@jbrowse/bandage-core 11.7.3 → 11.9.0

package/dist/chunks/{chunk-QXBQDHKL.js → chunk-3BOREHCJ.js}

@@ -2,7 +2,7 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-PKGPSTRW.js";
+} from "./chunk-JO2T77NW.js";
 import {
   Canvas2DRenderer
 } from "./chunk-4DMSPNYV.js";
@@ -13,7 +13,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-EPOPGV5G.js";
+} from "./chunk-IXLT3JJX.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,45 +21,50 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   geneLabelCandidates
-} from "./chunk-QJC63NFR.js";
+} from "./chunk-TQ26XEFL.js";
 import {
   nodesUnderBox
-} from "./chunk-LH436HS2.js";
+} from "./chunk-4JDO7ZLN.js";
 import {
   escapeAttr,
   serializeEl
 } from "./chunk-H2H4Y3TV.js";
 import {
   genePins
-} from "./chunk-BFUS3ENH.js";
+} from "./chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunk-AJQRKN3X.js";
+} from "./chunk-N3DCLT7M.js";
 import {
   axisScaleOf
-} from "./chunk-F4CDC72I.js";
+} from "./chunk-3DHGSHC3.js";
 import {
   figureScene
-} from "./chunk-UTDMFVC7.js";
+} from "./chunk-I5CHAYDZ.js";
 import {
   encodingStops
-} from "./chunk-6RB5ZQ34.js";
+} from "./chunk-UEWIGD52.js";
+import {
+  THREAD_PX,
+  passesKey,
+  threadsPasses
+} from "./chunk-3BDQQTXY.js";
 import {
   rangeText
-} from "./chunk-SG7VQB4F.js";
+} from "./chunk-IZKM4NY7.js";
 import {
   walkRowLabels
-} from "./chunk-SENPGW4O.js";
+} from "./chunk-VCUOYVLC.js";
 import {
   nodeInk
 } from "./chunk-ZANALBSX.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-4SN7R4UF.js";
+} from "./chunk-2MXFG3W7.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-XKPXOIWD.js";
+} from "./chunk-JVT3XTKN.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -79,6 +84,8 @@ var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
 var BAR_PX = 48;
 var SWATCH_PX = 18;
 var KEY_GAP_PX = 16;
+var KEY_LINE_PX = 16;
+var KEY_TALL_PX = 32;
 var STRIP_KEY_PX = 22;
 var FADED = "rgb(160,160,160)";
 var GENE_INK = "#1c1c22";
@@ -92,15 +99,45 @@ function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   );
   return {
     width,
+    height: under ? KEY_TALL_PX : KEY_LINE_PX,
     markup: `${defs}<g transform="translate(${x} ${y})" ${FONT}><rect y="5" width="${bar}" height="8" rx="2" ${fill}/><text x="${bar + 5}" y="13"><tspan font-weight="bold">${escapeAttr(label)}</tspan>${escapeAttr(after)}</text>${under ? `<text y="28">${escapeAttr(under)}</text>` : ""}</g>`
   };
 }
 function exonKeySvg(x, y) {
   return {
     width: SWATCH_PX + 5 + 4 * LABEL_CHAR_PX,
+    height: KEY_LINE_PX,
     markup: `<g transform="translate(${x} ${y})" ${FONT}><rect x="1" y="4" width="${SWATCH_PX - 2}" height="10" rx="4" fill="none" stroke="${EXON_COLOR}" stroke-width="2"/><text x="${SWATCH_PX + 5}" y="13">exon</text></g>`
   };
 }
+function passesKeySvg(x, y, note) {
+  const lines = [6, 9, 12].map(
+    (ly) => `<line y1="${ly}" y2="${ly}" x2="${SWATCH_PX}" stroke="#444" stroke-width="${THREAD_PX}"/>`
+  ).join("");
+  return {
+    width: SWATCH_PX + 5 + note.length * LABEL_CHAR_PX,
+    height: KEY_LINE_PX,
+    markup: `<g transform="translate(${x} ${y})" ${FONT}>${lines}<text x="${SWATCH_PX + 5}" y="13">${note}</text></g>`
+  };
+}
+function keyLines(keys, width) {
+  const markup = [];
+  let x = 6;
+  let y = 2;
+  let line = 0;
+  for (const key of keys) {
+    const size = key(0, 0);
