Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

[jalview.git] / src / jalview / analysis / TreeModel.java

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 4d5e4b2..11ca778 100644 (file)
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -81,8 +81,8 @@ public class TreeModel
   public TreeModel(SequenceI[] seqs, AlignmentView odata,
           NewickFile treefile)
   {
-    this(seqs, treefile.getTree(), treefile.HasDistances(),
-            treefile.HasBootstrap(), treefile.HasRootDistance());
+    this(seqs, treefile.getTree(), treefile.hasDistances(),
+            treefile.hasBootstrap(), treefile.hasRootDistance());
     seqData = odata;
 
     associateLeavesToSequences(seqs);
@@ -131,29 +131,27 @@ public class TreeModel
 
     Vector<SequenceNode> leaves = findLeaves(top);
 
-    int i = 0;
     int namesleft = seqs.length;
 
-    SequenceNode j;
-    SequenceI nam;
-    String realnam;
-    Vector<SequenceI> one2many = new Vector<SequenceI>();
+    SequenceI nodeSequence;
+    String nodeSequenceName;
+    Vector<SequenceI> one2many = new Vector<>();
     // int countOne2Many = 0;
-    while (i < leaves.size())
+
+    for (SequenceNode sn : leaves)
     {
-      j = leaves.elementAt(i++);
-      realnam = j.getName();
-      nam = null;
+      nodeSequenceName = sn.getName();
+      nodeSequence = null;
 
       if (namesleft > -1)
       {
-        nam = algnIds.findIdMatch(realnam);
+        nodeSequence = algnIds.findIdMatch(nodeSequenceName);
       }
 
-      if (nam != null)
+      if (nodeSequence != null)
       {
-        j.setElement(nam);
-        if (one2many.contains(nam))
+        sn.setElement(nodeSequence);
+        if (one2many.contains(nodeSequence))
         {
           // countOne2Many++;
           // if (Cache.isDebugEnabled())
@@ -162,14 +160,14 @@ public class TreeModel
         }
         else
         {
-          one2many.addElement(nam);
+          one2many.addElement(nodeSequence);
           namesleft--;
         }
       }
       else
       {
-        j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
-        j.setPlaceholder(true);
+        sn.setElement(new Sequence(nodeSequenceName, "THISISAPLACEHLDER"));
+        sn.setPlaceholder(true);
       }
     }
     // if (Cache.isDebugEnabled() && countOne2Many>0) {
@@ -296,7 +294,7 @@ public class TreeModel
    */
   public Vector<SequenceNode> findLeaves(SequenceNode nd)
   {
-    Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+    Vector<SequenceNode> leaves = new Vector<>();
     findLeaves(nd, leaves);
     return leaves;
   }
@@ -390,7 +388,7 @@ public class TreeModel
    */
   public List<SequenceNode> groupNodes(float threshold)
   {
-    List<SequenceNode> groups = new ArrayList<SequenceNode>();
+    List<SequenceNode> groups = new ArrayList<>();
     _groupNodes(groups, getTopNode(), threshold);
     return groups;
   }