X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeModel.java;h=b6c9caad68488ec9401c6e33193cd5de92d1f573;hb=89f0bcb459ed6acff9f7da0842bf967b8f941dee;hp=61c194d160f24f4a7babedd3d304d393f0973888;hpb=a58c1f3005f962f3d48043e38fd5e621081eb9b0;p=jalview.git

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 61c194d..b6c9caa 100644
--- 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);
@@ -93,9 +94,10 @@ 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();
+
   }
 
   /**
@@ -135,7 +137,7 @@ public class TreeModel
     SequenceNode j;
     SequenceI nam;
     String realnam;
-    Vector<SequenceI> one2many = new Vector<SequenceI>();
+    Vector<SequenceI> one2many = new Vector<>();
     // int countOne2Many = 0;
     while (i < leaves.size())
     {
@@ -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);
 
@@ -290,7 +296,7 @@ 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 +390,7 @@ 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;
   }
@@ -456,30 +462,6 @@ public class TreeModel
   }
 
   /**
-   * Returns original alignment data used for calculation - or null where not
-   * available.
-   * 
-   * @return null or cut'n'pasteable alignment
-   */
-  public String printOriginalSequenceData(char gapChar)
-  {
-    if (seqData == null)
-    {
-      return null;
-    }
-
-    StringBuffer sb = new StringBuffer();
-    String[] seqdatas = seqData.getSequenceStrings(gapChar);
-    for (int i = 0; i < seqdatas.length; i++)
-    {
-      sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequences[i]
-              .getName()));
-      sb.append(" " + seqdatas[i] + "\n");
-    }
-    return sb.toString();
-  }
-
-  /**
    * DOCUMENT ME!
    * 
    * @param nd
@@ -502,8 +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);
   }
 
   /**
@@ -532,7 +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)
     {
@@ -683,8 +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()))
     {
       ;
     }