Complete affinity migration from Graph to Layout

Fixes #6

Graph.js

@@ -16,7 +16,6 @@ class Graph {
     this.setPageRank();
     this.setSubgraph();
     this.bucketNodes();
-    this.setAffinity();
   }
 
   processList(list, soft=false) {
@@ -134,12 +133,6 @@ class Graph {
       nodes.sort();
     }
   }
-
-  setAffinity() {
-    for (let node of this.nodes) {
-      node.setAffinity(this.nodes);
-    }
-  }
 }
 
 <!--# include file="GraphGroup.js" -->

GraphNode.js

@@ -3,7 +3,6 @@ class GraphNode {
     this.links = [];
     this.linksIn = [];
     this.groups = new Set();
-    this.affinity = [];
     this.pageRank = 0;
     this.subgraph = null;
   }
@@ -41,38 +40,6 @@ class GraphNode {
     }
   }
 
-  // TODO: move this to LayoutNode, item by item
-  setAffinity(nodes) {
-    const INF = 999999;
-
-    for (let node of nodes) {
-    }
-
-    for (let link of this.links) {
-      // Stronger affinity for links
-      // Prefer to move toward the target instance
-      this.addAffinity(link.to, d => d <= 2 ? -INF : d * 11);
-      link.to.addAffinity(this, d => d <= 2 ? -INF : d * 9);
-    }
-
-    // Affinity for groups
-    for (let group of this.groups) {
-      for (let node of group.nodes) {
-        this.addAffinity(node, d => d * 100);
-      }
-    }
-  }
-
-  addAffinity(node, distanceToWeight) {
-    if (this == node) {
-      return;
-    }
-    this.affinity.push({
-      node: node,
-      distanceToWeight: distanceToWeight,
-    });
-  }
-
   static process(item, soft=false) {
     if (item.label == '') {
       return null;

Layout.js

@@ -12,7 +12,7 @@ class Layout {
     this.setInitialPositions();
     this.resolveGroups();
     this.resolveLinks();
-    this.resolveAffinity();
+    this.setAffinity();
     while (this.iterate());
     this.addGroupPos();
     this.drawLinks();
@@ -74,9 +74,9 @@ class Layout {
     }
   }
 
-  resolveAffinity() {
+  setAffinity() {
     for (let node of this.nodes_) {
-      node.resolveAffinity(this.nodesByGraphNode_);
+      node.setAffinity(this.nodesByGraphNode_);
     }
   }
 

LayoutNode.js

@@ -25,18 +25,9 @@ class LayoutNode {
     }
   }
 
-  resolveAffinity(nodesByGraphNode) {
+  setAffinity(nodesByGraphNode) {
     const INF = 999999;
 
-    // TODO: remove
-    // Transitional: copy GraphNode affinity
-    for (let aff of this.graphNode_.affinity) {
-      this.affinity_.push({
-        node: nodesByGraphNode.get(aff.node),
-        distanceToWeight: aff.distanceToWeight,
-      });
-    }
-
     for (let node of nodesByGraphNode.values()) {
       // Weak affinity full mesh
       // Keep unassociated subgroups together
@@ -78,6 +69,23 @@ class LayoutNode {
         });
       }
     }
+
+    for (let link of this.links) {
+      // Stronger affinity for links
+      // Prefer to move toward the target instance
+      this.addAffinity(link.to, d => d <= 2 ? -INF : d * 11);
+      link.to.addAffinity(this, d => d <= 2 ? -INF : d * 9);
+    }
+
+    // Affinity for groups
+    for (let group of this.groups) {
+      if (!group.hasGraphGroup()) {
+        continue;
+      }
+      for (let node of group.nodes) {
+        this.addAffinity(node, d => d * 100);
+      }
+    }
   }
 
   addAffinity(node, distanceToWeight) {