JAL-3436 move/rename/private fields refactoring only

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4d29919..2ef31a2 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -194,9 +194,9 @@ public class AlignFrame extends GAlignFrame
   /**
    * Current filename for this alignment
    */
-  String fileName = null;
+  private String fileName = null;
 
-  File fileObject;
+  private File fileObject;
 
   /**
    * Creates a new AlignFrame object with specific width and height.
@@ -851,25 +851,23 @@ public class AlignFrame extends GAlignFrame
   private PropertyChangeListener addServiceListeners()
   {
     PropertyChangeListener serviceListener = new PropertyChangeListener()
-            {
-              @Override
-              public void propertyChange(PropertyChangeEvent evt)
-              {
-                {
-                  SwingUtilities.invokeLater(new Runnable()
-                  {
-
-                    @Override
-                    public void run()
-                    {
-                      System.err.println(
-                              "Rebuild WS Menu for service change");
-                      BuildWebServiceMenu();
-                    }
+    {
+      @Override
+      public void propertyChange(PropertyChangeEvent evt)
+      {
+        {
+          SwingUtilities.invokeLater(new Runnable()
+          {
 
-                  });
-                }
-              }
+            @Override
+            public void run()
+            {
+              System.err.println("Rebuild WS Menu for service change");
+              BuildWebServiceMenu();
+            }
+          });
+        }
+      }
     };
 
     Desktop.getInstance().addJalviewPropertyChangeListener("services",
@@ -1055,6 +1053,7 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void reload_actionPerformed(ActionEvent e)
   {
+    System.out.println("AlignFrame.reload " + fileName);
     if (fileName != null)
     {
       // TODO: JAL-1108 - ensure all associated frames are closed regardless of
@@ -1086,7 +1085,9 @@ public class AlignFrame extends GAlignFrame
         DataSourceType protocol = fileName.startsWith("http:")
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
-        loader.loadFile(viewport, fileName, protocol, currentFileFormat);
+        loader.loadFile(viewport,
+                (fileObject == null ? fileName : fileObject), protocol,
+                currentFileFormat);
       }
       else
       {
@@ -3395,13 +3396,11 @@ public class AlignFrame extends GAlignFrame
     // undecorated overview with defined size
     frame.setName(Jalview.getAppID("overview"));
     //
-    Dimension dim = (Dimension) Platform.getEmbeddedAttribute(frame,
-            Platform.EMBEDDED_DIM);
+    Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1);
     if (dim != null && dim.width == 0)
     {
       dim = null; // hidden, not embedded
     }
-
     OverviewPanel overview = new OverviewPanel(alignPanel, dim);
 
     frame.setContentPane(overview);
@@ -3780,7 +3779,8 @@ public class AlignFrame extends GAlignFrame
 
     frameTitle += this.title;
 
-    Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+    Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+    Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
   }
 
   /**
@@ -4132,15 +4132,24 @@ public class AlignFrame extends GAlignFrame
       if (nf.getTree() != null)
       {
         tp = new TreePanel(alignPanel, nf, treeTitle, input);
-
-        tp.setSize(w, h);
+        Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
+        if (dim == null)
+        {
+          dim = new Dimension(w, h);
+        }
+        else
+        {
+          // no offset, either
+          x = 0;
+        }
+        tp.setSize(dim.width, dim.height);
 
         if (x > 0 && y > 0)
         {
           tp.setLocation(x, y);
         }
 
-        Desktop.addInternalFrame(tp, treeTitle, w, h);
+        Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height);
       }
     } catch (Exception ex)
     {
@@ -4530,7 +4539,6 @@ public class AlignFrame extends GAlignFrame
     {
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      alignPanel.getAlignment().resetColors();
     }
 
   }