From: kiramt <k.mourao@dundee.ac.uk>
Date: Thu, 16 Mar 2017 17:30:14 +0000 (+0000)
Subject: JAL-2388 Applied ViewportRanges to code
X-Git-Tag: Release_2_10_2~3^2~92^2~33
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=97b26ba418dec7a6e926378205d25470bf098633;p=jalview.git

JAL-2388 Applied ViewportRanges to code
---

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index c6312ab..bd43c60 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -47,11 +47,13 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  ViewportRanges getRanges();
-  
-  int getEndRes();
-
-  int getStartRes();
+  /**
+   * Get the ranges object containing details of the start and end sequences and
+   * residues
+   * 
+   * @return
+   */
+  public ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -461,8 +463,4 @@ public interface AlignViewportI extends ViewStyleI
    * @return search results or null
    */
   SearchResultsI getSearchResults();
-
-  int getStartSeq();
-
-  int getEndSeq();
 }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index dc622f5..e51131b 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -75,6 +75,7 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Canvas;
@@ -420,6 +421,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void keyPressed(KeyEvent evt)
   {
+    ViewportRanges ranges = viewport.getRanges();
+
     if (viewport.cursorMode
             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
@@ -571,8 +574,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               new String[] { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
-        alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
+        alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
+        alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
       }
       break;
 
@@ -598,8 +601,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.getStartRes(),
-                2 * viewport.getStartSeq() - viewport.getEndSeq());
+        alignPanel.setScrollValues(ranges.getStartRes(),
+                2 * ranges.getStartSeq() - ranges.getEndSeq());
       }
       break;
 
@@ -610,8 +613,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.getStartRes(),
-                viewport.getEndSeq());
+        alignPanel
+                .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
       }
       break;
 
@@ -2063,7 +2066,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             seqs, 0, viewport.getAlignment().getWidth(),
             viewport.getAlignment()));
 
-    viewport.setEndSeq(viewport.getAlignment().getHeight());
+    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
     viewport.getAlignment().getWidth();
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
@@ -2299,6 +2302,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   void trimAlignment(boolean trimLeft)
   {
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
@@ -2321,20 +2326,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        seqs = viewport.getAlignment().getSequencesArray();
+        seqs = al.getSequencesArray();
       }
 
       TrimRegionCommand trimRegion;
       if (trimLeft)
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
-                column, viewport.getAlignment());
-        viewport.setStartRes(0);
+                column, al);
+        ranges.setStartRes(0);
       }
       else
       {
         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
-                column, viewport.getAlignment());
+                column, al);
       }
 
       statusBar.setText(MessageManager.formatMessage(
@@ -2343,23 +2348,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                       .toString() }));
       addHistoryItem(trimRegion);
 
-      for (SequenceGroup sg : viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : al.getGroups())
       {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
-          viewport.getAlignment().deleteGroup(sg);
+          al.deleteGroup(sg);
         }
       }
 
-      viewport.firePropertyChange("alignment", null, viewport
-              .getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null, al.getSequences());
     }
   }
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.getAlignment().getWidth() - 1;
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
+    int start = 0;
+    int end = ranges.getAbsoluteAlignmentWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -2387,22 +2394,24 @@ 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.getStartRes());
+    SequenceI seq = al.getSequenceAt(0);
+    int startRes = seq.findPosition(ranges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.firePropertyChange("alignment", null, al.getSequences());
 
   }
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.getAlignment().getWidth() - 1;
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
+    int start = 0;
+    int end = ranges.getAbsoluteAlignmentWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -2419,16 +2428,15 @@ 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.getStartRes());
+    SequenceI seq = al.getSequenceAt(0);
+    int startRes = seq.findPosition(ranges.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
-            viewport.getAlignment()));
+            al));
 
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
+    viewport.firePropertyChange("alignment", null, al.getSequences());
 
   }
 
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 30817d5..065c503 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -297,7 +297,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public void resetSeqLimits(int height)
   {
-    setEndSeq(height / getCharHeight());
+    ranges.setEndSeq(height / getCharHeight());
   }
 
   public void setCurrentTree(NJTree tree)
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index e864337..3ae0394 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -65,6 +66,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   AnnotationLabels alabels;
 
