JAL-3130 Merge of JAL-3130_Java_11_investigations-Ben-2 and updated develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 25c6dd4..bd9f661 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -136,6 +136,7 @@ import java.util.Hashtable;
 import java.util.List;
 import java.util.Vector;
 
+import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
 import javax.swing.JInternalFrame;
@@ -1202,7 +1203,23 @@ 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(
@@ -2741,6 +2758,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     newap.av.setRedoList(viewport.getRedoList());
 
     /*
+     * copy any visualisation settings that are not saved in the project
+     */
+    newap.av.setColourAppliesToAllGroups(
+            viewport.getColourAppliesToAllGroups());
+
+    /*
      * Views share the same mappings; need to deregister any new mappings
      * created by copyAlignPanel, and register the new reference to the shared
      * mappings
@@ -3345,6 +3368,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * otherwise set the chosen colour scheme (or null for 'None')
      */
     ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
+            viewport,
             viewport.getAlignment(), viewport.getHiddenRepSequences());
     changeColour(cs);
   }
@@ -4481,7 +4505,8 @@ 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(
@@ -5301,7 +5326,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       PaintRefresher.Refresh(this, viewport.getSequenceSetId());
       alignPanel.updateAnnotation();
-      alignPanel.paintAlignment(true, true);
+      alignPanel.paintAlignment(true,
+              viewport.needToUpdateStructureViews());
     }
   }
 
@@ -5587,15 +5613,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(textColour);
     colourMenu.addSeparator();
 
-    ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
-            false);
+    ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+            viewport.getAlignment(), false);
 
+    colourMenu.add(annotationColour);
+    bg.add(annotationColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
     ColourMenuHelper.setColourSelected(colourMenu, colourScheme);