JAL-3390 pull-up refactoring towards functional changes...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 0239bb4..c847260 100644 (file)
--- 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();
-
                 }
               }
             });
@@ -2092,7 +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();
@@ -2139,7 +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();
@@ -4491,7 +4492,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              boolean autoAssociate = Cache
+                      .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
               if (!autoAssociate)
               {
                 String msg = MessageManager.formatMessage(
@@ -4934,6 +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();
               }
             });
@@ -5019,6 +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();
                                   }
                                 });