jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/dist/util/parseAssemblyName.test.js

@@ -0,0 +1,269 @@
+import { describe, expect, test } from 'vitest';
+import { parseAssemblyAndChr, parseAssemblyAndChrSimple, selectReferenceSequence, } from './parseAssemblyName';
+describe('parseAssemblyAndChr (MafTabix format)', () => {
+    test('no dot - entire string is assembly name', () => {
+        const result = parseAssemblyAndChr('hg38');
+        expect(result).toEqual({
+            assemblyName: 'hg38',
+            chr: '',
+        });
+    });
+    test('single dot - simple assembly.chr format', () => {
+        const result = parseAssemblyAndChr('hg38.chr1');
+        expect(result).toEqual({
+            assemblyName: 'hg38',
+            chr: 'chr1',
+        });
+    });
+    test('single dot - assembly.refName format with non-chr name', () => {
+        const result = parseAssemblyAndChr('mm10.scaffold_1');
+        expect(result).toEqual({
+            assemblyName: 'mm10',
+            chr: 'scaffold_1',
+        });
+    });
+    test('two dots with numeric version - assembly.version.chr format', () => {
+        const result = parseAssemblyAndChr('hg38.1.chr1');
+        expect(result).toEqual({
+            assemblyName: 'hg38.1',
+            chr: 'chr1',
+        });
+    });
+    test('two dots with multi-digit numeric version', () => {
+        const result = parseAssemblyAndChr('GRCh38.123.chrX');
+        expect(result).toEqual({
+            assemblyName: 'GRCh38.123',
+            chr: 'chrX',
+        });
+    });
+    test('two dots with non-numeric middle - assembly.chr.more format', () => {
+        const result = parseAssemblyAndChr('mm10.chr1.random');
+        expect(result).toEqual({
+            assemblyName: 'mm10',
+            chr: 'chr1.random',
+        });
+    });
+    test('two dots with non-numeric middle - chr_Un type naming', () => {
+        const result = parseAssemblyAndChr('hg38.chrUn_gl000220');
+        expect(result).toEqual({
+            assemblyName: 'hg38',
+            chr: 'chrUn_gl000220',
+        });
+    });
+    test('three dots with numeric version - assembly.version.chr.more format', () => {
+        const result = parseAssemblyAndChr('GRCh38.1.chr1.random');
+        expect(result).toEqual({
+            assemblyName: 'GRCh38.1',
+            chr: 'chr1.random',
+        });
+    });
+    test('empty string', () => {
+        const result = parseAssemblyAndChr('');
+        expect(result).toEqual({
+            assemblyName: '',
+            chr: '',
+        });
+    });
+    test('just a dot', () => {
+        const result = parseAssemblyAndChr('.');
+        expect(result).toEqual({
+            assemblyName: '',
+            chr: '',
+        });
+    });
+    test('leading dot', () => {
+        const result = parseAssemblyAndChr('.chr1');
+        expect(result).toEqual({
+            assemblyName: '',
+            chr: 'chr1',
+        });
+    });
+    test('trailing dot', () => {
+        const result = parseAssemblyAndChr('hg38.');
+        expect(result).toEqual({
+            assemblyName: 'hg38',
+            chr: '',
+        });
+    });
+    test('real world example - UCSC style', () => {
+        const result = parseAssemblyAndChr('hg19.chr6_ssto_hap7');
+        expect(result).toEqual({
+            assemblyName: 'hg19',
+            chr: 'chr6_ssto_hap7',
+        });
+    });
+    test('real world example - Ensembl style with numeric', () => {
+        const result = parseAssemblyAndChr('GRCh37.1.1');
+        expect(result).toEqual({
+            assemblyName: 'GRCh37.1',
+            chr: '1',
+        });
+    });
+});
+describe('parseAssemblyAndChrSimple (BigMaf format)', () => {
+    test('no dot - entire string is assembly name', () => {
+        const result = parseAssemblyAndChrSimple('hg38');
+        expect(result).toEqual({
+            assemblyName: 'hg38',
+            chr: '',
+        });
+    });
+    test('single dot - simple org.chr format', () => {
+        const result = parseAssemblyAndChrSimple('hg38.chr1');
+        expect(result).toEqual({
+            assemblyName: 'hg38',
+            chr: 'chr1',
+        });
+    });
+    test('multiple dots - only splits on first dot', () => {
+        const result = parseAssemblyAndChrSimple('mm10.chr1.random');
+        expect(result).toEqual({
+            assemblyName: 'mm10',
+            chr: 'chr1.random',
+        });
+    });
+    test('empty string', () => {
+        const result = parseAssemblyAndChrSimple('');
+        expect(result).toEqual({
+            assemblyName: '',
+            chr: '',
+        });
+    });
+});
+describe('selectReferenceSequence', () => {
+    const alignments = {
+        hg38: { seq: 'ACGTACGT' },
+        mm10: { seq: 'TGCATGCA' },
+        panTro6: { seq: 'GGGGGGGG' },
+    };
+    test('uses refAssemblyName when provided and exists', () => {
+        const result = selectReferenceSequence(alignments, 'mm10', 'hg38', 'panTro6');
+        expect(result).toBe('TGCATGCA');
+    });
+    test('falls back to queryAssemblyName when refAssemblyName is empty', () => {
+        const result = selectReferenceSequence(alignments, '', 'hg38', 'panTro6');
+        expect(result).toBe('ACGTACGT');
+    });
+    test('falls back to queryAssemblyName when refAssemblyName is undefined', () => {
+        const result = selectReferenceSequence(alignments, undefined, 'hg38', 'panTro6');
