@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/block.tk.junction-2KI3SPXW.js

@@ -0,0 +1,2358 @@
+import {
+  spliceevent_phrase_default
+} from "./chunk-IUT72AWA.js";
+import {
+  spliceevent_exonskip_getdefault_default
+} from "./chunk-4DXQJGJ7.js";
+import {
+  legend_newrow
+} from "./chunk-S4XD4GGN.js";
+import "./chunk-V2OJLJSK.js";
+import "./chunk-IGJOH5LV.js";
+import {
+  appear2 as appear,
+  axisstyle,
+  category2legend,
+  export_data,
+  font,
+  gmmode,
+  keyupEnter,
+  sayerror,
+  tkt
+} from "./chunk-NQDF3U2C.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-CCYVGZGI.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import "./chunk-N7DVQTPC.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import {
+  dofetch2,
+  dofetch3
+} from "./chunk-GRVO7RW4.js";
+import "./chunk-7CJKL3LK.js";
+import "./chunk-HZ3TCGBK.js";
+import {
+  IN_frame,
+  OUT_frame,
+  bplen,
+  defaultcolor,
+  spliceeventchangegmexon
+} from "./chunk-IZUYLFOX.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import {
+  axisRight,
+  category10_default
+} from "./chunk-Z2ZITHT4.js";
+import {
+  linear,
+  log,
+  ordinal
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __commonJS,
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// ../node_modules/d3-beeswarm/build/d3-beeswarm.js
+var require_d3_beeswarm = __commonJS({
+  "../node_modules/d3-beeswarm/build/d3-beeswarm.js"(exports, module) {
+    (function(global, factory) {
+      typeof exports === "object" && typeof module !== "undefined" ? factory(exports) : typeof define === "function" && define.amd ? define(["exports"], factory) : factory(global.d3 = global.d3 || {});
+    })(exports, function(exports2) {
+      "use strict";
+      function beeswarm2() {
+        var data = [];
+        var radius = 4;
+        var orientation = "horizontal";
+        var side = "symetric";
+        var distributeOn = (
+          // accessor to the x value
+          function(datum) {
+            return datum.x;
+          }
+        );
+        var minDistanceBetweenCircles;
+        var minSquareDistanceBetweenCircles;
+        var xBasedDataManager;
+        var xBasedColliderManager;
+        var yBasedColliderManager;
+        var arrangement;
+        var totalPossibleColliders, maxPossibleColliders, totalTestedPlacements, visitedColliderCount, totalVisitedColliders, maxVisitedColliders;
+        function _beeswarm() {
+        }
+        _beeswarm.data = function(_) {
+          if (!arguments.length) {
+            return data;
+          }
+          data = _;
+          return _beeswarm;
+        };
+        _beeswarm.radius = function(_) {
+          if (!arguments.length) {
+            return radius;
+          }
+          radius = _;
+          return _beeswarm;
+        };
+        _beeswarm.orientation = function(_) {
+          if (!arguments.length) {
+            return orientation;
+          }
+          if (_ === "horizontal" || _ === "vertical") {
+            orientation = _;
+          }
+          return _beeswarm;
+        };
+        _beeswarm.side = function(_) {
+          if (!arguments.length) {
+            return side;
+          }
+          if (_ === "symetric" || _ === "positive" || _ === "negative") {
+            side = _;
+          }
+          return _beeswarm;
+        };
+        _beeswarm.distributeOn = function(_) {
+          if (!arguments.length) {
+            return distributeOn;
+          }
+          distributeOn = _;
+          return _beeswarm;
+        };
+        _beeswarm.arrange = function() {
+          initArrangement();
+          arrangement.forEach(function(d) {
+            var bestYPosition = -Infinity, relativeYPos, xBasedPossibleColliders = gatherXBasedPossibleColliders(d);
+            if (xBasedPossibleColliders.length === 0) {
+              bestYPosition = 0;
+            } else {
+              yBasedColliderManager.clear();
+              yBasedColliderManager.addMany(xBasedPossibleColliders);
+              d.free = 0;
+              if (!collidesWithOther(d, yBasedColliderManager.closestTo0())) {
+                bestYPosition = 0;
+                totalVisitedColliders += visitedColliderCount;
+                if (visitedColliderCount > maxVisitedColliders) {
+                  maxVisitedColliders = visitedColliderCount;
+                }
+                visitedColliderCount = 0;
+                totalTestedPlacements += 1;
+              } else {
+                xBasedPossibleColliders.forEach(function(xbpc) {
+                  relativeYPos = yPosRelativeToXbpc(xbpc, d);
+                  placeBelow(d, xbpc, relativeYPos);
+                  if (isAuthorizedPlacement(d) && isBetterPlacement(d, bestYPosition) && !collidesWithOther(d, yBasedColliderManager.dln(xbpc))) {
+                    bestYPosition = d.free;
+                  }
+                  totalVisitedColliders += visitedColliderCount;
+                  if (visitedColliderCount > maxVisitedColliders) {
+                    maxVisitedColliders = visitedColliderCount;
+                  }
+                  visitedColliderCount = 0;
+                  totalTestedPlacements += 1;
+                  placeAbove(d, xbpc, relativeYPos);
+                  if (isAuthorizedPlacement(d) && isBetterPlacement(d, bestYPosition) && !collidesWithOther(d, yBasedColliderManager.dln(xbpc))) {
+                    bestYPosition = d.free;
+                  }
+                  totalVisitedColliders += visitedColliderCount;
+                  if (visitedColliderCount > maxVisitedColliders) {
+                    maxVisitedColliders = visitedColliderCount;
+                  }
+                  visitedColliderCount = 0;
+                  totalTestedPlacements += 1;
+                });
+              }
+            }
+            ;
+            d.free = bestYPosition;
+            if (orientation === "horizontal") {
+              d.x = d.fixed;
+              d.y = bestYPosition;
+            } else {
+              d.x = bestYPosition;
+              d.y = d.fixed;
+            }
+            xBasedColliderManager.add(d);
+          });
+          return arrangement;
+        };
+        _beeswarm.metrics = function() {
+          return {
+            totalPossibleColliders,
+            maxPossibleColliders,
+            totalTestedPlacements,
+            visitedColliderCount,
+            totalVisitedColliders,
+            maxVisitedColliders
+          };
+        };
+        function initArrangement() {
+          arrangement = data.map(function(d, i) {
+            return {
+              datum: d,
+              id: i,
+              fixed: distributeOn(d),
+              free: -Infinity
+            };
+          });
+          minDistanceBetweenCircles = 2 * radius;
+          minSquareDistanceBetweenCircles = Math.pow(minDistanceBetweenCircles, 2);
+          xBasedDataManager = new SortedDirectAccessDoublyLinkedList().valueAccessor(function(d) {
+            return d.fixed;
+          }).addMany(arrangement);
+          xBasedColliderManager = new SortedDirectAccessDoublyLinkedList().valueAccessor(function(d) {
+            return d.fixed;
+          });
+          yBasedColliderManager = new SortedDirectAccessDoublyLinkedList().valueAccessor(function(d) {
+            return d.free;
+          });
+          totalPossibleColliders = maxPossibleColliders = 0;
+          totalTestedPlacements = 0;
+          visitedColliderCount = totalVisitedColliders = maxVisitedColliders = 0;
+        }
+        function findNearestPossibleCollider(dln, visitedDln, direction) {
+          if (visitedDln === null) {
+            return null;
+          } else if (direction === "prev" ? dln.value - visitedDln.value > minDistanceBetweenCircles : visitedDln.value - dln.value > minDistanceBetweenCircles) {
+            return null;
+          } else {
+            if (isFinite(visitedDln.datum.free)) {
+              return visitedDln.datum;
+            }
+            return findNearestPossibleCollider(dln, visitedDln[direction], direction);
+          }
+        }
+        function visitToGatherXBasedPossibleColliders(dln, visitedDln, direction, xBasedPossibleColliders) {
+          if (visitedDln === null) {
+            return;
+          } else if (direction === "prev" ? dln.value - visitedDln.value > minDistanceBetweenCircles : visitedDln.value - dln.value > minDistanceBetweenCircles) {
+            return;
+          } else {
+            xBasedPossibleColliders.push(visitedDln.datum);
+            visitToGatherXBasedPossibleColliders(dln, visitedDln[direction], direction, xBasedPossibleColliders);
+          }
+        }
+        function gatherXBasedPossibleColliders(datum) {
+          var xBasedPossibleColliders = [];
+          var dln = xBasedDataManager.dln(datum);
+          var nearestXPrevAlreadyArrangedData = findNearestPossibleCollider(dln, dln.prev, "prev");
+          var nearestXNextAlreadyArrangedData = findNearestPossibleCollider(dln, dln.next, "next");
+          if (nearestXPrevAlreadyArrangedData != null) {
+            dln = xBasedColliderManager.dln(nearestXPrevAlreadyArrangedData);
+            visitToGatherXBasedPossibleColliders(dln, dln, "prev", xBasedPossibleColliders);
+          }
+          if (nearestXNextAlreadyArrangedData != null) {
+            dln = xBasedColliderManager.dln(nearestXNextAlreadyArrangedData);
+            visitToGatherXBasedPossibleColliders(dln, dln, "next", xBasedPossibleColliders);
+          }
+          totalPossibleColliders += xBasedPossibleColliders.length;
+          if (xBasedPossibleColliders.length > maxPossibleColliders) {
+            maxPossibleColliders = xBasedPossibleColliders.length;
+          }
+          return xBasedPossibleColliders;
+        }
+        function isAuthorizedPlacement(datum) {
+          if (side === "symetric") {
+            return true;
+          } else if (side === "positive") {
+            return datum.free >= 0;
+          } else {
+            return datum.free <= 0;
+          }
+        }
+        function isBetterPlacement(datum, bestYPosition) {
+          return Math.abs(datum.free) < Math.abs(bestYPosition);
+        }
+        function yPosRelativeToXbpc(xbpc, d) {
+          return Math.sqrt(minSquareDistanceBetweenCircles - Math.pow(d.fixed - xbpc.fixed, 2)) + 1e-6;
+        }
+        function placeBelow(d, aad, relativeYPos) {
+          d.free = aad.free - relativeYPos;
