add spotted gar genome with comparison with zebrafish

frontend/src/components/trackContainers/TrackViewManager.tsx

@@ -38,8 +38,8 @@ export function withTrackView(WrappedComponent: React.ComponentType<WrappedCompo
         constructor(props: DataManagerProps) {
             super(props);
             this._primaryGenome = props.genome;
-            const queryGenomes = this.getSecondaryGenomes(props.tracks);
-            this._multialignmentCalculator = new MultiAlignmentViewCalculator(this._primaryGenome, queryGenomes);
+            // const queryGenomes = this.getSecondaryGenomes(props.tracks);
+            // this._multialignmentCalculator = new MultiAlignmentViewCalculator(this._primaryGenome, queryGenomes);
 
             this.state = {
                 primaryView: 
@@ -84,8 +84,11 @@ export function withTrackView(WrappedComponent: React.ComponentType<WrappedCompo
 
         fetchAlignments(viewRegion: DisplayedRegionModel, tracks: TrackModel[]): Promise<MultiAlignment> {
             const visData = this.props.expansionAmount.calculateExpansion(viewRegion, this.getVisualizationWidth());
+            const queryGenomes = this.getSecondaryGenomes(this.props.tracks);
+            this._multialignmentCalculator = new MultiAlignmentViewCalculator(this._primaryGenome, queryGenomes);
             const alignmentCalculator = this._multialignmentCalculator;
-            return alignmentCalculator.multiAlign(visData);
+            const fetchedAlignment = alignmentCalculator.multiAlign(visData);
+            return fetchedAlignment;
         }
 
         async componentDidUpdate(prevProps: DataManagerProps) {

frontend/src/model/genomes/allGenomes.ts

@@ -15,6 +15,7 @@ import DM6 from "./dm6/dm6";
 import CE11 from "./ce11/ce11";
 import APLCAL3 from "./aplCal3/aplCal3";
 import SACCER3 from "./sacCer3/sacCer3";
+import LEPOCU1 from "./lepOcu1/lepOcu1";
 import { GenomeConfig } from "./GenomeConfig";
 
 /**
@@ -37,6 +38,7 @@ export const allGenomes = [
     DM6,
     CE11,
     APLCAL3,
+    LEPOCU1,
     SACCER3
 ];
 
@@ -97,6 +99,11 @@ export const treeOfLife: { [speciesName: string]: SpeciesConfig } = {
         assemblies: [DAN_RER11.genome.getName(), DAN_RER10.genome.getName()],
         color: "yellow"
     },
+    "spotted Gar":{
+        logoUrl: "https://wangftp.wustl.edu/~xzhuo/lepOcu1/SpottedGar.png",
+        assemblies: [LEPOCU1.genome.getName()],
+        color: "white"
+    },
     "fruit fly": {
         logoUrl: "https://epigenomegateway.wustl.edu/legacy/images/Fruit%20fly.png",
         assemblies: [DM6.genome.getName()],

frontend/src/model/genomes/danRer11/annotationTracks.json

@@ -23,6 +23,15 @@
                 "height": 30
             }
         ]
-    }
+    },
+    "Genome Comparison": [
+        {
+            "name": "querylepOcu1 to danRer11",
+            "label": "spotted gar to zebrafish lastz ensembl",
+            "querygenome": "lepOcu1",
+            "filetype": "genomealign",
+            "url": "https://wangftp.wustl.edu/~xzhuo/lepOcu1/danRer11.lepocu1.gz"
+        }
+    ]
 }
 

frontend/src/model/genomes/danRer11/danRer11.js

@@ -50,7 +50,7 @@ const defaultTracks = [
     new TrackModel({
         type: 'repeatmasker',
         name: 'RepeatMasker',
-        url: 'https://vizhub.wustl.edu/public/bosTau8/rmsk16.bb',
+        url: 'https://vizhub.wustl.edu/public/danRer11/rmsk16.bb',
     }),
 ];
 

frontend/src/model/genomes/lepOcu1/annotationTracks.json

@@ -0,0 +1,27 @@
+{
+    "Ruler": [
+        {
+            "type": "ruler",
+            "label": "Ruler",
+            "name": "Ruler"
+        }
+    ],
+    "Genes": [
+        {
+            "type": "refbed",
+            "name": "ensembl_gene",
+            "url": "https://wangftp.wustl.edu/~xzhuo/lepOcu1/lepOcu1_Gene.bed.gz"
+        }
+    ],
+    "RepeatMasker": {
+        "All Repeats": [
+            {
+                "name": "rmsk_all",
+                "label": "RepeatMasker",
+                "filetype": "repeatmasker",
+                "url": "https://wangftp.wustl.edu/~xzhuo/lepOcu1/lepOcu1.bb",
+                "height": 30
+            }
+        ]
+    }
+}