@jbrowse/bandage-core 0.1.10 → 0.1.12

package/dist/index.js

@@ -1982,19 +1982,6 @@ function tubeMapReferenceLayout(graph) {
   };
 }
 
-// src/layout/variantMapLayout.ts
-function variantMapLayout(graph) {
-  const backbone = backboneNodes(graph);
-  if (backbone.length === 0) {
-    return void 0;
-  }
-  return {
-    nodePositions: backbonePositions(backbone),
-    referenceAxis: true,
-    pixelRows: true
-  };
-}
-
 // src/layout/walkRows.ts
 function sampleOf(path) {
   return path.sample ?? panSNSample(path.name);
@@ -2095,12 +2082,18 @@ function walkRows(graph, region, unit) {
       runs
     };
   };
+  const meetsReference = (p) => p.nodeIds.some((id) => span2.has(id));
+  const placedWalks = new Set(
+    paths.filter((p) => p !== reference && meetsReference(p)).map((p) => p.name)
+  );
   const origin = cut ? cut.start : referenceStart;
   return {
     origin,
     unit,
     reference: rowOf(reference),
-    rows: paths.filter((p) => p !== reference).map(rowOf).sort(
+    rows: paths.filter(
+      (p) => p !== reference && (meetsReference(p) || !placedWalks.has(p.name))
+    ).map(rowOf).sort(
       (a, b) => Number(b.complete) - Number(a.complete) || b.bp - a.bp || a.label.localeCompare(b.label)
     )
   };
@@ -2184,15 +2177,6 @@ var LAYOUT_MODES = [
     available: hasBackbone,
     drawsLocally: hasBackbone
   },
-  {
-    value: "variants",
-    label: "Variant map",
-    description: "The reference as a line with one typed glyph per bubble, from the bubble index or from the graph itself: SNP, indel, deletion, inversion, repeat array. Click a glyph to open the graph inside it.",
-    run: variantMapLayout,
-    cutMargins: true,
-    available: hasBackbone,
-    drawsLocally: hasBackbone
-  },
   {
     value: "tubemap",
     label: "Tube map",
@@ -5606,8 +5590,6 @@ var LEGEND_INSET_PX = 6;
 var ROUTE_STACK = 8;
 var GENE_PIN_DROP_PX = 18;
 var GENE_STACK = 2;
-var GLYPH_ROOM_PX = 60;
-var MAX_GLYPH_LABEL_ROWS = 8;
 var TOPMOST_BASELINE = LABEL_PX + LABEL_PAD;
 function byExtent(items, extent) {
   return [...items].sort((a, b) => extent(b) - extent(a));
@@ -5665,32 +5647,6 @@ function layoutLabels(m) {
     frame,
     take
   );
-  const glyphRows = Math.max(
-    2,
-    Math.min(
-      MAX_GLYPH_LABEL_ROWS,
-      Math.floor((translateY - GLYPH_ROOM_PX) / (LABEL_PX + LABEL_PAD * 2))
-    )
-  );
-  const glyphs = placeLabels(
-    byExtent(m.bubbleGlyphs, (g) => g.bubble.end - g.bubble.start).flatMap(
-      (glyph) => {
-        const glyphX = (glyph.bubble.start + glyph.bubble.end) / 2 * scaleX + translateX;
-        const half = labelWidth(glyph.label) / 2;
-        return glyphX < 0 || glyphX > width ? [] : [
-          {
-            item: { glyph, glyphX },
-            x: Math.min(Math.max(glyphX, half), width - half),
-            y: TOPMOST_BASELINE,
-            text: glyph.label,
-            stack: glyphRows - 1
-          }
-        ];
-      }
-    ),
-    frame,
-    take
-  );
   const genes = placeLabels(
     byExtent(m.genePins, (pin) => pin.gene.end - pin.gene.start).map((pin) => {
       const { x, y } = screen(pin.at);
@@ -5741,7 +5697,6 @@ function layoutLabels(m) {
   );
   return {
     bubbles,
-    glyphs,
     genes,
     routes: routes2,
     sizes: [...deletionLabels, ...nodeLabels]

package/dist/types/index.d.ts

@@ -45,7 +45,7 @@ export type { WalkRows } from './layout/walkRows.js';
 export { walkRowsExtent } from './layout/walkRowLayout.js';
 export { ROW_HEIGHT_PX } from './layout/rowSpacing.js';
 export { HALO_FACTOR, LEGEND_INSET_PX, layoutLabels } from './labelLayout.js';
-export type { BubbleGlyph, LabelLayout, LabelLayoutSource } from './labelLayout.js';
+export type { LabelLayout, LabelLayoutSource } from './labelLayout.js';
 export { formatBp } from './graphLabels.js';
 export { genePins } from './genes/genePins.js';
 export type { GeneModel, GenePin } from './genes/genePins.js';