+        }
+        function placeAbove(d, aad, relativeYPos) {
+          d.free = aad.free + relativeYPos;
+        }
+        function areCirclesColliding(d0, d1) {
+          visitedColliderCount++;
+          return Math.pow(d1.free - d0.free, 2) + Math.pow(d1.fixed - d0.fixed, 2) < minSquareDistanceBetweenCircles;
+        }
+        function visitToDetectCollisionWithOther(datum, visitedDln, direction, visitCount) {
+          if (visitedDln === null) {
+            return false;
+          } else if (direction === "prev" ? datum.free - visitedDln.datum.free > minDistanceBetweenCircles : visitedDln.datum.free - datum.free > minDistanceBetweenCircles) {
+            return false;
+          } else if (areCirclesColliding(datum, visitedDln.datum)) {
+            return true;
+          } else {
+            return visitToDetectCollisionWithOther(datum, visitedDln[direction], direction, visitCount++);
+          }
+        }
+        function collidesWithOther(datum, visitedDln) {
+          var visitCount = 0;
+          if (visitToDetectCollisionWithOther(datum, visitedDln, "prev", visitCount++)) {
+            return true;
+          } else {
+            return visitToDetectCollisionWithOther(datum, visitedDln, "next", visitCount++);
+          }
+        }
+        function SortedDirectAccessDoublyLinkedList() {
+          this._valueAccesor = // accessor to the value to sort on
+          function(obj) {
+            return obj.value;
+          };
+          this._min = null;
+          this._max = null;
+          this._closestTo0 = null;
+          this.size = 0;
+          this._idToNode = {};
+        }
+        SortedDirectAccessDoublyLinkedList.prototype.valueAccessor = function(_) {
+          if (!arguments.length) {
+            return this._valueAccesor;
+          }
+          this._valueAccesor = _;
+          return this;
+        };
+        SortedDirectAccessDoublyLinkedList.prototype.closestTo0 = function() {
+          return this._closestTo0;
+        };
+        SortedDirectAccessDoublyLinkedList.prototype.clear = function() {
+          this._min = null;
+          this._max = null;
+          this._closestTo0 = null;
+          this.size = 0;
+          this._idToNode = {};
+          return this;
+        };
+        SortedDirectAccessDoublyLinkedList.prototype.dln = function(datum) {
+          return this._idToNode[datum.id];
+        };
+        SortedDirectAccessDoublyLinkedList.prototype.addMany = function(data2) {
+          data2.forEach(function(datum, item) {
+            this.add(datum);
+          }, this);
+          return this;
+        };
+        SortedDirectAccessDoublyLinkedList.prototype.add = function(datum) {
+          var dln = {
+            datum,
+            // original datum
+            value: this._valueAccesor(datum),
+            prev: null,
+            // previous value-based node
+            next: null
+            // next value-based node
+          };
+          if (this.size === 0) {
+            this._min = this._max = this._closestTo0 = dln;
+          } else {
+            if (dln.value <= this._min.value) {
+              dln.next = this._min;
+              dln.next.prev = dln;
+              this._min = dln;
+            } else if (dln.value >= this._max.value) {
+              dln.prev = this._max;
+              dln.prev.next = dln;
+              this._max = dln;
+            } else {
+              var current = this._max;
+              while (current.value > dln.value) {
+                current = current.prev;
+              }
+              dln.prev = current;
+              dln.next = current.next;
+              dln.next.prev = dln;
+              dln.prev.next = dln;
+            }
+            if (Math.abs(dln.value) < Math.abs(this._closestTo0.value)) {
+              this._closestTo0 = dln;
+            }
+          }
+          this._idToNode[dln.datum.id] = dln;
+          this.size++;
+          return this;
+        };
+        SortedDirectAccessDoublyLinkedList.prototype.remove = function(datum) {
+          var dln = this.dln(datum);
+          if (this.size === 1) {
+            this._min = this._max = this._closestTo0 = null;
+          } else {
+            if (dln === this._closestTo0) {
+              if (this._closestTo0.next === null) {
+                this._closestTo0 = dln.prev;
+              } else if (this.closestToZero.prev === null) {
+                this._closestTo0 = dln.prev;
+              } else {
+                var prevAbsValue = Math.abs(this._closestTo0.prev.value);
+                var nextAbsValue = Math.abs(this._closestTo0.next.value);
+                if (prevAbsValue < nextAbsValue) {
+                  this._closestTo0 = this._closestTo0.prev;
+                } else {
+                  this._closestTo0 = this._closestTo0.next;
+                }
+              }
+            }
+            if (dln === this._min) {
+              this._min = this._min.next;
+              this._min.prev = null;
+            } else if (dln === this._max) {
+              this._max = this._max.prev;
+              this._max.next = null;
+            } else {
+              dln.next.prev = dln.prev;
+              dln.prev.next = dln.next;
+            }
+          }
+          dln = null;
+          delete this._idToNode[datum.id];
+          this.size--;
+          return this;
+        };
+        return _beeswarm;
+      }
+      ;
+      exports2.beeswarm = beeswarm2;
+      Object.defineProperty(exports2, "__esModule", { value: true });
+    });
+  }
+});
+
+// src/spliceevent.prep.js
+function mapjunctiontoexons(junctions, genes) {
+  for (const j of junctions) {
+    j.exonleft = [];
+    j.exonright = [];
+    j.exonleftin = [];
+    j.exonrightin = [];
+    j.intronleft = [];
+    j.intronright = [];
+    j.leftout = [];
+    j.rightout = [];
+    j.matchisoform = [];
+  }
+  const usegenes = [];
+  for (const gene of genes) {
+    let use = false;
+    for (const j of junctions) {
+      if (gene.chr == j.chr && Math.max(gene.start, j.start) < Math.min(gene.stop, j.stop)) {
+        use = true;
+        break;
+      }
+    }
+    if (use) {
+      usegenes.push(gene);
+    }
+  }
+  if (usegenes.length == 0) {
+    return;
+  }
+  const leftpos = /* @__PURE__ */ new Map();
+  const rightpos = /* @__PURE__ */ new Map();
+  for (const j of junctions) {
+    if (!leftpos.has(j.start)) {
+      leftpos.set(j.start, []);
+    }
+    leftpos.get(j.start).push(j);
+    if (!rightpos.has(j.stop)) {
+      rightpos.set(j.stop, []);
+    }
+    rightpos.get(j.stop).push(j);
+  }
+  for (const [pos, jlst] of leftpos) {
+    for (const gm of usegenes) {
+      if (!gm.exon) continue;
+      for (let i = 0; i < gm.exon.length; i++) {
+        if (gm.exon[i][1] - 1 == pos) {
+          for (const j of jlst) {
+            j.exonleft.push({
+              gm,
+              exonidx: i
+            });
+          }
+        }
+        if (gm.exon[i][0] <= pos && gm.exon[i][1] - 1 > pos) {
+          for (const j of jlst) {
+            j.exonleftin.push({
+              gm,
+              exonidx: i
+            });
+          }
+        }
+      }
+      if (gm.intron) {
+        for (let i = 0; i < gm.intron.length; i++) {
+          if (gm.intron[i][0] <= pos && gm.intron[i][1] > pos) {
+            for (const j of jlst) {
+              j.intronleft.push({
+                gm,
+                intronidx: i
+              });
+            }
+          }
+        }
+      }
+    }
+  }
+  for (const [pos, jlst] of rightpos) {
+    for (const gm of usegenes) {
+      if (!gm.exon) continue;
+      for (let i = 0; i < gm.exon.length; i++) {
+        if (gm.exon[i][0] == pos) {
+          for (const j of jlst) {
+            j.exonright.push({
+              gm,
+              exonidx: i
+            });
+          }
+        }
+        if (gm.exon[i][0] < pos && gm.exon[i][1] > pos) {
+          for (const j of jlst) {
+            j.exonrightin.push({
+              gm,
+              exonidx: i
+            });
+          }
+        }
+      }
+      if (gm.intron) {
+        for (let i = 0; i < gm.intron.length; i++) {
+          if (gm.intron[i][0] <= pos && gm.intron[i][1] > pos) {
+            for (const j of jlst) {
+              j.intronright.push({
+                gm,
+                intronidx: i
+              });
+            }
+          }
+        }
+      }
+    }
+  }
+  for (const j of junctions) {
+    {
+      const isoforms = /* @__PURE__ */ new Set();
+      for (const q of j.exonleft) isoforms.add(q.gm.isoform);
+      for (const q of j.exonleftin) isoforms.add(q.gm.isoform);
+      for (const q of j.intronleft) isoforms.add(q.gm.isoform);
+      if (isoforms.size) {
+        for (const gm of usegenes) {
+          if (!isoforms.has(gm.isoform)) continue;
+          if (gm.stop <= j.stop) {
+            j.rightout.push({
+              gm
+            });
+          }
+        }
+      }
+    }
+    {
+      const isoforms = /* @__PURE__ */ new Set();
+      for (const q of j.exonright) isoforms.add(q.gm.isoform);
+      for (const q of j.exonrightin) isoforms.add(q.gm.isoform);
+      for (const q of j.intronright) isoforms.add(q.gm.isoform);
+      if (isoforms.size) {
+        for (const gm of usegenes) {
+          if (!isoforms.has(gm.isoform)) continue;
+          if (gm.start > j.start) {
+            j.leftout.push({
+              gm
+            });
+          }
+        }
+      }
+    }
+  }
+  for (const j of junctions) {
+    if (j.exonleft.length == 0 || j.exonright.length == 0) continue;
+    for (const el of j.exonleft) {
+      for (const er of j.exonright) {
+        if (el.gm.isoform == er.gm.isoform) {
+          j.matchisoform.push({
+            gm: el.gm,
+            leftexonidx: el.exonidx,
+            rightexonidx: er.exonidx
+          });
+        }
+      }
+    }
+  }
+}
+
+// src/spliceevent.exonskip.js
+var exonskipcolor = "#99004d";
+var exonaltcolor = "#004d99";
+function findexonskipping(multisample, junctions, gmdata) {
+  const allevents = [];
+  for (const j0 of junctions) {
+    if (!j0.matchisoform || j0.matchisoform.length == 0) {
+      continue;
+    }
+    for (const j0isoform of j0.matchisoform) {
+      const j0exonbegin = Math.min(j0isoform.leftexonidx, j0isoform.rightexonidx);
+      const j0exonend = Math.max(j0isoform.leftexonidx, j0isoform.rightexonidx);
+      if (j0exonend - j0exonbegin <= 1) {