+  ViewportRanges vpRanges;
+
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
@@ -73,6 +76,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     alignFrame = null;
     av = null;
+    vpRanges = null;
     seqPanel = null;
     seqPanelHolder = null;
     sequenceHolderPanel = null;
@@ -96,6 +100,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     alignFrame = af;
     this.av = av;
+    vpRanges = av.getRanges();
     seqPanel = new SeqPanel(av, this);
     idPanel = new IdPanel(av, this);
     scalePanel = new ScalePanel(av, this);
@@ -126,7 +131,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       @Override
       public void componentResized(ComponentEvent evt)
       {
-        setScrollValues(av.getStartRes(), av.getStartSeq());
+        setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
         if (getSize().height > 0
                 && annotationPanelHolder.getSize().height > 0)
         {
@@ -383,7 +388,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
        */
       if (centre)
       {
-        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
         end = Math.min(end + offset, seq.getEnd() - 1);
       }
@@ -468,33 +473,34 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       // setScrollValues(start, seqIndex);
       // }
       // logic copied from jalview.gui.AlignmentPanel:
-      if ((startv = av.getStartRes()) >= start)
+      if ((startv = vpRanges.getStartRes()) >= start)
       {
         /*
          * Scroll left to make start of search results visible
          */
         setScrollValues(start - 1, seqIndex);
       }
-      else if ((endv = av.getEndRes()) <= end)
+      else if ((endv = vpRanges.getEndRes()) <= end)
       {
         /*
          * Scroll right to make end of search results visible
          */
         setScrollValues(startv + 1 + end - endv, seqIndex);
       }
-      else if ((starts = av.getStartSeq()) > seqIndex)
+      else if ((starts = vpRanges.getStartSeq()) > seqIndex)
       {
         /*
          * Scroll up to make start of search results visible
          */
-        setScrollValues(av.getStartRes(), seqIndex);
+        setScrollValues(vpRanges.getStartRes(), seqIndex);
       }
-      else if ((ends = av.getEndSeq()) <= seqIndex)
+      else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
       {
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+        setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+                + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -516,10 +522,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     int cwidth = seqPanel.seqCanvas
             .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    if (res <= vpRanges.getStartRes()
+            || res >= (vpRanges.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
-      av.setStartRes(vscroll.getValue() * cwidth);
+      vpRanges.setStartRes(vscroll.getValue() * cwidth);
     }
   }
 
@@ -632,8 +639,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   public void setWrapAlignment(boolean wrap)
   {
-    av.setStartSeq(0);
-    av.setStartRes(0);
+    vpRanges.setStartSeq(0);
+    vpRanges.setStartRes(0);
     scalePanelHolder.setVisible(!wrap);
 
     hscroll.setVisible(!wrap);
@@ -762,10 +769,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       x = 0;
     }
 
-    av.setStartSeq(y);
-    av.setEndSeq(y + vextent);
-    av.setStartRes(x);
-    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+    vpRanges.setStartSeq(y);
+    vpRanges.setEndSeq(y + vextent);
+    vpRanges.setStartRes(x);
+    vpRanges.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
             .getCharWidth())) - 1);
 
     hscroll.setValues(x, hextent, 0, width);
@@ -782,8 +789,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+    int oldX = vpRanges.getStartRes();
+    int oldY = vpRanges.getStartSeq();
 
     if (evt == null || evt.getSource() == apvscroll)
     {
@@ -797,8 +804,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     if (evt == null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+      vpRanges.setStartRes(x);
+      vpRanges.setEndRes(x + seqPanel.seqCanvas.getSize().width
               / av.getCharWidth() - 1);
     }
 
@@ -809,13 +816,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         int rowSize = seqPanel.seqCanvas
                 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes((vscroll.getValue() + 1) * rowSize);
+        vpRanges.setStartRes(vscroll.getValue() * rowSize);
+        vpRanges.setEndRes((vscroll.getValue() + 1) * rowSize);
       }
       else
       {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+        vpRanges.setStartSeq(offy);
+        vpRanges.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
                 / av.getCharHeight() - 1);
       }
     }
@@ -825,8 +832,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.getStartRes() - oldX;
-    int scrollY = av.getStartSeq() - oldY;
+    int scrollX = vpRanges.getStartRes() - oldX;
+    int scrollY = vpRanges.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
@@ -836,13 +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.getEndRes() - av.getStartRes())
+      if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
       {
-        scrollX = av.getEndRes() - av.getStartRes();
+        scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
       }
-      else if (scrollX < av.getStartRes() - av.getEndRes())
+      else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
       {
-        scrollX = av.getStartRes() - av.getEndRes();
+        scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
       }
 
       idPanel.idCanvas.fastPaint(scrollY);
@@ -851,7 +858,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       scalePanel.repaint();
       if (av.isShowAnnotation())
       {
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
+        annotationPanel.fastPaint(vpRanges.getStartRes() - oldX);
       }
     }
     sendViewPosition();
@@ -948,8 +955,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   private void sendViewPosition()
   {
     StructureSelectionManager.getStructureSelectionManager(av.applet)
-            .sendViewPosition(this, av.getStartRes(), av.getEndRes(),
-                    av.getStartSeq(), av.getEndSeq());
+            .sendViewPosition(this, vpRanges.getStartRes(),
+                    vpRanges.getEndRes(), vpRanges.getStartSeq(),
+                    vpRanges.getEndSeq());
   }
 
