X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fviewmodel%2FOverviewDimensionsShowHiddenTest.java;h=b890e48352f8c640d9439d3a46d74270a51177b2;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=8297159e2f6bf770872f9f736cc4b21a95967812;hpb=460c037bef9ec113c2a46010c443d85e73347592;p=jalview.git

diff --git a/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java b/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
index 8297159..b890e48 100644
--- a/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
@@ -21,6 +21,8 @@
 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.Alignment;
@@ -43,19 +45,25 @@ import org.testng.annotations.Test;
 public class OverviewDimensionsShowHiddenTest
 {
   AlignmentI al;
+
   OverviewDimensionsShowHidden od;
 
   // cached widths and heights
   int boxWidth;
+
   int boxHeight;
+
   int viewHeight;
+
   int viewWidth;
+
   int alheight;
+
   int alwidth;
 
   ViewportRanges vpranges;
 
-  Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+  Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
 
   HiddenColumns hiddenCols = new HiddenColumns();
 
@@ -76,12 +84,10 @@ public class OverviewDimensionsShowHiddenTest
     }
     ColumnSelection colsel = new ColumnSelection();
     hiddenCols.revealAllHiddenColumns(colsel);
-    
+
     vpranges = new ViewportRanges(al);
-    vpranges.setStartRes(0);
-    vpranges.setEndRes(62);
-    vpranges.setStartSeq(0);
-    vpranges.setEndSeq(17);
+    vpranges.setViewportStartAndHeight(0, 18);
+    vpranges.setViewportStartAndWidth(0, 63);
 
     viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
     viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
@@ -99,12 +105,12 @@ public class OverviewDimensionsShowHiddenTest
     alheight = vpranges.getAbsoluteAlignmentHeight();
     alwidth = vpranges.getAbsoluteAlignmentWidth();
 
-    boxWidth = Math.round((float) (vpranges.getEndRes()
-            - vpranges.getStartRes() + 1)
-            * od.getWidth() / alwidth);
-    boxHeight = Math.round((float) (vpranges.getEndSeq()
-            - vpranges.getStartSeq() + 1)
-            * od.getSequencesHeight() / alheight);
+    boxWidth = Math.round(
+            (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+                    * od.getWidth() / alwidth);
+    boxHeight = Math.round(
+            (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+                    * od.getSequencesHeight() / alheight);
   }
 
   @AfterClass(alwaysRun = true)
@@ -203,89 +209,85 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // negative boxX value reset to 0
     mouseClick(od, -5, 10);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollRow(),
+    assertEquals(vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
             Math.round((float) 10 * alheight / od.getSequencesHeight()));
-    assertEquals(od.getScrollCol(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
 
     // negative boxY value reset to 0
     mouseClick(od, 6, -2);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
-            Math.round((float) 6 * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // overly large boxX value reset to width-boxWidth
-    mouseClick(od, 100, 6);
+    mouseClick(od, 101, 6);
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
-    assertEquals(od.getBoxY(), 6);
+    assertEquals(od.getBoxY(), 1);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(),
-            Math.round((float) od.getBoxY() * alheight
-                    / od.getSequencesHeight()));
+    assertEquals(vpranges.getStartSeq(), Math.round(
+            (float) od.getBoxY() * alheight / od.getSequencesHeight()));
 
     // overly large boxY value reset to sequenceHeight - boxHeight
     mouseClick(od, 10, 520);
-    assertEquals(od.getBoxX(), 10);
+    assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(0,
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
 
     // here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
     // and round rounds to 508; however we get 507 working with row values
     // hence the subtraction of 1
-    assertEquals(od.getScrollRow(),
-            Math.round((float) od.getBoxY() * alheight
-                    / od.getSequencesHeight()) - 1);
+    assertEquals(vpranges.getStartSeq(), Math.round(
+            (float) od.getBoxY() * alheight / od.getSequencesHeight()) - 1);
 
     // click past end of alignment, as above
     mouseClick(od, 3000, 5);
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(),
-            Math.round((float) od.getBoxY() * alheight
-                    / od.getSequencesHeight()));
+    assertEquals(vpranges.getStartSeq(), Math.round(
+            (float) od.getBoxY() * alheight / od.getSequencesHeight()));
 
