X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FTreeModel.java;h=1c19dbfd42e6e4abf4eddabf20ead77c267ca3b3;hb=c58f08345070f16bdc228c5e272db1bfd9cb6241;hp=2f8d7883f40d2fe37f1b875eb7026b8da517af8a;hpb=be27d7b3cadbfb5c488066034c48b1735799b429;p=jalview.git

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 2f8d788..1c19dbf 100644
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -46,7 +46,7 @@ public class TreeModel
    * SequenceData is a string representation of what the user
    * sees. The display may contain hidden columns.
    */
-  public AlignmentView seqData;
+  private AlignmentView seqData;
 
   int noseqs;
 
@@ -68,7 +68,7 @@ public class TreeModel
 
   /**
    * Create a new TreeModel object with leaves associated with sequences in
-   * seqs, and original alignment data represented by Cigar strings
+   * seqs, and (optionally) original alignment data represented by Cigar strings
    * 
    * @param seqs
    *          SequenceI[]
@@ -77,24 +77,12 @@ 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);
+    this(seqs, treefile.getTree(), treefile.hasDistances(),
+            treefile.hasBootstrap(), treefile.hasRootDistance());
     seqData = odata;
-  }
-
-  /**
-   * Creates a new TreeModel object from a tree from an external source
-   * 
-   * @param seqs
-   *          SequenceI which should be associated with leafs of treefile
-   * @param treefile
-   *          A parsed tree
-   */
-  public TreeModel(SequenceI[] seqs, NewickFile treefile)
-  {
-    this(seqs, treefile.getTree(), treefile.HasDistances(), treefile
-            .HasBootstrap(), treefile.HasRootDistance());
 
     associateLeavesToSequences(seqs);
   }
@@ -106,8 +94,9 @@ 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();
   }
 
   /**
@@ -141,29 +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())
@@ -172,14 +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) {
@@ -199,8 +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
   }
 
   /**
@@ -260,8 +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);
 
@@ -302,7 +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;
   }
@@ -396,7 +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;
   }
@@ -468,39 +459,6 @@ public class TreeModel
   }
 
   /**
-   * 
-   * @return true if original sequence data can be recovered
-   */
-  public boolean hasOriginalSequenceData()
-  {
-    return seqData != null;
-  }
-
-  /**
-   * 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
@@ -523,8 +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);
   }
 
   /**
@@ -553,7 +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)
     {
@@ -704,10 +663,15 @@ 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()))
     {
       ;
     }
   }
+
+  public AlignmentView getOriginalData()
+  {
+    return seqData;
+  }
 }