X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fviewmodel%2FViewportRangesTest.java;h=41a313f2ba26270e8c68f643ae6a4d50715fb00d;hb=8e820dadfebf0ced59476338df0fa391590f5401;hp=3cd20964743e9a07d14c93509bb333ef472e5c25;hpb=557859a3ea9a1e86899ef2033de90eadb6d87118;p=jalview.git

diff --git a/test/jalview/viewmodel/ViewportRangesTest.java b/test/jalview/viewmodel/ViewportRangesTest.java
index 3cd2096..41a313f 100644
--- a/test/jalview/viewmodel/ViewportRangesTest.java
+++ b/test/jalview/viewmodel/ViewportRangesTest.java
@@ -1,16 +1,23 @@
 package jalview.viewmodel;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
 import jalview.analysis.AlignmentGenerator;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenSequences;
 
 import java.beans.PropertyChangeEvent;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class ViewportRangesTest {
@@ -19,6 +26,26 @@ public class ViewportRangesTest {
 
   AlignmentI al = gen.generate(20, 30, 1, 5, 5);
 
+  AlignmentI smallAl = gen.generate(7, 2, 2, 5, 5);
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    gen = new AlignmentGenerator(false);
+    al = gen.generate(20, 30, 1, 5, 5);
+    smallAl = gen.generate(7, 2, 2, 5, 5);
+  }
+
+  @BeforeMethod(alwaysRun = true)
+  public void cleanUp()
+  {
+    ColumnSelection sel = new ColumnSelection();
+    al.getHiddenColumns().revealAllHiddenColumns(sel);
+    al.getHiddenSequences().showAll(null);
+    smallAl.getHiddenColumns().revealAllHiddenColumns(sel);
+    smallAl.getHiddenSequences().showAll(null);
+  }
+
   @Test(groups = { "Functional" })
   public void testViewportRanges() 
   {
@@ -49,17 +76,6 @@ public class ViewportRangesTest {
   }
 
   @Test(groups = { "Functional" })
-  public void testSetEndRes()
-  {
-    ViewportRanges vr = new ViewportRanges(al);
-    vr.setEndRes(-1);
-    assertEquals(vr.getEndRes(), 0);
-
-    vr.setEndRes(al.getWidth() - 1);
-    assertEquals(vr.getEndRes(), al.getWidth() - 1);
-  }
-
-  @Test(groups = { "Functional" })
   public void testSetEndSeq()
   {
     ViewportRanges vr = new ViewportRanges(al);
@@ -69,7 +85,7 @@ public class ViewportRangesTest {
     vr.setEndSeq(al.getHeight());
     assertEquals(vr.getEndSeq(), al.getHeight() - 1);
 
-    vr.setEndRes(al.getHeight() - 1);
+    vr.setEndSeq(al.getHeight() - 1);
     assertEquals(vr.getEndSeq(), al.getHeight() - 1);
   }
 
@@ -114,7 +130,17 @@ public class ViewportRangesTest {
     assertEquals(vr.getEndRes(), 19);
 
     vr.setStartEndRes(al.getWidth(), al.getWidth());
-    assertEquals(vr.getEndRes(), al.getWidth());
+    assertEquals(vr.getEndRes(), al.getWidth() - 1);
+
+    ViewportRanges vrsmall = new ViewportRanges(smallAl);
+    vrsmall.setStartEndRes(al.getWidth(), al.getWidth());
+    assertEquals(vrsmall.getEndRes(), 6);
+
+    // make visible alignment width = 0
+    smallAl.getHiddenColumns().hideColumns(0, 6);
+    vrsmall.setStartEndRes(0, 4);
+    assertEquals(vrsmall.getStartRes(), 0);
+    assertEquals(vrsmall.getEndRes(), 0);
   }
 
