X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=c8472603881862df6d58bdbb193238e6778fb2ab;hb=9811278f9e18ee6cb88470dbae98da046734a0af;hp=bd9f661cfd4c1afe7775c01e6f3428bc841d5b77;hpb=994a386819147f73fa47f3c29ba6c438f0e4b15a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bd9f661..c847260 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -33,6 +33,7 @@ import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -397,8 +398,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     addKeyListener();
 
-    final List<AlignmentPanel> selviews = new ArrayList<>();
-    final List<AlignmentPanel> origview = new ArrayList<>();
+    final List<AlignmentViewPanel> selviews = new ArrayList<>();
+    final List<AlignmentViewPanel> origview = new ArrayList<>();
     final String menuLabel = MessageManager
             .getString("label.copy_format_from");
     ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
@@ -406,7 +407,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             {
 
               @Override
-              public AlignmentPanel[] getAllAlignmentPanels()
+              public AlignmentViewPanel[] getAllAlignmentPanels()
               {
                 origview.clear();
                 origview.add(alignPanel);
@@ -424,7 +425,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               {
                 if (origview.size() > 0)
                 {
-                  final AlignmentPanel ap = origview.get(0);
+                  final AlignmentViewPanel avp = origview.get(0);
 
                   /*
                    * Copy the ViewStyle of the selected panel to 'this one'.
@@ -437,10 +438,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           .getAlignViewport().getCodingComplement() != null;
                   if (!fromSplitFrame)
                   {
-                    vs.setScaleProteinAsCdna(ap.getAlignViewport()
+                    vs.setScaleProteinAsCdna(avp.getAlignViewport()
                             .getViewStyle().isScaleProteinAsCdna());
                   }
-                  ap.getAlignViewport().setViewStyle(vs);
+                  avp.getAlignViewport().setViewStyle(vs);
 
                   /*
                    * Also rescale ViewStyle of SplitFrame complement if there is
@@ -448,7 +449,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                    * the whole ViewStyle (allow cDNA protein to have different
                    * fonts)
                    */
-                  AlignViewportI complement = ap.getAlignViewport()
+                  AlignViewportI complement = avp.getAlignViewport()
                           .getCodingComplement();
                   if (complement != null && vs.isScaleProteinAsCdna())
                   {
@@ -458,10 +459,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     af.setMenusForViewport();
                   }
 
+                  AlignmentPanel ap = (AlignmentPanel) avp;
                   ap.updateLayout();
                   ap.setSelected(true);
                   ap.alignFrame.setMenusForViewport();
-
                 }
               }
             });
@@ -974,7 +975,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void setStatus(String text)
   {
-    statusBar.setText(text);
+    statusBar.setText(text == null || text.isEmpty() ? " " : text);
   }
 
   /*
@@ -1203,23 +1204,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           PrintWriter out = new PrintWriter(
                   new FileWriter(backupfiles.getTempFilePath()));
 
-          // TESTING code here
-          boolean TESTING = true;
-          if (TESTING)
-          {
-            out.print("; TESTSTART\n");
-            int count = 20;
-            for (int i = 0; i < count; i++)
-            {
-              // Thread.sleep(1000);
-              out.println("; TEST: " + (count - 1 - i));
-            }
-          }
           out.print(output);
-          if (TESTING)
-          {
-            out.print("; TESTEND\n");
-          }
           out.close();
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
@@ -2108,7 +2093,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2155,7 +2140,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -3120,7 +3105,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
     viewport.setScaleAboveWrapped(scaleAbove.isSelected());
-    // TODO: do we actually need to update overview for scale above change ?
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3134,6 +3119,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
     viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -3147,6 +3133,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
     viewport.setScaleRightWrapped(scaleRight.isSelected());
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, false);
   }
 
@@ -4949,6 +4936,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void finished()
               {
+
+                for (FeatureSettingsModelI srcSettings : dbRefFetcher
+                        .getFeatureSettingsModels())
+                {
+
+                  alignPanel.av.mergeFeaturesStyle(srcSettings);
+                }
                 AlignFrame.this.setMenusForViewport();
               }
             });
@@ -5034,6 +5028,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   @Override
                                   public void finished()
                                   {
+                                    FeatureSettingsModelI srcSettings = dassource[0]
+                                            .getFeatureColourScheme();
+                                    alignPanel.av.mergeFeaturesStyle(
+                                            srcSettings);
                                     AlignFrame.this.setMenusForViewport();
                                   }
                                 });