   /**
@@ -1017,7 +1025,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
     else
     {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
     }
 
     seqPanel.seqCanvas.repaint();
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index b28ccc7..ad74b25 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -339,7 +339,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
                 av.calcPanelHeight());
         f.height += dif;
         ap.seqPanelHolder.setPreferredSize(f);
-        ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+        ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges()
+                .getStartSeq());
         ap.validate();
         // ap.paintAlignment(true);
         ap.addNotify();
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 8b1bb26..0ec7adf 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -462,7 +462,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    int column = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int column = evt.getX() / av.getCharWidth()
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -618,7 +619,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawComponent(gg, av.getStartRes(), av.getEndRes() + 1);
+    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+            .getEndRes() + 1);
 
     g.drawImage(image, 0, 0, this);
   }
@@ -635,7 +637,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.copyArea(0, 0, imgWidth, getSize().height,
             -horizontal * av.getCharWidth(), 0);
-    int sr = av.getStartRes(), er = av.getEndRes() + 1, transX = 0;
+    int sr = av.getRanges().getStartRes(), er = av.getRanges().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 18281d9..abcbd70 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -103,17 +104,20 @@ public class IdCanvas extends Panel
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     gg.copyArea(0, 0, getSize().width, imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.getStartSeq(), es = av.getEndSeq(), transY = 0;
+    int ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transY = 0;
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+      if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+                                     // at a
                                  // time
       {
-        ss = av.getStartSeq();
+        ss = ranges.getStartSeq();
       }
       else
       {
@@ -123,9 +127,9 @@ public class IdCanvas extends Panel
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.getEndSeq())
+      if (es > ranges.getEndSeq())
       {
-        es = av.getEndSeq();
+        es = ranges.getEndSeq();
       }
     }
 
@@ -181,7 +185,7 @@ public class IdCanvas extends Panel
     gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds(av.getStartSeq(), av.getEndSeq());
+    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
     g.drawImage(image, 0, 0, this);
   }
 
@@ -234,9 +238,10 @@ public class IdCanvas extends Panel
 
       int cHeight = alheight * avcharHeight + hgap + annotationHeight;
 
-      int rowSize = av.getEndRes() - av.getStartRes();
+      int rowSize = av.getRanges().getEndRes()
+              - av.getRanges().getStartRes();
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.getStartRes(); (ypos <= getSize().height)
+      for (int ypos = hgap, row = av.getRanges().getStartRes(); (ypos <= getSize().height)
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b03a638..e47c50a 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -253,13 +253,13 @@ public class IdPanel extends Panel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+    if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && e.getY() >= getSize().height
-            && av.getAlignment().getHeight() > av.getEndSeq())
+            && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -398,9 +398,10 @@ public class IdPanel extends Panel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if (av.getStartSeq() > index || av.getEndSeq() < index)
+    if (av.getRanges().getStartSeq() > index
+            || av.getRanges().getEndSeq() < index)
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
     }
   }
 
@@ -431,10 +432,10 @@ public class IdPanel extends Panel implements MouseListener,
         if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index ed07b63..15d82a5 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -76,7 +76,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int x = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes();
     final int res;
 
     if (av.hasHiddenColumns())
@@ -229,7 +229,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
   {
     mouseDragging = false;
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (res > av.getAlignment().getWidth())
     {
@@ -276,7 +277,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     mouseDragging = true;
     ColumnSelection cs = av.getColumnSelection();
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
     res = Math.max(0, res);
     res = cs.adjustForHiddenColumns(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
@@ -324,7 +326,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
@@ -350,7 +353,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
   @Override
   public void paint(Graphics g)
   {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
+    drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+            getSize().width,
             getSize().height);
   }
 
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index cd5aa74..b28b800 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -211,17 +212,19 @@ public class SeqCanvas extends Panel
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     updateViewport();
 
     // 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.getStartRes())
+    if (lastsr + horizontal != ranges.getStartRes())
     {
-      horizontal = av.getStartRes() - lastsr;
+      horizontal = ranges.getStartRes() - lastsr;
     }
 
-    lastsr = av.getStartRes();
+    lastsr = ranges.getStartRes();
 
     fastPaint = true;
     gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
@@ -229,7 +232,8 @@ public class SeqCanvas extends Panel
             imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
             -vertical * avcharHeight);
 
-    int sr = av.getStartRes(), er = av.getEndRes(), ss = av.getStartSeq(), es = av
+    int sr = ranges.getStartRes(), er = ranges.getEndRes(), ss = ranges
+            .getStartSeq(), es = ranges
             .getEndSeq(), transX = 0, transY = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
@@ -245,10 +249,11 @@ public class SeqCanvas extends Panel
     else if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.getStartSeq()) // ie scrolling too fast, more than a page at a
+      if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+                                     // at a
                                  // time
       {
-        ss = av.getStartSeq();
+        ss = ranges.getStartSeq();
       }
       else
       {
@@ -258,9 +263,9 @@ public class SeqCanvas extends Panel
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.getEndSeq())
+      if (es > ranges.getEndSeq())
       {
-        es = av.getEndSeq();
+        es = ranges.getEndSeq();
       }
     }
 
