Merge branch 'bug/JAL-2831' into develop

[jalview.git] / src / jalview / appletgui / SeqPanel.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 9a61f5f..d74bbb7 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -43,7 +43,6 @@ import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Font;
@@ -148,13 +147,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   void setCursorRow()
   {
     seqCanvas.cursorY = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorColumn()
   {
     seqCanvas.cursorX = getKeyboardNo1() - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void setCursorRowAndColumn()
@@ -167,7 +166,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       seqCanvas.cursorX = getKeyboardNo1() - 1;
       seqCanvas.cursorY = getKeyboardNo2() - 1;
-      scrollToVisible();
+      scrollToVisible(true);
     }
   }
 
@@ -176,7 +175,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
 
     seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
-    scrollToVisible();
+    scrollToVisible(true);
   }
 
   void moveCursor(int dx, int dy)
@@ -202,10 +201,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         seqCanvas.cursorX = original;
       }
     }
-    scrollToVisible();
+    scrollToVisible(false);
   }
 
-  void scrollToVisible()
+  /**
+   * Scroll to make the cursor visible in the viewport.
+   * 
+   * @param jump
+   *          just jump to the location rather than scrolling
+   */
+  void scrollToVisible(boolean jump)
   {
     if (seqCanvas.cursorX < 0)
     {
@@ -226,44 +231,34 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     endEditing();
-    if (av.getWrapAlignment())
+
+    boolean repaintNeeded = true;
+    if (jump)
     {
-      av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
+      // only need to repaint if the viewport did not move, as otherwise it will
+      // get a repaint
+      repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX,
+              seqCanvas.cursorY);
     }
     else
     {
-      ViewportRanges ranges = av.getRanges();
-      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      while (seqCanvas.cursorY < ranges.getStartSeq())
+      if (av.getWrapAlignment())
       {
-        ranges.scrollUp(true);
+        av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
       }
-      while (seqCanvas.cursorY > ranges.getEndSeq())
-      {
-        ranges.scrollUp(false);
-      }
-      while (seqCanvas.cursorX < hidden
-              .adjustForHiddenColumns(ranges.getStartRes()))
-      {
-
-        if (!ranges.scrollRight(false))
-        {
-          break;
-        }
-      }
-      while (seqCanvas.cursorX > hidden
-              .adjustForHiddenColumns(ranges.getEndRes()))
+      else
       {
-        if (!ranges.scrollRight(true))
-        {
-          break;
-        }
+        av.getRanges().scrollToVisible(seqCanvas.cursorX,
+                seqCanvas.cursorY);
       }
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
 
-    seqCanvas.repaint();
+    if (repaintNeeded)
+    {
+      seqCanvas.repaint();
+    }
   }
 
   void setSelectionAreaAtCursor(boolean topLeft)