jbrowse-plugin-msaview 2.2.1 → 2.2.3

package/src/MsaViewPanel/model.ts

@@ -65,6 +65,10 @@ export default function stateModelFactory() {
          * #property
          */
         blastParams: types.frozen<BlastParams | undefined>(),
+        /**
+         * #property
+         */
+        querySeqName: 'QUERY',
 
         /**
          * #property
@@ -198,7 +202,46 @@ export default function stateModelFactory() {
       setBlastParams(args?: BlastParams) {
         self.blastParams = args
       },
+      /**
+       * #action
+       */
+      handleMsaClick(coord: number) {
+        const { connectedView, zoomToBaseLevel } = self
+        const { assemblyManager } = getSession(self)
+        const r2 = msaCoordToGenomeCoord({ model: self, coord })
+
+        if (!r2 || !connectedView) {
+          return
+        }
+
+        if (zoomToBaseLevel) {
+          connectedView.navTo(r2)
+        } else {
+          const r =
+            assemblyManager
+              .get(connectedView.assemblyNames[0]!)
+              ?.getCanonicalRefName(r2.refName) ?? r2.refName
+          connectedView.centerAt(r2.start, r)
+        }
+      },
     }))
+    .actions(self => {
+      // store reference to the original action from react-msaview
+      const superSetMouseClickPos = self.setMouseClickPos
+
+      return {
+        /**
+         * #action
+         * overrides base setMouseClickPos to trigger navigation
+         */
+        setMouseClickPos(col?: number, row?: number) {
+          superSetMouseClickPos(col, row)
+          if (col !== undefined) {
+            self.handleMsaClick(col)
+          }
+        },
+      }
+    })
 
     .views(self => ({
       /**
@@ -241,12 +284,12 @@ export default function stateModelFactory() {
             if (self.blastParams) {
               try {
                 self.setProgress('Submitting query')
+                self.setError(undefined)
                 const data = await doLaunchBlast({
-                  self: self as JBrowsePluginMsaViewModel,
+                  self,
                 })
                 self.setData(data)
                 self.setBlastParams(undefined)
-                self.setProgress('')
               } catch (e) {
                 self.setError(e)
                 console.error(e)
@@ -273,33 +316,6 @@ export default function stateModelFactory() {
             self.setConnectedHighlights([r1, r2].filter(f => !!f))
           }),
         )
-
-        // nav to genome position after click
-        addDisposer(
-          self,
-          autorun(() => {
-            const { connectedView, zoomToBaseLevel, mouseClickCol } = self
-            const { assemblyManager } = getSession(self)
-            const r2 =
-              mouseClickCol === undefined
-                ? undefined
-                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
-
-            if (!r2 || !connectedView) {
-              return
-            }
-
-            if (zoomToBaseLevel) {
-              connectedView.navTo(r2)
-            } else {
-              const r =
-                assemblyManager
-                  .get(connectedView.assemblyNames[0]!)
-                  ?.getCanonicalRefName(r2.refName) ?? r2.refName
-              connectedView.centerAt(r2.start, r)
-            }
-          }),
-        )
       },
     }))
 }

package/src/MsaViewPanel/msaCoordToGenomeCoord.ts

@@ -1,28 +1,53 @@
-import { JBrowsePluginMsaViewModel } from './model'
+/**
+ * Convert gapped MSA column coordinate to ungapped sequence coordinate
+ * This is the inverse of ungappedCoordMap
+ */
+function gappedToUngappedCoord(seq: string, gappedPos: number): number {
+  let ungappedPos = 0
+  for (let i = 0; i < gappedPos && i < seq.length; i++) {
+    if (seq[i] !== '-') {
+      ungappedPos++
+    }
+  }
+  return ungappedPos
+}
 
 export function msaCoordToGenomeCoord({
   model,
   coord: mouseCol,
 }: {
-  model: JBrowsePluginMsaViewModel
+  model: { querySeqName: string; transcriptToMsaMap: any; rows: string[][] }
   coord: number
 }) {
-  const { transcriptToMsaMap } = model
+  const { querySeqName, transcriptToMsaMap } = model
   if (transcriptToMsaMap === undefined) {
-    return
-  }
+    return undefined
+  } else {
+    // Get the query sequence
+    const queryRow = model.rows.find(f => f[0] === querySeqName)
+    const querySeq = queryRow?.[1]
+    if (!querySeq) {
+      return undefined
+    }
 
