JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / io / vamsas / Tree.java

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index dbfaf37..a3781a7 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,12 +20,6 @@
  */
 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.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -35,10 +29,17 @@ 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;
@@ -290,8 +291,10 @@ 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 +308,18 @@ 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;
@@ -370,8 +376,7 @@ public class Tree extends DatastoreItem
    */
   public Treenode[] makeTreeNodes(NJTree ntree, Newick newick)
   {
-    Vector leaves = new Vector();
-    ntree.findLeaves(ntree.getTopNode(), leaves);
+    Vector<SequenceNode> leaves = ntree.findLeaves(ntree.getTopNode());
     Vector tnv = new Vector();
     Enumeration l = leaves.elements();
     Hashtable nodespecs = new Hashtable();
@@ -421,8 +426,7 @@ public class Tree extends DatastoreItem
       tnv.copyInto(tn);
       return tn;
     }
-    return new Treenode[]
-    {};
+    return new Treenode[] {};
   }
 
   private String makeNodeSpec(Hashtable nodespecs,
@@ -473,7 +477,9 @@ public class Tree extends DatastoreItem
         --occurence;
       }
       else
+      {
         bn = null;
+      }
     }
     return bn;
   }
@@ -510,7 +516,7 @@ 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 +601,7 @@ 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 +609,7 @@ 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)
     {