@jbrowse/plugin-config 2.1.7 → 2.2.1

package/src/FromConfigAdapter/fromConfig.ts

@@ -0,0 +1,22 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config FromConfigAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'FromConfigAdapter',
+  {
+    /**
+     * #slot
+     */
+    features: {
+      type: 'frozen',
+      defaultValue: [],
+    },
+  },
+  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
+)
+
+export default configSchema

package/src/FromConfigAdapter/fromConfigRegions.ts

@@ -0,0 +1,24 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+/**
+ * #config FromConfigRegionsAdapter
+ * used for specifying refNames+sizes of an assembly
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const regionsConfigSchema = ConfigurationSchema(
+  'FromConfigRegionsAdapter',
+  {
+    /**
+     * #slot
+     */
+    features: {
+      type: 'frozen',
+      defaultValue: [],
+    },
+  },
+  {
+    explicitlyTyped: true,
+    implicitIdentifier: 'adapterId',
+  },
+)
+export default regionsConfigSchema

package/src/FromConfigAdapter/fromConfigSequence.ts

@@ -0,0 +1,21 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+/**
+ * #config FromConfigSequenceAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const sequenceConfigSchema = ConfigurationSchema(
+  'FromConfigSequenceAdapter',
+  {
+    /**
+     * #slot
+     */
+    features: {
+      type: 'frozen',
+      defaultValue: [],
+    },
+  },
+  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
+)
+
+export default sequenceConfigSchema

package/src/FromConfigAdapter/index.ts

@@ -1,8 +1,6 @@
 export { default as AdapterClass } from './FromConfigAdapter'
 export { default as RegionsAdapterClass } from './FromConfigRegionsAdapter'
 export { default as SequenceAdapterClass } from './FromConfigSequenceAdapter'
-export {
-  configSchema,
-  regionsConfigSchema,
-  sequenceConfigSchema,
-} from './configSchema'
+export { default as configSchema } from './fromConfig'
+export { default as regionsConfigSchema } from './fromConfig'
+export { default as sequenceConfigSchema } from './fromConfigSequence'

package/src/RefNameAliasAdapter/configSchema.ts

@@ -1,8 +1,18 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
-export default ConfigurationSchema(
+/**
+ * #config RefNameAliasAdapter
+ * can read "chromAliases" type files from UCSC or any tab separated file of
+ * refName aliases
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const RefNameAliasAdapter = ConfigurationSchema(
   'RefNameAliasAdapter',
   {
+    /**
+     * #slot
+     */
     location: {
       type: 'fileLocation',
       defaultValue: {
@@ -10,6 +20,11 @@ export default ConfigurationSchema(
         locationType: 'UriLocation',
       },
     },
+    /**
+     * #slot
+     * by default, the "ref names that match the fasta" are assumed to be in the
+     * first column (0), change this variable if needed
+     */
     refNameColumn: {
       type: 'number',
       defaultValue: 0,
@@ -17,3 +32,5 @@ export default ConfigurationSchema(
   },
   { explicitlyTyped: true },
 )
+
+export default RefNameAliasAdapter

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

@@ -1,9 +1,9 @@
 // Jest Snapshot v1, https://goo.gl/fbAQLP
 
-exports[`Config editing adds config editor widget 1`] = `Object {}`;
+exports[`Config editing adds config editor widget 1`] = `{}`;
 
 exports[`Config editing creates proper FromConfigAdapter 1`] = `
-Object {
+{
   "adapterId": "testFromConfigAdapterId",
   "type": "FromConfigAdapter",
 }

package/dist/FromConfigAdapter/configSchema.d.ts

@@ -1,3 +0,0 @@
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare const regionsConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare const sequenceConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/dist/FromConfigAdapter/configSchema.js

@@ -1,35 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.sequenceConfigSchema = exports.regionsConfigSchema = exports.configSchema = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('FromConfigAdapter', {
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-exports.regionsConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfigRegionsAdapter', {
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-exports.sequenceConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfigSequenceAdapter', {
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-//# sourceMappingURL=configSchema.js.map

package/dist/FromConfigAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/FromConfigAdapter/configSchema.d.ts

@@ -1,3 +0,0 @@
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare const regionsConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export declare const sequenceConfigSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/FromConfigAdapter/configSchema.js

@@ -1,32 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-export const configSchema = ConfigurationSchema('FromConfigAdapter', {
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-export const regionsConfigSchema = ConfigurationSchema('FromConfigRegionsAdapter', {
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-export const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
-    features: {
-        type: 'frozen',
-        defaultValue: [],
-    },
-    featureClass: {
-        type: 'string',
-        defaultValue: 'SimpleFeature',
-    },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
-//# sourceMappingURL=configSchema.js.map

package/esm/FromConfigAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/src/FromConfigAdapter/configSchema.ts

@@ -1,46 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-export const configSchema = ConfigurationSchema(
-  'FromConfigAdapter',
-  {
-    features: {
-      type: 'frozen',
-      defaultValue: [],
-    },
-    featureClass: {
-      type: 'string',
-      defaultValue: 'SimpleFeature',
-    },
-  },
-  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
-)
-
-export const regionsConfigSchema = ConfigurationSchema(
-  'FromConfigRegionsAdapter',
-  {
-    features: {
-      type: 'frozen',
-      defaultValue: [],
-    },
-    featureClass: {
-      type: 'string',
-      defaultValue: 'SimpleFeature',
-    },
-  },
-  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
-)
-
-export const sequenceConfigSchema = ConfigurationSchema(
-  'FromConfigSequenceAdapter',
-  {
-    features: {
-      type: 'frozen',
-      defaultValue: [],
-    },
-    featureClass: {
-      type: 'string',
-      defaultValue: 'SimpleFeature',
-    },
-  },
-  { explicitlyTyped: true, implicitIdentifier: 'adapterId' },
-)