Merge branch 'Jalview-BH/JAL-3026-JAL-3063-JAXB' into trialMerge

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 01464fd..56ef63b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -125,7 +125,6 @@ import java.awt.event.MouseEvent;
 import java.awt.print.PageFormat;
 import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
@@ -761,9 +760,9 @@ 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);
     }
@@ -776,7 +775,7 @@ 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);
     }
@@ -799,7 +798,7 @@ 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);
   }
 
@@ -900,7 +899,7 @@ 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());
@@ -1011,9 +1010,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed()
   {
-    new jalview.gui.SequenceFetcher(this);
+    new SequenceFetcher(this);
   }
 
   @Override
@@ -1236,8 +1235,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         shortName = shortName.substring(
                 shortName.lastIndexOf(File.separatorChar) + 1);
       }
-      lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
+      lastSaveSuccessful = new jalview.project.Jalview2XML().saveAlignment(this, file,
               shortName);
+      
+      statusBar.setText(MessageManager.formatMessage(
+              "label.successfully_saved_to_file_in_format", new Object[]
+              { fileName, format }));
+      
       return;
     }
 
@@ -2761,7 +2765,8 @@ 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)
     {
       /*
@@ -2773,10 +2778,10 @@ 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"));
     }
 
     /*
@@ -2800,7 +2805,7 @@ 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();
@@ -2863,9 +2868,9 @@ 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());
         }
       }
     }
@@ -3679,9 +3684,9 @@ 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;
@@ -4858,12 +4863,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (e.isPopupTrigger())
     {
       String msg = MessageManager.getString("label.enter_view_name");
-      String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
-              JvOptionPane.QUESTION_MESSAGE);
+      String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
+      String reply = JvOptionPane.showInputDialog(msg, ttl);
 
       if (reply != null)
       {
-        viewport.viewName = reply;
+        viewport.setViewName(reply);
         // TODO warn if reply is in getExistingViewNames()?
         tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
       }
@@ -5014,22 +5019,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     });
     rfetch.add(fetchr);
-    final AlignFrame me = this;
     new Thread(new Runnable()
     {
       @Override
       public void run()
       {
         final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
-                .getSequenceFetcherSingleton(me);
+                .getSequenceFetcherSingleton();
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
           {
-            String[] dbclasses = sf.getOrderedSupportedSources();
-            // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
-            // jalview.util.QuickSort.sort(otherdb, otherdb);
+            String[] dbclasses = sf.getNonAlignmentSources();
             List<DbSourceProxy> otherdb;
             JMenu dfetch = new JMenu();
             JMenu ifetch = new JMenu();
@@ -5046,12 +5048,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 continue;
               }
-              // List<DbSourceProxy> dbs=otherdb;
-              // otherdb=new ArrayList<DbSourceProxy>();
-              // for (DbSourceProxy db:dbs)
-              // {
-              // if (!db.isA(DBRefSource.ALIGNMENTDB)
-              // }
               if (mname == null)
               {
                 mname = "From " + dbclass;
@@ -5401,6 +5397,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.createGroup())
     {
+      if (applyAutoAnnotationSettings.isSelected())
+      {
+        alignPanel.updateAnnotation(true, false);
+      }
       alignPanel.alignmentChanged();
     }
   }
@@ -5491,7 +5491,9 @@ 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;
   }
 
   /**