+        continue;
+      }
+      const jB = j0;
+      const thisevent = {
+        skippedexon: [],
+        junctionB: jB,
+        junctionAlst: []
+      };
+      for (let i = j0exonbegin + 1; i < j0exonend; i++) {
+        thisevent.skippedexon.push(i);
+      }
+      let gmB = null;
+      for (const gm of gmdata) {
+        if (!gm.intron) continue;
+        for (const i of gm.intron) {
+          if (i[0] - 1 == jB.start && i[1] == jB.stop) {
+            gmB = gm;
+            break;
+          }
+        }
+        if (gmB) {
+          break;
+        }
+      }
+      if (gmB) {
+        thisevent.isaltexon = true;
+        thisevent.color = exonaltcolor;
+        thisevent.gmA = j0isoform.gm;
+        thisevent.gmB = gmB;
+      } else {
+        thisevent.isskipexon = true;
+        thisevent.color = exonskipcolor;
+        thisevent.gm = j0isoform.gm;
+        const [utr3, utr5, coding] = checkexoncodingutr(thisevent.skippedexon, thisevent.gm);
+        if (utr3) thisevent.utr3 = true;
+        if (utr5) thisevent.utr5 = true;
+        if (coding) thisevent.coding = true;
+      }
+      {
+        const jAlst = findjunctionAlst(junctions, j0isoform.gm, j0exonbegin, j0exonend);
+        for (const ja of jAlst) {
+          thisevent.junctionAlst.push(ja);
+        }
+      }
+      if (thisevent.isskipexon) {
+        findupdown1junction4exonskip(thisevent, j0isoform.gm, junctions);
+      }
+      if (multisample) {
+        if (!jB.data) {
+          console.error("exonskip: jB.data missing when it is multi-sample");
+          continue;
+        }
+        if (jB.data.length == 0) {
+          console.error("exonskip: jB.data.length==0");
+          continue;
+        }
+        let percentagesamplesum = 0;
+        for (const sampleBdata of jB.data) {
+          const bcount = sampleBdata.v;
+          let acountsum = 0;
+          for (const junctionA of thisevent.junctionAlst) {
+            if (!junctionA) {
+              continue;
+            }
+            if (!junctionA.data) {
+              console.log("exonskip: jA.data missing when multi-sample");
+              continue;
+            }
+            for (const sampleAdata of junctionA.data) {
+              if (sampleAdata.tkid == sampleBdata.tkid) {
+                acountsum += sampleAdata.v;
+                break;
+              }
+            }
+          }
+          percentagesamplesum += 100 * bcount / (bcount + acountsum / thisevent.junctionAlst.length);
+        }
+        thisevent.percentage = Math.ceil(percentagesamplesum / jB.data.length);
+      } else {
+        let asum = 0;
+        for (const _j of thisevent.junctionAlst) {
+          asum += _j ? _j.data[0].v : 0;
+        }
+        thisevent.percentage = Math.ceil(
+          100 * thisevent.junctionB.data[0].v / (thisevent.junctionB.data[0].v + asum / thisevent.junctionAlst.length)
+        );
+      }
+      allevents.push(thisevent);
+    }
+  }
+  const exoncoords = /* @__PURE__ */ new Map();
+  for (const evt of allevents) {
+    const positionlst = [];
+    for (const eid of evt.skippedexon) {
+      let thisexon;
+      if (evt.isskipexon) {
+        thisexon = evt.gm.exon[eid];
+      } else {
+        thisexon = evt.gmA.exon[eid];
+      }
+      positionlst.push(thisexon[0]);
+      positionlst.push(thisexon[1]);
+    }
+    if (positionlst.length == 0) {
+      console.error("not possible: no skipped exon position for exon-skip");
+      console.log(evt);
+      continue;
+    }
+    positionlst.sort();
+    const posstr = positionlst.join(".") + "|" + evt.junctionB.start + "." + evt.junctionB.stop;
+    if (!exoncoords.has(posstr)) {
+      exoncoords.set(posstr, []);
+    }
+    exoncoords.get(posstr).push(evt);
+  }
+  const eventsetlst = [];
+  for (const eventlst of exoncoords.values()) {
+    const thisset = {
+      eventlst,
+      exonlst: []
+      // each exon: {start:, stop:}
+    };
+    eventsetlst.push(thisset);
+    const firstevent = eventlst[0];
+    for (const eid of firstevent.skippedexon) {
+      const gm = firstevent.isskipexon ? firstevent.gm : firstevent.gmA;
+      const thisexon = gm.exon[eid];
+      thisset.exonlst.push({
+        chr: gm.chr,
+        start: thisexon[0],
+        stop: thisexon[1]
+      });
+    }
+    let eventcount_skip = 0, eventcount_alt = 0;
+    for (const evt of eventlst) {
+      if (evt.isskipexon) {
+        eventcount_skip++;
+      } else {
+        eventcount_alt++;
+      }
+    }
+    thisset.color = eventcount_skip > 0 ? exonskipcolor : exonaltcolor;
+    const exonnumberset = /* @__PURE__ */ new Set();
+    for (const evt of eventlst) {
+      const thisexonnumbers = [];
+      for (const eid of evt.skippedexon) {
+        thisexonnumbers.push(eid + 1);
+      }
+      exonnumberset.add(thisexonnumbers.join(","));
+    }
+    if (exonnumberset.size == 1) {
+      thisset.toplabelsays = "exon " + [...exonnumberset][0] + " ";
+    } else {
+      thisset.toplabelsays = "exon ";
+    }
+    thisset.toplabelsays += eventcount_skip ? "skip" + (eventcount_alt ? "|alt" : "") : "alt";
+    if (multisample) {
+      let samplecount = 0;
+      for (const evt of eventlst) {
+        samplecount = Math.max(samplecount, evt.junctionB.data.length);
+      }
+      thisset.middlelabelsays = samplecount + " sample" + (samplecount > 1 ? "s" : "");
+    }
+    thisset.bottomlabelsays = firstevent.percentage + "%";
+  }
+  return eventsetlst;
+}
+function findjunctionbystartstop(lst, p1, p2) {
+  const start = Math.min(p1, p2);
+  const stop = Math.max(p1, p2);
+  for (const j of lst) {
+    if (j.start == start && j.stop == stop) return j;
+  }
+  return null;
+}
+function findjunctionAlst(junctions, gm, exonbegin, exonend) {
+  const lst = [];
+  const exonstart = Math.min(exonbegin, exonend);
+  const exonstop = Math.max(exonbegin, exonend);
+  if (gm.strand == "+") {
+    for (let i = exonstart; i < exonstop; i++) {
+      const p1 = gm.exon[i][1] - 1;
+      const p2 = gm.exon[i + 1][0];
+      lst.push(findjunctionbystartstop(junctions, p1, p2));
+    }
+  } else {
+    for (let i = exonstop; i > exonstart; i--) {
+      const p1 = gm.exon[i][1] - 1;
+      const p2 = gm.exon[i - 1][0];
+      lst.unshift(findjunctionbystartstop(junctions, p1, p2));
+    }
+  }
+  return lst;
+}
+function findupdown1junction4exonskip(evt, gm, junctions) {
+  let exonidx = evt.skippedexon[0];
+  if (exonidx > 1) {
+    let p1, p2;
+    if (gm.strand == "+") {
+      p1 = gm.exon[exonidx - 2][1] - 1;
+      p2 = gm.exon[exonidx - 1][0];
+    } else {
+      p1 = gm.exon[exonidx - 1][1] - 1;
+      p2 = gm.exon[exonidx - 2][0];
+    }
+    evt.up1junction = findjunctionbystartstop(junctions, p1, p2);
+  }
+  exonidx = evt.skippedexon[evt.skippedexon.length - 1];
+  if (exonidx < gm.exon.length - 2) {
+    let p1, p2;
+    if (gm.strand == "+") {
+      p1 = gm.exon[exonidx + 1][1] - 1;
+      p2 = gm.exon[exonidx + 2][0];
+    } else {
+      p1 = gm.exon[exonidx + 2][1] - 1;
+      p2 = gm.exon[exonidx + 1][0];
+    }
+    evt.down1junction = findjunctionbystartstop(junctions, p1, p2);
+  }
+}
+function checkexoncodingutr(exonidlst, gm) {
+  if (!gm.coding) {
+    return [false, false, false];
+  }
+  let exonstart = gm.exon[exonidlst[0]][0];
+  let exonstop = gm.exon[exonidlst[0]][1];
+  for (const idx of exonidlst) {
+    exonstart = Math.min(gm.exon[idx][0], exonstart);
+    exonstop = Math.max(gm.exon[idx][1], exonstop);
+  }
+  const forward = gm.strand == "+";
+  let utr3 = false, utr5 = false, coding = false;
+  if (exonstop <= gm.codingstart) {
+    if (forward) {
+      utr5 = true;
+    } else {
+      utr3 = true;
+    }
+  } else if (exonstart >= gm.codingstop) {
+    if (forward) {
+      utr3 = true;
+    } else {
+      utr5 = true;
+    }
+  } else {
+    coding = true;
+  }
+  return [utr3, utr5, coding];
+}
+
+// src/block.tk.junction.spliceevent.js
+function spliceeventanalyze(tk, block) {
+  if (tk.eventsg) {
+    tk.eventsg.selectAll("*").remove();
+  }
+  if (tk.type != tkt.junction) {
+    return;
+  }
+  if (!tk.data) {
+    return;
+  }
+  if (tk.data.length == 0) {
+    return;
+  }
+  const [gmdataerr, gmdata] = getgmdata(block);
+  if (gmdataerr) {
+    const fontsize = 12;
+    const pad = 2;
+    tk.eventsg.append("rect").attr("width", block.width).attr("height", pad * 2 + fontsize).attr("fill", "#f1f1f1");
+    tk.eventsg.append("text").text(gmdataerr).attr("font-family", font).attr("font-size", fontsize).attr("fill", "#858585").attr("text-anchor", "middle").attr("x", block.width / 2).attr("y", pad + fontsize / 2).attr("dominant-baseline", "central");
+    tk.height_main += pad * 2 + fontsize;
+    block.block_setheight();
+    return;
+  }
+  if (!gmdata) {
+    return;
+  }
+  for (const junction of tk.data) {
+    delete junction.spliceevents;
+  }
+  mapjunctiontoexons(tk.data, gmdata);
+  const allevents = [];
+  const exonskipalt = findexonskipping(tk.totalsamplecount > 1, tk.data, gmdata);
+  if (exonskipalt.length > 0) {
+    for (const exonset of exonskipalt) {
+      if (exonlstoutofrange(exonset.exonlst, block)) {
+        continue;
+      }
+      allevents.push(exonset);
+      for (const thisevt of exonset.eventlst) {
+        if (!thisevt.junctionB.spliceevents) {
+          thisevt.junctionB.spliceevents = [];
+        }
+        thisevt.junctionB.spliceevents.push(thisevt);
+      }
+    }
+  }
+  if (allevents.length) {
+    rendereventsintrack(allevents, tk, block);
+  }
+}
+function rendereventsintrack(allevents, tk, block) {
+  const labelfontsize = 10;
+  const stackspace = 1;
+  const boxlabelspacing = 2;
+  let stackheight;
+  if (tk.totalsamplecount > 1) {
+    stackheight = labelfontsize * 3 + stackspace * 2;
+  } else {
+    stackheight = labelfontsize * 2 + stackspace;
+  }
+  for (const eventset of allevents) {
+    eventset.g = tk.eventsg.append("g");
+    const junctionB = eventset.eventlst[0].junctionB;
+    const jbstr = junctionB.chr + "-" + junctionB.start + "-" + junctionB.stop;
+    eventset.toplabel = eventset.g.append("text").text(eventset.toplabelsays).attr("font-size", labelfontsize).attr("font-family", font).attr("fill", eventset.color).attr("y", labelfontsize / 2).attr("dominant-baseline", "central");
+    if (tk.totalsamplecount > 1) {
+      eventset.middlelabel = eventset.g.append("text").text(eventset.middlelabelsays).attr("font-size", labelfontsize).attr("font-family", font).attr("fill", eventset.color).attr("y", labelfontsize * 1.5).attr("dominant-baseline", "central");