+        expect(result).toBe('ACGTACGT');
+    });
+    test('falls back to firstAssemblyNameFound when queryAssemblyName does not match', () => {
+        const result = selectReferenceSequence(alignments, undefined, 'galGal6', // not in alignments
+        'hg38');
+        expect(result).toBe('ACGTACGT');
+    });
+    test('falls back to firstAssemblyNameFound when both config values are empty', () => {
+        const result = selectReferenceSequence(alignments, '', '', 'panTro6');
+        expect(result).toBe('GGGGGGGG');
+    });
+    test('returns undefined when refAssemblyName does not exist in alignments', () => {
+        const result = selectReferenceSequence(alignments, 'nonexistent', undefined, undefined);
+        expect(result).toBeUndefined();
+    });
+    test('returns undefined when no matches and all params undefined', () => {
+        const result = selectReferenceSequence(alignments, undefined, undefined, undefined);
+        expect(result).toBeUndefined();
+    });
+    test('returns undefined for empty alignments object', () => {
+        const result = selectReferenceSequence({}, 'hg38', 'mm10', 'panTro6');
+        expect(result).toBeUndefined();
+    });
+    test('skips refAssemblyName when it does not exist and uses queryAssemblyName', () => {
+        const result = selectReferenceSequence(alignments, 'galGal6', // not in alignments
+        'hg38', 'panTro6');
+        expect(result).toBe('ACGTACGT');
+    });
+    test('skips both refAssemblyName and queryAssemblyName when neither exists', () => {
+        const result = selectReferenceSequence(alignments, 'galGal6', // not in alignments
+        'rn6', // not in alignments
+        'mm10');
+        expect(result).toBe('TGCATGCA');
+    });
+});
+describe('assembly name lookup integration scenarios', () => {
+    test('refAssemblyName config takes precedence over query.assemblyName', () => {
+        const alignments = {
+            hg38: { seq: 'REFERENCE_SEQ' },
+            mm10: { seq: 'QUERY_SEQ' },
+        };
+        const result = selectReferenceSequence(alignments, 'hg38', 'mm10', 'mm10');
+        expect(result).toBe('REFERENCE_SEQ');
+    });
+    test('query.assemblyName works when refAssemblyName not configured', () => {
+        const alignments = {
+            hg38: { seq: 'QUERY_SEQ' },
+            mm10: { seq: 'OTHER_SEQ' },
+        };
+        const result = selectReferenceSequence(alignments, '', 'hg38', 'mm10');
+        expect(result).toBe('QUERY_SEQ');
+    });
+    test('firstAssemblyNameFound is used as last resort fallback', () => {
+        const alignments = {
+            panTro6: { seq: 'FIRST_FOUND' },
+            mm10: { seq: 'OTHER_SEQ' },
+        };
+        // When query assemblyName does not match any alignment
+        const result = selectReferenceSequence(alignments, '', 'hg38', 'panTro6');
+        expect(result).toBe('FIRST_FOUND');
+    });
+});
+describe('real-world MAF format parsing', () => {
+    test('ce10.chrI from UCSC 7-way alignment', () => {
+        const result = parseAssemblyAndChr('ce10.chrI');
+        expect(result).toEqual({
+            assemblyName: 'ce10',
+            chr: 'chrI',
+        });
+    });
+    test('caePb3.Scfld02_18 scaffold format', () => {
+        const result = parseAssemblyAndChr('caePb3.Scfld02_18');
+        expect(result).toEqual({
+            assemblyName: 'caePb3',
+            chr: 'Scfld02_18',
+        });
+    });
+    test('caeRem4.Crem_Contig16 contig format', () => {
+        const result = parseAssemblyAndChr('caeRem4.Crem_Contig16');
+        expect(result).toEqual({
+            assemblyName: 'caeRem4',
+            chr: 'Crem_Contig16',
+        });
+    });
+    test('cb4.chrI C. briggsae format', () => {
+        const result = parseAssemblyAndChr('cb4.chrI');
+        expect(result).toEqual({
+            assemblyName: 'cb4',
+            chr: 'chrI',
+        });
+    });
+    test('multiple assemblies from same MAF block produce correct lookup', () => {
+        const alignments = {
+            ce10: { seq: 'TCTTTTAGTATTTGTAA' },
+            caePb3: { seq: 'tcTTTTCGC-TTTATAA' },
+        };
+        // When querying with ce10 assembly
+        expect(selectReferenceSequence(alignments, '', 'ce10', 'ce10')).toBe('TCTTTTAGTATTTGTAA');
+        // When refAssemblyName is configured to override
+        expect(selectReferenceSequence(alignments, 'caePb3', 'ce10', 'ce10')).toBe('tcTTTTCGC-TTTATAA');
+    });
+});
+describe('refName renaming compatibility', () => {
+    test('parseAssemblyAndChr extracts chr correctly for refName alias matching', () => {
+        // When a file uses "chrI" but assembly has alias "I" -> "chrI"
+        // The chr portion extracted here should match what renameRegionsIfNeeded expects
+        const { chr } = parseAssemblyAndChr('ce10.chrI');
+        expect(chr).toBe('chrI');
+    });
+    test('parseAssemblyAndChrSimple extracts chr correctly for refName alias matching', () => {
+        const { chr } = parseAssemblyAndChrSimple('ce10.chrI');
+        expect(chr).toBe('chrI');
+    });
+    test('assembly name is isolated from chr for assembly-based lookups', () => {
+        // The assembly name (e.g., "ce10") is used to look up reference sequence
+        // It should not include the chr portion
+        const { assemblyName } = parseAssemblyAndChr('ce10.chrI');
+        expect(assemblyName).toBe('ce10');
+    });
+});
+//# sourceMappingURL=parseAssemblyName.test.js.map

