@jbrowse/plugin-sv-inspector 2.6.1

package/src/SvInspectorView/models/adhocFeatureUtils.js

@@ -0,0 +1,152 @@
+// this file contains the rather verbose functions for
+// creating features from CSV/TSV lines
+import { parseLocString } from '@jbrowse/core/util'
+
+export function makeAdHocFeature(
+  columns,
+  columnsAlreadyUsedInLocations,
+  row,
+  loc1,
+  loc2,
+  rowNumber,
+) {
+  // load all the other data in the row into an `otherData` object
+  const otherData = {}
+  columns.forEach((column, columnNumber) => {
+    if (columnsAlreadyUsedInLocations.includes(columnNumber)) {
+      return
+    }
+    let { text } = row.cells[columnNumber]
+    if (column.dataType.type === 'Number') {
+      text = parseFloat(text)
+    }
+    otherData[column.name] = text
+  })
+
+  // make the final feature data out of otherData + the parsed locations
+  return {
+    ...otherData,
+    uniqueId: `sv-inspector-adhoc-${rowNumber}`,
+    refName: loc1.refName,
+    start: loc1.start,
+    end: loc1.end,
+    mate: {
+      refName: loc2.refName,
+      start: loc2.start,
+      end: loc2.end,
+    },
+  }
+}
+
+export function makeAdHocSvFeatureFromTwoLocations(
+  columns,
+  locationColumnNumbers,
+  row,
+  rowNumber,
+  isValidRefName,
+) {
+  // use the first two locations we found (first according to *displayed* order)
+  const loc1 = parseLocString(
+    row.cells[locationColumnNumbers[0]].text,
+    isValidRefName,
+  )
+  const loc2 = parseLocString(
+    row.cells[locationColumnNumbers[1]].text,
+    isValidRefName,
+  )
+
+  const columnsAlreadyUsedInLocations = [
+    locationColumnNumbers[0],
+    locationColumnNumbers[1],
+  ]
+
+  return makeAdHocFeature(
+    columns,
+    columnsAlreadyUsedInLocations,
+    row,
+    loc1,
+    loc2,
+    rowNumber,
+  )
+}
+
+export function makeAdHocSvFeatureFromTwoRefStartEndSets(
+  columns,
+  locRefColumnNumbers,
+  locStartColumnNumbers,
+  locEndColumnNumbers,
+  row,
+  rowNumber,
+) {
+  const textOf = colno => row.cells[colno].text
+  const loc1 = {
+    refName: textOf(locRefColumnNumbers[0]),
+    start: parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
+    end: parseInt(textOf(locEndColumnNumbers[0]), 10),
+  }
+  const loc2 = {
+    refName: textOf(locRefColumnNumbers[1]),
+    start: parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
+    end: parseInt(textOf(locEndColumnNumbers[1]), 10),
+  }
+  const columnsAlreadyUsedInLocations = [
+    locRefColumnNumbers[0],
+    locStartColumnNumbers[0],
+    locEndColumnNumbers[0],
+    locRefColumnNumbers[1],
+    locStartColumnNumbers[1],
+    locEndColumnNumbers[1],
+  ]
+  return makeAdHocFeature(
+    columns,
+    columnsAlreadyUsedInLocations,
+    row,
+    loc1,
+    loc2,
+    rowNumber,
+  )
+}
+
+// makes a feature data object (passed as `data` to a SimpleFeature constructor)
+// out of table row if the row has 2 location columns. undefined if not
+export function makeAdHocSvFeature(sheet, rowNumber, row, isValidRefName) {
+  const { columns, columnDisplayOrder } = sheet
+  const columnTypes = {}
+  columnDisplayOrder.forEach(columnNumber => {
+    const columnDefinition = columns[columnNumber]
+    if (!columnTypes[columnDefinition.dataType.type]) {
+      columnTypes[columnDefinition.dataType.type] = []
+    }
+    columnTypes[columnDefinition.dataType.type].push(columnNumber)
+  })
+  const locationColumnNumbers = columnTypes.LocString || []
+  const locStartColumnNumbers = columnTypes.LocStart || []
+  const locEndColumnNumbers = columnTypes.LocEnd || []
+  const locRefColumnNumbers = columnTypes.LocRef || []
+
+  // if we have 2 or more columns of type location, make a feature from them
+  if (locationColumnNumbers.length >= 2) {
+    return makeAdHocSvFeatureFromTwoLocations(
+      columns,
+      locationColumnNumbers,
+      row,
+      rowNumber,
+      isValidRefName,
+    )
+  }
+  if (
+    locRefColumnNumbers.length >= 2 &&
+    locStartColumnNumbers.length >= 2 &&
+    locEndColumnNumbers.length >= 2
+  ) {
+    return makeAdHocSvFeatureFromTwoRefStartEndSets(
+      columns,
+      locRefColumnNumbers,
+      locStartColumnNumbers,
+      locEndColumnNumbers,
+      row,
+      rowNumber,
+    )
+  }
+  return undefined
+}