+    }
+    let willshowframe = false;
+    let thiseventframe = null;
+    for (const evt of eventset.eventlst) {
+      if (evt.isaltexon) {
+        evt.framenocheck = true;
+        continue;
+      }
+      if (evt.isskipexon) {
+        if (!evt.gm.coding) {
+          evt.framenocheck = true;
+          continue;
+        }
+        if (evt.utr3 || evt.utr5) {
+          evt.framenocheck = true;
+          continue;
+        }
+      }
+      willshowframe = true;
+      if (block.genome.junctionframecache.has(jbstr)) {
+        let isoform;
+        if (evt.isskipexon) {
+          isoform = evt.gm.isoform;
+        }
+        const thisframe = block.genome.junctionframecache.get(jbstr).get(isoform);
+        if (thisframe == void 0) {
+        } else {
+          evt.frame = thisframe;
+          if (thiseventframe == null) {
+            thiseventframe = thisframe;
+          } else {
+            if (thisframe == IN_frame) {
+              thiseventframe = IN_frame;
+            }
+          }
+        }
+      } else {
+      }
+    }
+    eventset.bottomlabel = eventset.g.append("text").text(
+      eventset.bottomlabelsays + (willshowframe ? ", " + (thiseventframe == null ? "checking" : thiseventframe == IN_frame ? "IN" : "OUT") : "")
+    ).attr("font-size", labelfontsize).attr("font-family", font).attr("fill", eventset.color).attr("y", stackheight - labelfontsize / 2).attr("dominant-baseline", "central");
+    if (willshowframe && thiseventframe == null) {
+      for (const evt of eventset.eventlst) {
+        let gm;
+        if (evt.isaltexon) {
+          gm = evt.gmB;
+        } else if (evt.isskipexon) {
+          gm = evt.gm;
+        }
+        if (!block.genome.junctionframecache.has(jbstr)) {
+          checkjunctionframe({
+            jbstr,
+            evt,
+            gm,
+            block,
+            eventset
+          });
+          continue;
+        }
+        if (!block.genome.junctionframecache.get(jbstr).has(gm.isoform)) {
+          checkjunctionframe({
+            jbstr,
+            evt,
+            gm,
+            block,
+            eventset
+          });
+        }
+      }
+    }
+    const exonobjlst = [];
+    let boxstart = null, boxstop;
+    for (const exon of eventset.exonlst) {
+      const pointa = block.seekcoord(exon.chr, exon.start)[0];
+      if (!pointa) {
+        console.log("skipped exon start position not mapped: " + exon.start);
+        return;
+      }
+      const pointb = block.seekcoord(exon.chr, exon.stop - 1)[0];
+      if (!pointb) {
+        console.log("skipped exon stop position not mapped: " + exon.stop);
+        return;
+      }
+      const exonobj = {
+        x: Math.min(pointa.x, pointb.x),
+        w: Math.max(1, Math.abs(pointa.x - pointb.x))
+      };
+      exonobj.rect = eventset.g.append("rect").attr("fill", eventset.color).attr("width", exonobj.w).attr("height", stackheight).attr("shape-rendering", "crispEdges").on("click", () => {
+        console.log(eventset);
+      });
+      if (boxstart == null) {
+        boxstart = exonobj.x;
+        boxstop = exonobj.x + exonobj.w;
+      } else {
+        boxstart = Math.min(boxstart, exonobj.x);
+        boxstop = Math.max(boxstop, exonobj.x + exonobj.w);
+      }
+      exonobjlst.push(exonobj);
+    }
+    for (const exon of exonobjlst) {
+      exon.rect.attr("x", exon.x - boxstart);
+    }
+    eventset.boxstart = boxstart;
+    eventset.boxwidth = boxstop - boxstart;
+    if (eventset.exonlst.length > 1) {
+      eventset.g.append("line").attr("stroke", eventset.color).attr("stroke-opacity", 0.2).attr("stroke-width", 2).attr("shape-rendering", "crispEdges").attr("x1", 0).attr("x2", eventset.boxwidth).attr("y1", stackheight / 2 - 0.5).attr("y2", stackheight / 2 - 0.5);
+    }
+    eventset.toplabel.each(function() {
+      eventset.labelwidth = this.getBBox().width;
+    });
+    if (eventset.middlelabel) {
+      eventset.middlelabel.each(function() {
+        eventset.labelwidth = this.getBBox().width;
+      });
+    }
+    eventset.bottomlabel.each(function() {
+      eventset.labelwidth = Math.max(eventset.labelwidth, this.getBBox().width);
+    });
+    if (eventset.labelwidth > eventset.boxstart) {
+      eventset.labelonright = true;
+      eventset.toplabel.attr("x", eventset.boxwidth + boxlabelspacing);
+      eventset.bottomlabel.attr("x", eventset.boxwidth + boxlabelspacing);
+      if (eventset.middlelabel) {
+        eventset.middlelabel.attr("x", eventset.boxwidth + boxlabelspacing);
+      }
+    } else {
+      eventset.toplabel.attr("text-anchor", "end").attr("x", -boxlabelspacing);
+      eventset.bottomlabel.attr("text-anchor", "end").attr("x", -boxlabelspacing);
+      if (eventset.middlelabel) {
+        eventset.middlelabel.attr("text-anchor", "end").attr("x", -boxlabelspacing);
+      }
+    }
+    eventset.cover = eventset.g.append("rect").attr("x", eventset.labelonright ? 0 : -eventset.labelwidth - boxlabelspacing).attr("width", eventset.labelwidth + boxlabelspacing + eventset.boxwidth).attr("height", stackheight).attr("fill", "#858585").attr("fill-opacity", 0).on("mouseover", () => {
+      eventset.cover.attr("fill-opacity", 0.1);
+    }).on("mouseout", () => {
+      eventset.cover.attr("fill-opacity", 0);
+    }).on("click", () => {
+      tk.tktip.clear();
+      displayspliceevents(eventset.eventlst, tk.tktip.d);
+      tk.tktip.showunder(eventset.cover.node());
+    });
+  }
+  const stacks = [0];
+  for (const eventset of allevents) {
+    let x1 = eventset.boxstart - (eventset.labelonright ? 0 : boxlabelspacing + eventset.labelwidth);
+    let x2 = eventset.boxstart + eventset.boxwidth + (eventset.labelonright ? boxlabelspacing + eventset.labelwidth : 0);
+    for (let stackidx = 0; stackidx < stacks.length; stackidx++) {
+      if (x1 > stacks[stackidx]) {
+        eventset.stackidx = stackidx;
+        stacks[stackidx] = x2;
+        break;
+      }
+      if (!eventset.labelonright) {
+        const newx1 = eventset.boxstart;
+        const newx2 = eventset.boxstart + eventset.boxwidth + boxlabelspacing + eventset.labelwidth;
+        if (newx1 > stacks[stackidx] && newx2 <= block.width) {
+          eventset.labelonright = true;
+          eventset.stackidx = stackidx;
+          stacks[stackidx] = newx2;
+          eventset.toplabel.attr("x", eventset.boxwidth + boxlabelspacing).attr("text-anchor", "start");
+          eventset.bottomlabel.attr("x", eventset.boxwidth + boxlabelspacing).attr("text-anchor", "start");
+          if (eventset.middlelabel) {
+            eventset.middlelabel.attr("x", eventset.boxwidth + boxlabelspacing).attr("text-anchor", "start");
+          }
+          eventset.cover.attr("x", 0);
+          break;
+        }
+      }
+    }
+    if (eventset.stackidx == void 0) {
+      eventset.stackidx = stacks.length;
+      stacks.push(x2);
+    }
+    eventset.g.attr(
+      "transform",
+      "translate(" + eventset.boxstart + "," + eventset.stackidx * (stackheight + stackspace) + ")"
+    );
+  }
+  tk.height_main += stacks.length * (stackheight + stackspace) + tk.bottompad;
+  block.block_setheight();
+}
+function checkjunctionframe(arg) {
+  if (!arg.block.genome.junctionframecache.has(arg.jbstr)) {
+    arg.block.genome.junctionframecache.set(arg.jbstr, /* @__PURE__ */ new Map());
+  }
+  if (!arg.gm.coding) {
+    arg.block.genome.junctionframecache.get(arg.jbstr).set(arg.gm.isoform, false);
+    mayupdateeventsetlabel(arg);
+    return;
+  }
+  const gm2 = spliceeventchangegmexon(arg.gm, arg.evt);
+  dofetch2("translategm", { method: "POST", body: JSON.stringify({ genome: arg.block.genome.name, gm: gm2 }) }).then((data) => {
+    if (!data) {
+      console.log("server error");
+      return;
+    }
+    if (data.error) {
+      console.log(data.error);
+      return;
+    }
+    if (typeof data.frame != "boolean") {
+      console.log("invalid result from translategm: " + data.frame);
+      return;
+    }
+    arg.evt.frame = data.frame;
+    arg.block.genome.junctionframecache.get(arg.jbstr).set(arg.gm.isoform, data.frame);
+    mayupdateeventsetlabel(arg);
+  });
+}
+function mayupdateeventsetlabel(arg) {
+  if (!arg.block.genome.junctionframecache.has(arg.jbstr)) {
+    return;
+  }
+  let frame = OUT_frame;
+  for (const evt of arg.eventset.eventlst) {
+    if (evt.framenocheck) {
+      continue;
+    }
+    let isoform;
+    if (evt.isskipexon) {
+      isoform = evt.gm.isoform;
+    }
+    const thisframe = arg.block.genome.junctionframecache.get(arg.jbstr).get(isoform);
+    if (thisframe == void 0) {
+      return;
+    }
+    if (thisframe == IN_frame) {
+      frame = IN_frame;
+    }
+  }
+  arg.eventset.bottomlabel.text(arg.eventset.bottomlabelsays + ", " + (frame == IN_frame ? "IN" : "OUT"));
+}
+function displayspliceevents(events, holder) {
+  const evt2showidx = spliceevent_exonskip_getdefault_default(events);
+  if (events.length > 1) {
+    holder.append("div").style("margin", "3px 0px").style("color", "#858585").text("Additional interpretations:");
+    const name = Math.random().toString();
+    for (const [idx, evt] of events.entries()) {
+      const id = name + idx;
+      const row = holder.append("div").style("margin-top", "3px");
+      row.append("input").attr("type", "radio").property("checked", idx == evt2showidx).attr("name", name).attr("id", id).on("change", () => {
+        displayspliceevents_show(events, idx, showdiv);
+      });
+      row.append("label").attr("for", id).html("&nbsp;" + spliceevent_phrase_default(evt));
+    }
+  }
+  const showdiv = holder.append("div");
+  displayspliceevents_show(events, evt2showidx, showdiv);
+}
+function displayspliceevents_show(events, idx, div) {
+  div.selectAll("*").remove();
+  import("./spliceevent.exonskip.diagram-PHFR53DH.js").then((p) => {
+    p.default({
+      event: events[idx],
+      holder: div,
+      nophrase: events.length > 1
+    });
+  });
+}
+function exonlstoutofrange(lst, block) {
+  const chr = lst[0].chr;
+  let start = lst[0].start;
+  let stop = lst[0].stop;
+  for (const e of lst) {
+    start = Math.min(start, e.start);
+    stop = Math.max(stop, e.stop);
+  }
+  const starthit = block.seekcoord(chr, start)[0];
+  const stophit = block.seekcoord(chr, stop)[0];
+  if (!starthit || !stophit) {
+    return true;
+  }
+  let startoutleft = false;
+  let startoutright = false;
