From: kiramt <k.mourao@dundee.ac.uk>
Date: Mon, 27 Feb 2017 16:10:21 +0000 (+0000)
Subject: JAL-2388 Make startRes,startSeq,endRes,endSeq private with get/setters
X-Git-Tag: Release_2_10_2~3^2~92^2~63
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d559b47886de6427219011e6e355320a0babd757;p=jalview.git

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6a0b390..dc622f5 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -571,8 +571,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               new String[] { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+        alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
+        alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
       }
       break;
 
@@ -598,8 +598,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                - viewport.endSeq + viewport.startSeq);
+        alignPanel.setScrollValues(viewport.getStartRes(),
+                2 * viewport.getStartSeq() - viewport.getEndSeq());
       }
       break;
 
@@ -610,8 +610,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                + viewport.endSeq - viewport.startSeq);
+        alignPanel.setScrollValues(viewport.getStartRes(),
+                viewport.getEndSeq());
       }
       break;
 
@@ -2388,7 +2388,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // 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();
@@ -2420,7 +2420,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // 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()));
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 951a651..f927e63 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -76,10 +76,10 @@ public class AlignViewport extends AlignmentViewport implements
     alignment = al;
     // we always pad gaps
     this.setPadGaps(true);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
+    this.setStartRes(0);
+    this.setEndRes(al.getWidth() - 1);
+    this.setStartSeq(0);
+    this.setEndSeq(al.getHeight() - 1);
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index e97c347..af7e9cd 100644
--- 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);
@@ -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());
   }
 
   /**
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 6012c1a..8b1bb26 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -618,7 +618,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getStartRes(), av.getEndRes() + 1);
 
     g.drawImage(image, 0, 0, this);
   }
@@ -635,7 +635,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.copyArea(0, 0, imgWidth, getSize().height,
             -horizontal * av.getCharWidth(), 0);
-    int sr = av.startRes, er = av.endRes + 1, transX = 0;
+    int sr = av.getStartRes(), er = av.getEndRes() + 1, transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index d72e91f..8f8ed35 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -106,13 +106,14 @@ public class IdCanvas extends Panel
     gg.copyArea(0, 0, getSize().width, imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.startSeq, es = av.endSeq, transY = 0;
+    int ss = av.getStartSeq(), es = av.getEndSeq(), transY = 0;
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+                                 // time
       {
-        ss = av.startSeq;
+        ss = av.getStartSeq();
       }
       else
       {
@@ -122,9 +123,9 @@ public class IdCanvas extends Panel
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.endSeq)
+      if (es > av.getEndSeq())
       {
-        es = av.endSeq;
+        es = av.getEndSeq();
       }
     }
 
@@ -180,7 +181,7 @@ public class IdCanvas extends Panel
     gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds(av.startSeq, av.endSeq);
+    drawIds(av.getStartSeq(), av.getEndSeq());
     g.drawImage(image, 0, 0, this);
   }
 
@@ -235,7 +236,7 @@ public class IdCanvas extends Panel
 
       int rowSize = av.getEndRes() - av.getStartRes();
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+      for (int ypos = hgap, row = av.getStartRes(); (ypos <= getSize().height)
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 1b6df1d..0d3f058 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -253,7 +253,6 @@ public class OverviewPanel extends Panel implements Runnable,
       if ((int) (row * sampleRow) == lastrow)
       {
         sameRow++;
-        continue;
       }
       else
       {
@@ -261,10 +260,13 @@ public class OverviewPanel extends Panel implements Runnable,
         hiddenRow = false;
         if (hasHiddenRows)
         {
+          // look for sequence in hidden rows
           seq = av.getAlignment().getHiddenSequences()
                   .getHiddenSequence(lastrow);
           if (seq == null)
           {
+            // didn't find in hidden rows, adjust the index and retrieve from
+            // full row set
             int index = av.getAlignment().getHiddenSequences()
                     .findIndexWithoutHiddenSeqs(lastrow);
 
@@ -272,6 +274,7 @@ public class OverviewPanel extends Panel implements Runnable,
           }
           else
           {
+            // found in hidden rows, ergo this row is hidden
             hiddenRow = true;
           }
         }
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5d6bb07..fd74c4a 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -216,12 +216,12 @@ public class SeqCanvas extends Panel
     // Its possible on certain browsers that the call to fastpaint
     // is faster than it can paint, so this check here catches
     // this possibility
-    if (lastsr + horizontal != av.startRes)
+    if (lastsr + horizontal != av.getStartRes())
     {
-      horizontal = av.startRes - lastsr;
+      horizontal = av.getStartRes() - lastsr;
     }
 
