X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;fp=src%2Fjalview%2Fgui%2FTreePanel.java;h=ec4ef7b2552f02a83bd35ae0d69f57d7e42fa911;hb=c0501eaa85c0594f9275766f64de8ea44a59c368;hp=3463346c423268dfee3b63d60268328cb85740f5;hpb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 3463346..ec4ef7b 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -30,6 +30,8 @@ import jalview.analysis.TreeModel;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.Alignment;
@@ -323,9 +325,8 @@ public class TreePanel extends GTreePanel
       }
       else
       {
-        ScoreModelI sm = ScoreModels.getInstance()
-                .getScoreModel(scoreModelName,
-                        treeCanvas.getAssociatedPanel());
+        ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+                scoreModelName, treeCanvas.getAssociatedPanel());
         TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
                 ? new NJTree(av, sm, similarityParams)
                 : new AverageDistanceTree(av, sm, similarityParams);
@@ -411,7 +412,7 @@ public class TreePanel extends GTreePanel
   {
     // TODO: JAL-3048 save newick file for Jalview-JS
     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"));
@@ -422,7 +423,7 @@ public class TreePanel extends GTreePanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+      Cache.setProperty("LAST_DIRECTORY",
               chooser.getSelectedFile().getParent());
 
       try
@@ -461,7 +462,7 @@ public class TreePanel extends GTreePanel
     AlignmentView originalData = tree.getOriginalData();
     if (originalData == null)
     {
-      jalview.bin.Cache.log.info(
+      Console.info(
               "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
@@ -591,9 +592,8 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.getAssociatedPanel().alignFrame
-              .addHistoryItem(
-                      sortAlignmentIn(treeCanvas.getAssociatedPanel()));
+      treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+              sortAlignmentIn(treeCanvas.getAssociatedPanel()));
     }
 
   }
@@ -698,7 +698,8 @@ public class TreePanel extends GTreePanel
     String tree = MessageManager.getString("label.tree");
     ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
             tree);
-    exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT));
+    exporter.doExport(null, this, width, height,
+            tree.toLowerCase(Locale.ROOT));
   }
 
   /**
@@ -790,8 +791,8 @@ public class TreePanel extends GTreePanel
     /*
      * i18n description of Neighbour Joining or Average Distance method
      */
-    String treecalcnm = MessageManager
-            .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
+    String treecalcnm = MessageManager.getString(
+            "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
 
     /*
      * short score model name (long description can be too long)
@@ -820,8 +821,7 @@ public class TreePanel extends GTreePanel
       int width = treeCanvas.getWidth();
       int height = treeCanvas.getHeight();
 
-      FileOutputStream out = new FileOutputStream(
-              outFile);
+      FileOutputStream out = new FileOutputStream(outFile);
       EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
               height);
       pg.setAccurateTextMode(!textOption);
@@ -835,7 +835,7 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
-  
+
   public AlignViewport getViewport()
   {
     return av;