X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;fp=src%2Fjalview%2Fgui%2FTreePanel.java;h=cbcea768dded1d70ecbc21a6bd14c5382c511b73;hp=7177e43bfed2c9a5ab4540478f977478dab615e3;hb=aa91e8c4561c2dd0f18760e18fb0052979733bf8;hpb=b4b79402a4b3c95c0a79002fc3dacb67479a061c

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 7177e43..cbcea76 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -42,6 +42,7 @@ import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
 import jalview.jbgui.GTreePanel;
 import jalview.schemes.ResidueProperties;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -262,7 +263,7 @@ public class TreePanel extends GTreePanel
   {
     NewickFile newtree;
 
-    jalview.datamodel.AlignmentView odata = null;
+    AlignmentView odata = null;
 
     public TreeLoader(NewickFile newtree)
     {
@@ -413,8 +414,7 @@ public class TreePanel extends GTreePanel
       buffer.append("PID");
     }
 
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(
-            tree.getTopNode());
+    NewickFile fout = new NewickFile(tree.getTopNode());
     try
     {
       cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
@@ -437,7 +437,7 @@ public class TreePanel extends GTreePanel
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
@@ -447,13 +447,12 @@ public class TreePanel extends GTreePanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       try
       {
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(
-                tree.getTopNode());
+        NewickFile fout = new NewickFile(tree.getTopNode());
         String output = fout.print(tree.isHasBootstrap(),
                 tree.isHasDistances(), tree.isHasRootDistance());
         java.io.PrintWriter out = new java.io.PrintWriter(
@@ -483,7 +482,7 @@ public class TreePanel extends GTreePanel
   {
     if (!tree.hasOriginalSequenceData())
     {
-      jalview.bin.Cache.log
+      Cache.log
               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
@@ -702,7 +701,7 @@ public class TreePanel extends GTreePanel
   {
     boolean accurateText = true;
 
-    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+    String renderStyle = Cache.getDefault("EPS_RENDERING",
             "Prompt each time");
 
     // If we need to prompt, and if the GUI is visible then
@@ -731,8 +730,8 @@ public class TreePanel extends GTreePanel
 
     try
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              Cache.getProperty("LAST_DIRECTORY"), new String[]
               { "eps" }, new String[]
               { "Encapsulated Postscript" }, "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
@@ -741,12 +740,12 @@ public class TreePanel extends GTreePanel
 
       int value = chooser.showSaveDialog(this);
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      if (value != JalviewFileChooser.APPROVE_OPTION)
       {
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
@@ -777,23 +776,23 @@ public class TreePanel extends GTreePanel
 
     try
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              Cache.getProperty("LAST_DIRECTORY"), new String[]
               { "png" }, new String[]
               { "Portable network graphics" }, "Portable network graphics");
 
-      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      if (value != JalviewFileChooser.APPROVE_OPTION)
       {
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
@@ -836,7 +835,7 @@ public class TreePanel extends GTreePanel
           if (sq != null)
           {
             // search dbrefs, features and annotation
-            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+            DBRefEntry[] refs = DBRefUtils.selectRefs(
                     sq.getDBRef(), new String[]
                     { labelClass.toUpperCase() });
             if (refs != null)