-    lastsr = av.startRes;
+    lastsr = av.getStartRes();
 
     fastPaint = true;
     gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
@@ -229,7 +229,8 @@ public class SeqCanvas extends Panel
             imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
             -vertical * avcharHeight);
 
-    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+    int sr = av.getStartRes(), er = av.getEndRes(), ss = av.getStartSeq(), es = av
+            .getEndSeq(), transX = 0, transY = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -244,9 +245,10 @@ public class SeqCanvas extends Panel
     else if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+                                 // time
       {
-        ss = av.startSeq;
+        ss = av.getStartSeq();
       }
       else
       {
@@ -256,9 +258,9 @@ public class SeqCanvas extends Panel
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.endSeq)
+      if (es > av.getEndSeq())
       {
-        es = av.endSeq;
+        es = av.getEndSeq();
       }
     }
 
@@ -331,11 +333,12 @@ public class SeqCanvas extends Panel
 
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+      drawWrappedPanel(gg, imgWidth, imgHeight, av.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+      drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
+              av.getEndSeq(), 0);
     }
 
     g.drawImage(img, 0, 0, this);
@@ -421,7 +424,7 @@ public class SeqCanvas extends Panel
 
     av.setWrappedWidth(cWidth);
 
-    av.endRes = av.startRes + cWidth;
+    av.setEndRes(av.getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 1352fe9..946fc2a 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -226,16 +226,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.startSeq)
+      while (seqCanvas.cursorY < av.getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.endSeq)
+      while (seqCanvas.cursorY + 1 > av.getEndSeq())
       {
         ap.scrollUp(false);
       }
       while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(av.startRes))
+              .adjustForHiddenColumns(av.getStartRes()))
       {
 
         if (!ap.scrollRight(false))
@@ -244,7 +244,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
       }
       while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(av.endRes))
+              .adjustForHiddenColumns(av.getEndRes()))
       {
         if (!ap.scrollRight(true))
         {
@@ -1643,8 +1643,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = -1;
     }
 
-    if (res > av.endRes || res < av.startRes || y < av.startSeq
-            || y > av.endSeq)
+    if (res > av.getEndRes() || res < av.getStartRes()
+            || y < av.getStartSeq() || y > av.getEndSeq())
     {
       mouseExited(evt);
     }
@@ -1890,8 +1890,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollTo(int row, int column)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    column = column < 0 ? ap.av.startRes : column;
+    row = row < 0 ? ap.av.getStartSeq() : row;
+    column = column < 0 ? ap.av.getStartRes() : column;
     ap.scrollTo(column, column, row, true, true);
   }
 
@@ -1903,8 +1903,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToRow(int row)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
+    row = row < 0 ? ap.av.getStartSeq() : row;
+    ap.scrollTo(ap.av.getStartRes(), ap.av.getStartRes(), row, true, true);
   }
 
   /**
@@ -1915,8 +1915,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToColumn(int column)
   {
 
-    column = column < 0 ? ap.av.startRes : column;
-    ap.scrollTo(column, column, ap.av.startSeq, true, true);
+    column = column < 0 ? ap.av.getStartRes() : column;
+    ap.scrollTo(column, column, ap.av.getStartSeq(), true, true);
   }
 
   /**
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b5fc817..75d3677 100644
--- 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()));
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3d0eb21..4c888a1 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -237,10 +237,10 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    this.startRes = 0;
-    this.endRes = alignment.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = alignment.getHeight() - 1;
+    setStartRes(0);
+    setEndRes(alignment.getWidth() - 1);
+    setStartSeq(0);
+    setEndSeq(alignment.getHeight() - 1);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d793e6a..552d166 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -467,7 +467,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
-      av.startRes = vscroll.getValue() * cwidth;
+      av.setStartRes(vscroll.getValue() * cwidth);
     }
 
   }
@@ -591,7 +591,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
-    av.startSeq = 0;
+    av.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
@@ -810,8 +810,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       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)
     {
@@ -821,13 +821,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       // 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();
       }
 
       if (scrollX != 0 || scrollY != 0)
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index b1f0edb..c619dc1 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -55,7 +55,6 @@ import java.util.List;
 
