jbrowse-plugin-graphgenomeviewer 4.0.13 → 4.0.15

package/src/GraphGenomeView/model.ts

@@ -4,6 +4,7 @@ import {
 } from '@jbrowse/bandage-core/anchoredNodes'
 import { BUBBLE_SPREAD_VALUES } from '@jbrowse/bandage-core/bubbleSpreads'
 import { bubbleHalos } from '@jbrowse/bandage-core/bubbles/bubbleHalos'
+import { sameBubble } from '@jbrowse/bandage-core/bubbles/bubbleLine'
 import { bubblesFromGraph } from '@jbrowse/bandage-core/bubbles/bubblesFromGraph'
 import {
   BUBBLE_KIND_NAMES,
@@ -55,15 +56,18 @@ import {
   buildNeighbors,
   nodeReferenceSpan,
 } from '@jbrowse/bandage-core/referenceSpan'
+import {
+  REFERENCE_STRIP_ZONE_PX,
+  nodeAnchor,
+  referenceStripBlocks,
+  stripBlockAt,
+  stripOverhang,
+} from '@jbrowse/bandage-core/referenceStrip'
 import {
   buildGeometry,
   computeReferenceRamp,
 } from '@jbrowse/bandage-core/renderer/GeometryBuilder'
-import {
-  referenceBoxes,
-  rulerBoxes,
-  rulerMarks,
-} from '@jbrowse/bandage-core/tubeMap/axis'
+import { referenceBoxes, rulerBoxes } from '@jbrowse/bandage-core/tubeMap/axis'
 import { coarsenTubeMap } from '@jbrowse/bandage-core/tubeMap/coarsen'
 import {
   connectorAt,
@@ -71,7 +75,11 @@ import {
   tubeMapConnectors,
 } from '@jbrowse/bandage-core/tubeMap/connectors'
 import { deviationMarks } from '@jbrowse/bandage-core/tubeMap/deviations'
-import { tubeMapPicture } from '@jbrowse/bandage-core/tubeMap/draw'
+import {
+  mismatchOnScreen,
+  mismatchesLegible,
+  tubeMapPicture,
+} from '@jbrowse/bandage-core/tubeMap/draw'
 import {
   tubeMapFrame,
   tubeMapNodeAt,
@@ -412,11 +420,15 @@ export function GraphPaneMixin() {
         ),
         // Whether the node layouts draw each bubble as a halo along its nodes
         // with a label that opens it. The variant map draws glyphs instead.
-        showBubbles: types.optional(types.boolean, true),
+        // Off by default: on a base-level cut every SNP's halo is a blob.
+        showBubbles: types.optional(types.boolean, false),
         showDeletionEdges: types.optional(types.boolean, false),
         // The session's genes drawn onto the backbone: exons along the nodes
         // that carry them, names pinned at their midpoints. See genes/.
         showGenes: types.optional(types.boolean, true),
+        // Whether a drawing in its own coordinates inside a linear view gets
+        // the strip of reference segments at their bp. See referenceStrip.ts.
+        showReferenceStrip: types.optional(types.boolean, true),
         // Variants under this many bp fold into the reference before a tube map
         // is laid out, each kept as a tick on its walk's tube (coarsen.ts); 0
         // draws every one
@@ -521,6 +533,11 @@ export function GraphPaneMixin() {
       loadCanceled: false,
       statusMessage: '',
       hoveredNode: null as string | null,
+      // the bubble whose label the pointer is on
+      hoveredBubble: null as MinigraphBubble | null,
+      // whether the pointer is over this pane, whose own hit test then says
+      // what it is on
+      pointerInPane: false,
       hoveredEdge: null as number | null,
       selectedNode: null as string | null,
       viewportDirty: 0,
@@ -696,12 +713,14 @@ export function GraphPaneMixin() {
       // Empty unless the ribbons are actually on: a colour key beside a drawing
       // with no colours in it is a legend for nothing.