@@ -331,14 +336,16 @@ public class SeqCanvas extends Panel
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
+    ViewportRanges ranges = av.getRanges();
+
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, imgWidth, imgHeight, av.getStartRes());
+      drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
-              av.getEndSeq(), 0);
+      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq(), 0);
     }
 
     g.drawImage(img, 0, 0, this);
@@ -424,7 +431,7 @@ public class SeqCanvas extends Panel
 
     av.setWrappedWidth(cWidth);
 
-    av.setEndRes(av.getStartRes() + cWidth);
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 946fc2a..0e12703 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -41,6 +41,7 @@ import jalview.structure.VamsasSource;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Font;
@@ -226,16 +227,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.getStartSeq())
+      ViewportRanges ranges = av.getRanges();
+      while (seqCanvas.cursorY < ranges.getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.getEndSeq())
+      while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
       {
         ap.scrollUp(false);
       }
       while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(av.getStartRes()))
+              .adjustForHiddenColumns(ranges.getStartRes()))
       {
 
         if (!ap.scrollRight(false))
@@ -244,7 +246,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
       }
       while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(av.getEndRes()))
+              .adjustForHiddenColumns(ranges.getEndRes()))
       {
         if (!ap.scrollRight(true))
         {
@@ -624,14 +626,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getStartRes() / cwidth;
+      wrappedBlock += av.getRanges().getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
     }
     else
     {
-      res = (x / av.getCharWidth()) + av.getStartRes();
+      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
     }
 
     if (av.hasHiddenColumns())
@@ -681,7 +683,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+      seq = Math.min((y / av.getCharHeight())
+              + av.getRanges().getStartSeq(),
+              av
               .getAlignment().getHeight() - 1);
       if (seq < 0)
       {
@@ -1643,8 +1647,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = -1;
     }
 
-    if (res > av.getEndRes() || res < av.getStartRes()
-            || y < av.getStartSeq() || y > av.getEndSeq())
+    if (res > av.getRanges().getEndRes()
+            || res < av.getRanges().getStartRes()
+            || y < av.getRanges().getStartSeq()
+            || y > av.getRanges().getEndSeq())
     {
       mouseExited(evt);
     }
@@ -1742,13 +1748,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         if (evt != null)
         {
 
-          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+          if (mouseDragging && evt.getY() < 0
+                  && av.getRanges().getStartSeq() > 0)
           {
             running = ap.scrollUp(true);
           }
 
           if (mouseDragging && evt.getY() >= getSize().height
-                  && av.getAlignment().getHeight() > av.getEndSeq())
+                  && av.getAlignment().getHeight() > av.getRanges()
+                          .getEndSeq())
           {
             running = ap.scrollUp(false);
           }
@@ -1890,8 +1898,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollTo(int row, int column)
   {
 
-    row = row < 0 ? ap.av.getStartSeq() : row;
-    column = column < 0 ? ap.av.getStartRes() : column;
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
     ap.scrollTo(column, column, row, true, true);
   }
 
@@ -1903,8 +1911,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToRow(int row)
   {
 
-    row = row < 0 ? ap.av.getStartSeq() : row;
-    ap.scrollTo(ap.av.getStartRes(), ap.av.getStartRes(), row, true, true);
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges()
+            .getStartRes(), row, true, true);
   }
 
   /**
@@ -1915,8 +1924,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToColumn(int column)
   {
 
-    column = column < 0 ? ap.av.getStartRes() : column;
-    ap.scrollTo(column, column, ap.av.getStartSeq(), true, true);
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+    ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true);
   }
 
   /**
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 75d3677..ab1ac0e 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -86,6 +86,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.jws1.Discoverer;
@@ -160,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
+  ViewportRanges vpRanges;
+
   public AlignViewControllerI avc;
 
   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
@@ -331,6 +334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
+    vpRanges = viewport.getRanges();
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -640,9 +644,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   new String[] { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().seqCanvas.cursorX = viewport
+            alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
                     .getStartRes();
-            alignPanel.getSeqPanel().seqCanvas.cursorY = viewport
+            alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
                     .getStartSeq();
           }
           alignPanel.getSeqPanel().seqCanvas.repaint();
@@ -681,8 +685,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.setScrollValues(viewport.getStartRes(),
-                    2 * viewport.getStartSeq() - viewport.getEndSeq());
+            alignPanel.setScrollValues(vpRanges.getStartRes(),
+                    2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
@@ -692,8 +696,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.setScrollValues(viewport.getStartRes(),
-                    viewport.getEndSeq());
+            alignPanel.setScrollValues(vpRanges.getStartRes(),
+                    vpRanges.getEndSeq());
           }
           break;
         }
@@ -2143,7 +2147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        viewport.setEndSeq(alignment.getHeight());
+        vpRanges.setEndSeq(alignment.getHeight());
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
@@ -2547,7 +2551,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
                 column, viewport.getAlignment());
-        viewport.setStartRes(0);
+        vpRanges.setStartRes(0);
       }
       else
       {
@@ -2614,13 +2618,13 @@ 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.getStartRes());
+    int startRes = seq.findPosition(vpRanges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
 
