X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FTree.java;h=d800d201cd5f725fa81204e2be5b10586b2c5a96;hb=efa724edf32b5803396087cf7c94521e3d597836;hp=ae530742f8e465cd47afb3408d8288194d6776be;hpb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;p=jalview.git

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index ae53074..d800d20 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,30 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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.SequenceIdMatcher;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
@@ -33,11 +30,17 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
-import jalview.gui.AlignFrame;
-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;
@@ -104,6 +107,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
    */
+  @Override
   public void addFromDocument()
   {
     tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
@@ -134,6 +138,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#conflict()
    */
+  @Override
   public void conflict()
   {
     Cache.log
@@ -145,6 +150,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#update()
    */
+  @Override
   public void updateToDoc()
   {
     if (isModifiable(tree.getModifiable()))
@@ -165,6 +171,7 @@ public class Tree extends DatastoreItem
    * 
    * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
    */
+  @Override
   public void updateFromDoc()
   {
     // should probably just open a new tree panel in the same place as the old
@@ -213,15 +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);
@@ -233,12 +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();
@@ -266,25 +276,29 @@ public class Tree extends DatastoreItem
     System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
     Vector alsq = new Vector();
     List<SequenceI> jalsqs;
-    synchronized (jalsqs=jal.getSequences())
-    {for (SequenceI asq:jalsqs)
+    synchronized (jalsqs = jal.getSequences())
     {
-      for (int t = 0; t < sequences.length; t++)
+      for (SequenceI asq : jalsqs)
       {
-        if (tseqs[t] != null
-                && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
-                        .getDatasetSequence()))
-        // && tseqs[t].getStart()>=asq.getStart() &&
-        // tseqs[t].getEnd()<=asq.getEnd())
+        for (int t = 0; t < sequences.length; t++)
         {
-          tseqs[t] = null;
-          alsq.add(asq);
+          if (tseqs[t] != null
+                  && (tseqs[t].getRefSeq() == asq || tseqs[t].getRefSeq() == asq
+                          .getDatasetSequence()))
+          // && tseqs[t].getStart()>=asq.getStart() &&
+          // tseqs[t].getEnd()<=asq.getEnd())
+          {
+            tseqs[t] = null;
+            alsq.add(asq);
+          }
         }
       }
     }
     if (alsq.size() < sequences.length)
+    {
       Cache.log
               .warn("Not recovered all alignment sequences for given set of input sequence CIGARS");
+    }
     return alsq;
   }
 
@@ -298,15 +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;
@@ -357,14 +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();
@@ -414,8 +431,7 @@ public class Tree extends DatastoreItem
       tnv.copyInto(tn);
       return tn;
     }
-    return new Treenode[]
-    {};
+    return new Treenode[] {};
   }
 
   private String makeNodeSpec(Hashtable nodespecs,
@@ -466,7 +482,9 @@ public class Tree extends DatastoreItem
         --occurence;
       }
       else
+      {
         bn = null;
+      }
     }
     return bn;
   }
@@ -476,13 +494,14 @@ public class Tree extends DatastoreItem
    * add jalview object to vamsas document
    * 
    */
+  @Override
   public void addToDocument()
   {
     tree = new uk.ac.vamsas.objects.core.Tree();
     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));
@@ -502,7 +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++)
@@ -587,8 +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
@@ -596,7 +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)
     {