       // The tube map colours its tubes whether or not paths are drawn on the
-      // nodes, so under it the key follows the tubes.
+      // nodes, so under it the key follows the tubes, and names the colours
+      // the tubes were drawn in.
       get pathLegend() {
         const paths = self.graph?.paths
-        const colouring = self.drawPaths || self.layoutResult?.tubeMap
+        const tubeMap = self.layoutResult?.tubeMap
+        const colouring = self.drawPaths || tubeMap
         return colouring && paths && pathColorsLegible(paths.length)
-          ? pathLegend(paths)
+          ? pathLegend(paths, tubeMap?.pathColors)
           : []
       },
       // Every walk the graph carries, named for a picker, whatever the count.
@@ -1161,34 +1180,41 @@ export function GraphPaneMixin() {
           ? { start: ramp.start, end: ramp.start + ramp.span }
           : undefined
       },
-      // The reference interval of the hovered node, for a connected linear view
-      // to highlight. Only a graph cut from a track has one: a whole-file import
-      // has no region, and its stable names need not name anything in a loaded
-      // assembly.
+      // A node's reference interval, an allele's between its flanks
+      nodeSpan(nodeId: string) {
+        const { nodeById, nodeNeighbors: neighbors } = self
+        return nodeById && neighbors
+          ? nodeReferenceSpan({ nodeId, nodeById, neighbors })
+          : undefined
+      },
+    }))
+    .views(self => ({
+      // The reference interval under the pointer: the hovered node's, or the
+      // hovered bubble's
+      get hoveredSpan() {
+        const nodeId = self.hoveredNode
+        const bubble = self.hoveredBubble
+        return nodeId !== null
+          ? self.nodeSpan(nodeId)
+          : bubble
+            ? { start: bubble.start, end: bubble.end }
+            : undefined
+      },
+    }))
+    .views(self => ({
+      // The hovered span, for a connected linear view to highlight. Only a
+      // graph cut from a track has one: a whole-file import has no region, and
+      // its stable names need not name anything in a loaded assembly.
       get hoverHighlight() {
-        let result:
-          | {
-              refName: string
-              assemblyName: string
-              start: number
-              end: number
-            }
-          | undefined
         const region = self.graphRegion
-        const nodeId = self.hoveredNode
-        const nodeById = self.nodeById
-        const neighbors = self.nodeNeighbors
-        if (region && nodeId !== null && nodeById && neighbors) {
-          const span = nodeReferenceSpan({ nodeId, nodeById, neighbors })
-          if (span) {
-            result = {
+        const span = self.hoveredSpan
+        return region && span
+          ? {
               refName: region.refName,
               assemblyName: region.assemblyName,
               ...span,
             }
-          }
-        }
-        return result
+          : undefined
       },
     }))
     .views(self => ({
@@ -1397,6 +1423,102 @@ export function GraphPaneMixin() {
           ? tubeMapGenes(reference, self.backboneGenes)
           : []
       },
+      // A drawing of nodes in its own coordinates inside a linear view, whose
+      // reference segments the strip can put back at their bp. A tube map has
+      // its own bands, and walk rows' bars are lengths, not nodes.
+      get referenceStripApplies() {
+        const { host, layoutResult } = self
+        return (
+          !!host?.initialized &&
+          !!layoutResult &&
+          !layoutResult.tubeMap &&
+          !self.hostPlacesX &&
+          self.chosenLayoutMode !== 'walkrows'
+        )
+      },
+    }))
+    .views(self => ({
+      get referenceStripBlocks() {
+        const { graph } = self
+        return self.showReferenceStrip && self.referenceStripApplies && graph
+          ? referenceStripBlocks(graph, {
+              colorScheme: self.effectiveColorScheme,
+              referenceRamp: self.referenceRamp,
+              walkNodes: self.walkHighlight?.nodeIds,
+            })
+          : []
+      },
+      // Read off the live blocks, so the strip follows every frame of a pan
+      // in the linear view
+      get referenceStripFrame() {
+        const { host, graphRegion } = self
+        return host?.initialized && graphRegion
+          ? hostFrame(host, graphRegion)
+          : undefined
+      },
+    }))
+    .views(self => ({
+      get referenceStripShown() {
+        return (
+          self.referenceStripBlocks.length > 0 &&
+          self.referenceStripFrame !== undefined
+        )
+      },
+      // Whether the graph draws reference past the window's edges. A boolean
+      // rather than the bp, which moves on every frame of a pan and would
+      // resize the legend with it.
