@jbrowse/plugin-hic 2.6.1

package/src/LinearHicDisplay/index.ts

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+import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
+
+import configSchemaFactory from './configSchema'
+import stateModelFactory from './model'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addDisplayType(() => {
+    const configSchema = configSchemaFactory(pluginManager)
+    return new DisplayType({
+      name: 'LinearHicDisplay',
+      displayName: 'Hi-C contact matrix display',
+      configSchema,
+      stateModel: stateModelFactory(configSchema),
+      trackType: 'HicTrack',
+      viewType: 'LinearGenomeView',
+      ReactComponent: BaseLinearDisplayComponent,
+    })
+  })
+}

package/src/LinearHicDisplay/model.ts

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+import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
+import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view'
+import { types, getEnv } from 'mobx-state-tree'
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+
+/**
+ * #stateModel LinearHicDisplay
+ * #category display
+ * extends `BaseLinearDisplay`
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+export default (configSchema: AnyConfigurationSchemaType) =>
+  types
+    .compose(
+      'LinearHicDisplay',
+      BaseLinearDisplay,
+      types.model({
+        /**
+         * #property
+         */
+        type: types.literal('LinearHicDisplay'),
+        /**
+         * #property
+         */
+        configuration: ConfigurationReference(configSchema),
+        /**
+         * #property
+         */
+        resolution: types.optional(types.number, 1),
+      }),
+    )
+    .views(self => {
+      const { renderProps: superRenderProps } = self
+      return {
+        /**
+         * #getter
+         */
+        get blockType() {
+          return 'dynamicBlocks'
+        },
+        /**
+         * #getter
+         */
+        get rendererTypeName() {
+          return 'HicRenderer'
+        },
+        /**
+         * #method
+         */
+        renderProps() {
+          const config = self.rendererType.configSchema.create(
+            getConf(self, 'renderer') || {},
+            getEnv(self),
+          )
+
+          return {
+            ...superRenderProps(),
+            config,
+            rpcDriverName: self.rpcDriverName,
+            displayModel: self,
+            resolution: self.resolution,
+          }
+        },
+      }
+    })
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setResolution(n: number) {
+        self.resolution = n
+      },
+    }))
+    .views(self => {
+      const { trackMenuItems: superTrackMenuItems } = self
+      return {
+        /**
+         * #getter
+         */
+        trackMenuItems() {
+          return [
+            ...superTrackMenuItems(),
+            {
+              label: 'Resolution',
+              subMenu: [
+                {
+                  label: 'Finer resolution',
+                  onClick: () => {
+                    self.setResolution(self.resolution * 2)
+                  },
+                },
+                {
+                  label: 'Coarser resolution',
+                  onClick: () => {
+                    self.setResolution(self.resolution / 2)
+                  },
+                },
+              ],
+            },
+          ]
+        },
+      }
+    })

package/src/declare.d.ts

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+declare module '@jbrowse/core/util/offscreenCanvasPonyfill'
+declare module 'hic-straw'

package/src/index.ts

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+import Plugin from '@jbrowse/core/Plugin'
+import PluginManager from '@jbrowse/core/PluginManager'
+import { FileLocation } from '@jbrowse/core/util/types'
+import Color from 'color'
+import HicRendererF from './HicRenderer'
+import HicTrackF from './HicTrack'
+import LinearHicDisplayF from './LinearHicDisplay'
+import HicAdapterF from './HicAdapter'
+import {
+  AdapterGuesser,
+  getFileName,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
+
+export default class HicPlugin extends Plugin {
+  name = 'HicPlugin'
+
+  install(pluginManager: PluginManager) {
+    HicAdapterF(pluginManager)
+    HicRendererF(pluginManager)
+    HicTrackF(pluginManager)
+    LinearHicDisplayF(pluginManager)
+
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.hic/i
+          const adapterName = 'HicAdapter'
+          const fileName = getFileName(file)
+          const obj = {
+            type: adapterName,
+            hicLocation: file,
+          }
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj
+          } else if (adapterHint === adapterName) {
+            return obj
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+    pluginManager.addToExtensionPoint(
+      'Core-guessTrackTypeForLocation',
+      (trackTypeGuesser: TrackTypeGuesser) => {
+        return (adapterName: string) => {
+          if (adapterName === 'HicAdapter') {
+            return 'HicTrack'
+          }
+          return trackTypeGuesser(adapterName)
+        }
+      },
+    )
+  }
+
+  configure(pluginManager: PluginManager) {
+    pluginManager.jexl.addFunction('alpha', (color: Color, value: number) =>
+      color.alpha(value),
+    )
+    pluginManager.jexl.addFunction('hsl', (color: Color) => color.hsl())
+    pluginManager.jexl.addFunction('colorString', (color: Color) =>
+      color.string(),
+    )
+  }
+}