Fix overlapping groups

GraphNode.js

@@ -41,6 +41,7 @@ class GraphNode {
     }
   }
 
+  // TODO: move this to LayoutNode, item by item
   setAffinity(nodes) {
     const INF = 999999;
 

Layout.js

@@ -9,9 +9,9 @@ class Layout {
     this.links_ = [];
 
     this.setInitialPositions();
+    this.resolveGroups();
     this.resolveLinks();
     this.resolveAffinity();
-    this.resolveGroups();
     while (this.iterate());
     this.addGroupPos();
     this.drawLinks();

LayoutGroup.js

@@ -4,6 +4,10 @@ class LayoutGroup {
     this.nodesByPos_ = nodesByPos;
     this.nodes = new Set(nodes);
     this.tension = 0;
+
+    for (let node of nodes) {
+      node.groups.push(this);
+    }
   }
 
   setTension() {
@@ -68,6 +72,12 @@ class LayoutGroup {
     return [min, max];
   }
 
+  isContained(pos) {
+    let [min, max] = this.getMinMax();
+    return (pos[0] >= min[0] && pos[0] <= max[0] &&
+            pos[1] >= min[1] && pos[1] <= max[1]);
+  }
+
   getStep() {
     if (!this.graphGroup_) {
       return null;

LayoutNode.js

@@ -3,6 +3,7 @@ class LayoutNode {
     this.graphNode_ = graphNode;
     this.nodesByPos_ = nodesByPos;
     this.pos = pos;
+    this.groups = [];
 
     this.nodesByPos_.set(this.pos, this);
   }
@@ -15,6 +16,9 @@ class LayoutNode {
   }
 
   resolveAffinity(nodesByGraphNode) {
+    const INF = 999999;
+
+    // Transitional: copy GraphNode affinity
     this.affinity_ = [];
     for (let aff of this.graphNode_.affinity) {
       this.affinity_.push({
@@ -22,6 +26,19 @@ class LayoutNode {
         distanceToWeight: aff.distanceToWeight,
       });
     }
+
+    for (let node of nodesByGraphNode.values()) {
+      for (let group of this.groups) {
+        // Ensure groups do not overlap
+        if (group.nodes.has(node)) {
+          continue;
+        }
+        this.affinity_.push({
+          node: node,
+          distanceToWeight: (d, v, p) => group.isContained(p) ? -INF : 0,
+        });
+      }
+    }
   }
 
   setTension() {
@@ -35,7 +52,7 @@ class LayoutNode {
       };
       // Avoid calling sqrt(), since the results are used relatively
       let distanceSquared = vec[0] * vec[0] + vec[1] * vec[1];
-      let weight = aff.distanceToWeight(distanceSquared, vec);
+      let weight = aff.distanceToWeight(distanceSquared, vec, aff.node.pos);
       if (weight instanceof Array) {
         for (let i of [0, 1]) {
           this.vec[i] += weight[i];