+      get referenceStripOverhangs() {
+        const frame = self.referenceStripFrame
+        if (!frame || self.referenceStripBlocks.length === 0) {
+          return false
+        }
+        const { left, right } = stripOverhang(
+          self.referenceStripBlocks,
+          frame,
+          self.paneWidth,
+        )
+        return left > 0 || right > 0
+      },
+    }))
+    .views(self => ({
+      // The lit span on the strip, and where the graph drew what it is of:
+      // the hovered node, the hovered bubble's name, or the selected node
+      get referenceStripLit() {
+        if (!self.referenceStripShown) {
+          return undefined
+        }
+        const toScreen = (p: { x: number; y: number }) => ({
+          x: p.x * self.scaleX + self.translateX,
+          y: p.y * self.scaleY + self.translateY,
+        })
+        const bubble = self.hoveredNode === null ? self.hoveredBubble : null
+        if (bubble) {
+          const halo = self.bubbleHalos.find(h => sameBubble(h.bubble, bubble))
+          return {
+            start: bubble.start,
+            end: bubble.end,
+            anchor: halo ? toScreen(halo.labelAt) : undefined,
+          }
+        }
+        const nodeId = self.hoveredNode ?? self.selectedNode
+        const span = nodeId === null ? undefined : self.nodeSpan(nodeId)
+        return span && nodeId !== null
+          ? {
+              ...span,
+              anchor: nodeAnchor(self.nodePositions?.[nodeId], toScreen),
+            }
+          : undefined
+      },
+      referenceStripNodeAt(sx: number, sy: number) {
+        const frame = self.referenceStripFrame
+        return self.referenceStripShown && frame
+          ? stripBlockAt(self.referenceStripBlocks, frame, sx, sy)
+          : undefined
+      },
+      // the strip, and the gap the fit leaves under it
+      get referenceStripZonePx() {
+        return self.referenceStripShown ? REFERENCE_STRIP_ZONE_PX : 0
+      },
     }))
     .views(self => ({
       // `paneHeight` replaces the built-in ceiling rather than adding a second
@@ -1407,10 +1529,15 @@ export function GraphPaneMixin() {
         return Math.max(MIN_CANVAS_HEIGHT, self.paneHeight ?? MAX_CANVAS_HEIGHT)
       },
       // Room over a tube map for the rows its genes need, one inside the
-      // padding and one more for each further gene that overlaps it
+      // padding and one more for each further gene that overlaps it, and
+      // room for the reference strip
       get fitPadTop() {
         const rows = tubeMapGeneRows(self.tubeMapGenes)
-        return FIT_PADDING + Math.max(0, rows - 1) * GENE_ROW_PX
+        return (
+          FIT_PADDING +
+          Math.max(0, rows - 1) * GENE_ROW_PX +
+          self.referenceStripZonePx
+        )
       },
       // A tube map on its own axis reads by panning along it, as in
       // sequenceTubeMap. Rather than shrink a long cut to a strip, the fit
@@ -1536,19 +1663,27 @@ export function GraphPaneMixin() {
       },
     }))
     .views(self => ({
-      // What the tube map's legend has to explain: a zigzag where the ruler
-      // squeezes a box on screen, and the fold its walks' ticks stand for
+      // What the tube map's legend has to explain: that on the own axis a
+      // box is as wide as the log of its length, the fold its walks' ticks
+      // stand for, the reads' strands, and the marks on the reads in view
       get tubeMapKeys() {
