Fix the set feature height ability

packages/core/pluggableElementTypes/renderers/BoxRendererType.ts

@@ -57,7 +57,7 @@ export class LayoutSession implements LayoutSessionProps {
       maxHeight: readConfObject(this.config, 'maxHeight'),
       displayMode: readConfObject(this.config, 'displayMode'),
       pitchX: this.bpPerPx,
-      spacing: readConfObject(this.config, 'noSpacing') ? 0 : 2,
+      pitchY: readConfObject(this.config, 'noSpacing') ? 1 : 3,
     })
   }
 

packages/core/util/layouts/GranularRectLayout.ts

@@ -338,7 +338,7 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
     pitchX = 10,
     pitchY = 10,
     maxHeight = 10000,
-    hardRowLimit = 3000,
+    hardRowLimit = 10000,
     displayMode = 'normal',
   }: {
     pitchX?: number
@@ -428,9 +428,7 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
 
   collides(rect: Rectangle<T>, top: number): boolean {
     const { bitmap } = this
-    // var mY = top + rect.h/2; // Y midpoint: ( top+height  + top ) / 2
 
-    // test exhaustively
     const maxY = top + rect.h
     for (let y = top; y < maxY; y += 1) {
       const row = bitmap[y]
@@ -470,12 +468,11 @@ export default class GranularRectLayout<T> implements BaseLayout<T> {
     const { bitmap } = this
     const yEnd = rect.top + rect.h
     if (rect.r - rect.l > maxFeaturePitchWidth) {
-      // the rect is very big in relation to the view size, just
-      // pretend, for the purposes of layout, that it extends
-      // infinitely.  this will cause weird layout if a user
-      // scrolls manually for a very, very long time along the
-      // genome at the same zoom level.  but most users will not
-      // do that.  hopefully.
+      // the rect is very big in relation to the view size, just pretend, for
+      // the purposes of layout, that it extends infinitely.  this will cause
+      // weird layout if a user scrolls manually for a very, very long time
+      // along the genome at the same zoom level.  but most users will not do
+      // that.  hopefully.
       for (let y = rect.top; y < yEnd; y += 1) {
         this.autovivifyRow(bitmap, y).setAllFilled(data)
       }

products/jbrowse-web/src/__snapshots__/jbrowseModel.test.ts.snap

@@ -2836,6 +2836,71 @@ Object {
       "trackId": "volvox.inv.vcf",
       "type": "VariantTrack",
     },
+    Object {
+      "adapter": Object {
+        "craiLocation": Object {
+          "internetAccountId": undefined,
+          "internetAccountPreAuthorization": undefined,
+          "locationType": "UriLocation",
+          "uri": "deep_sequencing.cram.crai",
+        },
+        "cramLocation": Object {
+          "internetAccountId": undefined,
+          "internetAccountPreAuthorization": undefined,
+          "locationType": "UriLocation",
+          "uri": "deep_sequencing.cram",
+        },
+        "sequenceAdapter": Object {
+          "chromSizesLocation": Object {
+            "internetAccountId": undefined,
+            "internetAccountPreAuthorization": undefined,
+            "locationType": "UriLocation",
+            "uri": "/path/to/default.chrom.sizes",
+          },
+          "twoBitLocation": Object {
+            "internetAccountId": undefined,
+            "internetAccountPreAuthorization": undefined,
+            "locationType": "UriLocation",
+            "uri": "volvox.2bit",
+          },
+          "type": "TwoBitAdapter",
+        },
+        "type": "CramAdapter",
+      },
+      "assemblyNames": Array [
+        "volvox",
+      ],
+      "category": Array [
+        "Alignments",
+      ],
+      "displays": Array [
+        Object {
+          "displayId": "deep_seq_alignments",
+          "pileupDisplay": Object {
+            "displayId": "deep_seq_pileup",
+            "renderers": Object {
+              "PileupRenderer": Object {
+                "maxHeight": 10000,
+                "type": "PileupRenderer",
+              },
+            },
+            "type": "LinearPileupDisplay",
+          },
+          "type": "LinearAlignmentsDisplay",
+        },
+        Object {
+          "displayId": "Deep sequencing-LinearPileupDisplay",
+          "type": "LinearPileupDisplay",
+        },
+        Object {
+          "displayId": "Deep sequencing-LinearSNPCoverageDisplay",
+          "type": "LinearSNPCoverageDisplay",
+        },
+      ],
+      "name": "deep_sequencing",
+      "trackId": "Deep sequencing",
+      "type": "AlignmentsTrack",
+    },
   ],
 }
 `;

products/jbrowse-web/src/tests/__snapshots__/BreakpointSplitView.test.js.snap

@@ -7,12 +7,12 @@ exports[`breakpoint split view open a split view 1`] = `
   stroke="#333"
 >
   <path
-    d="M 410.99312656000257 80.5 C 610.9931265600026 80.5 203.41868021525443 89.5 403.4186802152544 89.5"
+    d="M 407.99312656000257 143.5 C 607.9931265600026 143.5 203.41868021525443 173.5 403.4186802152544 173.5"
     data-testid="r1"
     stroke-width="1"
   />
   <path
-    d="M 660.4186802152544 89.5 C 860.4186802152544 89.5 206.99312656000257 53.5 406.99312656000257 53.5"
+    d="M 660.4186802152544 173.5 C 860.4186802152544 173.5 206.99312656000257 53.5 406.99312656000257 53.5"
     data-testid="r1"
     stroke-width="1"
   />
@@ -27,7 +27,7 @@ exports[`breakpoint split view open a split view 2`] = `
   stroke-width="5"
 >
   <path
-    d="M 388.99312656000257 20 L 408.99312656000257 20 L 403.4186802152544 20 L 423.4186802152544 20"
+    d="M 387.99312656000257 20 L 407.99312656000257 20 L 403.4186802152544 20 L 423.4186802152544 20"
     stroke-width="5"
   />
 </g>