Merge branch 'develop' into ben/gecos_colour_schemes

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 2d8e729..d735402 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -20,6 +20,8 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AverageDistanceTree;
 import jalview.analysis.NJTree;
@@ -28,6 +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;
@@ -318,9 +322,8 @@ 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);
@@ -406,7 +409,7 @@ 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"));
@@ -417,7 +420,7 @@ 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
@@ -456,7 +459,7 @@ 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;
     }
@@ -586,9 +589,8 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.getAssociatedPanel().alignFrame
-              .addHistoryItem(
-                      sortAlignmentIn(treeCanvas.getAssociatedPanel()));
+      treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+              sortAlignmentIn(treeCanvas.getAssociatedPanel()));
     }
 
   }
@@ -693,7 +695,8 @@ 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());
+    exporter.doExport(null, this, width, height,
+            tree.toLowerCase(Locale.ROOT));
   }
 
   /**
@@ -723,7 +726,7 @@ public class TreePanel extends GTreePanel
             // search dbrefs, features and annotation
             List<DBRefEntry> refs = jalview.util.DBRefUtils
                     .selectRefs(sq.getDBRefs(), new String[]
-                    { labelClass.toUpperCase() });
+                    { labelClass.toUpperCase(Locale.ROOT) });
             if (refs != null)
             {
               for (int i = 0, ni = refs.size(); i < ni; i++)
@@ -785,8 +788,8 @@ public class TreePanel extends GTreePanel
     /*
      * i18n description of Neighbour Joining or Average Distance method
      */
-    String treecalcnm = MessageManager
-            .getString("label.tree_calc_" + treeType.toLowerCase());
+    String treecalcnm = MessageManager.getString(
+            "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
 
     /*
      * short score model name (long description can be too long)
@@ -815,8 +818,7 @@ 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);
@@ -830,7 +832,7 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
-  
+
   public AlignViewport getViewport()
   {
     return av;