     // move viewport so startRes non-zero and then mouseclick
-    moveViewportH(50);
+    moveViewportH(20);
 
     // click at viewport position
     int oldboxx = od.getBoxX();
     int oldboxy = od.getBoxY();
-    mouseClick(od, od.getBoxX() + 5, od.getBoxY() + 2);
-    assertEquals(od.getBoxX(), oldboxx + 5);
+    mouseClick(od, od.getBoxX() + od.getBoxWidth() / 2 + 6,
+            od.getBoxY() + od.getBoxHeight() / 2 + 3);
+    assertEquals(od.getBoxX(), oldboxx + 6);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getBoxY(), oldboxy + 2);
-    assertEquals(od.getScrollRow(),
-            Math.round((float) od.getBoxY() * alheight
-                    / od.getSequencesHeight()));
+    assertEquals(od.getBoxY(), oldboxy + 3);
+    assertEquals(vpranges.getStartSeq(), Math.round(
+            (float) od.getBoxY() * alheight / od.getSequencesHeight()));
 
     // click at top corner
     mouseClick(od, 0, 0);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getScrollCol(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
   }
@@ -301,8 +303,8 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide cols at start and check updated box position is correct
     // changes boxX but not boxwidth
@@ -310,30 +312,31 @@ public class OverviewDimensionsShowHiddenTest
     hiddenCols.hideColumns(0, lastHiddenCol);
 
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
-    assertEquals(od.getBoxX(),
-            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
-                    / alwidth));
+    assertEquals(od.getBoxX(), Math
+            .round((float) (lastHiddenCol + 1) * od.getWidth() / alwidth));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // try to click in hidden cols, check box does not move
     int xpos = 10;
     mouseClick(od, xpos, 0);
-    assertEquals(
-            od.getBoxX(),
-            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
-                    / alwidth));
+    assertEquals(od.getBoxX(), Math
+            .round((float) (lastHiddenCol + 1) * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
 
     // click to right of hidden columns, box moves to click point
-    testBoxIsAtClickPoint(40, 0);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(),
-            Math.round((float) 40 * alwidth / od.getWidth())
+    mouseClick(od, 60 + boxWidth / 2, boxHeight / 2);
+    assertEquals(od.getBoxX(), 60);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartRes(),
+            Math.round((float) 60 * alwidth / od.getWidth())
                     - (lastHiddenCol + 1));
 
     // click to right of hidden columns such that box runs over right hand side
@@ -341,17 +344,16 @@ public class OverviewDimensionsShowHiddenTest
     // box position is adjusted away from the edge
     // overly large boxX value reset to width-boxWidth
     xpos = 100;
-    mouseClick(od, xpos, 5);
+    mouseClick(od, xpos + boxWidth / 2, 5 + boxHeight / 2);
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 5);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth())
                     - (lastHiddenCol + 1));
-    assertEquals(od.getScrollRow(),
-            Math.round((float) od.getBoxY() * alheight
-                    / od.getSequencesHeight()));
+    assertEquals(vpranges.getStartSeq(), Math.round(
+            (float) od.getBoxY() * alheight / od.getSequencesHeight()));
   }
 
