X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5ff7c6cb239edda0b3e9fd73f05c8e54ef3ca8f1;hb=a6b324e3f5edac3df0b968f0037b1cc8b651598e;hp=e8eb03b92e93cfacbae41f9498801c7d5220a32e;hpb=e0401a6563eb1fb58b2f4b6d594b4b3826135950;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e8eb03b..5ff7c6c 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2548,7 +2548,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
-    if (colSel.size() > 0)
+    if (!colSel.isEmpty())
     {
       if (trimLeft)
       {
@@ -2573,18 +2573,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       TrimRegionCommand trimRegion;
       if (trimLeft)
       {
-        trimRegion = new TrimRegionCommand("Remove Left",
-                TrimRegionCommand.TRIM_LEFT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+                column, viewport.getAlignment());
         viewport.setStartRes(0);
       }
       else
       {
-        trimRegion = new TrimRegionCommand("Remove Right",
-                TrimRegionCommand.TRIM_RIGHT, seqs, column,
-                viewport.getAlignment(), viewport.getColumnSelection(),
-                viewport.getSelectionGroup());
+        trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+                column, viewport.getAlignment());
       }
 
       statusBar.setText(MessageManager.formatMessage(
@@ -2971,6 +2967,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.showAllHiddenColumns();
     repaint();
+    viewport.sendSelection();
   }
 
   @Override
@@ -3061,6 +3058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
     toggleHiddenRegions(false, false);
+    viewport.sendSelection();
   }
 
   /*
@@ -3078,6 +3076,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   /*
@@ -3093,6 +3092,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.showAllHiddenColumns();
     viewport.showAllHiddenSeqs();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
@@ -3100,6 +3100,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport.hideSelectedColumns();
     alignPanel.paintAlignment(true);
+    viewport.sendSelection();
   }
 
   @Override
@@ -5513,8 +5514,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           @Override
           public void run()
           {
+            boolean isNuclueotide = alignPanel.alignFrame
+                    .getViewport().getAlignment()
+                    .isNucleotide();
             new jalview.ws.DBRefFetcher(alignPanel.av
-                    .getSequenceSelection(), alignPanel.alignFrame)
+                    .getSequenceSelection(),
+                    alignPanel.alignFrame, null,
+                    alignPanel.alignFrame.featureSettings,
+                    isNuclueotide)
                     .fetchDBRefs(false);
           }
         }).start();
@@ -5583,9 +5590,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
+                        boolean isNuclueotide = alignPanel.alignFrame
+                                .getViewport().getAlignment()
+                                .isNucleotide();
                         new jalview.ws.DBRefFetcher(alignPanel.av
                                 .getSequenceSelection(),
-                                alignPanel.alignFrame, dassource)
+                                alignPanel.alignFrame, dassource,
+                                alignPanel.alignFrame.featureSettings,
+                                isNuclueotide)
                                 .fetchDBRefs(false);
                       }
                     }).start();
@@ -5619,9 +5631,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
+                        boolean isNuclueotide = alignPanel.alignFrame
+                                .getViewport().getAlignment()
+                                .isNucleotide();
                         new jalview.ws.DBRefFetcher(alignPanel.av
                                 .getSequenceSelection(),
-                                alignPanel.alignFrame, dassource)
+                                alignPanel.alignFrame, dassource,
+                                alignPanel.alignFrame.featureSettings,
+                                isNuclueotide)
                                 .fetchDBRefs(false);
                       }
                     }).start();
@@ -5670,9 +5687,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         @Override
                         public void run()
                         {
+                          boolean isNuclueotide = alignPanel.alignFrame
+                                  .getViewport().getAlignment()
+                                  .isNucleotide();
                           new jalview.ws.DBRefFetcher(alignPanel.av
                                   .getSequenceSelection(),
-                                  alignPanel.alignFrame, dassrc)
+                                  alignPanel.alignFrame, dassrc,
+                                  alignPanel.alignFrame.featureSettings,
+                                  isNuclueotide)
                                   .fetchDBRefs(false);
                         }
                       }).start();