+    if (x > 6 && x + size.width > width - 6) {
+      x = 6;
+      y += line + 4;
+      line = 0;
+    }
+    markup.push(key(x, y).markup);
+    x += size.width + KEY_GAP_PX;
+    line = Math.max(line, size.height);
+  }
+  return { markup, height: y + line };
+}
 function walkKeySvg(id, x, y, walk, label, key) {
   return keySvg(
     id,
@@ -264,22 +301,18 @@ function figureSvg(graph, layout, o = {}) {
     });
     height = grid.total;
   } else {
-    let x = 6;
-    const push = (key) => {
-      parts.push(key.markup);
-      x += key.width + KEY_GAP_PX;
-    };
+    const keys = [];
     if (lift) {
       lift.walks.forEach((walk, i) => {
-        push(
-          walkKeySvg(`key${i}`, x, 2, walk, labelOf(walk.name), keyText(walk))
+        keys.push(
+          (x, y) => walkKeySvg(`key${i}`, x, y, walk, labelOf(walk.name), keyText(walk))
         );
       });
-      push(
-        keySvg(
+      keys.push(
+        (x, y) => keySvg(
           "faded",
           x,
-          2,
+          y,
           [{ offset: 0, color: FADED }],
           "",
           `not on ${lift.walks.length === 1 ? labelOf(lift.walks[0].name) : "these walks"}`,
@@ -287,24 +320,31 @@ function figureSvg(graph, layout, o = {}) {
           0.3
         )
       );
+      if (threadsPasses(lift.walks)) {
+        keys.push((x, y) => passesKeySvg(x, y, passesKey(lift.walks)));
+      }
     }
     if (rows) {
-      const key = walkRowsKeyTree(
-        walkRowsKey(rows, {
-          ramp: rampInterval,
-          genes: o.rowGenes?.size ? o.rowGeneGaps : void 0
-        }),
-        x,
-        2,
-        "rows-key"
-      );
-      push({ width: key.width, markup: serializeEl(key.tree) });
+      const entries = walkRowsKey(rows, {
+        ramp: rampInterval,
+        genes: o.rowGenes?.size ? o.rowGeneGaps : void 0
+      });
+      entries.forEach((entry, i) => {
+        keys.push((x, y) => {
+          const key = walkRowsKeyTree([entry], x, y, `rows-key-${i}`);
+          return {
+            width: key.width - KEY_GAP_PX,
+            height: KEY_LINE_PX,
+            markup: serializeEl(key.tree)
+          };
+        });
+      });
     } else if (!lift && referenceRamp) {
-      push(
-        keySvg(
+      keys.push(
+        (x, y) => keySvg(
           "ramp",
           x,
-          2,
+          y,
           encodingStops({ field: "reference", scheme: "rainbow" }),
           referenceName ? `${referenceName} position` : "Reference position",
           "",
@@ -317,9 +357,11 @@ function figureSvg(graph, layout, o = {}) {
       );
     }
     if (pins.some((pin) => pin.exonsByNode.length > 0)) {
-      push(exonKeySvg(x, 2));
+      keys.push((x, y) => exonKeySvg(x, y));
     }
-    const header = parts.length > 0 ? FACET_TITLE_PX : 0;
+    const keyed = keyLines(keys, width);
+    parts.push(...keyed.markup);
+    const header = keys.length > 0 ? Math.max(FACET_TITLE_PX, keyed.height) : 0;
     const usable = width - 2 * FIT_PADDING;
     const drawn = pixelRows || !(bounds.w > 0) ? bounds.h : bounds.h * usable / bounds.w;
     const h = Math.max(

package/dist/chunks/{chunk-F4CDC72I.js → chunk-3DHGSHC3.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-XKPXOIWD.js";
+} from "./chunk-JVT3XTKN.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-P276TWPM.js → chunk-3GORESBG.js}