-  const c = mouseCol
-  const k1 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c) || 0
-  const k2 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c + 1) || 0
-  const { refName, p2g } = transcriptToMsaMap
-  const s = p2g[k1]
-  const e = p2g[k2]
-  return s !== undefined && e !== undefined
-    ? {
-        refName,
-        start: Math.min(s, e),
-        end: Math.max(s, e),
-      }
-    : undefined
+    // Check if the position in the query sequence is a gap
+    if (querySeq[mouseCol] === '-') {
+      return undefined
+    }
+
+    // Convert gapped MSA column to ungapped sequence coordinate
+    const ungappedPos = gappedToUngappedCoord(querySeq, mouseCol)
+
+    // Use the ungapped position to look up in the p2g map
+    const { refName, p2g } = transcriptToMsaMap
+    const s = p2g[ungappedPos]
+    const e = p2g[ungappedPos + 1]
+    return s !== undefined && e !== undefined
+      ? {
+          refName,
+          start: Math.min(s, e),
+          end: Math.max(s, e),
+        }
+      : undefined
+  }
 }

package/src/MsaViewPanel/util.ts

@@ -5,8 +5,8 @@ export function checkHovered(hovered: unknown): hovered is {
   hoverPosition: { coord: number; refName: string }
 } {
   return (
-    !!hovered &&
-    typeof hovered == 'object' &&
+    typeof hovered === 'object' &&
+    hovered !== null &&
     'hoverFeature' in hovered &&
     'hoverPosition' in hovered
   )

package/src/index.ts

@@ -1,10 +1,13 @@
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { AbstractSessionModel, isAbstractMenuManager } from '@jbrowse/core/util'
 import GridOn from '@mui/icons-material/GridOn'
+import { types } from 'mobx-state-tree'
 
 import { version } from '../package.json'
 import AddHighlightModelF from './AddHighlightModel'
+import BgzipFastaMsaAdapterF from './BgzipFastaMsaAdapter'
 import LaunchMsaViewF from './LaunchMsaView'
 import MsaViewF from './MsaViewPanel'
 
@@ -16,6 +19,7 @@ export default class MsaViewPlugin extends Plugin {
     MsaViewF(pluginManager)
     LaunchMsaViewF(pluginManager)
     AddHighlightModelF(pluginManager)
+    BgzipFastaMsaAdapterF(pluginManager)
   }
 
   configure(pluginManager: PluginManager) {
@@ -29,4 +33,31 @@ export default class MsaViewPlugin extends Plugin {
       })
     }
   }
+
+  // @ts-expect-error
+  rootConfigurationSchema(pluginManager: PluginManager) {
+    return {
+      msa: ConfigurationSchema('MSA', {
+        datasets: types.maybe(
+          types.array(
+            ConfigurationSchema('MSAEntry', {
+              datasetId: {
+                type: 'string',
+                defaultValue: '',
+              },
+              description: {
+                type: 'string',
+                defaultValue: '',
+              },
+              name: {
+                type: 'string',
+                defaultValue: '',
+              },
+              adapter: pluginManager.pluggableConfigSchemaType('adapter'),
+            }),
+          ),
+        ),
+      }),
+    }
+  }
 }

package/src/utils/fetch.ts

@@ -1,4 +1,6 @@
-export async function myfetch(url: string, args?: RequestInit) {
+import { ungzip } from 'pako'
+
+export async function handleFetch(url: string, args?: RequestInit) {
   const response = await fetch(url, args)
 
   if (!response.ok) {
@@ -11,15 +13,41 @@ export async function myfetch(url: string, args?: RequestInit) {
 }
 
 export async function textfetch(url: string, args?: RequestInit) {
-  const response = await myfetch(url, args)
+  const response = await handleFetch(url, args)
   return response.text()
 }
 
 export async function jsonfetch<T>(url: string, args?: RequestInit) {
-  const response = await myfetch(url, args)
+  const response = await handleFetch(url, args)
   return response.json() as Promise<T>
 }
 