@@ -2653,12 +2657,12 @@ 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.getStartRes());
+    int startRes = seq.findPosition(vpRanges.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
 
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
 
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 11321eb..602e3a1 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -852,7 +852,7 @@ public class AlignViewport extends AlignmentViewport implements
       }
     }
 
-    setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 631638f..ac137b9 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -35,6 +35,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -69,6 +70,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 {
   public AlignViewport av;
 
+  ViewportRanges vpRanges;
+
   OverviewPanel overviewPanel;
 
   private SeqPanel seqPanel;
@@ -113,6 +116,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
+    vpRanges = av.getRanges();
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
@@ -377,7 +381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       if (centre)
       {
-        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
         end = end + offset - 1;
       }
@@ -413,7 +417,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
-        if ((startv = av.getStartRes()) >= start)
+        if ((startv = vpRanges.getStartRes()) >= start)
         {
           /*
            * Scroll left to make start of search results visible
@@ -421,7 +425,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(start - 1, seqIndex); // plus one residue
           setScrollValues(start, seqIndex);
         }
-        else if ((endv = av.getEndRes()) <= end)
+        else if ((endv = vpRanges.getEndRes()) <= end)
         {
           /*
            * Scroll right to make end of search results visible
@@ -429,19 +433,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
           setScrollValues(startv + end - endv, seqIndex);
         }
-        else if ((starts = av.getStartSeq()) > seqIndex)
+        else if ((starts = vpRanges.getStartSeq()) > seqIndex)
         {
           /*
            * Scroll up to make start of search results visible
            */
-          setScrollValues(av.getStartRes(), seqIndex);
+          setScrollValues(vpRanges.getStartRes(), seqIndex);
         }
-        else if ((ends = av.getEndSeq()) <= seqIndex)
+        else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
         {
           /*
            * Scroll down to make end of search results visible
            */
-          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+          setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+                  + 1);
         }
         /*
          * Else results are already visible - no need to scroll
@@ -464,10 +469,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int cwidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-    if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    if (res < vpRanges.getStartRes()
+            || res >= (vpRanges.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
-      av.setStartRes(vscroll.getValue() * cwidth);
+      vpRanges.setStartRes(vscroll.getValue() * cwidth);
     }
 
   }
@@ -591,7 +597,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
-    av.setStartSeq(0);
+    vpRanges.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
@@ -735,7 +741,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
 
     // update endRes after x has (possibly) been adjusted
-    av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+    vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
             .getCharWidth())) - 1);
 
     /*
@@ -758,14 +764,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+    int oldX = vpRanges.getStartRes();
+    int oldY = vpRanges.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+      vpRanges.setStartRes(x);
+      vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
               .getCharWidth())) - 1);
     }
 
@@ -779,8 +785,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           int rowSize = getSeqPanel().seqCanvas
                   .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          av.setStartRes(offy * rowSize);
-          av.setEndRes((offy + 1) * rowSize);
+          vpRanges.setStartRes(offy * rowSize);
+          vpRanges.setEndRes((offy + 1) * rowSize);
         }
         else
         {
@@ -792,15 +798,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
             @Override
             public void run()
             {
-              setScrollValues(av.getStartRes(), av.getStartSeq());
+              setScrollValues(vpRanges.getStartRes(),
+                      vpRanges.getStartSeq());
             }
           });
         }
       }
       else
       {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy
+        vpRanges.setStartSeq(offy);
+        vpRanges.setEndSeq(offy
                 + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
                 - 1);
       }
@@ -811,8 +818,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.getStartRes() - oldX;
-    int scrollY = av.getStartSeq() - oldY;
+    int scrollX = vpRanges.getStartRes() - oldX;
+    int scrollY = vpRanges.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint)
     {
@@ -822,13 +829,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if (scrollX > av.getEndRes() - av.getStartRes())
+      if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
       {
-        scrollX = av.getEndRes() - av.getStartRes();
+        scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
       }
-      else if (scrollX < av.getStartRes() - av.getEndRes())
+      else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
       {
-        scrollX = av.getStartRes() - av.getEndRes();
+        scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
       }
 
       if (scrollX != 0 || scrollY != 0)
@@ -928,7 +935,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
     }
   }
 
