Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 5a41802..4d5e4b2 100644 (file)
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.NodeTransformI;
@@ -77,10 +78,11 @@ 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 +95,8 @@ 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();
   }
 
@@ -154,8 +156,8 @@ public class TreeModel
         if (one2many.contains(nam))
         {
           // countOne2Many++;
-          // if (jalview.bin.Cache.log.isDebugEnabled())
-          // jalview.bin.Cache.log.debug("One 2 many relationship for
+          // if (Cache.isDebugEnabled())
+          // Cache.debug("One 2 many relationship for
           // "+nam.getName());
         }
         else
@@ -170,8 +172,8 @@ public class TreeModel
         j.setPlaceholder(true);
       }
     }
-    // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
-    // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+    // if (Cache.isDebugEnabled() && countOne2Many>0) {
+    // Cache.debug("There were "+countOne2Many+" alignment
     // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
     // more leaves.");
     // }
@@ -187,8 +189,12 @@ 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 +254,8 @@ 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);
 
@@ -478,8 +484,8 @@ 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 +514,8 @@ 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 +666,8 @@ 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()))
     {
       ;
     }