Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 32c5702..5e14fce 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -158,8 +158,8 @@ public class TreePanel extends GTreePanel
           }
           if (evt.getNewValue() == null)
           {
-            System.out
-                    .println("new alignment sequences vector value is null");
+            System.out.println(
+                    "new alignment sequences vector value is null");
           }
 
           tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
@@ -183,8 +183,8 @@ public class TreePanel extends GTreePanel
 
   void buildAssociatedViewMenu()
   {
-    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
-            .getSequenceSetId());
+    AlignmentPanel[] aps = PaintRefresher
+            .getAssociatedPanels(av.getSequenceSetId());
     if (aps.length == 1 && treeCanvas.ap == aps[0])
     {
       associateLeavesMenu.setVisible(false);
@@ -193,7 +193,8 @@ public class TreePanel extends GTreePanel
 
     associateLeavesMenu.setVisible(true);
 
-    if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+    if ((viewMenu
+            .getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
     {
       viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
     }
@@ -275,11 +276,11 @@ public class TreePanel extends GTreePanel
       }
       else
       {
-        ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
-                scoreModelName, treeCanvas.ap);
-        TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
-                av, sm, similarityParams) : new AverageDistanceTree(av, sm,
-                similarityParams);
+        ScoreModelI sm = ScoreModels.getInstance()
+                .getScoreModel(scoreModelName, treeCanvas.ap);
+        TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
+                ? new NJTree(av, sm, similarityParams)
+                : new AverageDistanceTree(av, sm, similarityParams);
         tree = new TreeModel(njtree);
         showDistances(true);
       }
@@ -363,8 +364,8 @@ public class TreePanel extends GTreePanel
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager
-            .getString("label.save_tree_as_newick"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.save_tree_as_newick"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(null);
@@ -372,15 +373,15 @@ public class TreePanel extends GTreePanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
-              .getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+              chooser.getSelectedFile().getParent());
 
       try
       {
         jalview.io.NewickFile fout = new jalview.io.NewickFile(
                 tree.getTopNode());
-        String output = fout.print(tree.hasBootstrap(),
-                tree.hasDistances(), tree.hasRootDistance());
+        String output = fout.print(tree.hasBootstrap(), tree.hasDistances(),
+                tree.hasRootDistance());
         java.io.PrintWriter out = new java.io.PrintWriter(
                 new java.io.FileWriter(choice));
         out.println(output);
@@ -411,8 +412,8 @@ public class TreePanel extends GTreePanel
     AlignmentView originalData = tree.getOriginalData();
     if (originalData == null)
     {
-      jalview.bin.Cache.log
-              .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+      jalview.bin.Cache.log.info(
+              "Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
     // decide if av alignment is sufficiently different to original data to
@@ -439,8 +440,9 @@ public class TreePanel extends GTreePanel
       // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
 
       AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
-      AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
-              .getAlignment().getDataset() : null;
+      AlignmentI dataset = (av != null && av.getAlignment() != null)
+              ? av.getAlignment().getDataset()
+              : null;
       if (dataset != null)
       {
         al.setDataset(dataset);
@@ -450,8 +452,7 @@ public class TreePanel extends GTreePanel
       {
         // make a new frame!
         AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
-                AlignFrame.DEFAULT_WIDTH,
-                AlignFrame.DEFAULT_HEIGHT);
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
         // >>>This is a fix for the moment, until a better solution is
         // found!!<<<
@@ -461,8 +462,8 @@ public class TreePanel extends GTreePanel
         // msaorder);
 
         Desktop.addInternalFrame(af, MessageManager.formatMessage(
-                "label.original_data_for_params",
-                new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+                "label.original_data_for_params", new Object[]
+                { this.title }), AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
       }
     }
@@ -493,8 +494,8 @@ public class TreePanel extends GTreePanel
     if (treeCanvas.applyToAllViews)
     {
       final ArrayList<CommandI> commands = new ArrayList<CommandI>();
-      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
-              .getSequenceSetId()))
+      for (AlignmentPanel ap : PaintRefresher
+              .getAssociatedPanels(av.getSequenceSetId()))
       {
         commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
       }
@@ -532,8 +533,8 @@ public class TreePanel extends GTreePanel
           }
         }
       });
-      for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
-              .getSequenceSetId()))
+      for (AlignmentPanel ap : PaintRefresher
+              .getAssociatedPanels(av.getSequenceSetId()))
       {
         // ensure all the alignFrames refresh their GI after adding an undo item
         ap.alignFrame.updateEditMenuBar();
@@ -668,8 +669,8 @@ public class TreePanel extends GTreePanel
       JalviewFileChooser chooser = new JalviewFileChooser(
               ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
       chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle(MessageManager
-              .getString("label.create_eps_from_tree"));
+      chooser.setDialogTitle(
+              MessageManager.getString("label.create_eps_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -679,11 +680,13 @@ public class TreePanel extends GTreePanel
         return;
       }
 
-      Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
-              .getParent());
+      Cache.setProperty("LAST_DIRECTORY",
+              chooser.getSelectedFile().getParent());
 
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
+      FileOutputStream out = new FileOutputStream(
+              chooser.getSelectedFile());
+      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+              height);
 
       pg.setAccurateTextMode(accurateText);
 
@@ -715,8 +718,8 @@ public class TreePanel extends GTreePanel
               ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
 
       chooser.setFileView(new jalview.io.JalviewFileView());
-      chooser.setDialogTitle(MessageManager
-              .getString("label.create_png_from_tree"));
+      chooser.setDialogTitle(
+              MessageManager.getString("label.create_png_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
@@ -726,10 +729,11 @@ public class TreePanel extends GTreePanel
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
-              .getSelectedFile().getParent());
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+              chooser.getSelectedFile().getParent());
 
-      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+      FileOutputStream out = new FileOutputStream(
+              chooser.getSelectedFile());
 
       BufferedImage bi = new BufferedImage(width, height,
               BufferedImage.TYPE_INT_RGB);
@@ -770,9 +774,9 @@ public class TreePanel extends GTreePanel
           if (sq != null)
           {
             // search dbrefs, features and annotation
-            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
-                    sq.getDBRefs(),
-                    new String[] { labelClass.toUpperCase() });
+            DBRefEntry[] refs = jalview.util.DBRefUtils
+                    .selectRefs(sq.getDBRefs(), new String[]
+                    { labelClass.toUpperCase() });
             if (refs != null)
             {
               for (int i = 0; i < refs.length; i++)
@@ -821,6 +825,7 @@ public class TreePanel extends GTreePanel
    * Neighbour Joining Using BLOSUM62
    * <p>
    * For a tree loaded from file, just uses the file name
+   * 
    * @return
    */
   public String getPanelTitle()
@@ -833,8 +838,8 @@ 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());
 
     /*
      * short score model name (long description can be too long)