attributes
               </p>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
                   aria-label="reference base(s): Each base must be one of A,C,G,T,N (case insensitive)."
-                  class="tss-1qe2j6j-fieldDescription-fieldName"
+                  class="css-1qe2j6j-fieldDescription-fieldName"
                   data-mui-internal-clone-element="true"
                 >
                   REF
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     A
@@ -137,17 +137,17 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
                   aria-label="alternate base(s): Comma-separated list of alternate non-reference alleles"
-                  class="tss-1qe2j6j-fieldDescription-fieldName"
+                  class="css-1qe2j6j-fieldDescription-fieldName"
                   data-mui-internal-clone-element="true"
                 >
                   ALT
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     &lt;TRA&gt;
@@ -155,17 +155,17 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
                   aria-label="quality: Phred-scaled quality score for the assertion made in ALT"
-                  class="tss-1qe2j6j-fieldDescription-fieldName"
+                  class="css-1qe2j6j-fieldDescription-fieldName"
                   data-mui-internal-clone-element="true"
                 >
                   QUAL
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     10.4
@@ -173,16 +173,16 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 62px;"
                 >
                   INFO.MQ
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     5
@@ -190,7 +190,7 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                 </div>
               </div>
               <div
-                class="tss-1upvn7b-container2"
+                class="css-1upvn7b-container2"
               >
                 <button
                   class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
@@ -203,7 +203,7 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
                   />
                 </button>
                 <div
-                  class="MuiFormControl-root tss-1x17dzq-formControl css-1nrlq1o-MuiFormControl-root"
+                  class="MuiFormControl-root css-147opmv-MuiFormControl-root-formControl"
                 >
                   <button
                     class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"

package/src/VariantTrack/configSchema.ts

@@ -0,0 +1,24 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+/**
+ * #config VariantTrack
+ * Mostly similar to feature track, but has `ChordDisplayType` registered to it,
+ * and custom feature details in `LinearVariantDisplay`
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = (pluginManager: PluginManager) =>
+  ConfigurationSchema(
+    'VariantTrack',
+    {},
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+    },
+  )
+
+export default configSchema

package/src/VariantTrack/index.ts

@@ -1,26 +1,15 @@
 import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
+import configSchemaF from './configSchema'
 
-export default (pluginManager: PluginManager) => {
-  pluginManager.addTrackType(() => {
-    const configSchema = ConfigurationSchema(
-      'VariantTrack',
-      {},
-      { baseConfiguration: createBaseTrackConfig(pluginManager) },
-    )
+export default (pm: PluginManager) => {
+  pm.addTrackType(() => {
+    const configSchema = configSchemaF(pm)
     return new TrackType({
       name: 'VariantTrack',
       configSchema,
-      stateModel: createBaseTrackModel(
-        pluginManager,
-        'VariantTrack',
-        configSchema,
-      ),
+      stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
     })
   })
 }

package/src/VcfAdapter/configSchema.ts

@@ -1,8 +1,16 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config VcfAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const VcfAdapter = ConfigurationSchema(
   'VcfAdapter',
   {
+    /**
+     * #slot
+     */
     vcfLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },
@@ -10,3 +18,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default VcfAdapter

package/src/VcfTabixAdapter/configSchema.ts

@@ -1,19 +1,33 @@
 import { types } from 'mobx-state-tree'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config VcfTabixAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const VcfTabixAdapter = ConfigurationSchema(
   'VcfTabixAdapter',
   {
+    /**
+     * #slot
+     */
     vcfGzLocation: {
       type: 'fileLocation',
       defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('VcfIndex', {
+      /**
+       * #slot index.indexType
+       */
       indexType: {
         model: types.enumeration('IndexType', ['TBI', 'CSI']),
         type: 'stringEnum',
         defaultValue: 'TBI',
       },
+      /**
+       * #slot index.location
+       */
       location: {
         type: 'fileLocation',
         defaultValue: {
@@ -25,3 +39,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default VcfTabixAdapter

package/src/index.ts

@@ -4,9 +4,9 @@ import ExtensionPointsF from './extensionPoints'
 import VariantTrackF from './VariantTrack'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import ChordVariantDisplay from './ChordVariantDisplay'
+import ChordVariantDisplayF from './ChordVariantDisplay'
 import LinearVariantDisplayF from './LinearVariantDisplay'
-import StructuralVariantChordRendererFactory from './StructuralVariantChordRenderer'
+import StructuralVariantChordRendererF from './StructuralVariantChordRenderer'
 import VariantFeatureWidgetF from './VariantFeatureWidget'
 
 export default class VariantsPlugin extends Plugin {
@@ -19,14 +19,8 @@ export default class VariantsPlugin extends Plugin {
     VariantTrackF(pluginManager)
     ExtensionPointsF(pluginManager)
     LinearVariantDisplayF(pluginManager)
-
-    pluginManager.addRendererType(() =>
-      pluginManager.jbrequire(StructuralVariantChordRendererFactory),
-    )
-
-    pluginManager.addDisplayType(() =>
-      pluginManager.jbrequire(ChordVariantDisplay),
-    )
+    StructuralVariantChordRendererF(pluginManager)
+    ChordVariantDisplayF(pluginManager)
   }
 }