X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=d800d201cd5f725fa81204e2be5b10586b2c5a96;hb=efa724edf32b5803396087cf7c94521e3d597836;hp=1cbc848d3531b5ded0e7222c333d24dd8d6e8759;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 1cbc848..d800d20 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -20,13 +20,8 @@
  */
 package jalview.io.vamsas;
 
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -35,10 +30,17 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignViewport;
 import jalview.gui.TreePanel;
 import jalview.io.NewickFile;
 import jalview.io.VamsasAppDatastore;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 import uk.ac.vamsas.client.Vobject;
 import uk.ac.vamsas.objects.core.AlignmentSequence;
 import uk.ac.vamsas.objects.core.Entry;
@@ -218,15 +220,17 @@ public class Tree extends DatastoreItem
     prov.getEntry(0).setUser(provEntry.getUser());
     prov.getEntry(0).setApp(provEntry.getApp());
     prov.getEntry(0).setDate(provEntry.getDate());
-    if (tp.getTree().hasOriginalSequenceData())
+
+    AlignmentView originalData = tp.getTree().getOriginalData();
+    if (originalData != null)
     {
       Input vInput = new Input();
       // LATER: check to see if tree input data is contained in this alignment -
       // or just correctly resolve the tree's seqData to the correct alignment
       // in
       // the document.
-      Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal,
-              tp.getTree().seqData.getSequences()));
+      Vector alsqrefs = getjv2vObjs(findAlignmentSequences(jal, tp
+              .getTree().getOriginalData().getSequences()));
       Object[] alsqs = new Object[alsqrefs.size()];
       alsqrefs.copyInto(alsqs);
       vInput.setObjRef(alsqs);
@@ -238,12 +242,13 @@ public class Tree extends DatastoreItem
       prov.getEntry(0).addParam(new Param());
       prov.getEntry(0).getParam(0).setName("treeType");
       prov.getEntry(0).getParam(0).setType("utf8");
-      prov.getEntry(0).getParam(0).setContent("NJ"); // TODO: type of tree is a
-      // general parameter
-      int ranges[] = tp.getTree().seqData.getVisibleContigs();
+      prov.getEntry(0).getParam(0)
+              .setContent(TreeBuilder.NEIGHBOUR_JOINING);
+      // TODO: type of tree is a general parameter
+      int ranges[] = originalData.getVisibleContigs();
       // VisibleContigs are with respect to alignment coordinates. Still need
       // offsets
-      int start = tp.getTree().seqData.getAlignmentOrigin();
+      int start = tp.getTree().getOriginalData().getAlignmentOrigin();
       for (int r = 0; r < ranges.length; r += 2)
       {
         Seg visSeg = new Seg();
@@ -290,8 +295,10 @@ public class Tree extends DatastoreItem
       }
     }
     if (alsq.size() < sequences.length)
+    {
       Cache.log
               .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+    }
     return alsq;
   }
 
@@ -305,15 +312,18 @@ public class Tree extends DatastoreItem
   public void UpdateSequenceTreeMap(TreePanel tp)
   {
     if (tp == null || tree == null)
+    {
       return;
-    Vector leaves = new Vector();
+    }
+
     if (tp.getTree() == null)
     {
       Cache.log.warn("Not updating SequenceTreeMap for "
               + tree.getVorbaId());
       return;
     }
-    tp.getTree().findLeaves(tp.getTree().getTopNode(), leaves);
+    Vector<SequenceNode> leaves = tp.getTree().findLeaves(
+            tp.getTree().getTopNode());
     Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
     // particular tree
     int sz = tn.length;
@@ -364,14 +374,14 @@ public class Tree extends DatastoreItem
   /**
    * construct treenode mappings for mapped sequences
    * 
-   * @param ntree
+   * @param treeModel
    * @param newick
    * @return
    */
-  public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
+  public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
   {
-    Vector leaves = new Vector();
-    ntree.findLeaves(ntree.getTopNode(), leaves);
+    Vector<SequenceNode> leaves = treeModel.findLeaves(treeModel
+            .getTopNode());
     Vector tnv = new Vector();
     Enumeration l = leaves.elements();
     Hashtable nodespecs = new Hashtable();
@@ -421,8 +431,7 @@ public class Tree extends DatastoreItem
       tnv.copyInto(tn);
       return tn;
     }
-    return new Treenode[]
-    {};
+    return new Treenode[] {};
   }
 
   private String makeNodeSpec(Hashtable nodespecs,
@@ -473,7 +482,9 @@ public class Tree extends DatastoreItem
         --occurence;
       }
       else
+      {
         bn = null;
+      }
     }
     return bn;
   }
@@ -490,7 +501,7 @@ public class Tree extends DatastoreItem
     bindjvvobj(tp, tree);
     tree.setTitle(tp.getTitle());
     Newick newick = new Newick();
-    newick.setContent(tp.getTree().toString());
+    newick.setContent(tp.getTree().print());
     newick.setTitle(tp.getTitle());
     tree.addNewick(newick);
     tree.setProvenance(makeTreeProvenance(jal, tp));
@@ -510,7 +521,7 @@ public class Tree extends DatastoreItem
    */
   public Object[] recoverInputData(Provenance tp)
   {
-    AlignViewport javport = null;
+    AlignmentViewport javport = null;
     jalview.datamodel.AlignmentI jal = null;
     jalview.datamodel.CigarArray view = null;
     for (int pe = 0; pe < tp.getEntryCount(); pe++)
@@ -595,8 +606,7 @@ public class Tree extends DatastoreItem
           // off by
           // one for to
         }
-        return new Object[]
-        { new AlignmentView(view), jal };
+        return new Object[] { new AlignmentView(view), jal };
       }
     }
     Cache.log
@@ -604,7 +614,7 @@ public class Tree extends DatastoreItem
     return null;
   }
 
-  private AlignViewport getViewport(Vobject v_parent)
+  private AlignmentViewport getViewport(Vobject v_parent)
   {
     if (v_parent instanceof uk.ac.vamsas.objects.core.Alignment)
     {