package/dist/util/parseAssemblyName.test.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.4.5",
+  "version": "1.4.6",
   "license": "MIT",
   "name": "jbrowse-plugin-mafviewer",
   "keywords": [
@@ -15,7 +15,7 @@
   ],
   "scripts": {
     "clean": "rimraf dist",
-    "start": "node esbuild.mjs",
+    "start": "node esbuild.mjs --watch",
     "test": "vitest",
     "format": "prettier --write .",
     "prebuild": "yarn clean",
@@ -29,9 +29,10 @@
     "@babel/preset-react": "^7.10.4",
     "@emotion/react": "^11.10.4",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^3.0.1",
-    "@jbrowse/plugin-data-management": "^3.0.1",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.1",
+    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/mobx-state-tree": "^5.4.1",
+    "@jbrowse/plugin-data-management": "^4.1.1",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
     "@mui/material": "^7.0.1",
     "@mui/system": "^7.0.1",
     "@mui/x-data-grid": "^8.2.0",
@@ -48,7 +49,6 @@
     "eslint-plugin-unicorn": "^62.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.1",
-    "mobx-state-tree": "^5.4.1",
     "prettier": "^3.4.2",
     "pretty-bytes": "^7.0.0",
     "react": "^19.0.0",
@@ -62,7 +62,7 @@
     "vitest": "^4.0.5"
   },
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^5.0.2",
+    "@gmod/bgzf-filehandle": "^6.0.12",
     "abortable-promise-cache": "^1.5.0",
     "buffer": "^6.0.3",
     "d3-array": "^3.2.4",