+  if (starthit.x <= 0) {
+    startoutleft = true;
+  } else if (starthit.x >= block.width) {
+    startoutright = true;
+  }
+  let stopoutleft = false;
+  let stopoutright = false;
+  if (stophit.x <= 0) {
+    stopoutleft = true;
+  } else if (stophit.x >= block.width) {
+    stopoutright = true;
+  }
+  if (startoutleft && stopoutleft) return true;
+  if (startoutright && stopoutright) return true;
+  return false;
+}
+function getgmdata(block) {
+  if (!block.gmmode || block.gmmode == gmmode.genomic) {
+    const genetk = [];
+    for (const t of block.tklst) {
+      if (t.__isgene) {
+        genetk.push(t);
+      }
+    }
+    if (genetk.length == 0) {
+      return ["Add a gene track to analyze splice junctions."];
+    }
+    const gmdatalst = [];
+    for (const t of genetk) {
+      if (t.gmdata) {
+        for (const m of t.gmdata) {
+          gmdatalst.push(m);
+        }
+      }
+    }
+    if (gmdatalst.length == 0) {
+      return [null];
+    }
+    const regions = [];
+    for (const m of gmdatalst) {
+      let overlap = false;
+      for (const r of regions) {
+        if (Math.max(r.start, m.start) < Math.min(r.stop, m.stop)) {
+          overlap = true;
+          r.start = Math.min(r.start, m.start);
+          r.stop = Math.max(r.stop, m.stop);
+          break;
+        }
+      }
+      if (!overlap) {
+        regions.push({ start: m.start, stop: m.stop });
+      }
+    }
+    if (regions.length >= 3) {
+      return ["Zoom in on a single gene to analyze splice junctions."];
+    }
+    return [null, gmdatalst];
+  }
+  if (block.gmmode == gmmode.gmsum) {
+    if (!block.allgm) {
+      return ["Error: block.allgm[] is missing"];
+    }
+    return [null, block.allgm];
+  }
+  if (!block.usegm) {
+    return ["Error: block.usegm is missing"];
+  }
+  return [null, [block.usegm]];
+}
+
+// src/block.tk.junction.renderjunctions.js
+var import_d3_beeswarm = __toESM(require_d3_beeswarm(), 1);
+var colorfunc = ordinal(category10_default);
+var minfontsize = 12;
+function rendertk(junctions, tk, block) {
+  if (tk.data) {
+    const map = /* @__PURE__ */ new Map();
+    for (const j of tk.data) {
+      map.set(j.chr + "." + j.start + "." + j.stop, j);
+    }
+    const pannedpx = Number.isInteger(block.pannedpx) ? block.pannedpx : 0;
+    for (const i of junctions) {
+      const j = map.get(i.chr + "." + i.start + "." + i.stop);
+      if (j) {
+        i.x = j.x + pannedpx;
+        i.mode = j.mode;
+        i.modefix = j.modefix;
+        if (i.mode == modesample) {
+          i.mode = moderaise;
+        }
+      }
+    }
+  }
+  tk.data = junctions;
+  tk.glider.selectAll("*").remove();
+  tk.leftaxis.selectAll("*").remove();
+  if (tk.readcountcutoff) {
+    const newj = [];
+    for (const j of tk.data) {
+      if (j.data) {
+        const newsamples = [];
+        for (const s of j.data) {
+          if (s.v >= tk.readcountcutoff) {
+            newsamples.push(s);
+          }
+        }
+        if (newsamples.length == 0) {
+          continue;
+        }
+        j.data = newsamples;
+        newj.push(j);
+      } else {
+        if (j.v >= tk.readcountcutoff) {
+          newj.push(j);
+        }
+      }
+    }
+    tk.data = newj;
+  }
+  if (tk.data.length == 0) {
+    tk.height_main = 50;
+    block.tkcloakoff(tk, { error: tk.name + ": No junction in view range" });
+    tk.label_mcount.text("");
+    if (tk.label_samplecount) {
+      tk.label_samplecount.text("");
+    }
+    get_leftLabelMaxwidth(tk);
+    block.setllabel();
+    block.block_setheight();
+    return;
+  }
+  tk.label_mcount.text(tk.data.length + " junction" + (tk.data.length > 1 ? "s" : ""));
+  get_leftLabelMaxwidth(tk);
+  block.setllabel();
+  junctiontype2color(tk, block);
+  const mg = tk.glider.append("g");
+  tk.data.sort((a, b) => {
+    return a._x - b._x;
+  });
+  let maxsamplecount = 0;
+  if (tk.totalsamplecount > 1) {
+    maxsamplecount = tk.data.reduce((max, j) => Math.max(max, j.data.length), 0);
+    const radius = 5;
+    let mrd = 0;
+    const w = Math.pow(radius, 2) * Math.PI;
+    if (maxsamplecount <= 10) {
+      mrd = w * maxsamplecount * 0.9;
+    } else if (maxsamplecount <= 100) {
+      mrd = w * 10;
+    } else if (maxsamplecount <= 1e3) {
+      mrd = w * 14;
+    } else {
+      mrd = w * 20;
+    }
+    const sf_discradius = linear().domain([
+      1,
+      maxsamplecount * 0.5 + 0.1,
+      maxsamplecount * 0.6 + 0.1,
+      maxsamplecount * 0.7 + 0.1,
+      maxsamplecount * 0.8 + 0.1,
+      maxsamplecount
+    ]).range([w, w + (mrd - w) * 0.8, w + (mrd - w) * 0.85, w + (mrd - w) * 0.9, w + (mrd - w) * 0.95, mrd]);
+    let maxradius = 0;
+    for (const j of tk.data) {
+      j.radius = Math.sqrt(sf_discradius(j.data.length) / Math.PI);
+      if (j.data.length > 1) {
+        mg.append("text").attr("font-family", font).attr("font-size", Math.max(minfontsize, j.radius)).text(j.data.length).each(function() {
+          const b = this.getBBox();
+          const newrad = Math.sqrt(Math.pow(b.width, 2) + Math.pow(b.height, 2)) / 2;
+          j.radius = Math.max(j.radius, newrad);
+        }).remove();
+      }
+      j.rimwidth = j.rimcount ? Math.max(2, j.radius / 6) : 0;
+      j.radius2 = j.radius + j.rimwidth + (j.rimwidth > 0 ? 1 : 0);
+      maxradius = Math.max(maxradius, j.radius2);
+    }
+    tk.maxradius = maxradius;
+  } else {
+    maxsamplecount = tk.data.reduce((max, j) => Math.max(max, j.data[0].v), 0);
+    const radius = 5;
+    let mrd = 0;
+    const w = Math.pow(radius, 2) * Math.PI;
+    if (maxsamplecount <= 10) {
+      mrd = w * maxsamplecount * 0.9;
+    } else if (maxsamplecount <= 100) {
+      mrd = w * 5;
+    } else if (maxsamplecount <= 1e3) {
+      mrd = w * 7;
+    } else {
+      mrd = w * 10;
+    }
+    const sf_discradius = linear().domain([
+      1,
+      maxsamplecount * 0.5 + 0.1,
+      maxsamplecount * 0.6 + 0.1,
+      maxsamplecount * 0.7 + 0.1,
+      maxsamplecount * 0.8 + 0.1,
+      maxsamplecount
+    ]).range([w, w + (mrd - w) * 0.8, w + (mrd - w) * 0.85, w + (mrd - w) * 0.9, w + (mrd - w) * 0.95, mrd]);
+    let maxradius = 0;
+    for (const j of tk.data) {
+      j.radius = Math.sqrt(sf_discradius(j.data[0].v) / Math.PI);
+      j.rimwidth = j.rimcount ? Math.max(2, j.radius / 6) : 0;
+      j.radius2 = j.radius + j.rimwidth + (j.rimwidth > 0 ? 1 : 0);
+      maxradius = Math.max(maxradius, j.radius2);
+    }
+    tk.maxradius = maxradius;
+  }
+  let maxread = 0, maxmedian = 0, maxmedianradius = 0;
+  for (const j of tk.data) {
+    for (const s of j.data) {
+      maxread = Math.max(s.v, maxread);
+    }
+    if (j.data.length == 1) {
+      j.median = j.data[0].v;
+    } else {
+      const readlst = j.data.map((s) => s.v);
+      readlst.sort((a, b) => a - b);
+      j.median = readlst[Math.floor(j.data.length / 2)];
+    }
+    if (j.median > maxmedian) {
+      maxmedian = j.median;
+      maxmedianradius = j.radius;
+    }
+  }
+  tk.yscale = log().domain([tk.readcountcutoff || 1, maxread]).range([tk.axisheight, 0]);
+  axisstyle({
+    axis: tk.leftaxis.call(axisRight().scale(tk.yscale).ticks(6, ".0f")),
+    color: "black",
+    showline: true
+  });
+  tk.height_main = tk.toppad + tk.axisheight + tk.maxradius * 4 + tk.padheight + tk.lowpad + tk.legheight + tk.bottompad;
+  tk.eventsg = tk.glider.append("g").attr("transform", "translate(0," + (tk.height_main - tk.toppad) + ")");
+  automode(tk, null, block.width);
+  mg.attr("transform", "translate(0," + (tk.height_main - tk.toppad - tk.bottompad) + ")");
+  {
+    const topy = -tk.legheight - tk.lowpad - tk.maxradius * 4 - tk.padheight - tk.axisheight;
+    mg.append("line").attr("x1", 0).attr("y1", topy).attr("y2", topy).attr("x2", block.width).attr("stroke", "#858585").attr("stroke-opacity", 0.2).attr("shape-rendering", "crispEdges");
+    mg.append("line").attr("x1", 0).attr("y1", topy + tk.axisheight).attr("y2", topy + tk.axisheight).attr("x2", block.width).attr("stroke", "#858585").attr("stroke-opacity", 0.2).attr("shape-rendering", "crispEdges");
+    let v = 10;
+    while (v <= maxread) {
+      mg.append("line").attr("x1", 0).attr("y1", topy + tk.yscale(v)).attr("y2", topy + tk.yscale(v)).attr("x2", block.width).attr("stroke", "#858585").attr("stroke-opacity", 0.2).attr("stroke-dasharray", "4,4").attr("shape-rendering", "crispEdges");
+      v *= 10;
+    }
+  }
+  const jug = mg.selectAll().data(tk.data).enter().append("g").attr("transform", (d) => set_jug(d)).each(function(j) {
+    j.jugg = this;
+  });
+  tk.jug = jug;
+  if (tk.hljunctions) {
+    jug.attr("class", (d) => {
+      for (const j of tk.hljunctions) {
+        if (d.chr == j.chr && d.start == j.start && d.stop == j.stop) {
+          return "sja_pulse";
+        }
+      }
+      return null;
+    });
+  }
+  jug.append("line").attr("stroke", (d) => d.color).attr("x1", (d) => set_leg_x1(d)).attr("y2", (d) => set_leg_y(d, tk)).attr("stroke-opacity", (d) => set_lineopacity(d)).each(function(d) {
+    d.leg1 = this;
+  }).classed("sja_jug_leg1", true);
+  jug.append("line").attr("stroke", (d) => d.color).attr("x2", (d) => set_leg_x2(d)).attr("y1", (d) => set_leg_y(d, tk)).attr("stroke-opacity", (d) => set_lineopacity(d)).classed("sja_jug_leg2", true).each(function(d) {
+    d.leg2 = this;
+  });
+  const jug2 = jug.append("g").attr("class", "sja_jug_jug2").attr("transform", (d) => set_jug2(d, tk));
+  jug2.append("line").attr("stroke", (d) => d.color).classed("sja_jug_stem", true).attr("stroke-dasharray", "2,2").attr("shape-rendering", "crispEdges").attr("y1", (d) => set_stem_y1(d)).attr("y2", (d) => set_stem_y2(d, tk)).attr("stroke-opacity", (d) => set_lineopacity(d)).each(function(d) {
+    d.stem = this;
+  });
+  jug2.append("circle").attr("r", (d) => d.radius).attr("fill", (d) => d.color).attr("stroke", "white").attr("fill-opacity", 0.5);
+  jug2.filter((d) => d.data.length > 1).append("text").text((d) => d.data.length).attr("font-size", (d) => Math.max(minfontsize, d.radius)).attr("fill-opacity", (d) => set_discnum(d)).classed("sja_jug_discnum", true).attr("fill", "white").attr("font-family", font).attr("text-anchor", "middle").attr("dominant-baseline", "central");
+  jug2.append("circle").attr("r", (d) => d.radius).attr("stroke", (d) => d.color).classed("sja_aa_disckick", true).attr("fill", "white").attr("fill-opacity", 0).attr("stroke-opacity", 0).on("mouseover", (event, d) => {
+    jug.selectAll(".sja_jug_leg1").attr("stroke-opacity", 0.2);
