jbrowse-plugin-msaview 2.2.11 → 2.3.2

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -0,0 +1,299 @@
+import { getSession } from '@jbrowse/core/util'
+
+import { doLaunchBlast } from './doLaunchBlast'
+import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
+import {
+  cleanupOldData,
+  generateDataStoreId,
+  retrieveMsaData,
+  storeMsaData,
+} from './msaDataStore'
+import { gappedToUngappedPosition } from './structureConnection'
+import { getUniprotIdFromAlphaFoldUrl } from './util'
+
+import type { JBrowsePluginMsaViewModel } from './model'
+
+export function loadStoredData(self: JBrowsePluginMsaViewModel) {
+  const { dataStoreId, rows } = self
+  if (dataStoreId && rows.length === 0) {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        self.setLoadingStoredData(true)
+        const storedData = await retrieveMsaData(dataStoreId)
+        if (storedData) {
+          if (storedData.msa) {
+            self.setMSA(storedData.msa)
+          }
+          if (storedData.tree) {
+            self.setTree(storedData.tree)
+          }
+        }
+      } catch (e) {
+        console.error('Failed to load MSA data from IndexedDB:', e)
+      } finally {
+        self.setLoadingStoredData(false)
+      }
+    })()
+  }
+}
+
+export function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel) {
+  const { rows, dataStoreId } = self
+  if (rows.length > 0 && !dataStoreId) {
+    const hasFilehandle = !!(self.msaFilehandle ?? self.treeFilehandle)
+    if (hasFilehandle) {
+      return
+    }
+
+    const msaData = self.data.msa
+    const treeData = self.data.tree
+
+    if (msaData || treeData) {
+      // eslint-disable-next-line @typescript-eslint/no-floating-promises
+      ;(async () => {
+        try {
+          const newId = generateDataStoreId()
+          const success = await storeMsaData(newId, {
+            msa: msaData,
+            tree: treeData,
+            treeMetadata: self.data.treeMetadata,
+          })
+          if (success) {
+            self.setDataStoreId(newId)
+          }
+        } catch (e) {
+          console.error('Failed to store MSA data to IndexedDB:', e)
+        }
+      })()
+    }
+  }
+}
+
+export function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel) {
+  if (self.blastParams) {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        self.setProgress('Submitting query')
+        self.setError(undefined)
+        const data = await doLaunchBlast({ self })
+        self.setData(data)
+        self.setBlastParams(undefined)
+      } catch (e) {
+        self.setError(e)
+        console.error(e)
+      } finally {
+        self.setProgress('')
+      }
+    })()
+  }
+}
+
+export function processInit(self: JBrowsePluginMsaViewModel) {
+  const { init } = self
+  if (init) {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        self.setError(undefined)
+        const { msaData, msaUrl, treeData, treeUrl, querySeqName } = init
+
+        if (msaUrl) {
+          const id = getUniprotIdFromAlphaFoldUrl(msaUrl)
+          if (id) {
+            self.setUniprotId(id)
+            self.setQuerySeqName('query')
+          }
+        }
+
+        if (querySeqName) {
+          self.setQuerySeqName(querySeqName)
+        }
+
+        if (msaData) {
+          self.setMSA(msaData)
+        } else if (msaUrl) {
+          const response = await fetch(msaUrl)
+          if (!response.ok) {
+            throw new Error(`Failed to fetch MSA: ${response.status}`)
+          }
+          const data = await response.text()
+          self.setMSA(data)
+        }
+
+        if (treeData) {
+          self.setTree(treeData)
+        } else if (treeUrl) {
+          const response = await fetch(treeUrl)
+          if (!response.ok) {
+            throw new Error(`Failed to fetch tree: ${response.status}`)
+          }
+          const data = await response.text()
+          self.setTree(data)
+        }
+
+        self.setInit(undefined)
+      } catch (e) {
+        self.setError(e)
+        console.error(e)
+      }
+    })()
+  }
+}
+
