@jbrowse/plugin-linear-genome-view 1.7.10 → 2.0.1

package/src/LinearGenomeView/components/util.ts

@@ -1,4 +1,8 @@
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
+import { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager'
+import { TextSearchManager } from '@jbrowse/core/util'
 
 export function dedupe(
   results: BaseResult[] = [],
@@ -8,3 +12,42 @@ export function dedupe(
     (elt, idx, self) => idx === self.findIndex(t => cb(t) === cb(elt)),
   )
 }
+
+export async function fetchResults({
+  queryString,
+  searchType,
+  searchScope,
+  rankSearchResults,
+  textSearchManager,
+  assembly,
+}: {
+  queryString: string
+  searchScope: SearchScope
+  rankSearchResults: (results: BaseResult[]) => BaseResult[]
+  searchType?: SearchType
+  textSearchManager?: TextSearchManager
+  assembly?: Assembly
+}) {
+  if (!textSearchManager) {
+    console.warn('No text search manager')
+  }
+
+  const textSearchResults = await textSearchManager?.search(
+    {
+      queryString,
+      searchType,
+    },
+    searchScope,
+    rankSearchResults,
+  )
+
+  const refNameResults = assembly?.allRefNames
+    ?.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase()))
+    .slice(0, 10)
+    .map(r => new BaseResult({ label: r }))
+
+  return dedupe(
+    [...(refNameResults || []), ...(textSearchResults || [])],
+    elt => elt.getId(),
+  )
+}

package/src/LinearGenomeView/index.test.ts

@@ -88,6 +88,7 @@ function initialize() {
       assemblyManager: types.optional(AssemblyManager, {
         assemblies: {
           volvox: {
+            // @ts-ignore
             regions: volvoxDisplayedRegions,
           },
         },
@@ -289,13 +290,13 @@ test('can navToMultiple', () => {
     { refName: 'ctgC', start: 0, end: 5000 },
   ])
   expect(model.offsetPx).toBe(199)
-  expect(model.bpPerPx).toBeCloseTo(25.126)
+  expect(model.bpPerPx).toBeCloseTo(25.125)
 
   model.navToMultiple([
     { refName: 'ctgA', start: 5000, end: 10000 },
     { refName: 'ctgC', start: 0, end: 5000 },
   ])
-  expect(model.offsetPx).toBe(2799)
+  expect(model.offsetPx).toBe(2793)
   expect(model.bpPerPx).toBeCloseTo(12.531)
 })
 
@@ -329,7 +330,7 @@ describe('Zoom to selected displayed regions', () => {
     // 'ctgA' 15000  bp+ 'ctgA' 10000 bp+ 'ctgB' 3000 bp = 28000 totalbp
     expect(model.totalBp).toEqual(28000)
 
-    model.zoomToDisplayedRegions(
+    model.moveTo(
       {
         start: 5000,
         index: 0,
@@ -353,32 +354,8 @@ describe('Zoom to selected displayed regions', () => {
     expect(model.bpPerPx).toBeCloseTo(31.408)
   })
 
-  it('can select if start and end object are swapped', () => {
-    // should be same results as above test
-    model.zoomToDisplayedRegions(
-      {
-        start: 0,
-        index: 2,
-        coord: 1,
-        end: 3000,
-        offset: 1,
-        refName: 'ctgB',
-      },
-      {
-        start: 5000,
-        index: 0,
-        end: 20000,
-        coord: 5001,
-        offset: 0,
-        refName: 'ctgA',
-      },
-    )
-    expect(model.offsetPx).toEqual(0)
-    expect(model.bpPerPx).toBeCloseTo(31.408)
-  })
-
   it('can select over one refSeq', () => {
-    model.zoomToDisplayedRegions(
+    model.moveTo(
       {
         start: 5000,
         index: 0,
@@ -403,7 +380,7 @@ describe('Zoom to selected displayed regions', () => {
   })
 
   it('can select one region with start or end outside of displayed region', () => {
-    model.zoomToDisplayedRegions(
+    model.moveTo(
       {
         start: 5000,
         index: 0,
@@ -422,7 +399,8 @@ describe('Zoom to selected displayed regions', () => {
       },
     )
     // offsetPx is still 0 since we are starting from the first coord
-    expect(model.offsetPx).toBe(0)
+    // needed Math.abs since it was giving negative-zero (-0)
+    expect(Math.abs(model.offsetPx)).toEqual(0)
     // endOffset 19000 - (-1) = 19001 /  800 = zoomTo(23.75)
     expect(model.bpPerPx).toBeCloseTo(23.75)
     expect(model.bpPerPx).toBeLessThan(largestBpPerPx)
@@ -433,7 +411,7 @@ describe('Zoom to selected displayed regions', () => {
     model.showAllRegions()
     expect(model.bpPerPx).toBeCloseTo(38.8888)
     // totalBp = 28000 / 1000 = 28 as maxBpPerPx
-    model.zoomToDisplayedRegions(
+    model.moveTo(
       {
         start: 5000,
         index: 0,
@@ -467,7 +445,7 @@ describe('Zoom to selected displayed regions', () => {
     // totalBp 15000 + 3000 + 35000 = 53000
     // then 53000 / (width*0.9) = 73.6111
     expect(model.bpPerPx).toBeCloseTo(73.61111)
-    model.zoomToDisplayedRegions(
+    model.moveTo(
       {
         start: 5000,
         coord: 15000,
@@ -532,7 +510,7 @@ test('can instantiate a model that >2 regions', () => {
     { refName: 'ctgB', index: 1, offset: 0, start: 0, end: 10000 },
     { refName: 'ctgC', index: 2, offset: 0, start: 0, end: 10000 },
   )
-  expect(model.offsetPx).toEqual(10000 / model.bpPerPx + 2)
+  expect(model.offsetPx).toEqual(10000 / model.bpPerPx)
   expect(model.displayedRegionsTotalPx).toEqual(30000 / model.bpPerPx)
   model.showAllRegions()
   expect(model.offsetPx).toEqual(-40)
@@ -658,7 +636,7 @@ test('can perform pxToBp on human genome things with ellided blocks (zoomed out)
 
   // chrX after an ellided block, this tests a specific coord but should just be
   // probably somewhat around here
-  expect(model.pxToBp(1228).coord).toBe(99349155)
+  expect(model.pxToBp(1228).coord).toBe(118604872)
   expect(model.pxToBp(1228).refName).toBe('X')
 
   // chrY_random at the end
@@ -687,7 +665,7 @@ test('can showAllRegionsInAssembly', async () => {
   ])
 })
 
-describe('Get Sequence for selected displayed regions', () => {
+describe('get sequence for selected displayed regions', () => {
   const { Session, LinearGenomeModel } = initialize()
   /* the start of all the results should be +1
   the sequence dialog then handles converting from 1-based closed to interbase
@@ -777,7 +755,7 @@ describe('Get Sequence for selected displayed regions', () => {
       model.rightOffset,
     )
 
-    expect(outOfBounds.length).toEqual(0)
+    expect(outOfBounds.length).toEqual(1)
   })
 
   it('selects multiple regions with a region in between', () => {