X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d03b2c77698be7ebbb055e2154d3d40662b596e4;hb=c43bf66142660933dbe5b62c8d1a9e18eb75e439;hp=de82fd8322002ac4a130f59834d9d261876752d2;hpb=0d69df1fcdf53cd75eae383f8dcf62ea211edce6;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index de82fd8..d03b2c7 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -536,7 +536,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1,
+                    evt.isShiftDown() && !evt.isAltDown());
           }
           break;
 
@@ -547,9 +548,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1,
+                    evt.isShiftDown() && !evt.isAltDown());
           }
-
           break;
 
         case KeyEvent.VK_LEFT:
@@ -560,7 +561,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
           }
 
           break;
@@ -572,7 +573,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
           }
           break;
 
@@ -1740,19 +1741,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   synchronized void slideSequences(boolean right, int size)
   {
     List<SequenceI> sg = new ArrayList<>();
-    if (viewport.cursorMode)
-    {
-      sg.add(viewport.getAlignment()
-              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
-    }
-    else if (viewport.getSelectionGroup() != null
-            && viewport.getSelectionGroup().getSize() != viewport
-                    .getAlignment().getHeight())
+    if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup()
+            .getSize() != viewport.getAlignment().getHeight())
     {
       sg = viewport.getSelectionGroup()
               .getSequences(viewport.getHiddenRepSequences());
     }
 
+    if (sg.size() == 0 && viewport.cursorMode)
+    {
+      sg.add(viewport.getAlignment()
+              .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
+    }
+
     if (sg.size() < 1)
     {
       return;
@@ -2450,7 +2451,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     viewport.setSelectionGroup(null);
     viewport.getColumnSelection().clear();
-    viewport.setSelectionGroup(null);
+    viewport.setSearchResults(null);
     alignPanel.getIdPanel().getIdCanvas().searchResults = null;
     // JAL-2034 - should delegate to
     // alignPanel to decide if overview needs
@@ -4694,7 +4695,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             if (parseFeaturesFile(file, sourceType))
             {
-              alignPanel.paintAlignment(true, true);
+              SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+              if (splitFrame != null)
+              {
+                splitFrame.repaint();
+              }
+              else
+              {
+                alignPanel.paintAlignment(true, true);
+              }
             }
           }
           else