JAL-1951 added comment to NexusFile clarifying Forester's broken parser

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

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 5a41802..1c19dbf 100644 (file)
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -77,10 +77,11 @@ public class TreeModel
    * @param treefile
    *          NewickFile
    */
-  public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile)
+  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);
@@ -93,8 +94,8 @@ public class TreeModel
    */
   public TreeModel(TreeBuilder tree)
   {
-    this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(), tree
-            .hasBootstrap(), tree.hasRootDistance());
+    this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
+            tree.hasBootstrap(), tree.hasRootDistance());
     seqData = tree.getOriginalData();
   }
 
@@ -129,29 +130,27 @@ 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 (jalview.bin.Cache.log.isDebugEnabled())
@@ -160,14 +159,14 @@ 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 (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
@@ -187,8 +186,12 @@ public class TreeModel
   {
     NewickFile fout = new NewickFile(getTopNode());
 
-    return fout.print(hasBootstrap(), hasDistances(),
-            hasRootDistance()); // output all data available for tree
+    return fout.print(hasBootstrap(), hasDistances(), hasRootDistance()); // output
+                                                                          // all
+                                                                          // data
+                                                                          // available
+                                                                          // for
+                                                                          // tree
   }
 
   /**
@@ -248,8 +251,8 @@ public class TreeModel
           if (!leaf.isPlaceholder())
           {
             // Construct a new placeholder sequence object for this leaf
-            leaf.setElement(new Sequence(leaf.getName(),
-                    "THISISAPLACEHLDER"));
+            leaf.setElement(
+                    new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
           }
           leaf.setPlaceholder(true);
 
@@ -290,7 +293,7 @@ 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;
   }
@@ -384,7 +387,7 @@ 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;
   }
@@ -478,8 +481,8 @@ public class TreeModel
       System.out.println(" name = " + ((SequenceI) nd.element()).getName());
     }
 
-    System.out.println(" dist = " + nd.dist + " " + nd.count + " "
-            + nd.height);
+    System.out.println(
+            " dist = " + nd.dist + " " + nd.count + " " + nd.height);
   }
 
   /**
@@ -508,7 +511,8 @@ public class TreeModel
   {
     // if (_lycount<_lylimit)
     // {
-    // System.err.println("Warning: depth of _recount greater than number of nodes.");
+    // System.err.println("Warning: depth of _recount greater than number of
+    // nodes.");
     // }
     if (nd == null)
     {
@@ -659,8 +663,8 @@ public class TreeModel
   public void applyToNodes(NodeTransformI nodeTransformI)
   {
     for (Enumeration<SequenceNode> nodes = node.elements(); nodes
-            .hasMoreElements(); nodeTransformI.transform(nodes
-            .nextElement()))
+            .hasMoreElements(); nodeTransformI
+                    .transform(nodes.nextElement()))
     {
       ;
     }