package/src/BigMafAdapter/BigMafAdapter.ts

@@ -2,11 +2,12 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { SimpleFeature, updateStatus } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { getSnapshot } from 'mobx-state-tree'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import { firstValueFrom, toArray } from 'rxjs'
 
 import parseNewick from '../parseNewick'
 import { normalize } from '../util'
+import { parseAssemblyAndChrSimple } from '../util/parseAssemblyName'
 
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'
 import type { Feature, Region } from '@jbrowse/core/util'
@@ -103,10 +104,9 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
                 referenceSeq = sequence
               }
 
-              // Parse organism and chromosome once
-              const dotIndex = organismChr.indexOf('.')
-              const org = organismChr.slice(0, Math.max(0, dotIndex))
-              const chr = organismChr.slice(Math.max(0, dotIndex + 1))
+              // Parse organism and chromosome
+              const { assemblyName: org, chr } =
+                parseAssemblyAndChrSimple(organismChr)
 
               // Create alignment record directly
               alignments[org] = {

package/src/LinearMafDisplay/components/LinearMafDisplayComponent.tsx

@@ -1,14 +1,20 @@
-import React, { useCallback, useEffect, useRef, useState } from 'react'
+import React, { useRef } from 'react'
 
 import { Menu } from '@jbrowse/core/ui'
-import { getContainingView, getEnv } from '@jbrowse/core/util'
+import {
+  getContainingView,
+  getEnv,
+  getSession,
+  isSessionModelWithWidgets,
+} from '@jbrowse/core/util'
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 
 import Crosshairs from './Crosshairs'
-import SequenceDialog from './GetSequenceDialog/GetSequenceDialog'
 import MAFTooltip from './MAFTooltip'
+import MsaHighlightOverlay from './MsaHighlightOverlay'
 import YScaleBars from './Sidebar/YScaleBars'
+import { useDragSelection } from './useDragSelection'
 
 import type { LinearMafDisplayModel } from '../stateModel'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -18,123 +24,34 @@ const LinearMafDisplay = observer(function (props: {
 }) {
   const { model } = props
   const { pluginManager } = getEnv(model)
-  const { rowHeight, height, scrollTop, samples: sources } = model
+  const { height, scrollTop, samples: sources } = model
   const ref = useRef<HTMLDivElement>(null)
   const theme = useTheme()
+  const session = getSession(model)
 
   const LinearGenomePlugin = pluginManager.getPlugin(
     'LinearGenomeViewPlugin',
   ) as import('@jbrowse/plugin-linear-genome-view').default
   const { BaseLinearDisplayComponent } = LinearGenomePlugin.exports
 