+    jug.selectAll(".sja_jug_leg2").attr("stroke-opacity", 0.2);
+    jug.selectAll(".sja_jug_stem").attr("stroke-opacity", 0.2);
+    select_default(d.leg1).attr("stroke-opacity", 1);
+    select_default(d.leg2).attr("stroke-opacity", 1);
+    select_default(d.stem).attr("stroke-opacity", 1);
+    if (d.mode == modefold) {
+      foldedjunctioninfo(d, tk);
+      return;
+    }
+    const circle = event.target.getBoundingClientRect();
+    expandedjunctioninfo(d, tk, circle);
+  }).on("mouseout", () => {
+    tk.pica.g.selectAll("*").remove();
+    tk.tktip.hide();
+    jug.selectAll(".sja_jug_leg1").attr("stroke-opacity", (d) => set_lineopacity(d));
+    jug.selectAll(".sja_jug_leg2").attr("stroke-opacity", (d) => set_lineopacity(d));
+    jug.selectAll(".sja_jug_stem").attr("stroke-opacity", (d) => set_lineopacity(d));
+  }).on("mousedown", (event) => {
+    event.stopPropagation();
+  }).on("click", (event, d) => {
+    if (d.mode == modefold) {
+      d.mode = moderaise;
+    } else if (d.mode == moderaise) {
+      if (d.data.length == 1) {
+        d.mode = modefold;
+      } else {
+        d.mode = modesample;
+        junctionsamplespread(d, tk, block);
+      }
+    } else {
+      d.mode = modefold;
+    }
+    d.modefix = true;
+    horiplace(tk.data, block.width, tk);
+  });
+  horiplace(tk.data, block.width, tk);
+  function set_lineopacity(d) {
+    return 0.5;
+  }
+  block.onloadalltk.push(() => {
+    spliceeventanalyze(tk, block);
+  });
+  block.tkcloakoff(tk, {});
+  block.block_setheight();
+}
+function horiplace(lst, width, tk) {
+  const todo = [];
+  for (const i of lst) {
+    if (i.x0 < 0) {
+      i.tox = i.x1 - i.radius2 * 2;
+    } else if (i.x1 > width) {
+      i.tox = i.x0 + i.radius2 * 2;
+    } else {
+      i.tox = i._x;
+    }
+    if (i.mode == modefold) {
+      i.x = i.tox;
+    } else {
+      todo.push(i);
+    }
+  }
+  for (const i of lst) {
+    i.x = i.tox;
+  }
+  set_all(tk);
+  return;
+}
+function automode(tk, usemode, blockwidth) {
+  for (const i of tk.data) {
+    if (!i.mode) i.mode = moderaise;
+  }
+  return;
+  const samplecountlst = [];
+  for (let i = 0; i < tk.data.length; i++) {
+    samplecountlst.push({
+      idx: i,
+      count: tk.data[i].data ? tk.data[i].data.length : tk.data[i].v
+    });
+  }
+  samplecountlst.sort((a, b) => b.count - a.count);
+  let cumx = 0;
+  for (const cc of samplecountlst) {
+    const d = tk.data[cc.idx];
+    if (!d.mode) {
+      cumx += d.radius2 * 2;
+      d.mode = cumx >= blockwidth ? modefold : moderaise;
+    } else {
+      if (d.modefix) {
+        if (d.mode != modefold) {
+          cumx += d.radius2 * 2;
+        }
+      } else {
+        if (usemode) {
+          d.mode = usemode;
+          if (d.mode != modefold) {
+            cumx += d.radius2 * 2;
+          }
+        } else {
+          cumx += d.radius2 * 2;
+          d.mode = cumx >= blockwidth ? modefold : moderaise;
+        }
+      }
+    }
+  }
+}
+function set_jug(d) {
+  return "translate(" + d.x + ",0)";
+}
+function set_leg_x1(d) {
+  return d.x0 - d.x;
+}
+function set_leg_x2(d) {
+  return d.x1 - d.x;
+}
+function set_discnum(d) {
+  return d.mode == modefold ? 0 : 1;
+}
+function set_stem_y1(d) {
+  if (d.mode == modefold) return d.radius;
+  return d.radius2;
+}
+function set_qmg(d, tk) {
+  if (d.mode == modesample)
+    return "translate(0,-" + (tk.legheight + tk.maxradius * 4 + tk.lowpad + tk.padheight) + ") scale(1)";
+  return "translate(0,0) scale(0)";
+}
+function set_leg_y(d, tk) {
+  if (d.mode == modefold) return -tk.legheight;
+  return -tk.legheight - tk.lowpad - tk.maxradius * 2;
+}
+function set_jug2(d, tk) {
+  if (d.mode == modefold) return "translate(0,-" + (tk.legheight + tk.lowpad + d.radius) + ")";
+  if (d.mode == moderaise)
+    return "translate(0,-" + (tk.legheight + tk.lowpad + tk.maxradius * 4 + tk.padheight + tk.axisheight - tk.yscale(d.median)) + ")";
+  return "translate(0,-" + (tk.legheight + tk.lowpad + tk.maxradius * 3 + tk.padheight) + ")";
+}
+function set_stem_y2(d, tk) {
+  if (d.mode == modefold) return d.radius + tk.lowpad;
+  if (d.mode == moderaise) return tk.padheight + tk.maxradius * 2 + tk.axisheight - tk.yscale(d.median);
+  return tk.maxradius + tk.padheight;
+}
+function set_all(tk) {
+  const dur = 500;
+  if (tk.totalsamplecount > 1) {
+    tk.jug.selectAll(".sja_jug_qmg").transition().duration(dur).attr("transform", (d) => set_qmg(d, tk));
+    tk.jug.selectAll(".sja_jug_discnum").transition().duration(dur).attr("fill-opacity", (d) => set_discnum(d));
+  }
+  tk.jug.selectAll(".sja_jug_leg1").transition().duration(dur).attr("y2", (d) => set_leg_y(d, tk)).attr("x1", (d) => set_leg_x1(d));
+  tk.jug.selectAll(".sja_jug_leg2").transition().duration(dur).attr("y1", (d) => set_leg_y(d, tk)).attr("x2", (d) => set_leg_x2(d));
+  tk.jug.selectAll(".sja_jug_jug2").transition().duration(dur).attr("transform", (d) => set_jug2(d, tk));
+  tk.jug.selectAll(".sja_jug_stem").transition().duration(dur).attr("y2", (d) => set_stem_y2(d, tk)).attr("y1", (d) => set_stem_y1(d));
+  tk.jug.transition().duration(dur).attr("transform", (d) => set_jug(d));
+}
+function junctiontype2color(tk, block) {
+  for (const j of tk.data) {
+    j.color = defaultcolor;
+  }
+  if (tk.nocatepreconfig) {
+    let categories = {};
+    if (tk.categories) {
+      categories = tk.categories;
+    }
+    let hasnewtype = false;
+    for (const j of tk.data) {
+      if (j.type) {
+        if (!categories[j.type]) {
+          hasnewtype = true;
+          categories[j.type] = {
+            label: j.type
+          };
+          if (j.type.toLowerCase() == "known") {
+            categories[j.type].color = "#0C72A8";
+          } else if (j.type.toLowerCase() == "novel") {
+            categories[j.type].color = "#A80C33";
+          } else {
+            categories[j.type].color = colorfunc(j.type);
+          }
+        }
+      }
+    }
+    if (hasnewtype) {
+      tk.categories = categories;
+      if (!tk.tr_legend) {
+        const [tr, td] = legend_newrow(block, tk.name);
+        tk.tr_legend = tr;
+        tk.td_legend = td;
+        tr.style("display", "none");
+        appear(tr, "table-row");
+      }
+      category2legend(tk.categories, tk.td_legend);
+    }
+  }
+  if (tk.categories) {
+    for (const j of tk.data) {
+      if (j.type && tk.categories[j.type]) {
+        j.color = tk.categories[j.type].color;
+      }
+    }
+  }
+}
+function foldedjunctioninfo(d, tk) {
+  const fontsize = 15;
+  let pad = 5, y = pad, width = 0;
+  const bg = tk.pica.g.append("rect").attr("stroke", d.color).attr("shape-rendering", "crispEdges").attr("fill", "white").attr("fill-opacity", 0.8);
+  if (d.type) {
+    tk.pica.g.append("text").text(d.type).attr("fill", d.color).attr("font-size", fontsize - 2).attr("font-family", font).attr("x", pad).attr("y", y + fontsize / 2).attr("dominant-baseline", "central").each(function() {
+      width = this.getBBox().width;
+    });
+    y += fontsize;
+  }
+  if (d.data) {
+    tk.pica.g.append("text").text(d.data.length + " sample" + (d.data.length > 1 ? "s" : "")).attr("fill", "#858585").attr("font-size", fontsize - 2).attr("font-family", font).attr("x", pad).attr("y", y + fontsize / 2).attr("dominant-baseline", "central").each(function() {
+      width = Math.max(width, this.getBBox().width);
+    });
+    y += fontsize;
+    tk.pica.g.append("text").text(d.median + " median").attr("fill", "#858585").attr("font-size", fontsize - 2).attr("font-family", font).attr("x", pad).attr("y", y + fontsize / 2).attr("dominant-baseline", "central").each(function() {
+      width = Math.max(width, this.getBBox().width);
+    });
+    y += fontsize;
+  } else {
+    tk.pica.g.append("text").text(d.v + " reads").attr("fill", "#858585").attr("font-size", fontsize - 2).attr("font-family", font).attr("x", pad).attr("y", y + fontsize / 2).attr("dominant-baseline", "central").each(function() {
+      width = Math.max(width, this.getBBox().width);
+    });
+    y += fontsize;
+  }
+  y += pad;
+  bg.attr("width", pad * 2 + width).attr("height", y);
+  tk.pica.g.append("line").attr("stroke", d.color).attr("shape-rendering", "crispEdges").attr("x1", 30).attr("x2", 30).attr("y1", y).attr("y2", y + 15);
+  y += 15;
+  tk.pica.g.attr(
+    "transform",
+    "translate(" + (d.x - 30) + "," + (tk.toppad + tk.axisheight + tk.maxradius * 4 + tk.padheight - d.radius * 2 - y) + ")"
+  );
+}
+function expandedjunctioninfo(d, tk, circle) {
+  tk.tktip.clear();
+  const holder = tk.tktip.d;
+  if (d.type) {
+    holder.append("div").style("display", "inline-block").text(d.type).classed("sja_mcdot", true).style("background-color", d.color).style("padding", "1px 8px").style("margin-bottom", "3px");
+  }
+  holder.append("div").html(
+    bplen(d.stop - d.start) + ' <span style="font-size:.8em;">' + d.chr + ":" + (d.start + 1) + "-" + (d.stop + 1) + "</span>"
+  );
+  if (d.data) {
+    if (d.data.length > 1) {
+      holder.append("div").html(d.data.length + ' <span style="font-size:.8em;color:#858585">samples</span>');
+      if (d.rimcount) {
+        holder.append("div").html(d.rimcount + ' <span style="font-size:.8em;color:#858585">show ' + tk.rimwhat + "</span>");
+      }
+      holder.append("div").html(d.median + ' <span style="font-size:.8em;color:#858585">median read count</span>');
+    } else if (d.data.length == 1) {
+      samplejunctiontooltip(d, d.data[0], tk, holder);
+    }
+  } else {
+    holder.append("div").html(d.v + ' <span style="font-size:.8em;color:#858585">read count</span>');
+  }
+  if (d.spliceevents && d.spliceevents.length > 0) {
+    const renderdiv = holder.append("div").style("margin", "10px 0px");
+    displayspliceevents(d.spliceevents, renderdiv);
+  }
+  tk.tktip.show(circle.left + circle.width, circle.top - 50);
+}
+function junctionsamplespread(j, tk, block) {
+  if (j.qmg) {
+    j.qmg.remove();
+  }
+  if (tk.cohortsetting && tk.cohortsetting.uselevelidx != void 0) {
+    for (const d of j.data) {
+      if (!d[tk.cohortsetting.cohort.levels[0].k]) {
+        d.color = "gray";
+        continue;
+      }
+      const levelkeys = [];
+      for (let lidx = 0; lidx <= tk.cohortsetting.uselevelidx; lidx++) {
+        const levelvalue = d[tk.cohortsetting.cohort.levels[lidx].k];
+        if (levelvalue) {
+          levelkeys.push(levelvalue);
+        }
+      }
+      const str = levelkeys.join(tk.cohortsetting.levelseparator);