   @Test(groups = { "Functional" })
@@ -131,6 +157,32 @@ public class ViewportRangesTest {
 
     vr.setStartEndSeq(al.getHeight(), al.getHeight());
     assertEquals(vr.getEndSeq(), al.getHeight() - 1);
+
+    // make visible alignment height = 0
+    smallAl.getHiddenSequences().hideSequence(smallAl.getSequenceAt(0));
+    smallAl.getHiddenSequences().hideSequence(smallAl.getSequenceAt(0));
+    ViewportRanges vrsmall = new ViewportRanges(smallAl);
+    vrsmall.setStartEndSeq(0, 3);
+    assertEquals(vrsmall.getStartSeq(), 0);
+    assertEquals(vrsmall.getEndSeq(), 0);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetStartResAndSeq()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    vr.setViewportHeight(10);
+    vr.setStartResAndSeq(3, 6);
+    assertEquals(vr.getStartRes(), 3);
+    assertEquals(vr.getStartSeq(), 6);
+    assertEquals(vr.getEndRes(), 3 + vr.getViewportWidth() - 1);
+    assertEquals(vr.getEndSeq(), 6 + vr.getViewportHeight() - 1);
+
+    vr.setStartResAndSeq(10, 25);
+    assertEquals(vr.getStartRes(), 10);
+    assertEquals(vr.getStartSeq(), 19);
+    assertEquals(vr.getEndRes(), 10 + vr.getViewportWidth() - 1);
+    assertEquals(vr.getEndSeq(), 19 + vr.getViewportHeight() - 1);
   }
 
   @Test(groups = { "Functional" })
@@ -184,7 +236,13 @@ public class ViewportRangesTest {
     // reset out of bounds start values to within bounds
     vr.setViewportStartAndWidth(35, 5);
     assertEquals(vr.getViewportWidth(), 5);
-    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getStartRes(), 16);
+
+    // small alignment doesn't get bounds reset
+    ViewportRanges vrsmall = new ViewportRanges(smallAl);
+    vrsmall.setViewportStartAndWidth(0, 63);
+    assertEquals(vrsmall.getViewportWidth(), 7);
+    assertEquals(vrsmall.getStartRes(), 0);
   }
 
   @Test(groups = { "Functional" })
@@ -213,7 +271,7 @@ public class ViewportRangesTest {
     vr.pageDown();
 
     // pagedown to bottom does not go beyond end, and height stays same
-    assertEquals(vr.getStartSeq(), 23);
+    assertEquals(vr.getStartSeq(), 24);
     assertEquals(vr.getViewportHeight(), 6);
   }
 
@@ -228,6 +286,30 @@ public class ViewportRangesTest {
     vr.scrollUp(true);
     assertEquals(vr.getStartSeq(), 0);
 
+    vr.setViewportStartAndHeight(24, 5);
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 25);
+    // can't scroll beyond bottom
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 25);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testScrollUpWithHidden()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+
+    // hide last sequence
+    HiddenSequences hidden = new HiddenSequences(al);
+    hidden.hideSequence(al.getSequenceAt(29));
+
+    vr.setViewportStartAndHeight(1, 5);
+    vr.scrollUp(true);
+    assertEquals(vr.getStartSeq(), 0);
+    // can't scroll above top
+    vr.scrollUp(true);
+    assertEquals(vr.getStartSeq(), 0);
+
     vr.setViewportStartAndHeight(23, 5);
     vr.scrollUp(false);
     assertEquals(vr.getStartSeq(), 24);
@@ -247,38 +329,86 @@ public class ViewportRangesTest {
     vr.scrollRight(false);
     assertEquals(vr.getStartRes(), 0);
 
-    vr.setViewportStartAndWidth(19, 5);
+    vr.setViewportStartAndWidth(15, 5);
     vr.scrollRight(true);
-    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getStartRes(), 16);
     // can't scroll right past end
     vr.scrollRight(true);
-    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getStartRes(), 16);
   }
 