-  const [mouseY, setMouseY] = useState<number>()
-  const [mouseX, setMouseX] = useState<number>()
-  const [isDragging, setIsDragging] = useState(false)
-  const [dragStartX, setDragStartX] = useState<number>()
-  const [dragEndX, setDragEndX] = useState<number>()
-  const [showSelectionBox, setShowSelectionBox] = useState(false)
-  const [contextCoord, setContextCoord] = useState<{
-    coord: [number, number]
-    dragStartX: number
-    dragEndX: number
-  }>()
-  const [showSequenceDialog, setShowSequenceDialog] = useState(false)
-  const [selectionCoords, setSelectionCoords] = useState<
-    | {
-        dragStartX: number
-        dragEndX: number
-      }
-    | undefined
-  >()
-  const { width } = getContainingView(model) as LinearGenomeViewModel
-
-  const handleMouseDown = (event: React.MouseEvent) => {
-    const rect = ref.current?.getBoundingClientRect()
-    const left = rect?.left || 0
-    const clientX = event.clientX - left
-
-    // Clear the previous selection box when starting a new drag
-    setShowSelectionBox(false)
-    setIsDragging(true)
-    setDragStartX(clientX)
-    setDragEndX(clientX)
-    event.stopPropagation()
-  }
-
-  const handleMouseMove = (event: React.MouseEvent) => {
-    const rect = ref.current?.getBoundingClientRect()
-    const top = rect?.top || 0
-    const left = rect?.left || 0
-    const clientX = event.clientX - left
-    const clientY = event.clientY - top
-
-    setMouseY(clientY)
-    setMouseX(clientX)
-
-    if (isDragging) {
-      setDragEndX(clientX)
-    }
-  }
-
-  const handleMouseUp = (event: React.MouseEvent) => {
-    if (isDragging && dragStartX !== undefined && dragEndX !== undefined) {
-      // Calculate the drag distance
-      const dragDistanceX = Math.abs(dragEndX - dragStartX)
-
-      // Only show context menu if the drag distance is at least 2 pixels in either direction
-      if (dragDistanceX >= 2) {
-        setContextCoord({
-          coord: [event.clientX, event.clientY],
-          dragEndX: event.clientX,
-          dragStartX: dragStartX,
-        })
-
-        // Set showSelectionBox to true to keep the selection visible
-        setShowSelectionBox(true)
-      } else {
-        // For very small drags (less than 2px), don't show selection box or context menu
-        clearSelectionBox()
-      }
-    }
-
-    // Only set isDragging to false, but keep the coordinates
-    setIsDragging(false)
-  }
-
-  // Function to clear the selection box
-  const clearSelectionBox = useCallback(() => {
-    setShowSelectionBox(false)
-    setDragStartX(undefined)
-    setDragEndX(undefined)
-  }, [])
-
-  // Add keydown event handler to clear selection box when Escape key is pressed
-  useEffect(() => {
-    const handleKeyDown = (event: KeyboardEvent) => {
-      if (event.key === 'Escape' && showSelectionBox) {
-        clearSelectionBox()
-      }
-    }
-
-    // Add click handler to clear selection box when clicking outside of it
-    const handleClickOutside = (event: MouseEvent) => {
-      if (
-        ref.current &&
-        !ref.current.contains(event.target as Node) &&
-        showSelectionBox
-      ) {
-        clearSelectionBox()
-      }
-    }
-
-    document.addEventListener('keydown', handleKeyDown)
-    document.addEventListener('click', handleClickOutside)
-
-    return () => {
-      document.removeEventListener('keydown', handleKeyDown)
-      document.removeEventListener('click', handleClickOutside)
-    }
-  }, [showSelectionBox, clearSelectionBox])
+  const {
+    isDragging,
+    dragStartX,
+    dragEndX,
+    showSelectionBox,
+    mouseX,
+    mouseY,
+    contextCoord,
+    setContextCoord,
+    handleMouseDown,
+    handleMouseMove,
+    handleMouseUp,
+    handleMouseLeave,
+    clearSelectionBox,
+  } = useDragSelection(ref)
+
+  const view = getContainingView(model) as LinearGenomeViewModel
+  const { width } = view
 