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index c619dc1..84f3e6c 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -707,7 +707,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int column = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -904,7 +905,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.getEndRes() - av.getStartRes() + 1) * av.getCharWidth();
+    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
+            * av.getCharWidth();
     if (imgWidth < 1)
     {
       return;
@@ -945,7 +947,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       imageFresh = true;
     }
 
-    drawComponent(gg, av.getStartRes(), av.getEndRes() + 1);
+    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+            .getEndRes() + 1);
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -975,8 +978,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
-    int sr = av.getStartRes();
-    int er = av.getEndRes() + 1;
+    int sr = av.getRanges().getStartRes();
+    int er = av.getRanges().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 11bb14b..aad0776 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -158,20 +159,22 @@ public class IdCanvas extends JPanel
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     gg.copyArea(0, 0, getWidth(), imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.getStartSeq();
-    int es = av.getEndSeq();
+    int ss = ranges.getStartSeq();
+    int es = ranges.getEndSeq();
     int transY = 0;
 
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
 
-      if (ss < av.getStartSeq())
+      if (ss < ranges.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.getStartSeq();
+        ss = ranges.getStartSeq();
       }
       else
       {
@@ -182,9 +185,9 @@ public class IdCanvas extends JPanel
     {
       es = ss - vertical;
 
-      if (es > av.getEndSeq())
+      if (es > ranges.getEndSeq())
       {
-        es = av.getEndSeq();
+        es = ranges.getEndSeq();
       }
     }
 
@@ -240,7 +243,7 @@ public class IdCanvas extends JPanel
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
 
-    drawIds(av.getStartSeq(), av.getEndSeq());
+    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
 
     g.drawImage(image, 0, 0, this);
   }
@@ -314,10 +317,11 @@ public class IdCanvas extends JPanel
 
       int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
 
-      int rowSize = av.getEndRes() - av.getStartRes();
+      int rowSize = av.getRanges().getEndRes()
+              - av.getRanges().getStartRes();
 
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.getStartRes(); (ypos <= getHeight())
+      for (int ypos = hgap, row = av.getRanges().getStartRes(); (ypos <= getHeight())
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 6ae19f0..2074900 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -242,13 +242,14 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+    if (mouseDragging && (e.getY() < 0)
+            && (av.getRanges().getStartSeq() > 0))
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.getAlignment().getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -442,9 +443,10 @@ public class IdPanel extends JPanel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getRanges().getStartSeq() > index)
+            || (av.getRanges().getEndSeq() < index))
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
     }
   }
 
@@ -486,11 +488,11 @@ public class IdPanel extends JPanel implements MouseListener,
         if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
 
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 55d29d5..e8b832d 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -87,6 +87,7 @@ import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -755,6 +756,7 @@ public class Jalview2XML
     List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
 
     AlignViewport av = ap.av;
+    ViewportRanges vpRanges = av.getRanges();
 
     JalviewModel object = new JalviewModel();
     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
@@ -1270,8 +1272,8 @@ public class Jalview2XML
       view.setWidth(size.width);
       view.setHeight(size.height);
 
-      view.setStartRes(av.getStartRes());
-      view.setStartSeq(av.getStartSeq());
+      view.setStartRes(vpRanges.getStartRes());
+      view.setStartSeq(vpRanges.getStartSeq());
 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
@@ -4448,8 +4450,8 @@ public class Jalview2XML
     af.viewport.setThresholdTextColour(view.getTextColThreshold());
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+    af.viewport.getRanges().setStartSeq(view.getStartSeq());
     af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
     // apply colourschemes
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index e751a2c..6235cbe 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -367,8 +367,8 @@ public class Jalview2XML_V1
 
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+    af.viewport.getRanges().setStartSeq(view.getStartSeq());
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
     af.viewport.setColourText(view.getShowColourText());
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 8961f21..de21be6 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -101,7 +101,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int x = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes();
     final int res;
 
     if (av.hasHiddenColumns())
@@ -282,7 +282,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   {
     mouseDragging = false;
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -337,7 +338,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     mouseDragging = true;
     ColumnSelection cs = av.getColumnSelection();
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
     res = Math.max(0, res);
     res = cs.adjustForHiddenColumns(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
@@ -389,7 +391,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
@@ -419,7 +422,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   @Override
   public void paintComponent(Graphics g)
   {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
+    drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+            getWidth(), getHeight());
   }
 
   // scalewidth will normally be screenwidth,
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 226e0df..0593e24 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -26,6 +26,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
@@ -279,10 +280,11 @@ public class SeqCanvas extends JComponent
     gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
             imgHeight, -horizontal * charWidth, -vertical * charHeight);
 
-    int sr = av.getStartRes();
-    int er = av.getEndRes();
-    int ss = av.getStartSeq();
-    int es = av.getEndSeq();
+    ViewportRanges ranges = av.getRanges();
+    int sr = ranges.getStartRes();
+    int er = ranges.getEndRes();
+    int ss = ranges.getStartSeq();
+    int es = ranges.getEndSeq();
     int transX = 0;
     int transY = 0;
 