-        const boxes = self.tubeMapRulerBoxes
+        const layout = self.layoutResult
+        const reads = layout?.tubeMap?.layout.reads ?? []
+        const picture = self.tubeMapPicture
         const frame = self.tubeMapFrame
-        const marks =
-          boxes && frame
-            ? rulerMarks(boxes, frame.x, self.paneWidth, () => 0)
-            : undefined
+        const shown =
+          picture && frame && mismatchesLegible(frame.yScale)
+            ? picture.mismatches.filter(m =>
+                mismatchOnScreen(m, { x: frame.x, width: self.paneWidth }),
+              )
+            : []
         return {
-          squeezed: (marks?.squeezed.length ?? 0) > 0,
+          logWidths: layout?.tubeMap !== undefined && !layout.referenceAxis,
           foldBp:
             self.tubeMapDeviations.length > 0 ? self.tubeMapFold : undefined,
+          forwardReads: reads.some(r => !r.is_reverse),
+          reverseReads: reads.some(r => r.is_reverse),
+          mismatches: new Set(shown.map(m => m.kind)),
         }
       },
       tubeMapNodeAt(sx: number, sy: number) {
@@ -1644,6 +1779,9 @@ export function GraphPaneMixin() {
       setShowGenes(show: boolean) {
         self.showGenes = show
       },
+      setShowReferenceStrip(show: boolean) {
+        self.showReferenceStrip = show
+      },
       setTubeMapFold(bp: number) {
         self.tubeMapFold = bp
       },
@@ -1690,6 +1828,12 @@ export function GraphPaneMixin() {
       setHoveredNode(nodeId: string | null) {
         self.hoveredNode = nodeId
       },
+      setHoveredBubble(bubble: MinigraphBubble | null) {
+        self.hoveredBubble = bubble
+      },
+      setPointerInPane(inside: boolean) {
+        self.pointerInPane = inside
+      },
       setLegendSize(size: { width: number; height: number }) {
         self.legendSize = size
       },
@@ -1713,6 +1857,7 @@ export function GraphPaneMixin() {
       // is replaced, and by clearGraph.
       clearInteractionState() {
         self.hoveredNode = null
+        self.hoveredBubble = null
         self.hoveredEdge = null
         self.selectedNode = null
         self.draggingNode = null
@@ -2554,6 +2699,9 @@ export function GraphPaneMixin() {
           // LGV writes `{hoverPosition, hoverFeature}` to session.hovered on
           // every mousemove; neither field names the source view, so the guard
           // is that the position lies in the region this graph was cut from.
+          // A pointer over the pane itself is the host's too, at a bp its x
+          // only means on a reference-axis layout, so there the pane's own hit
+          // test is the hover.
           //
           // Only `hovered` is tracked — the graph reads are untracked, so a
           // geometry rebuild can't re-fire this and clobber a hover the canvas
@@ -2566,7 +2714,7 @@ export function GraphPaneMixin() {
               untracked(() => {
                 const region = self.graphRegion
                 const graph = self.graph
-                if (region && graph) {
+                if (region && graph && !self.pointerInPane) {
                   self.setHoveredNode(
                     hover && hoverInRegion(hover, region)
                       ? nodeForLgvHover({ hover, nodes: graph.nodes })
@@ -2606,6 +2754,7 @@ export function GraphPaneMixin() {
               () => `${self.scale}-${self.translateX}-${self.translateY}`,
               () => {
                 self.setHoveredNode(null)