 export function timeout(time: number) {
   return new Promise(res => setTimeout(res, time))
 }
+
+export async function fetchWithLocalStorageCache<T>(
+  key: string,
+  fetchFn: () => Promise<T>,
+): Promise<T> {
+  const cachedData = localStorage.getItem(key)
+
+  if (cachedData) {
+    try {
+      return JSON.parse(cachedData) as T
+    } catch (error) {
+      console.error(`Error parsing cached data for ${key}:`, error)
+      // Continue to fetch fresh data if parsing fails
+      localStorage.removeItem(key)
+    }
+  }
+
+  const data = await fetchFn()
+  localStorage.setItem(key, JSON.stringify(data))
+  return data
+}
+
+export async function unzipfetch(url: string, arg?: RequestInit) {
+  const res = await handleFetch(url, arg)
+  return ungzip(await res.arrayBuffer(), { to: 'string' })
+}

package/dist/ExternalLink.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"ExternalLink.js","sourceRoot":"","sources":["../src/ExternalLink.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,aAAa,MAAM,+BAA+B,CAAA;AACzD,OAAO,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAIpC,MAAM,CAAC,OAAO,UAAU,YAAY,CAAC,KAAgB;IACnD,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,KAAK,CAAA;IACnC,OAAO,CACL,oBAAC,IAAI,OAAK,IAAI,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY;QAC7C,QAAQ;;QAAE,oBAAC,aAAa,IAAC,QAAQ,EAAC,OAAO,GAAG,CACxC,CACR,CAAA;AACH,CAAC"}

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.d.ts

@@ -1 +0,0 @@
-export declare function fetchGeneList(): Promise<string[]>;

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.js

@@ -1,12 +0,0 @@
-export async function fetchGeneList() {
-    const res = await fetch('https://jbrowse.org/demos/msaview/knownCanonical/list.txt');
-    if (!res.ok) {
-        throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`);
-    }
-    const result = await res.text();
-    return result
-        .split('\n')
-        .map(f => f.trim())
-        .filter(f => !!f);
-}
-//# sourceMappingURL=fetchGeneList.js.map

package/dist/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"fetchGeneList.js","sourceRoot":"","sources":["../../../../src/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,KAAK,UAAU,aAAa;IACjC,MAAM,GAAG,GAAG,MAAM,KAAK,CACrB,2DAA2D,CAC5D,CAAA;IACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,kBAAkB,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IACzE,CAAC;IACD,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;IAC/B,OAAO,MAAM;SACV,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrB,CAAC"}

package/dist/ReadOnlyTextField2.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"ReadOnlyTextField2.js","sourceRoot":"","sources":["../src/ReadOnlyTextField2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,UAAU,MAAM,cAAc,CAAA;AAErC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAEF,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EAAE,KAAK,EAAqB;IACrE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,CACL,oBAAC,UAAU,IACT,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,KAAK,EACZ,SAAS,EAAE;YACT,KAAK,EAAE;gBACL,QAAQ,EAAE,IAAI;gBACd,OAAO,EAAE;oBACP,KAAK,EAAE,OAAO,CAAC,YAAY;iBAC5B;aACF;SACF,GACD,CACH,CAAA;AACH,CAAC"}

package/dist/TextField2.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"TextField2.js","sourceRoot":"","sources":["../src/TextField2.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAIzC,SAAS,UAAU,CAAC,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAkB;IACvD,OAAO,CACL;QACE,oBAAC,SAAS,OAAK,IAAI,IAAG,QAAQ,CAAa,CACvC,CACP,CAAA;AACH,CAAC;AAED,eAAe,UAAU,CAAA"}

package/src/LaunchMsaView/components/PreLoadedMSA/fetchGeneList.ts

@@ -1,13 +0,0 @@
-export async function fetchGeneList() {
-  const res = await fetch(
-    'https://jbrowse.org/demos/msaview/knownCanonical/list.txt',
-  )
-  if (!res.ok) {
-    throw new Error(`HTTP ${res.status} fetching list ${await res.text()}`)
-  }
-  const result = await res.text()
-  return result
-    .split('\n')
-    .map(f => f.trim())
-    .filter(f => !!f)
-}