@@ -300,9 +302,9 @@ public class SeqCanvas extends JComponent
     {
       ss = es - vertical;
 
-      if (ss < av.getStartSeq())
+      if (ss < ranges.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.getStartSeq();
+        ss = ranges.getStartSeq();
       }
       else
       {
@@ -313,9 +315,9 @@ public class SeqCanvas extends JComponent
     {
       es = ss - vertical;
 
-      if (es > av.getEndSeq())
+      if (es > ranges.getEndSeq())
       {
-        es = av.getEndSeq();
+        es = ranges.getEndSeq();
       }
     }
 
@@ -395,14 +397,15 @@ public class SeqCanvas extends JComponent
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
+    ViewportRanges ranges = av.getRanges();
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getWidth(), getHeight(), av.getStartRes());
+      drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.getStartRes(), av.getEndRes(), av.getStartSeq(),
-              av.getEndSeq(), 0);
+      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq(), 0);
     }
 
     g.drawImage(lcimg, 0, 0, this);
@@ -504,7 +507,7 @@ public class SeqCanvas extends JComponent
 
     av.setWrappedWidth(cWidth);
 
-    av.setEndRes(av.getStartRes() + cWidth);
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 16415cc..db7aa36 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -209,7 +209,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getStartRes() / cwidth;
+      wrappedBlock += av.getRanges().getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
@@ -222,11 +222,11 @@ public class SeqPanel extends JPanel implements MouseListener,
         // right-hand gutter
         x = seqCanvas.getX() + seqCanvas.getWidth();
       }
-      res = (x / av.getCharWidth()) + av.getStartRes();
-      if (res > av.getEndRes())
+      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+      if (res > av.getRanges().getEndRes())
       {
         // moused off right
-        res = av.getEndRes();
+        res = av.getRanges().getEndRes();
       }
     }
 
@@ -262,7 +262,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+      seq = Math.min((y / av.getCharHeight())
+              + av.getRanges().getStartSeq(),
+              av
               .getAlignment().getHeight() - 1);
     }
 
@@ -385,18 +387,18 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.getStartSeq())
+      while (seqCanvas.cursorY < av.getRanges().getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.getEndSeq())
+      while (seqCanvas.cursorY + 1 > av.getRanges().getEndSeq())
       {
         ap.scrollUp(false);
       }
       if (!av.getWrapAlignment())
       {
         while (seqCanvas.cursorX < av.getColumnSelection()
-                .adjustForHiddenColumns(av.getStartRes()))
+                .adjustForHiddenColumns(av.getRanges().getStartRes()))
         {
           if (!ap.scrollRight(false))
           {
@@ -404,7 +406,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
         }
         while (seqCanvas.cursorX > av.getColumnSelection()
-                .adjustForHiddenColumns(av.getEndRes()))
+                .adjustForHiddenColumns(av.getRanges().getEndRes()))
         {
           if (!ap.scrollRight(true))
           {
@@ -1772,9 +1774,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       changeStartRes = true;
     }
 
-    if (res < av.getStartRes())
+    if (res < av.getRanges().getStartRes())
     {
-      res = av.getStartRes();
+      res = av.getRanges().getStartRes();
     }
 
     if (changeEndRes)
@@ -1908,13 +1910,15 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         if (evt != null)
         {
-          if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
+          if (mouseDragging && (evt.getY() < 0)
+                  && (av.getRanges().getStartSeq() > 0))
           {
             running = ap.scrollUp(true);
           }
 
           if (mouseDragging && (evt.getY() >= getHeight())
-                  && (av.getAlignment().getHeight() > av.getEndSeq()))
+                  && (av.getAlignment().getHeight() > av.getRanges()
+                          .getEndSeq()))
           {
             running = ap.scrollUp(false);
           }
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 6f84a2e..3a27c7d 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -307,7 +307,7 @@ public class AnnotationRenderer
   public void updateFromAlignViewport(AlignViewportI av)
   {
     charWidth = av.getCharWidth();
-    endRes = av.getEndRes();
+    endRes = av.getRanges().getEndRes();
     charHeight = av.getCharHeight();
     hasHiddenColumns = av.hasHiddenColumns();
     validCharWidth = av.isValidCharWidth();
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 1f91935..5f84a5d 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1287,14 +1287,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean followHighlight = true;
 
-  /*private int startRes;
-
-  private int endRes;
-
-  private int startSeq;
-
-  private int endSeq;*/
-
   /**
    * Property change listener for changes in alignment
    * 
@@ -2652,50 +2644,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ranges;
   }
 