   @Test(groups = { "Functional" })
-  public void testScrollToWrappedVisible()
+  public void testScrollRightWithHidden()
   {
     ViewportRanges vr = new ViewportRanges(al);
+
+    // hide last 2 columns
+    HiddenColumns cols = new HiddenColumns();
+    cols.hideColumns(19, 20);
+    al.setHiddenColumns(cols);
+
+    vr.setViewportStartAndWidth(1, 5);
+    vr.scrollRight(false);
+    assertEquals(vr.getStartRes(), 0);
+    // can't scroll left past start
+    vr.scrollRight(false);
+    assertEquals(vr.getStartRes(), 0);
+
+    vr.setViewportStartAndWidth(13, 5);
+    vr.scrollRight(true);
+    assertEquals(vr.getStartRes(), 14);
+    // can't scroll right past last visible col
+    vr.scrollRight(true);
+    assertEquals(vr.getStartRes(), 14);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testScrollToWrappedVisible()
+  {
+    AlignmentI al2 = gen.generate(60, 30, 1, 5, 5);
+
+    ViewportRanges vr = new ViewportRanges(al2);
+
+    // start with viewport on 5-14
     vr.setViewportStartAndWidth(5, 10);
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 14);
 
-    vr.scrollToWrappedVisible(0);
+    // scroll to 12 - no change
+    assertFalse(vr.scrollToWrappedVisible(12));
+    assertEquals(vr.getStartRes(), 5);
+
+    // scroll to 2 - back to 0-9
+    assertTrue(vr.scrollToWrappedVisible(2));
     assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 9);
 
-    vr.scrollToWrappedVisible(10);
-    assertEquals(vr.getStartRes(), 10);
+    // scroll to 9 - no change
+    assertFalse(vr.scrollToWrappedVisible(9));
+    assertEquals(vr.getStartRes(), 0);
 
-    vr.scrollToWrappedVisible(15);
+    // scroll to 12 - moves to 10-19
+    assertTrue(vr.scrollToWrappedVisible(12));
     assertEquals(vr.getStartRes(), 10);
+    assertEquals(vr.getEndRes(), 19);
+
+    vr.setStartRes(13);
+    assertEquals(vr.getStartRes(), 13);
+    assertEquals(vr.getEndRes(), 22);
+
+    // scroll to 45 - jumps to 43-52
+    assertTrue(vr.scrollToWrappedVisible(45));
+    assertEquals(vr.getStartRes(), 43);
+    assertEquals(vr.getEndRes(), 52);
   }
 
-  // leave until JAL-2388 is merged and we can do without viewport
-  /*@Test(groups = { "Functional" })
+  @Test(groups = { "Functional" })
   public void testScrollToVisible()
   {
     ViewportRanges vr = new ViewportRanges(al);
     vr.setViewportStartAndWidth(12,5);
     vr.setViewportStartAndHeight(10,6);
-    vr.scrollToVisible(13,14)
+    vr.scrollToVisible(13, 14);
     
     // no change
     assertEquals(vr.getStartRes(), 12);
@@ -289,14 +419,22 @@ public class ViewportRangesTest {
     assertEquals(vr.getStartSeq(), 6);
     
     // test for hidden columns too
-  }*/
+    al.getHiddenColumns().hideColumns(1, 3);
+    vr.scrollToVisible(13, 3);
+    assertEquals(vr.getStartRes(), 6);
+    assertEquals(vr.getStartSeq(), 3);
+
+    vr.scrollToVisible(2, 9);
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getStartSeq(), 4);
+  }
 
   @Test(groups = { "Functional" })
   public void testEventFiring()
   {
     ViewportRanges vr = new ViewportRanges(al);
     MockPropChangeListener l = new MockPropChangeListener(vr);
-    List<String> emptylist = new ArrayList<String>();
+    List<String> emptylist = new ArrayList<>();
 
     vr.setViewportWidth(5);
     vr.setViewportHeight(5);
@@ -304,7 +442,7 @@ public class ViewportRangesTest {
 
     // one event fired when startRes is called with new value
     vr.setStartRes(4);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRES)));
     l.reset();
 
     // no event fired for same value
@@ -312,17 +450,8 @@ public class ViewportRangesTest {
     assertTrue(l.verify(0, emptylist));
     l.reset();
 