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.Scrollable;
@@ -905,7 +904,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+    imgWidth = (av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth();
     if (imgWidth < 1)
     {
       return;
@@ -946,7 +945,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       imageFresh = true;
     }
 
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getStartRes(), av.getEndRes() + 1);
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -976,8 +975,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
-    int sr = av.startRes;
-    int er = av.endRes + 1;
+    int sr = av.getStartRes();
+    int er = av.getEndRes() + 1;
     int transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 37be8bc..c753cae 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -161,17 +161,17 @@ public class IdCanvas extends JPanel
     gg.copyArea(0, 0, getWidth(), imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    int ss = av.getStartSeq();
+    int es = av.getEndSeq();
     int transY = 0;
 
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < av.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = av.getStartSeq();
       }
       else
       {
@@ -182,9 +182,9 @@ public class IdCanvas extends JPanel
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > av.getEndSeq())
       {
-        es = av.endSeq;
+        es = av.getEndSeq();
       }
     }
 
@@ -240,7 +240,7 @@ public class IdCanvas extends JPanel
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
 
-    drawIds(av.getStartSeq(), av.endSeq);
+    drawIds(av.getStartSeq(), av.getEndSeq());
 
     g.drawImage(image, 0, 0, this);
   }
@@ -317,7 +317,7 @@ public class IdCanvas extends JPanel
       int rowSize = av.getEndRes() - av.getStartRes();
 
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+      for (int ypos = hgap, row = av.getStartRes(); (ypos <= getHeight())
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3ac453f..55d29d5 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1270,8 +1270,8 @@ public class Jalview2XML
       view.setWidth(size.width);
       view.setHeight(size.height);
 
-      view.setStartRes(av.startRes);
-      view.setStartSeq(av.startSeq);
+      view.setStartRes(av.getStartRes());
+      view.setStartSeq(av.getStartSeq());
 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d015292..54d2be7 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -279,10 +279,10 @@ public class SeqCanvas extends JComponent
     gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
             imgHeight, -horizontal * charWidth, -vertical * charHeight);
 
-    int sr = av.startRes;
-    int er = av.endRes;
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    int sr = av.getStartRes();
+    int er = av.getEndRes();
+    int ss = av.getStartSeq();
+    int es = av.getEndSeq();
     int transX = 0;
     int transY = 0;
 
@@ -300,9 +300,9 @@ public class SeqCanvas extends JComponent
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < av.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = av.getStartSeq();
       }
       else
       {
@@ -313,9 +313,9 @@ public class SeqCanvas extends JComponent
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > av.getEndSeq())
       {
-        es = av.endSeq;
+        es = av.getEndSeq();
       }
     }
 
@@ -397,11 +397,12 @@ public class SeqCanvas extends JComponent
 
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+      drawWrappedPanel(gg, getWidth(), getHeight(), av.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+      drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
+              av.getEndSeq(), 0);
     }
 
     g.drawImage(lcimg, 0, 0, this);
@@ -503,7 +504,7 @@ public class SeqCanvas extends JComponent
 
     av.setWrappedWidth(cWidth);
 
-    av.endRes = av.startRes + cWidth;
+    av.setEndRes(av.getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 37b4852..16415cc 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -385,18 +385,18 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.startSeq)
+      while (seqCanvas.cursorY < av.getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.endSeq)
+      while (seqCanvas.cursorY + 1 > av.getEndSeq())
       {
         ap.scrollUp(false);
       }
       if (!av.getWrapAlignment())
       {
         while (seqCanvas.cursorX < av.getColumnSelection()
-                .adjustForHiddenColumns(av.startRes))
+                .adjustForHiddenColumns(av.getStartRes()))
         {
           if (!ap.scrollRight(false))
           {
@@ -404,7 +404,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
         }
         while (seqCanvas.cursorX > av.getColumnSelection()
-                .adjustForHiddenColumns(av.endRes))
+                .adjustForHiddenColumns(av.getEndRes()))
         {
           if (!ap.scrollRight(true))
           {
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index fb2b4071..b728efc 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1285,14 +1285,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean followHighlight = true;
 
-  // TODO private with getters and setters?
-  public int startRes;
+  private int startRes;
 
-  public int endRes;
+  private int endRes;
 
-  public int startSeq;
+  private int startSeq;
 
-  public int endSeq;
+  private int endSeq;
 
   /**
    * Property change listener for changes in alignment