JAL-1807 explicit imports (jalview.io.*)

[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 b5ada26..f007463 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -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 +29,18 @@ import jalview.datamodel.SeqCigar;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
+import jalview.gui.AlignFrame;
 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;
@@ -68,14 +70,12 @@ public class Tree extends DatastoreItem
   private AlignmentView inputData = null;
 
   public static void updateFrom(VamsasAppDatastore datastore,
-          jalview.gui.AlignFrame alignFrame,
-          uk.ac.vamsas.objects.core.Tree vtree)
+          AlignFrame alignFrame, uk.ac.vamsas.objects.core.Tree vtree)
   {
     Tree toTree = new Tree(datastore, alignFrame, vtree);
   }
 
-  public Tree(VamsasAppDatastore datastore,
-          jalview.gui.AlignFrame alignFrame,
+  public Tree(VamsasAppDatastore datastore, AlignFrame alignFrame,
           uk.ac.vamsas.objects.core.Tree vtree)
   {
     super(datastore, vtree, TreePanel.class);
@@ -84,7 +84,7 @@ public class Tree extends DatastoreItem
 
   private NewickFile getNtree() throws IOException
   {
-    return new jalview.io.NewickFile(tree.getNewick(0).getContent());
+    return new NewickFile(tree.getNewick(0).getContent());
   }
 
   public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
@@ -290,8 +290,10 @@ 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;
   }
 
@@ -305,7 +307,9 @@ public class Tree extends DatastoreItem
   public void UpdateSequenceTreeMap(TreePanel tp)
   {
     if (tp == null || tree == null)
+    {
       return;
+    }
     Vector leaves = new Vector();
     if (tp.getTree() == null)
     {
@@ -473,7 +477,9 @@ public class Tree extends DatastoreItem
         --occurence;
       }
       else
+      {
         bn = null;
+      }
     }
     return bn;
   }
@@ -511,7 +517,7 @@ public class Tree extends DatastoreItem
   public Object[] recoverInputData(Provenance tp)
   {
     AlignmentViewport javport = null;
-    jalview.datamodel.AlignmentI jal = null;
+    AlignmentI jal = null;
     jalview.datamodel.CigarArray view = null;
     for (int pe = 0; pe < tp.getEntryCount(); pe++)
     {