-    vr.setEndRes(10);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
-    l.reset();
-
-    // no event fired for same value
-    vr.setEndRes(10);
-    assertTrue(l.verify(0, emptylist));
-    l.reset();
-
     vr.setStartSeq(4);
-    assertTrue(l.verify(1, Arrays.asList("startseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ)));
     l.reset();
 
     vr.setStartSeq(4);
@@ -330,7 +459,7 @@ public class ViewportRangesTest {
     l.reset();
 
     vr.setEndSeq(10);
-    assertTrue(l.verify(1, Arrays.asList("startseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ)));
     l.reset();
 
     vr.setEndSeq(10);
@@ -338,7 +467,7 @@ public class ViewportRangesTest {
     l.reset();
 
     vr.setStartEndRes(2, 15);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRES)));
     l.reset();
 
     vr.setStartEndRes(2, 15);
@@ -347,16 +476,18 @@ public class ViewportRangesTest {
 
     // check new value fired by event is corrected startres
     vr.setStartEndRes(-1, 5);
-    assertTrue(l.verify(1, Arrays.asList("startres"), Arrays.asList(0)));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRES),
+            Arrays.asList(0)));
     l.reset();
 
     // check new value fired by event is corrected endres
     vr.setStartEndRes(0, -1);
-    assertTrue(l.verify(1, Arrays.asList("endres"), Arrays.asList(0)));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.ENDRES),
+            Arrays.asList(0)));
     l.reset();
 
     vr.setStartEndSeq(2, 15);
-    assertTrue(l.verify(1, Arrays.asList("startseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ)));
     l.reset();
 
     vr.setStartEndSeq(2, 15);
@@ -369,12 +500,14 @@ public class ViewportRangesTest {
 
     // check new value fired by event is corrected startseq
     vr.setStartEndSeq(-1, 5);
-    assertTrue(l.verify(1, Arrays.asList("startseq"), Arrays.asList(0)));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ),
+            Arrays.asList(0)));
     l.reset();
 
     // check new value fired by event is corrected endseq
     vr.setStartEndSeq(0, -1);
-    assertTrue(l.verify(1, Arrays.asList("endseq"), Arrays.asList(0)));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.ENDSEQ),
+            Arrays.asList(0)));
     l.reset();
 
     // reset for later tests
@@ -383,57 +516,419 @@ public class ViewportRangesTest {
 
     // test viewport height and width setting triggers event
     vr.setViewportHeight(10);
-    assertTrue(l.verify(1, Arrays.asList("endseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.ENDSEQ)));
     l.reset();
 
     vr.setViewportWidth(18);
-    assertTrue(l.verify(1, Arrays.asList("endres")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.ENDRES)));
     l.reset();
 
     // already has seq start set to 2, so triggers endseq
     vr.setViewportStartAndHeight(2, 16);
-    assertTrue(l.verify(1, Arrays.asList("endseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.ENDSEQ)));
     l.reset();
 
     vr.setViewportStartAndWidth(1, 14);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRES)));
     l.reset();
 
     // test page up/down triggers event
     vr.pageUp();
-    assertTrue(l.verify(1, Arrays.asList("startseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ)));
     l.reset();
 
     vr.pageDown();
-    assertTrue(l.verify(1, Arrays.asList("startseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ)));
     l.reset();
 
     // test scrolling triggers event
     vr.scrollUp(true);
-    assertTrue(l.verify(1, Arrays.asList("startseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ)));
     l.reset();
 
     vr.scrollUp(false);
-    assertTrue(l.verify(1, Arrays.asList("startseq")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTSEQ)));
     l.reset();
 
     vr.scrollRight(true);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRES)));
     l.reset();
 
     vr.scrollRight(false);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRES)));
     l.reset();
 
-    // TODO test scrollToVisibble once hidden columns JAL-2388 merged in
-    // to avoid somersaults with align viewport
-    /*vr.scrollToVisible(10, 10);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
-    l.reset();*/
+    vr.scrollToVisible(10, 10);
+    assertTrue(l.verify(4,
+            Arrays.asList(ViewportRanges.STARTSEQ, ViewportRanges.STARTSEQ,
+                    ViewportRanges.STARTSEQ, ViewportRanges.STARTSEQ)));
+    l.reset();
 