-  @Override
-  public int getStartRes()
-  {
-    return ranges.getStartRes();
-  }
-
-  @Override
-  public int getEndRes()
-  {
-    return ranges.getEndRes();
-  }
-
-  @Override
-  public int getStartSeq()
-  {
-    return ranges.getStartSeq();
-  }
-
-  public void setStartRes(int res)
-  {
-    ranges.setStartRes(res);
-  }
-
-  public void setStartSeq(int seq)
-  {
-    ranges.setStartSeq(seq);
-  }
-
-  public void setEndRes(int res)
-  {
-    ranges.setEndRes(res);
-  }
-
-  public void setEndSeq(int seq)
-  {
-    ranges.setEndSeq(seq);
-  }
-
-  @Override
-  public int getEndSeq()
-  {
-    return ranges.getEndSeq();
-  }
-
   /**
    * Helper method to populate the SearchResults with the location in the
    * complementary alignment to scroll to, in order to match this one.
@@ -2733,7 +2681,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
      * locate 'middle' column (true middle if an odd number visible, left of
      * middle if an even number visible)
      */
-    int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+    int middleColumn = ranges.getStartRes()
+            + (ranges.getEndRes() - ranges.getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
 
@@ -2743,7 +2692,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
-    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+    for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 5c8cdb6..c91d2d9 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -25,7 +25,9 @@ import jalview.datamodel.AlignmentI;
 /**
  * Embryonic class which: Supplies and updates viewport properties relating to
  * position such as: start and end residues and sequences; ideally will serve
- * hidden columns/rows too
+ * hidden columns/rows too. Intention also to support calculations for
+ * positioning, scrolling etc. such as finding the middle of the viewport,
+ * checking for scrolls off screen
  */
 public class ViewportRanges extends ViewportProperties
 {
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 676a4b6..4d3dd2f 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -617,8 +617,8 @@ public class DasSequenceFeatureFetcher
     }
     af.getFeatureRenderer().featuresAdded();
 
-    int start = af.getViewport().getStartSeq();
-    int end = af.getViewport().getEndSeq();
+    int start = af.getViewport().getRanges().getStartSeq();
+    int end = af.getViewport().getRanges().getEndSeq();
     int index;
     for (index = start; index < end; index++)
     {
diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
index f3b6876..c580a88 100644
--- a/test/jalview/gui/AlignmentPanelTest.java
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -28,6 +28,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.ViewportRanges;
 
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -164,27 +165,29 @@ public class AlignmentPanelTest
   @Test(groups = "Functional")
   public void TestSetScrollValues()
   {
-    int oldres = af.getViewport().getEndRes();
+    ViewportRanges ranges = af.getViewport().getRanges();
+
+    int oldres = ranges.getEndRes();
     af.alignPanel.setScrollValues(-1, 5);
 
     // setting -ve x value does not change residue
-    assertEquals(af.getViewport().getEndRes(), oldres);
+    assertEquals(ranges.getEndRes(), oldres);
 
     af.alignPanel.setScrollValues(0, 5);
 
     // setting 0 as x value does not change residue
-    assertEquals(af.getViewport().getEndRes(), oldres);
+    assertEquals(ranges.getEndRes(), oldres);
 
     af.alignPanel.setScrollValues(5, 5);
     // setting x value to 5 extends endRes by 5 residues
-    assertEquals(af.getViewport().getEndRes(), oldres + 5);
+    assertEquals(ranges.getEndRes(), oldres + 5);
 
     // scroll to position after hidden columns sets endres to oldres (width) +
     // position
     int scrollpos = 60;
     af.getViewport().hideColumns(30, 50);
     af.alignPanel.setScrollValues(scrollpos, 5);
-    assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
+    assertEquals(ranges.getEndRes(), oldres + scrollpos);
 
     // scroll to position within hidden columns, still sets endres to oldres +
     // position
@@ -194,14 +197,14 @@ public class AlignmentPanelTest
     af.getViewport().showAllHiddenColumns();
     af.getViewport().hideColumns(30, 50);
     af.alignPanel.setScrollValues(scrollpos, 5);
-    assertEquals(af.getViewport().getEndRes(), oldres + scrollpos);
+    assertEquals(ranges.getEndRes(), oldres + scrollpos);
 
     // scroll to position within <width> distance of the end of the alignment
     // endRes should be set to width of alignment - 1
     scrollpos = 130;
     af.getViewport().showAllHiddenColumns();
     af.alignPanel.setScrollValues(scrollpos, 5);
-    assertEquals(af.getViewport().getEndRes(), af.getViewport()
+    assertEquals(ranges.getEndRes(), af.getViewport()
             .getAlignment().getWidth() - 1);
 
     // now hide some columns, and scroll to position within <width>
@@ -210,7 +213,7 @@ public class AlignmentPanelTest
     // columns
     af.getViewport().hideColumns(30, 50);
     af.alignPanel.setScrollValues(scrollpos, 5);
-    assertEquals(af.getViewport().getEndRes(), af.getViewport()
+    assertEquals(ranges.getEndRes(), af.getViewport()
             .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
                                                   // columns
   }