package/dist/types/labelLayout.d.ts

@@ -1,6 +1,4 @@
 import type { BubbleHalo, RouteLabel } from './bubbles/bubbleHalos.js';
-import type { MinigraphBubble } from './bubbles/bubbleLine.js';
-import type { BubbleKind } from './bubbles/classifyBubble.js';
 import type { DeletionEdge } from './deletionEdges.js';
 import type { GenePin } from './genes/genePins.js';
 import type { GraphLabel } from './graphLabels.js';
@@ -9,11 +7,6 @@ import type { AlleleDeletion, NodeSegment } from './types.js';
 import type { AxisScale } from './util/geometry.js';
 export declare const HALO_FACTOR = 3.4;
 export declare const LEGEND_INSET_PX = 6;
-export interface BubbleGlyph {
-    bubble: MinigraphBubble;
-    kind: BubbleKind;
-    label: string;
-}
 export interface LabelLayoutSource {
     paneWidth: number;
     canvasHeight: number;
@@ -31,7 +24,6 @@ export interface LabelLayoutSource {
         y: number;
     }[];
     bubbleHalos: BubbleHalo[];
-    bubbleGlyphs: BubbleGlyph[];
     genePins: GenePin[];
     poppedFrom?: {
         label: string;
@@ -46,10 +38,6 @@ export interface LabelLayoutSource {
 }
 export interface LabelLayout {
     bubbles: PlacedLabel<BubbleHalo>[];
-    glyphs: PlacedLabel<{
-        glyph: BubbleGlyph;
-        glyphX: number;
-    }>[];
     genes: PlacedLabel<GenePin>[];
     routes: PlacedLabel<{
         halo: BubbleHalo;

package/dist/types/layoutModes.d.ts

@@ -2,7 +2,6 @@ import { anchoredLayout } from './layout/anchoredLayout.js';
 import { orderedLayout } from './layout/orderedLayout.js';
 import { sampleRowLayout } from './layout/sampleRowLayout.js';
 import { hasTubeMapPaths, tubeMapLayout, tubeMapReferenceLayout } from './layout/tubeMapLayout.js';
-import { variantMapLayout } from './layout/variantMapLayout.js';
 import { walkRowLayout } from './layout/walkRowLayout.js';
 import type { Graph, LayoutResult } from './types.js';
 export declare const FORCE_LAYOUT_LABEL = "Force-directed layout";
@@ -50,14 +49,6 @@ export declare const LAYOUT_MODES: readonly [{
     readonly cutMargins: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
-}, {
-    readonly value: "variants";
-    readonly label: "Variant map";
-    readonly description: "The reference as a line with one typed glyph per bubble, from the bubble index or from the graph itself: SNP, indel, deletion, inversion, repeat array. Click a glyph to open the graph inside it.";
-    readonly run: typeof variantMapLayout;
-    readonly cutMargins: true;
-    readonly available: (graph: Graph) => boolean;
-    readonly drawsLocally: (graph: Graph) => boolean;
 }, {
     readonly value: "tubemap";
     readonly label: "Tube map";
@@ -84,7 +75,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly drawsLocally: () => false;
 }];
 export type LayoutModeValue = (typeof LAYOUT_MODES)[number]['value'];
-export declare const LAYOUT_MODE_VALUES: ("auto" | "ordered" | "samplerows" | "walkrows" | "variants" | "tubemap" | "tubemapref" | "force")[];
+export declare const LAYOUT_MODE_VALUES: ("auto" | "ordered" | "samplerows" | "walkrows" | "tubemap" | "tubemapref" | "force")[];
 export declare function modeUsesLayoutEngine(value: string, graph: Graph): boolean;
 export declare function layoutModeByValue(value: string): {
     readonly value: "auto";
@@ -118,14 +109,6 @@ export declare function layoutModeByValue(value: string): {
     readonly cutMargins: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
-} | {
-    readonly value: "variants";
-    readonly label: "Variant map";
-    readonly description: "The reference as a line with one typed glyph per bubble, from the bubble index or from the graph itself: SNP, indel, deletion, inversion, repeat array. Click a glyph to open the graph inside it.";
-    readonly run: typeof variantMapLayout;
-    readonly cutMargins: true;
-    readonly available: (graph: Graph) => boolean;
-    readonly drawsLocally: (graph: Graph) => boolean;
 } | {
     readonly value: "tubemap";
     readonly label: "Tube map";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "0.1.10",
+  "version": "0.1.12",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {

package/dist/types/layout/variantMapLayout.d.ts

@@ -1,2 +0,0 @@
-import type { Graph, LayoutResult } from '../types.js';
-export declare function variantMapLayout(graph: Graph): LayoutResult | undefined;