final fix for nucleotide positioning #86

src/App.js

@@ -651,14 +651,11 @@ class App extends Component {
         (schematizeComponent, i) => {
           // The dummy component (firstBin and lastBin equal to 0) is not loaded in this.schematic.components, but there is a nucleotide for it in the FASTA file.
           // If the first component has firstBin == 1, then in the FASTA there is a nucleotide not visualized, so the shift start from 0, and not 1
-          const nt_shift =
-            this.schematic.components[0].firstBin === 1
-              ? 0
-              : this.schematic.components[0].firstBin;
+          const nt_shift = this.schematic.components[0].firstBin || 1;
 
           const nucleotides_slice = this.schematic.nucleotides.slice(
-            schematizeComponent.firstBin - nt_shift,
-            schematizeComponent.lastBin - nt_shift + 1
+              schematizeComponent.firstBin - nt_shift, // firstBin is 1 indexed, but this is canceled by nt_shift
+              schematizeComponent.lastBin - nt_shift + 1 // inclusive end
           );
 
           //console.log("nucleotides_slice: " + nucleotides_slice);

src/ViewportInputsStore.js

@@ -33,7 +33,7 @@ RootStore = types
     chunkIndex: ChunkIndex,
     beginEndBin: types.optional(types.array(types.integer), [1, 100]),
     useVerticalCompression: false,
-    useWidthCompression: false,
+    useWidthCompression: true,
     binScalingFactor: 3,
     useConnector: true,
     pixelsPerColumn: 10,
@@ -43,7 +43,7 @@ RootStore = types
     highlightedLink: 0, // we will compare linkColumns
     maximumHeightThisFrame: 150,
     cellToolTipContent: "",
-    jsonName: "run1.B1phi1.i1.seqwish.v16",
+    jsonName: "SARS-CoV-b2",
     // Added attributes for the zoom level management
     availableZoomLevels: types.optional(types.array(types.string), ["1"]),
     indexSelectedZoomLevel: 0,