@@ -9,7 +9,7 @@ import {
   edgeJoinOf,
   routedEdgeCurves,
   strandSides
-} from "./chunk-VACK24HF.js";
+} from "./chunk-JJV2GT2Z.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-4KOYS5WR.js → chunk-4BYGFDQB.js}

@@ -1,6 +1,6 @@
 import {
   ownStrand
-} from "./chunk-VACK24HF.js";
+} from "./chunk-JJV2GT2Z.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-LH436HS2.js → chunk-4JDO7ZLN.js}

@@ -1,7 +1,7 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-2US43KNG.js";
+} from "./chunk-7YSIP3O2.js";
 import {
   weakMemo
 } from "./chunk-HMXCN6PG.js";
@@ -9,7 +9,7 @@ import {
   pathRibbonOffsets,
   translateCurves,
   yToXOf
-} from "./chunk-VACK24HF.js";
+} from "./chunk-JJV2GT2Z.js";
 
 // src/util/hitDetection.ts
 function distanceToSegment(px, py, x1, y1, x2, y2) {

package/dist/chunks/{chunk-2US43KNG.js → chunk-7YSIP3O2.js}

@@ -1,10 +1,10 @@
 import {
   baseEdgeCurves
-} from "./chunk-33KUO34R.js";
+} from "./chunk-P2GJBFNA.js";
 import {
   curveBounds,
   pathRibbonOffsets
-} from "./chunk-VACK24HF.js";
+} from "./chunk-JJV2GT2Z.js";
 
 // src/util/SpatialIndex.ts
 var FALLBACK_CELL_SIZE = 50;

package/dist/chunks/{chunk-VNF236GG.js → chunk-ARXDNQLF.js}

@@ -3,7 +3,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-63XWYNID.js";
+} from "./chunk-BDS5VZYZ.js";
 import {
   sampleRowLayout
 } from "./chunk-XR2HMGAS.js";
@@ -15,7 +15,7 @@ import {
 } from "./chunk-UAFATXYA.js";
 import {
   walkRowLayout
-} from "./chunk-SENPGW4O.js";
+} from "./chunk-VCUOYVLC.js";
 import {
   isBackbone,
   isOffReference

package/dist/chunks/{chunk-N73RA4DR.js → chunk-AURNOR27.js}

@@ -7,15 +7,15 @@ import {
 } from "./chunk-AB35TJST.js";
 import {
   polylineMidpoint
-} from "./chunk-2VMKQKVO.js";
+} from "./chunk-HNNP5QUN.js";
 import {
   edgeCurvesOf
-} from "./chunk-P276TWPM.js";
+} from "./chunk-3GORESBG.js";
 import {
   curveBounds,
   curveMidpoint,
   polylinePx
-} from "./chunk-VACK24HF.js";
+} from "./chunk-JJV2GT2Z.js";
 
 // src/graphLabels.ts
 var MIN_DELETION_LABEL_PX = 26;

package/dist/chunks/{chunk-63XWYNID.js → chunk-BDS5VZYZ.js}

@@ -1,21 +1,21 @@
 import {
   stepName,
   tubeMapReads
-} from "./chunk-SDI6BVG7.js";
+} from "./chunk-KKHXMJEE.js";
 import {
   referenceWalkName
-} from "./chunk-G7SG4XMK.js";
+} from "./chunk-LODKC7PJ.js";
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-GD6RUZU5.js";
+} from "./chunk-VQ353UDK.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";
 import {
   ownStrand,
   strandSides
-} from "./chunk-VACK24HF.js";
+} from "./chunk-JJV2GT2Z.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-BXE3SBBN.js → chunk-C3KAPREU.js}

@@ -1,7 +1,7 @@
 import {
   walkRowRuns,
   walkRowsOf
-} from "./chunk-G7SG4XMK.js";
+} from "./chunk-LODKC7PJ.js";
 
 // src/layout/walkRows.ts
 function filterSamples(rows, samples) {