+      d.color = tk.cohortsetting.colorfunc(str);
+    }
+  }
+  j.swarm = (0, import_d3_beeswarm.beeswarm)().data(j.data).distributeOn((d) => tk.axisheight - tk.yscale(d.v)).radius(tk.qmradius).orientation("vertical").side("symetric").arrange();
+  const jugg = select_default(j.jugg);
+  j.qmg = jugg.append("g").attr("class", "sja_jug_qmg").attr("transform", set_qmg(j, tk));
+  const opacity = 0.8;
+  j.qmg.selectAll().data(j.swarm).enter().append("circle").attr("cx", 0).attr("cy", (bee) => -bee.y).attr("r", tk.qmradius).attr("fill", (bee) => {
+    return bee.datum.color || "green";
+  }).attr("fill-opacity", opacity).on("mousedown", (event) => event.stopPropagation()).on("mousemove", (event) => event.stopPropagation()).on("mouseover", (event, bee) => {
+    select_default(event.target).attr("fill-opacity", 1);
+    const p = event.target.getBoundingClientRect();
+    tk.tktip.clear();
+    tk.tktip.show(p.left + 20, p.top - 40);
+    samplejunctiontooltip(j, bee.datum, tk, tk.tktip.d);
+  }).on("mouseout", (event) => select_default(event.target).attr("fill-opacity", opacity)).on("click", (event, bee) => {
+    if (tk.tracks) {
+      return;
+    }
+  }).transition().attr("cx", (bee) => bee.x);
+}
+function samplejunctiontooltip(j, sample, tk, holder) {
+  if (sample.sample) {
+    holder.append("div").html(sample.sample);
+  } else if (sample.name) {
+    holder.append("div").html(sample.name);
+  } else if (sample.patient || sample.sampletype) {
+    if (sample.patient) {
+      holder.append("div").html(sample.patient + ' <span style="font-size:.7em;color:#858585">patient</span>');
+    }
+    if (sample.sampletype) {
+      holder.append("div").html(sample.sampletype + ' <span style="font-size:.7em;color:#858585">sample type</span>');
+    }
+  } else if (sample.tkid) {
+    for (const t of tk.tracks) {
+      if (t.tkid == sample.tkid) {
+        holder.append("div").text(t.name || "unnamed member");
+        break;
+      }
+    }
+  }
+  if (tk.cohortsetting && tk.cohortsetting.cohort && tk.cohortsetting.cohort.levels) {
+    for (const lev of tk.cohortsetting.cohort.levels) {
+      if (sample[lev.k]) {
+        holder.append("div").html(sample[lev.k] + ' <span style="font-size:.7em;color:#858585">' + lev.label + "</span>");
+      }
+    }
+  }
+  holder.append("div").html(sample.v + ' <span style="font-size:.7em;color:#858585">read count</span>');
+  if (sample.metadata) {
+    holder.append("div").html(
+      '<span style="background-color:' + sample.metadata.color + '" class=sja_mcdot>&nbsp;</span> ' + sample.metadata.value + ' <span style="font-size:.7em;color:#858585">' + tk.metadata.m.label + "</span>"
+    );
+  }
+  if (sample.hasrim) {
+    holder.append("div").text(tk.rimwhat);
+  }
+  if (j.spliceevents) {
+    const evtidx = spliceevent_exonskip_getdefault_default(j.spliceevents);
+    const evt = j.spliceevents[evtidx];
+    const skipwhichexon = "exon " + evt.skippedexon.map((i) => i + 1).join(",") + " " + (evt.isskipexon ? "skip" : "alt. use");
+    let jbcount = 0;
+    if (evt.junctionB && evt.junctionB.data) {
+      for (const d of evt.junctionB.data) {
+        if (d.tkid == sample.tkid) {
+          jbcount = d.v;
+          break;
+        }
+      }
+    }
+    let acountsum = 0;
+    if (evt.junctionAlst) {
+      for (const ja of evt.junctionAlst) {
+        if (ja && ja.data) {
+          for (const d of ja.data) {
+            if (d.tkid == sample.tkid) {
+              acountsum += d.v;
+              break;
+            }
+          }
+        }
+      }
+    }
+    let percent;
+    if (jbcount == 0) {
+      percent = 0;
+    } else {
+      percent = Math.ceil(100 * jbcount / (jbcount + acountsum / evt.junctionAlst.length));
+    }
+    holder.append("div").html(percent + '% <span style="font-size:.7em;color:#858585;">' + skipwhichexon + "</span>");
+  }
+}
+function get_leftLabelMaxwidth(tk) {
+  const collectlabw = [];
+  tk.tklabel.each(function() {
+    collectlabw.push(this.getBBox().width);
+  });
+  if (tk.label_mcount) {
+    tk.label_mcount.each(function() {
+      collectlabw.push(this.getBBox().width);
+    });
+  }
+  tk.leftLabelMaxwidth = Math.max(...collectlabw);
+}
+
+// src/block.tk.junction.js
+var binpxw = 5;
+var modefold = 1;
+var moderaise = 2;
+var modesample = 3;
+var labyspace = 5;
+function makeTk(tk, block) {
+  tk.leftaxis = tk.gleft.append("g");
+  let laby = labyspace + block.labelfontsize;
+  const thistip = new Menu({ padding: "none" });
+  tk.label_mcount = block.maketklefthandle(tk, laby).on("click", (event) => {
+    label_mcount_fillpane(tk, block, thistip);
+  });
+  laby += labyspace + block.labelfontsize;
+  tk.totalsamplecount = 0;
+  tk.height_main = 100;
+  tk.config_handle = block.maketkconfighandle(tk).on("click", (event) => configpanel(tk, block));
+  if (tk.categories || tk.cohortsetting) {
+    const [tr, td] = legend_newrow(block, tk.name);
+    tk.tr_legend = tr;
+    tk.td_legend = td;
+  }
+  if (tk.categories) {
+    category2legend(tk.categories, tk.td_legend);
+  }
+  if (tk.cohortsetting) {
+    tk.cohortsetting.holder = tk.td_legend.append("div").style("margin-top", "10px");
+    tk.cohortsetting.legendholder = tk.cohortsetting.holder.append("div");
+  }
+}
+function junctionload(tk, block) {
+  if (tk.uninitialized) {
+    makeTk(tk, block);
+    delete tk.uninitialized;
+  }
+  if ((block.zoomedin || block.resized) && tk.data) {
+    const junc = [];
+    for (const i of tk.data) {
+      const oldx = i.x;
+      const e = j2block(i, block);
+      if (e) {
+        continue;
+      }
+      if (i.x0 >= 0 && i.x0 <= block.width || i.x1 >= 0 && i.x1 <= block.width) {
+        i.x = oldx;
+        junc.push(i);
+      }
+    }
+    rendertk(junc, tk, block);
+    return;
+  }
+  if (tk.fixeddata) {
+    block.tkcloakon(tk);
+    const junc2 = [];
+    for (const j of tk.fixeddata) {
+      const j2 = {
+        chr: j.chr,
+        start: j.start,
+        stop: j.stop,
+        data: j.data,
+        type: j.type
+      };
+      const e = j2block(j2, block);
+      if (e) {
+        continue;
+      }
+      junc2.push(j2);
+    }
+    tk.totalsamplecount = tk.tracks[0].samplecount;
+    tk.axisheight = 200;
+    tk.legheight = 50;
+    tk.bottompad = 0;
+    tk.qmradius = 2;
+    tk.lowpad = 15;
+    tk.padheight = 10;
+    rendertk(junc2, tk, block);
+    return;
+  }
+  if (!tk.tracks) {
+    block.tkcloakoff(tk, { error: "neither .tracks[] or .fixeddata[] are available" });
+    tk.height_main = 50;
+    block.block_setheight();
+    return;
+  }
+  block.block_setheight();
+  block.tkcloakon(tk);
+  const bincount = Math.ceil(block.width / binpxw);
+  let bins = null;
+  let donenum = 0;
+  const tasks = [];
+  const allfiledata = [];
+  for (const t of tk.tracks) {
+    const getheader = new Promise((resolve, reject) => {
+      if (t.rnapegfile) {
+        t.samplecount = 1;
+        return resolve();
+      }
+      if (t.samplecount != void 0 && t.checkedheader) return resolve();
+      const par = {};
+      if (t.file) {
+        par.file = t.file;
+      } else {
+        par.url = t.url;
+        if (t.indexURL) par.indexURL = t.indexURL;
+      }
+      dofetch3("tabixheader", { body: par }).then((data) => {
+        if (data.error) return reject("cannot load header for member track " + t.name + ": " + data.error);
+        t.checkedheader = true;
+        const str = data.lines.join("");
+        if (!str) {
+        } else {
+          const l = str.trim().split("	");
+          t.headersamples = [];
+          for (let i = 5; i < l.length; i++) {
+            const str2 = l[i];
+            let j = null;
+            if (str2[0] == "{" && str2[str2.length - 1] == "}") {
+              try {
+                j = JSON.parse(str2);
+              } catch (e) {
+                console.error("header line field [" + i + "] is broken json: " + str2);
+              }
+            }
+            if (j) {
+              j.tkid = Math.random().toString();
+              t.headersamples.push(j);
+            } else {
+              t.headersamples.push({
+                name: l[i],
+                tkid: Math.random().toString()
+              });
+            }
+          }
+          t.samplecount = t.headersamples.length;
+          tk.totalsamplecount += t.samplecount;
+        }
+        resolve();
+      });
+    });
+    const getdata = new Promise((resolve, reject) => {
+      getheader.then(() => {
+        const par = {
+          genome: block.genome.name,
+          rglst: block.tkarg_maygm(t)
+        };
+        if (bincount) par.bincount = bincount;
+        if (t.file || t.rnapegfile) {
+          par.file = t.file || t.rnapegfile;
+        } else {
+          par.url = t.url;
+          if (t.indexURL) par.indexURL = t.indexURL;
+        }
+        if (t.rnapegfile) {
+          par.isrnapeg = 1;
+        }
+        dofetch3("termdb/junction/onesampletk", { body: par }).then((data) => {
+          donenum++;
+          if (tk.tracks.length > 1) {
+            block.tkprogress(tk, donenum / tk.tracks.length);
+          }
+          if (!data) reject("server error for getting member track " + t.name);
+          if (data.error) reject("Cannot get data: " + data.error);
+          if (!data.lst && !data.bins) reject("wrong response when getting data for " + t.name);
+          if (data.lst) {
+            if (data.lst[0] && data.lst[0].rawdata && t.samplecount == void 0) {
+              t.samplecount = data.lst[0].rawdata.length;
+              tk.totalsamplecount += t.samplecount;
+            }
+            if (bins) {
+            } else {
+              const thisfilejunctions = [];
+              for (const k of data.lst) {
+                k.data = [];
+                for (let i = 0; i < k.rawdata.length; i++) {
+                  const v = k.rawdata[i];
+                  if (!Number.isInteger(v) || v <= 0) {
+                    continue;
+                  }
+                  const s = { v };
+                  if (t.headersamples) {
+                    const s0 = t.headersamples[i];
+                    if (s0) {
+                      for (const _k in s0) {
+                        s[_k] = s0[_k];
+                      }
+                    }
+                  } else {
+                    if (t.name) s.name = t.name;
+                    if (t.sample) s.sample = t.sample;
+                    if (t.patient) s.patient = t.patient;