-    vr.scrollToWrappedVisible(5);
-    assertTrue(l.verify(1, Arrays.asList("startres")));
+    /*
+     * scrollToWrappedVisible does nothing if the target position is
+     * within the current startRes-endRes range
+     */
+    assertFalse(vr.scrollToWrappedVisible(5));
+    assertTrue(l.verify(0, Collections.<String> emptyList()));
     l.reset();
+
+    vr.scrollToWrappedVisible(25);
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRES)));
+    l.reset();
+
+    // test setStartResAndSeq triggers one event
+    vr.setStartResAndSeq(5, 7);
+    assertTrue(l.verify(1, Arrays.asList(ViewportRanges.STARTRESANDSEQ),
+            Arrays.asList(5, 7)));
+
+    l.reset();
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetWrappedScrollPosition()
+  {
+    AlignmentI al2 = gen.generate(157, 15, 1, 5, 5);
+    ViewportRanges vr = new ViewportRanges(al2);
+    vr.setStartEndRes(0, 39);
+    int width = vr.getViewportWidth(); // 40
+
+    /*
+     * scroll is 0 at column 0 (only)
+     */
+    assertEquals(vr.getWrappedScrollPosition(0), 0);
+
+    /*
+     * scroll is 1 at columns 1-40
+     */
+    int i = 1;
+    int j = width;
+    for (; i <= j; i++)
+    {
+      assertEquals(1, vr.getWrappedScrollPosition(i));
+    }
+
+    /*
+     * scroll is 2 at columns 41-80, etc
+     */
+    j += width;
+    for (; i <= j; i++)
+    {
+      assertEquals(2, vr.getWrappedScrollPosition(i), "For " + i);
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testPageUpDownWrapped()
+  {
+    /*
+     * 15 sequences, 110 residues wide (+gaps)
+     */
+    AlignmentI al2 = gen.generate(110, 15, 1, 5, 5);
+
+    ViewportRanges vr = new ViewportRanges(al2);
+    vr.setWrappedMode(true);
+
+    // first row
+    vr.setViewportStartAndWidth(0, 40);
+    int width = vr.getViewportWidth();
+    assertEquals(width, 40);
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 39);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), 14);
+
+    // second row
+    vr.pageDown();
+    assertEquals(vr.getStartRes(), 40);
+    assertEquals(vr.getEndRes(), 79);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), 14);
+
+    // third and last row
+    // note endRes is nominal (>width) to preserve viewport width
+    vr.pageDown();
+    assertEquals(vr.getStartRes(), 80);
+    assertEquals(vr.getEndRes(), 119);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), 14);
+
+    // another pageDown should do nothing
+    vr.pageDown();
+    assertEquals(vr.getStartRes(), 80);
+    assertEquals(vr.getEndRes(), 119);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), 14);
+
+    // back to second row
+    vr.pageUp();
+    assertEquals(vr.getStartRes(), 40);
+    assertEquals(vr.getEndRes(), 79);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), 14);
+
+    // back to first row
+    vr.pageUp();
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 39);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), 14);
+
+    // another pageUp should do nothing
+    vr.pageUp();
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 39);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), 14);
+
+    /*
+     * simulate scroll right a few positions
+     */
+    vr.setStartRes(5);
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 5 + width - 1); // 44
+
+    vr.pageDown(); // 5-44 shifts to 45-84
+    assertEquals(vr.getStartRes(), 45);
+    assertEquals(vr.getEndRes(), 84);
+
+    vr.pageDown(); // 45-84 shifts to 85-124
+    assertEquals(vr.getStartRes(), 85);
+    assertEquals(vr.getEndRes(), 124);
+
+    vr.pageDown(); // no change - at end already
+    assertEquals(vr.getStartRes(), 85);
+    assertEquals(vr.getEndRes(), 124);
+
+    vr.pageUp(); // back we go
+    assertEquals(vr.getStartRes(), 45);
+    assertEquals(vr.getEndRes(), 84);
+
+    vr.pageUp();
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 44);
