JAL-2388 Make startRes,startSeq,endRes,endSeq private with get/setters

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b5fc817..75d3677 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -640,8 +640,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   new String[] { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
-            alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+            alignPanel.getSeqPanel().seqCanvas.cursorX = viewport
+                    .getStartRes();
+            alignPanel.getSeqPanel().seqCanvas.cursorY = viewport
+                    .getStartSeq();
           }
           alignPanel.getSeqPanel().seqCanvas.repaint();
           break;
@@ -679,8 +681,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                    - viewport.endSeq + viewport.startSeq);
+            alignPanel.setScrollValues(viewport.getStartRes(),
+                    2 * viewport.getStartSeq() - viewport.getEndSeq());
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
@@ -690,8 +692,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                    + viewport.endSeq - viewport.startSeq);
+            alignPanel.setScrollValues(viewport.getStartRes(),
+                    viewport.getEndSeq());
           }
           break;
         }
@@ -2612,7 +2614,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(viewport.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
@@ -2651,7 +2653,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(viewport.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));