+                    if (t.sampeltype) s.sampletype = t.sampletype;
+                    if (t.tkid) s.tkid = t.tkid;
+                    if (t.file) s.file = t.file;
+                    if (t.url) s.url = t.url;
+                    if (t.indexURL) s.indexURL = t.indexURL;
+                  }
+                  k.data.push(s);
+                }
+                delete k.rawdata;
+                thisfilejunctions.push(k);
+              }
+              resolve(thisfilejunctions);
+            }
+          } else {
+          }
+        });
+      }).catch((err) => reject(err));
+    });
+    tasks.push(getdata);
+  }
+  Promise.all(tasks).then((data) => {
+    const junc = [];
+    data.forEach((dat) => {
+      if (!dat) return;
+      dat.forEach((k) => {
+        let notfound = true;
+        for (const j of junc) {
+          if (j.start == k.start && j.stop == k.stop) {
+            j.data = j.data.concat(k.data);
+            notfound = false;
+            break;
+          }
+        }
+        if (notfound) {
+          junc.push(k);
+        }
+      });
+    });
+    for (const j of junc) {
+      j2block(j, block);
+    }
+    for (const j of junc) {
+      smuggleattributes(j);
+    }
+    if (!tk.axisheight) {
+      if (tk.totalsamplecount > 1) {
+        tk.axisheight = 200;
+        tk.legheight = 50;
+        tk.bottompad = 0;
+        tk.qmradius = 2;
+        tk.lowpad = 15;
+        tk.padheight = 10;
+      } else {
+        tk.axisheight = 100;
+        tk.legheight = 20;
+        tk.bottompad = 0;
+        tk.lowpad = 10;
+        tk.padheight = 10;
+      }
+      if (tk.cohortsetting) {
+        initcohortsetting(tk, block);
+      }
+    }
+    rendertk(junc, tk, block);
+  }).catch((err) => {
+    tk.glider.selectAll("*").remove();
+    block.tkcloakoff(tk, { error: err });
+    block.block_setheight();
+  });
+}
+function j2block(j, block) {
+  const starthit = block.seekcoord(j.chr, j.start)[0];
+  if (!starthit) {
+    return true;
+  }
+  const stophit = block.seekcoord(j.chr, j.stop)[0];
+  if (!stophit) {
+    return true;
+  }
+  const startout = starthit.x < 0 || starthit.x > block.width;
+  const stopout = stophit.x < 0 || stophit.x > block.width;
+  if (startout && stopout) {
+    return true;
+  }
+  j.x0 = starthit.x;
+  j.x1 = stophit.x;
+  j.x = (j.x0 + j.x1) / 2;
+  j._x = j.x;
+  if (!j.modefix) {
+    j.mode = moderaise;
+  }
+  return false;
+}
+function smuggleattributes(j) {
+}
+function label_mcount_fillpane(tk, block, tip) {
+  tip.clear();
+  const holder = tip.d;
+  const types = /* @__PURE__ */ new Map();
+  for (const j of tk.data) {
+    if (!j.type) continue;
+    if (!types.has(j.type)) {
+      types.set(j.type, []);
+    }
+    if (j.data) {
+      types.get(j.type).push(j.data.map((i) => i.v));
+    } else {
+      types.get(j.type).push(j.v);
+    }
+  }
+  if (types.size) {
+    const d = holder.append("div").style("margin", "8px");
+    for (const [type, valuelst] of types) {
+      d.append("div").style("margin", "2px").html(
+        valuelst.length + ' <span style="font-size:.8em;color:' + tk.categories[type].color + '">' + type + " junction" + (valuelst.length > 1 ? "s" : "") + "</span>"
+      );
+      let vlst = valuelst;
+      if (tk.tracks) {
+        vlst = [];
+        for (const l of valuelst) {
+          vlst.push(...l);
+        }
+      }
+      if (vlst.length == 1) {
+      } else {
+        d.append("table").style("margin-left", "20px").html(
+          '<tr><td style="text-align:right;">' + Math.max(...vlst) + '</td><td style="color:#858585;font-size:.7em">max read count</td></tr><tr><td style="text-align:right;">' + Math.min(...vlst) + '</td><td style="color:#858585;font-size:.7em">min</td></tr><tr><td style="text-align:right;">' + Math.ceil(vlst.reduce((i, j) => j + i, 0) / vlst.length) + '</td><td style="color:#858585;font-size:.7em">mean</td></tr>'
+        );
+      }
+    }
+  } else {
+    let vlst = [];
+    if (tk.tracks) {
+      for (const j of tk.data) {
+        vlst.push(...j.data.map((i) => i.v));
+      }
+    } else {
+      vlst = tk.data.map((j) => j.v);
+    }
+    if (vlst.length > 1) {
+      holder.append("table").html(
+        '<tr><td style="text-align:right;">' + Math.max(...vlst) + '</td><td style="color:#858585;font-size:.7em">max read count</td></tr><tr><td style="text-align:right;">' + Math.min(...vlst) + '</td><td style="color:#858585;font-size:.7em">min</td></tr><tr><td style="text-align:right;">' + Math.ceil(vlst.reduce((i, j) => j + i, 0) / vlst.length) + '</td><td style="color:#858585;font-size:.7em">mean</td></tr>'
+      );
+    }
+  }
+  holder.append("div").text("Fold").classed("sja_menuoption", true).on("click", (event) => {
+    tip.hide();
+    for (const j of tk.data) {
+      j.mode = modefold;
+      j.modefix = true;
+    }
+    horiplace(tk.data, block.width, tk);
+  });
+  holder.append("div").text("Expand").classed("sja_menuoption", true).on("click", (event) => {
+    tip.hide();
+    for (const j of tk.data) {
+      j.modefix = false;
+    }
+    automode(tk, null, block.width);
+    for (const j of tk.data) {
+      j.modefix = true;
+    }
+    horiplace(tk.data, block.width, tk);
+  });
+  holder.append("div").text("Download").classed("sja_menuoption", true).on("click", (event) => {
+    tip.hide();
+    downloadjunctions(tk);
+  });
+  tip.showunder(tk.label_mcount.node());
+}
+function downloadjunctions(tk) {
+  const txt = [];
+  if (tk.file || tk.url) {
+    if (tk.data) {
+      txt.push("chromosome	start	stop	read_count" + (tk.categories ? "	type" : ""));
+      for (const j of tk.data) {
+        txt.push(j.chr + "	" + j.start + "	" + j.stop + "	" + j.v + (tk.categories ? "	" + j.type : ""));
+      }
+    }
+  } else if (tk.tracks) {
+    if (tk.data) {
+      const header = ["chromosome	start	stop" + (tk.categories ? "	type" : "")];
+      for (const t of tk.tracks) {
+        const lst = [];
+        if (t.patient) lst.push(t.patient);
+        if (t.sampletype) lst.push(t.sampletype);
+        if (lst.length == 0) {
+          lst.push(t.name);
+        }
+        header.push(lst.join(", "));
+      }
+      txt.push(header.join("	"));
+      for (const j of tk.data) {
+        const lst = [j.chr + "	" + j.start + "	" + j.stop + (tk.categories ? "	" + j.type : "")];
+        const hash = /* @__PURE__ */ new Map();
+        for (const jsample of j.data) {
+          hash.set(jsample.tkid, jsample.v);
+        }
+        for (const t of tk.tracks) {
+          lst.push(hash.has(t.tkid) ? hash.get(t.tkid) : "");
+        }
+        txt.push(lst.join("	"));
+      }
+    }
+  }
+  export_data(tk.name, [{ label: "Splice junction", text: txt.join("\n") }]);
+}
+function configpanel(tk, block) {
+  tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+  const holder = tk.tkconfigtip.d;
+  {
+    const row = holder.append("div").style("margin-bottom", "10px");
+    row.append("span").html("Read count cutoff&nbsp;");
+    row.append("input").property("value", tk.readcountcutoff || 0).attr("type", "number").style("width", "50px").on("keyup", (event) => {
+      if (!keyupEnter(event)) return;
+      const v = Number.parseFloat(event.target.value);
+      if (v == 0) {
+        if (tk.readcountcutoff) {
+          tk.readcountcutoff = 0;
+          junctionload(tk, block);
+        } else {
+        }
+        return;
+      }
+      if (!v || v < 0) {
+        return;
+      }
+      if (tk.readcountcutoff) {
+        if (tk.readcountcutoff == v) {
+        } else if (tk.readcountcutoff > v) {
+          tk.readcountcutoff = v;
+          junctionload(tk, block);
+        } else {
+          tk.readcountcutoff = v;
+          rendertk(tk.data, tk, block);
+        }
+      } else {
+        tk.readcountcutoff = v;
+        junctionload(tk, block);
+      }
+    });
+    const note = row.append("div").style("font-size", ".7em").style("color", "#858585");
+    if (tk.totalsamplecount > 1) {
+      note.text("For a junction, samples with read count lower than cutoff will not be shown.");
+    } else {
+      note.text("Junctions with read count lower than cutoff will not be shown.");
+    }
+  }
+}
+function initcohortsetting(tk, block) {
+  if (!tk.cohortsetting.cohort) {
+    sayerror(tk.cohortsetting.holder, ".cohort missing from tk.cohortsetting");
+    return;
+  }
+  if (!tk.cohortsetting.cohort.levels) {
+    sayerror(tk.cohortsetting.holder, ".levels missing from tk.cohortsetting.cohort");
+    return;
+  }
+  if (!tk.cohortsetting.cohort.levels[0]) {
+    sayerror(tk.cohortsetting.holder, "tk.cohortsetting.cohort.levels[0] is invalid");
+    return;
+  }
+  tk.cohortsetting.levelseperator = ".";
+  tk.cohortsetting.uselevelidx = 0;
+  setcohortlegend_usecohortlevel(tk, block);
+}
+function setcohortlegend_usecohortlevel(tk, block) {
+  tk.cohortsetting.legendholder.selectAll("*").remove();
+  tk.cohortsetting.colorfunc = ordinal(category10_default);
+  const stratkey2count = /* @__PURE__ */ new Map();
+  for (const t of tk.tracks) {
+    for (const s of t.headersamples) {
+      if (!s[tk.cohortsetting.cohort.levels[0].k]) {
+        continue;
+      }
+      const thissamplekeys = [];
+      for (let lidx = 0; lidx <= tk.cohortsetting.uselevelidx; lidx++) {
+        const thislevelkey = s[tk.cohortsetting.cohort.levels[lidx].k];
+        if (thislevelkey) {
+          thissamplekeys.push(thislevelkey);
+        }
+      }
+      const str = thissamplekeys.join(tk.cohortsetting.levelseperator);
+      if (!stratkey2count.has(str)) {
+        stratkey2count.set(str, {
+          count: 0,
+          label: s[tk.cohortsetting.cohort.levels[tk.cohortsetting.uselevelidx].full]
+        });
+      }
+      stratkey2count.get(str).count++;
+    }
+  }
+  const sorteditems = [...stratkey2count].sort((a, b) => b[1].count - a[1].count);
+  for (const item of sorteditems) {
+    const color = tk.cohortsetting.colorfunc(item[0]);
+    const label = item[1].label;
+    const row = tk.cohortsetting.legendholder.append("div").style("margin-top", "5px");
+    row.append("div").style("display", "inline-block").attr("class", "sja_mcdot").style("background-color", color).style("margin-right", "10px").html("&nbsp;&nbsp;");
+    row.append("div").style("display", "inline-block").text(label);
+  }
+}
+export {
+  junctionload,
+  modefold,
+  moderaise,
+  modesample
+};
+//# sourceMappingURL=block.tk.junction-2KI3SPXW.js.map