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

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

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index f77d6a1..af7e9cd 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -519,7 +519,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
-      av.startRes = vscroll.getValue() * cwidth;
+      av.setStartRes(vscroll.getValue() * cwidth);
     }
   }
 
@@ -632,8 +632,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   public void setWrapAlignment(boolean wrap)
   {
-    av.startSeq = 0;
-    av.startRes = 0;
+    av.setStartSeq(0);
+    av.setStartRes(0);
     scalePanelHolder.setVisible(!wrap);
 
     hscroll.setVisible(!wrap);
@@ -832,8 +832,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
+    int scrollX = av.getStartRes() - oldX;
+    int scrollY = av.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
@@ -843,13 +843,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if (scrollX > av.endRes - av.startRes)
+      if (scrollX > av.getEndRes() - av.getStartRes())
       {
-        scrollX = av.endRes - av.startRes;
+        scrollX = av.getEndRes() - av.getStartRes();
       }
-      else if (scrollX < av.startRes - av.endRes)
+      else if (scrollX < av.getStartRes() - av.getEndRes())
       {
-        scrollX = av.startRes - av.endRes;
+        scrollX = av.getStartRes() - av.getEndRes();
       }
 
       idPanel.idCanvas.fastPaint(scrollY);
@@ -920,7 +920,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
      * mapped), we can make the scroll-to location a sequence above the one
      * actually mapped.
      */
-    SequenceI mappedTo = sr.getResultSequence(0);
+    SequenceI mappedTo = sr.getResults().get(0).getSequence();
     List<SequenceI> seqs = av.getAlignment().getSequences();
 
     /*
@@ -955,8 +955,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   private void sendViewPosition()
   {
     StructureSelectionManager.getStructureSelectionManager(av.applet)
-            .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
-                    av.endSeq);
+            .sendViewPosition(this, av.getStartRes(), av.getEndRes(),
+                    av.getStartSeq(), av.getEndSeq());
   }
 
   /**