+export function updateGenomeHighlights(self: JBrowsePluginMsaViewModel) {
+  const { mouseCol, mouseClickCol } = self
+  const r1 =
+    mouseCol === undefined
+      ? undefined
+      : msaCoordToGenomeCoord({ model: self, coord: mouseCol })
+  const r2 =
+    mouseClickCol === undefined
+      ? undefined
+      : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+
+  self.setConnectedHighlights([r1, r2].filter(f => !!f))
+}
+
+export function highlightConnectedStructures(self: JBrowsePluginMsaViewModel) {
+  const { mouseCol, connectedProteinViews } = self
+  if (connectedProteinViews.length === 0) {
+    return
+  }
+
+  for (const conn of connectedProteinViews) {
+    const structure = conn.proteinView?.structures?.[conn.structureIdx]
+    if (!structure) {
+      continue
+    }
+
+    if (mouseCol === undefined) {
+      structure.clearHighlightFromExternal?.()
+      continue
+    }
+
+    const seq = self.getSequenceByRowName(conn.msaRowName)
+    if (!seq) {
+      continue
+    }
+
+    const msaUngapped = gappedToUngappedPosition(seq, mouseCol)
+    if (msaUngapped === undefined) {
+      structure.clearHighlightFromExternal?.()
+      continue
+    }
+
+    const structurePos = conn.msaToStructure[msaUngapped]
+    if (structurePos === undefined) {
+      structure.clearHighlightFromExternal?.()
+    } else {
+      structure.highlightFromExternal?.(structurePos)
+    }
+  }
+}
+
+export function autoConnectStructures(self: JBrowsePluginMsaViewModel) {
+  const { views } = getSession(self)
+  const { connectedViewId, uniprotId, rows, connectedStructures } = self
+
+  if (!uniprotId || rows.length === 0) {
+    return
+  }
+
+  for (const view of views) {
+    const v = view as any
+    if (v.type !== 'ProteinView' || !v.structures) {
+      continue
+    }
+
+    for (
+      let structureIdx = 0;
+      structureIdx < v.structures.length;
+      structureIdx++
+    ) {
+      const structure = v.structures[structureIdx]
+
+      if (structure.connectedViewId !== connectedViewId) {
+        continue
+      }
+
+      if (structure.uniprotId !== uniprotId) {
+        continue
+      }
+
+      const alreadyConnected = connectedStructures.some(
+        c => c.proteinViewId === v.id && c.structureIdx === structureIdx,
+      )
+      if (alreadyConnected) {
+        continue
+      }
+
+      if (!structure.structureSequences?.[0]) {
+        continue
+      }
+
+      try {
+        self.connectToStructure(v.id, structureIdx)
+      } catch (e) {
+        console.error('Failed to auto-connect to ProteinView:', e)
+      }
+    }
+  }
+}
+
+export function observeProteinHighlights(self: JBrowsePluginMsaViewModel) {
+  const { views } = getSession(self)
+  const { connectedViewId, transcriptToMsaMap, querySeqName } = self
+
+  if (!connectedViewId || !transcriptToMsaMap) {
+    return
+  }
+
+  const columns: number[] = []
+
+  for (const view of views) {
+    const v = view as any
+    if (v.type !== 'ProteinView' || !v.structures) {
+      continue
+    }
+
+    for (const structure of v.structures) {
+      if (structure.connectedViewId !== connectedViewId) {
+        continue
+      }
+
+      const highlights = structure.hoverGenomeHighlights
+      if (!highlights || highlights.length === 0) {
+        continue
+      }
+
+      const { g2p } = transcriptToMsaMap
+      for (const highlight of highlights) {
+        for (let coord = highlight.start; coord < highlight.end; coord++) {
+          const proteinPos = g2p[coord]
+          if (proteinPos !== undefined) {
+            const col = self.seqPosToGlobalCol(querySeqName, proteinPos)
+            if (!columns.includes(col)) {
+              columns.push(col)
+            }
+          }
+        }
+      }
+    }
+  }
+
+  const visibleColumns = columns
+    .map(col => self.globalColToVisibleCol(col))
+    .filter((col): col is number => col !== undefined)
+
+  self.setHighlightedColumns(
+    visibleColumns.length > 0 ? visibleColumns : undefined,
+  )
+}
+
+export function runCleanup() {
+  cleanupOldData().catch((e: unknown) => {
+    console.error('Failed to cleanup old MSA data:', e)
+  })
+}