+
+    vr.pageUp(); // back to the start
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 39);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetStartEndResWrapped()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    vr.setWrappedMode(true);
+    vr.setStartEndRes(-1, -1);
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 0);
+  
+    vr.setStartEndRes(5, 19);
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 19);
+  
+    // bounds are not constrained to alignment width
+    // when in wrapped mode
+    vr.setStartEndRes(88, 888);
+    assertEquals(vr.getStartRes(), 88);
+    assertEquals(vr.getEndRes(), 888);
+  
+    ViewportRanges vrsmall = new ViewportRanges(smallAl);
+    vrsmall.setWrappedMode(true);
+    vrsmall.setStartEndRes(88, 888);
+    assertEquals(vrsmall.getStartRes(), 88);
+    assertEquals(vrsmall.getEndRes(), 888);
+  
+    // make visible alignment width = 0
+    smallAl.getHiddenColumns().hideColumns(0, 6);
+    vrsmall.setStartEndRes(0, 4);
+    assertEquals(vrsmall.getStartRes(), 0);
+    assertEquals(vrsmall.getEndRes(), 4);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetViewportStartAndWidthWrapped()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    vr.setWrappedMode(true);
+    vr.setViewportStartAndWidth(2, 6);
+    assertEquals(vr.getViewportWidth(), 6);
+    assertEquals(vr.getStartRes(), 2);
+  
+    // reset -ve values of start to 0
+    vr.setViewportStartAndWidth(-1, 7);
+    assertEquals(vr.getViewportWidth(), 7);
+    assertEquals(vr.getStartRes(), 0);
+  
+    // out of bounds values are not forced to within bounds
+    vr.setViewportStartAndWidth(35, 5);
+    assertEquals(vr.getViewportWidth(), 5);
+    assertEquals(vr.getStartRes(), 35);
+  
+    // small alignment doesn't get bounds reset
+    ViewportRanges vrsmall = new ViewportRanges(smallAl);
+    vrsmall.setViewportStartAndWidth(0, 63);
+    assertEquals(vrsmall.getViewportWidth(), 7);
+    assertEquals(vrsmall.getStartRes(), 0);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetWrappedMaxScroll()
+  {
+    // generate an ungapped alignment of width 140
+    int alignmentWidth = 140;
+    AlignmentI al2 = gen.generate(alignmentWidth, 15, 1, 0, 5);
+    ViewportRanges vr = new ViewportRanges(al2);
+    vr.setStartEndRes(0, 39);
+    int width = vr.getViewportWidth(); // 40
+    int partWidth = alignmentWidth % width; // 20
+  
+    /*
+     * there are 3 * 40 remainder 20 residues
+     * number of widths depends on offset (scroll right)
+     * 4 widths (maxScroll = 3) if offset by 0 or more than 19 columns
+     * 5 widths (maxScroll = 4) if 1 <= offset <= 19
+     */
+    for (int col = 0; col < alignmentWidth; col++)
+    {
+      int offset = col % width;
+      if (offset > 0 && offset < partWidth)
+      {
+        assertEquals(vr.getWrappedMaxScroll(col), 4, "col " + col);
+      }
+      else
+      {
+        assertEquals(vr.getWrappedMaxScroll(col), 3, "col " + col);
+      }
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testScrollUp_wrapped()
+  {
+    /*
+     * alignment 30 tall and 45 wide
+     */
+    AlignmentI al2 = gen.generate(45, 30, 1, 0, 5);
+
+    /*
+     * wrapped view, 5 sequences high, start at sequence offset 1
+     */
+    ViewportRanges vr = new ViewportRanges(al2);
+    vr.setWrappedMode(true);
+    vr.setViewportStartAndHeight(1, 5);
+
+    /*
+     * offset wrapped view to column 3
+     */
+    vr.setStartEndRes(3, 22);
+
+    int startRes = vr.getStartRes();
+    int width = vr.getViewportWidth();
+    assertEquals(startRes, 3);
+    assertEquals(width, 20);
+
+    // in wrapped mode, we change startRes but not startSeq
+    // scroll down:
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 1);
+    assertEquals(vr.getStartRes(), 23);
+
+    // scroll up returns to original position