   return (
     <div
@@ -143,20 +60,19 @@ const LinearMafDisplay = observer(function (props: {
       onMouseMove={handleMouseMove}
       onMouseUp={handleMouseUp}
       onDoubleClick={() => {
-        // Clear selection box on double click
         if (showSelectionBox) {
           clearSelectionBox()
         }
       }}
-      onMouseLeave={() => {
-        setMouseY(undefined)
-        setMouseX(undefined)
-        setIsDragging(false)
-      }}
+      onMouseLeave={handleMouseLeave}
     >
       <BaseLinearDisplayComponent {...props} />
       {model.showSidebar ? <YScaleBars model={model} /> : null}
-      {mouseY && mouseX && sources && !contextCoord && !showSequenceDialog ? (
+      <MsaHighlightOverlay model={model} view={view} height={height} />
+      {mouseY !== undefined &&
+      mouseX !== undefined &&
+      sources &&
+      !contextCoord ? (
         <div style={{ position: 'relative' }}>
           <Crosshairs
             width={width}
@@ -168,10 +84,7 @@ const LinearMafDisplay = observer(function (props: {
           <MAFTooltip
             model={model}
             mouseX={mouseX}
-            mouseY={mouseY}
-            origMouseX={dragStartX}
-            rowHeight={rowHeight}
-            sources={sources}
+            origMouseX={isDragging ? dragStartX : undefined}
           />
         </div>
       ) : null}
@@ -224,32 +137,37 @@ const LinearMafDisplay = observer(function (props: {
                 return
               }
 
-              // Store the selection coordinates for the SequenceDialog to use
-              setSelectionCoords({
-                dragStartX: contextCoord.dragStartX,
-                dragEndX: contextCoord.dragEndX,
-              })
-
-              // Show the dialog
-              setShowSequenceDialog(true)
-
-              // Close the context menu
+              const { refName, assemblyName } = view.displayedRegions[0]!
+              const [s, e] = [
+                Math.min(contextCoord.dragStartX, contextCoord.dragEndX),
+                Math.max(contextCoord.dragStartX, contextCoord.dragEndX),
+              ]
+
+              if (isSessionModelWithWidgets(session)) {
+                const widget = session.addWidget(
+                  'MafSequenceWidget',
+                  'mafSequence',
+                  {
+                    adapterConfig: model.adapterConfig,
+                    samples: model.samples,
+                    regions: [
+                      {
+                        refName,
+                        start: view.pxToBp(s).coord - 1,
+                        end: view.pxToBp(e).coord,
+                        assemblyName,
+                      },
+                    ],
+                    connectedViewId: view.id,
+                  },
+                )
+                session.showWidget(widget)
+              }
               setContextCoord(undefined)
             },
           },
         ]}
       />
-
-      {showSequenceDialog ? (
-        <SequenceDialog
-          model={model}
-          selectionCoords={selectionCoords}
-          onClose={() => {
-            setShowSequenceDialog(false)
-            setSelectionCoords(undefined)
-          }}
-        />
-      ) : null}
     </div>
   )
 })

package/src/LinearMafDisplay/components/MAFTooltip.tsx

@@ -16,10 +16,7 @@ const MAFTooltip = observer(function ({
   mouseX,
   origMouseX,
 }: {
-  mouseY: number
   mouseX: number
-  rowHeight: number
-  sources: Record<string, any>[]
   model: LinearMafDisplayModel
   origMouseX?: number
 }) {