package/src/SvInspectorView/models/breakpointSplitViewFromTableRow.js

@@ -0,0 +1,84 @@
+import { SimpleFeature, getEnv, getSession } from '@jbrowse/core/util'
+import { makeAdHocSvFeature } from './adhocFeatureUtils'
+
+export function getFeatureForRow(session, spreadsheetView, row, rowNumber) {
+  return (
+    row.extendedData?.vcfFeature ||
+    row.extendedData?.feature ||
+    makeAdHocSvFeature(
+      spreadsheetView.spreadsheet,
+      rowNumber,
+      row,
+      session.assemblyManager.isValidRefName,
+    )
+  )
+}
+
+export function breakpointSplitViewSnapshotFromTableRow(
+  svInspectorView,
+  spreadsheetView,
+  spreadsheet,
+  row,
+  rowNumber,
+) {
+  const { pluginManager } = getEnv(svInspectorView)
+  const session = getSession(spreadsheetView)
+  const featureData = getFeatureForRow(session, spreadsheet, row, rowNumber)
+
+  if (featureData) {
+    const feature = new SimpleFeature(featureData)
+    session.setSelection(feature)
+    return pluginManager
+      .getViewType('BreakpointSplitView')
+      .snapshotFromBreakendFeature(feature, svInspectorView.circularView)
+  }
+  return undefined
+}
+
+export function openBreakpointSplitViewFromTableRow(
+  svInspectorView,
+  spreadsheetView,
+  spreadsheet,
+  row,
+  rowNumber,
+) {
+  const viewSnapshot = breakpointSplitViewSnapshotFromTableRow(
+    svInspectorView,
+    spreadsheetView,
+    spreadsheet,
+    row,
+    rowNumber,
+  )
+  if (viewSnapshot) {
+    // try to center the offsetPx
+    const { circularView } = svInspectorView
+    viewSnapshot.views[0].offsetPx -= circularView.width / 2 + 100
+    viewSnapshot.views[1].offsetPx -= circularView.width / 2 + 100
+
+    const session = getSession(spreadsheetView)
+    session.addView('BreakpointSplitView', viewSnapshot)
+  }
+}
+
+export function canOpenBreakpointSplitViewFromTableRow(
+  svInspectorView,
+  spreadsheetView,
+  spreadsheet,
+  row,
+  rowNumber,
+) {
+  try {
+    return Boolean(
+      breakpointSplitViewSnapshotFromTableRow(
+        svInspectorView,
+        spreadsheetView,
+        spreadsheet,
+        row,
+        rowNumber,
+      ),
+    )
+  } catch (e) {
+    console.error('Unable to open breakpoint split view from table row', e)
+    return false
+  }
+}

package/src/index.ts

@@ -0,0 +1,34 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import Plugin from '@jbrowse/core/Plugin'
+import {
+  AbstractSessionModel,
+  isAbstractMenuManager,
+} from '@jbrowse/core/util/types'
+
+// icons
+import TableChartIcon from '@mui/icons-material/TableChart'
+
+// locals
+import SvInspectorViewF from './SvInspectorView'
+import LaunchSvInspectorViewF from './LaunchSvInspectorView'
+
+export default class SvInspectorViewPlugin extends Plugin {
+  name = 'SvInspectorViewPlugin'
+
+  install(pluginManager: PluginManager) {
+    SvInspectorViewF(pluginManager)
+    LaunchSvInspectorViewF(pluginManager)
+  }
+
+  configure(pluginManager: PluginManager) {
+    if (isAbstractMenuManager(pluginManager.rootModel)) {
+      pluginManager.rootModel.appendToSubMenu(['Add'], {
+        label: 'SV inspector',
+        icon: TableChartIcon,
+        onClick: (session: AbstractSessionModel) => {
+          session.addView('SvInspectorView', {})
+        },
+      })
+    }
+  }
+}