+    vr.scrollUp(true);
+    assertEquals(vr.getStartSeq(), 1);
+    assertEquals(vr.getStartRes(), 3);
+
+    // scroll up again returns to 'origin'
+    vr.scrollUp(true);
+    assertEquals(vr.getStartSeq(), 1);
+    assertEquals(vr.getStartRes(), 0);
+
+    /*
+     * offset 3 columns once more and do some scroll downs
+     */
+    vr.setStartEndRes(3, 22);
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 1);
+    assertEquals(vr.getStartRes(), 23);
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 1);
+    assertEquals(vr.getStartRes(), 43);
+
+    /*
+     * scroll down beyond end of alignment does nothing
+     */
+    vr.scrollUp(false);
+    assertEquals(vr.getStartSeq(), 1);
+    assertEquals(vr.getStartRes(), 43);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetViewportLocation()
+  {
+    AlignmentI al2 = gen.generate(60, 80, 1, 0, 0);
+
+    ViewportRanges vr = new ViewportRanges(al2);
+
+    // start with viewport on 5-14
+    vr.setViewportStartAndWidth(5, 10);
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 14);
+
+    vr.setViewportStartAndHeight(3, 13);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // set location to (8,5) - no change
+    vr.setViewportLocation(8, 5);
+    assertEquals(vr.getStartRes(), 5);
+    assertEquals(vr.getEndRes(), 14);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // set location to (40,50) - change to top left (40,50)
+    vr.setViewportLocation(40, 50);
+    assertEquals(vr.getStartRes(), 40);
+    assertEquals(vr.getEndRes(), 49);
+    assertEquals(vr.getStartSeq(), 50);
+    assertEquals(vr.getEndSeq(), 62);
+
+    // set location past end of alignment - resets to leftmost pos
+    vr.setViewportLocation(63, 85);
+    assertEquals(vr.getStartRes(), 50);
+    assertEquals(vr.getEndRes(), 59);
+    assertEquals(vr.getStartSeq(), 67);
+    assertEquals(vr.getEndSeq(), 79);
+
+    // hide some columns
+    al2.getHiddenColumns().hideColumns(20, 50);
+    vr.setViewportLocation(55, 4);
+    assertEquals(vr.getStartRes(), 19);
+    assertEquals(vr.getEndRes(), 28);
+    assertEquals(vr.getStartSeq(), 4);
+    assertEquals(vr.getEndSeq(), 16);
+
+    // hide some sequences
+    al2.getHiddenSequences().hideSequence(al2.getSequenceAt(3));
+    al2.getHiddenSequences().hideSequence(al2.getSequenceAt(4));
+    vr.setViewportLocation(17, 5);
+    assertEquals(vr.getStartRes(), 17);
+    assertEquals(vr.getEndRes(), 26);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // set wrapped mode
+    vr.setWrappedMode(true);
+    vr.setViewportLocation(1, 8);
+    assertEquals(vr.getStartRes(), 0);
+    assertEquals(vr.getEndRes(), 9);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
+
+    // try further down the alignment
+    vr.setViewportLocation(57, 5);
+    assertEquals(vr.getStartRes(), 20);
+    assertEquals(vr.getEndRes(), 29);
+    assertEquals(vr.getStartSeq(), 3);
+    assertEquals(vr.getEndSeq(), 15);
   }
 }
 
@@ -442,9 +937,9 @@ class MockPropChangeListener implements ViewportListenerI
 {
   private int firecount = 0;
 
-  private List<String> events = new ArrayList<String>();
+  private List<String> events = new ArrayList<>();
 
-  private List<Integer> newvalues = new ArrayList<Integer>();
+  private List<Integer> newvalues = new ArrayList<>();
 
   public MockPropChangeListener(ViewportRanges vr)
   {
@@ -456,7 +951,15 @@ class MockPropChangeListener implements ViewportListenerI
   {
     firecount++;
     events.add(evt.getPropertyName());
-    newvalues.add((Integer) evt.getNewValue());
+    if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
+    {
+      newvalues.add(((int[]) evt.getNewValue())[0]);
+      newvalues.add(((int[]) evt.getNewValue())[1]);
+    }
+    else
+    {
+      newvalues.add((Integer) evt.getNewValue());
+    }
   }
 
   public boolean verify(int count, List<String> eventslist,