JAL-3198 SequenceGroup 'bulk constructor' without duplicates check

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a2336a0..936e714 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -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[]
@@ -2397,12 +2398,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = new SequenceGroup();
-
-    for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
-    {
-      sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
-    }
+    SequenceGroup sg = new SequenceGroup(
+            viewport.getAlignment().getSequences());
 
     sg.setEndRes(viewport.getAlignment().getWidth() - 1);
     viewport.setSelectionGroup(sg);
@@ -2701,7 +2698,8 @@ 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)
     {
       /*
@@ -2888,7 +2886,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.setFollowHighlight(state);
     if (state)
     {
-      alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+      alignPanel.scrollToPosition(viewport.getSearchResults());
     }
   }
 
@@ -5399,7 +5397,9 @@ 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;
   }
 
   /**