Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 94b38ed..477db0c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -733,9 +733,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     int aSize = alignPanels.size();
 
-    tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+    tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
 
-    if (aSize == 1 && ap.av.viewName == null)
+    if (aSize == 1 && ap.av.getViewName() == null)
     {
       this.getContentPane().add(ap, BorderLayout.CENTER);
     }
@@ -748,7 +748,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       expandViews.setEnabled(true);
       gatherViews.setEnabled(true);
-      tabbedPane.addTab(ap.av.viewName, ap);
+      tabbedPane.addTab(ap.av.getViewName(), ap);
 
       ap.setVisible(false);
     }
@@ -771,7 +771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     gatherViews.setEnabled(true);
     tabbedPane.setVisible(true);
     AlignmentPanel first = alignPanels.get(0);
-    tabbedPane.addTab(first.av.viewName, first);
+    tabbedPane.addTab(first.av.getViewName(), first);
     this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
   }
 
@@ -872,7 +872,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param av
    *          AlignViewport
    */
-  void setMenusFromViewport(AlignViewport av)
+  public void setMenusFromViewport(AlignViewport av)
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
     colourTextMenuItem.setSelected(av.isShowColourText());
@@ -1154,7 +1154,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 shortName.lastIndexOf(java.io.File.separatorChar) + 1);
       }
 
-      success = new Jalview2XML().saveAlignment(this, file, shortName);
+      success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+              shortName);
 
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
@@ -2701,7 +2702,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Create a new AlignmentPanel (with its own, new Viewport)
      */
-    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+    AlignmentPanel newap = new jalview.project.Jalview2XML()
+            .copyAlignPanel(alignPanel);
     if (!copyAnnotation)
     {
       /*
@@ -2713,10 +2715,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     newap.av.setGatherViewsHere(false);
 
-    if (viewport.viewName == null)
+    if (viewport.getViewName() == null)
     {
-      viewport.viewName = MessageManager
-              .getString("label.view_name_original");
+      viewport.setViewName(MessageManager
+              .getString("label.view_name_original"));
     }
 
     /*
@@ -2740,7 +2742,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       newap.refresh(true); // adjust layout of annotations
     }
 
-    newap.av.viewName = getNewViewName(viewTitle);
+    newap.av.setViewName(getNewViewName(viewTitle));
 
     addAlignmentPanel(newap, true);
     newap.alignmentChanged();
@@ -2803,9 +2805,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (comp instanceof AlignmentPanel)
       {
         AlignmentPanel ap = (AlignmentPanel) comp;
-        if (!existingNames.contains(ap.av.viewName))
+        if (!existingNames.contains(ap.av.getViewName()))
         {
-          existingNames.add(ap.av.viewName);
+          existingNames.add(ap.av.getViewName());
         }
       }
     }
@@ -3597,9 +3599,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     frameTitle += " from ";
 
-    if (viewport.viewName != null)
+    if (viewport.getViewName() != null)
     {
-      frameTitle += viewport.viewName + " of ";
+      frameTitle += viewport.getViewName() + " of ";
     }
 
     frameTitle += this.title;
@@ -4767,7 +4769,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (reply != null)
       {
-        viewport.viewName = reply;
+        viewport.setViewName(reply);
         // TODO warn if reply is in getExistingViewNames()?
         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
@@ -5399,7 +5401,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public List<? extends AlignmentViewPanel> getAlignPanels()
   {
-    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    // alignPanels is never null
+    // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    return alignPanels;
   }
 
   /**