JAL-1551 spotlessApply

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index b730df4..0e1fd42 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -20,8 +20,26 @@
  */
 package jalview.gui;
 
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Locale;
 
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import org.jibble.epsgraphics.EpsGraphics2D;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AverageDistanceTree;
 import jalview.analysis.NJTree;
@@ -30,9 +48,12 @@ 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;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.BinaryNode;
@@ -51,25 +72,6 @@ import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
-import org.jibble.epsgraphics.EpsGraphics2D;
-
 /**
  * DOCUMENT ME!
  * 
@@ -104,6 +106,7 @@ public class TreePanel extends GTreePanel
           SimilarityParamsI options)
   {
     super();
+    this.setFrameIcon(null);
     this.similarityParams = options;
     initTreePanel(ap, type, modelName, null, null);
 
@@ -116,10 +119,44 @@ public class TreePanel extends GTreePanel
           String theTitle, AlignmentView inputData)
   {
     super();
+    this.setFrameIcon(null);
     this.treeTitle = theTitle;
     initTreePanel(alignPanel, null, null, newtree, inputData);
   }
 
+  /**
+   * columnwise tree associated with positions in aa
+   * 
+   * @param alignPanel
+   * @param fin
+   * @param title
+   * @param aa
+   */
+  public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
+          AlignmentAnnotation aa, String title)
+  {
+    super();
+    columnWise = true;
+    assocAnnotation = aa;
+    this.setFrameIcon(null);
+    this.treeTitle = title;
+    initTreePanel(alignPanel, null, null, fin, null);
+  }
+
+  boolean columnWise = false;
+
+  AlignmentAnnotation assocAnnotation = null;
+
+  public boolean isColumnWise()
+  {
+    return columnWise;
+  }
+
+  public AlignmentAnnotation getAssocAnnotation()
+  {
+    return assocAnnotation;
+  }
+
   public AlignmentI getAlignment()
   {
     return getTreeCanvas().getViewport().getAlignment();
@@ -139,6 +176,15 @@ public class TreePanel extends GTreePanel
     this.treeType = type;
     this.scoreModelName = modelName;
 
+    if (columnWise)
+    {
+      bootstrapMenu.setVisible(false);
+      placeholdersMenu.setSelected(false);
+      placeholdersMenu.setVisible(false);
+      fitToWindow.setSelected(false);
+      sortAssocViews.setVisible(false);
+    }
+
     treeCanvas = new TreeCanvas(this, ap, scrollPane);
     scrollPane.setViewportView(treeCanvas);
 
@@ -320,9 +366,8 @@ 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);
@@ -408,7 +453,7 @@ 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"));
@@ -419,7 +464,7 @@ 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
@@ -458,7 +503,7 @@ 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;
     }
@@ -588,9 +633,8 @@ public class TreePanel extends GTreePanel
     }
     else
     {
-      treeCanvas.getAssociatedPanel().alignFrame
-              .addHistoryItem(
-                      sortAlignmentIn(treeCanvas.getAssociatedPanel()));
+      treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+              sortAlignmentIn(treeCanvas.getAssociatedPanel()));
     }
 
   }
@@ -695,7 +739,8 @@ 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));
   }
 
   /**
@@ -719,7 +764,7 @@ public class TreePanel extends GTreePanel
                 && !((SequenceNode) node).isDummy())
         {
           String newname = null;
-          SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+          SequenceI sq = (SequenceI) ((BinaryNode) node).element();
           if (sq != null)
           {
             // search dbrefs, features and annotation
@@ -761,7 +806,7 @@ public class TreePanel extends GTreePanel
           {
             // String oldname = ((SequenceNode) node).getName();
             // TODO : save oldname in the undo object for this modification.
-            ((SequenceNode) node).setName(newname);
+            ((BinaryNode) node).setName(newname);
           }
         }
       }
@@ -787,8 +832,8 @@ 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)
@@ -817,8 +862,7 @@ 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);
@@ -832,7 +876,7 @@ public class TreePanel extends GTreePanel
       ex.printStackTrace();
     }
   }
-  
+
   public AlignViewport getViewport()
   {
     return av;