+                self.setHoveredBubble(null)
                 self.setHoveredEdge(null)
               },
               { name: 'GraphClearHoverOnViewportChange' },
@@ -2996,6 +3145,18 @@ export function GraphPaneMixin() {
               self.setShowGenes(!self.showGenes)
             },
           },
+          ...(self.referenceStripApplies
+            ? [
+                {
+                  type: 'checkbox' as const,
+                  label: 'Reference strip at bp',
+                  checked: self.showReferenceStrip,
+                  onClick: () => {
+                    self.setShowReferenceStrip(!self.showReferenceStrip)
+                  },
+                },
+              ]
+            : []),
         ]
       },
       launchMenuItems(): MenuItem[] {

package/src/LinearGraphDisplay/model.ts

@@ -373,6 +373,8 @@ export function stateModelFactory(configSchema: LinearGraphDisplayConfigModel) {
             referencePath: self.referencePath,
             geneTrackId: self.geneTrackId,
             showGenes: self.showGenes,
+            showBubbles: self.showBubbles,
+            showDeletionEdges: self.showDeletionEdges,
           } satisfies GraphViewSpec
         },
       }))

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.0.13'
+export const version = '4.0.15'

package/dist/chunks/chunk-CJ56O2VG.js

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t=xa(e.filter(s=>s.type===n),s=>`${s.nodeStart},${s.nodeEnd}`);t.forEach(s=>{let a=.3,i=.4/s.length;s.length<=5&&(a=.5,i=0),s.sort(Ma),s.forEach(l=>{let c,f;l.yStart<l.yEnd?(c=l.xStart+(l.xEnd-l.xStart)*(1-a),a+=i,f=l.xStart+(l.xEnd-l.xStart)*(1-a)):(c=l.xStart+(l.xEnd-l.xStart)*a,a+=i,f=l.xStart+(l.xEnd-l.xStart)*a);let u=`M ${l.xStart} ${l.yStart}`;u+=` C ${c} ${l.yStart} ${c} ${l.yEnd} ${l.xEnd} ${l.yEnd}`,u+=` V ${l.yEnd+l.width}`,u+=` C ${f} ${l.yEnd+l.width} ${f} ${l.yStart+l.width} ${l.xStart} ${l.yStart+l.width}`,u+=" Z",l.path=u})});let r=Array.from(t.keys());r.sort(function(s,a){let i=s.split(",").map(Number),l=a.split(",").map(Number),c=i[0]??0,f=i[1]??0,u=l[0]??0,d=l[1]??0;return c<u?-1:c>u?1:f<d?-1:f>d?1:0});let o=[];for(let s of r){let a=t.get(s);a!==void 0&&o.push(...a)}return o}function Ao(e){let n=`M ${e.x-9} ${e.y} Q ${e.x-9} ${e.y-9} ${e.x} ${e.y-9}`,t=e.x,r=e.y-9;return e.width>1&&(t+=e.pixelWidth,n+=` L ${t} ${r}`),n+=` Q ${t+9} ${r} ${t+9} 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Na=["#6baed6","#4292c6","#2171b5","#08519c"],Sa=["#fb6a4a","#ef3b2c","#cb181d","#a50f15"];function Co(e){let n=e.is_reverse?Sa:Na;return n[e.id%n.length]}function Ra(e){let n=new Map;for(let[t,r]of e.pathVisits??[])for(let o of r){let s=`${o.path}	${t}`,a=n.get(s);a?a.push(o.strand):n.set(s,[o.strand])}return n}function Ea(e){let n=new Map(e.nodes.map(s=>[s.id,s])),t=Ra(e),r=(e.paths??[]).map((s,a)=>({path:s,index:a})),o=r.findIndex(s=>Le(s.path.name).name===e.referencePath);return o>0&&r.unshift(...r.splice(o,1)),r.flatMap(({path:s,index:a})=>{let i=Le(s.name).name,l=new Map,c=s.nodeIds.flatMap(f=>{let u=n.get(f);if(!u)return[];let d=l.get(u.name)??0;l.set(u.name,d+1);let h=t.get(`${i}	${u.name}`)?.[d]??Yn(u);return[kn(u,h)]});return c.length>0?[{id:a,name:s.name,sequence:c,sourceTrackID:0,type:"haplotype"}]:[]})}function Aa(e){return e.nodes.map(n=>({name:n.id,seq:"",sequenceLength:Math.max(1,n.length)}))}function Ae(e){return(e.paths?.length??0)>0}var Ta=600,Ca=3,Ia=15;function 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