   /**
@@ -365,9 +367,9 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
-    
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
+
     // hide columns 63-73, no change to box position or dimensions
     int firstHidden = 63;
     int lastHidden = 73;
@@ -377,81 +379,65 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // move box so that it overlaps with hidden cols on one side
     // box width changes, boxX and scrollCol as for unhidden case
-    int xpos = 55 - boxWidth; // 55 is position in overview approx halfway
-                              // between cols 60 and 70
-    mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(), xpos);
+    int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
+    // between cols 60 and 70
+    mouseClick(od, xpos, boxHeight / 2);
+    assertEquals(od.getBoxX(), xpos - boxWidth / 2);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(
-            od.getBoxWidth(),
+    assertEquals(od.getBoxWidth(),
             Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
                     * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
-            Math.round(xpos * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(),
+            Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth())
+                    + 1); // +1 for rounding
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // move box so that it completely covers hidden cols
     // box width changes, boxX and scrollCol as for hidden case
-    xpos = 33;
+    xpos = 24 + boxWidth / 2;
     mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxX(), 24);
     assertEquals(od.getBoxY(), 0);
-    assertEquals(
-            od.getBoxWidth(),
+    assertEquals(od.getBoxWidth(),
             Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
                     * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
-            Math.round((float) xpos * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
-
-    // move box so boxX is in hidden cols, box overhangs at right
-    // boxX and scrollCol at left of hidden area, box width extends across
-    // hidden region
-    xpos = 50;
-    mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(),
-            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth));
-    assertEquals(od.getBoxY(), 0);
-    assertEquals(
-            od.getBoxWidth(),
-            boxWidth
-                    + Math.round((float) (lastHidden - firstHidden + 1)
-                            * od.getWidth() / alwidth));
-    assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), firstHidden - 1);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(),
+            Math.round((float) 24 * alwidth / od.getWidth()));
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // move box so boxX is to right of hidden cols, but does not go beyond full
     // width of alignment
     // box width, boxX and scrollCol all as for non-hidden case
-    xpos = 75;
-    testBoxIsAtClickPoint(xpos, 0);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(),
-            Math.round(xpos * alwidth / od.getWidth())
-                    - (lastHidden - firstHidden + 1));
-    
+    xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
+    mouseClick(od, xpos, boxHeight / 2);
+    assertEquals(od.getBoxX(), xpos - boxWidth / 2);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(vpranges.getStartSeq(), 0);
+    assertEquals(vpranges.getStartRes(),
+            75 - (lastHidden - firstHidden + 1));
+
     // move box so it goes beyond full width of alignment
     // boxX, scrollCol adjusted back, box width normal
     xpos = 3000;
     mouseClick(od, xpos, 5);
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
-    assertEquals(od.getBoxY(), 5);
+    assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
                     - (lastHidden - firstHidden + 1)));
-    assertEquals(od.getScrollRow(),
-            Math.round((float) od.getBoxY() * alheight
-                    / od.getSequencesHeight()));
+    assertEquals(vpranges.getStartSeq(), Math.round(
+            (float) od.getBoxY() * alheight / od.getSequencesHeight()));
 
   }
 
@@ -466,8 +452,8 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide columns 140-164, no change to box position or dimensions
     int firstHidden = 140;
@@ -477,30 +463,32 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // click to left of hidden cols, without overlapping
     // boxX, scrollCol and width as normal
-    int xpos = 5;
-    testBoxIsAtClickPoint(xpos, 0);
-    assertEquals(od.getScrollRow(), 0);
-    assertEquals(od.getScrollCol(),
-            Math.round((float) xpos * alwidth / od.getWidth()));
+    int xpos = 30;
+    int ypos = 6;
+    testBoxIsAtClickPoint(xpos, ypos);
+    assertEquals(vpranges.getStartSeq(), Math.round(
+            (float) (ypos - boxHeight / 2) * alheight / od.getHeight()));
+    assertEquals(vpranges.getStartRes(), Math.round(
+            (float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
 
     // click to left of hidden cols, with overlap
     // boxX and scrollCol adjusted for hidden cols, width normal
     xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
-    mouseClick(od, xpos, 0);
+    mouseClick(od, xpos + boxWidth / 2, boxHeight / 2);
     assertEquals(od.getBoxX(),
             Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
                     - boxWidth + 1);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
-            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(),
+            Math.round((float) (od.getBoxX()) * alwidth / od.getWidth()));
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // click in hidden cols
     // boxX and scrollCol adjusted for hidden cols, width normal
@@ -511,9 +499,9 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // click off end of alignment
     // boxX and scrollCol adjusted for hidden cols, width normal
@@ -524,9 +512,9 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
   }
 
   /**
@@ -624,11 +612,9 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(),
             Math.round((float) 10 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(
-            od.getBoxWidth(),
-            boxWidth
-                    + Math.round((float) (lastHidden - firstHidden + 1)
-                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxWidth(),
+            boxWidth + Math.round((float) (lastHidden - firstHidden + 1)
+                    * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to straddle hidden columns
@@ -636,11 +622,8 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(),
             Math.round((float) 63 * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
-    assertEquals(
-            od.getBoxWidth(),
-            boxWidth
-                    + Math.round((lastHidden - firstHidden + 1)
-                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxWidth(), boxWidth + Math.round(
+            (lastHidden - firstHidden + 1) * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to right of hidden columns, no overlap
@@ -676,9 +659,8 @@ public class OverviewDimensionsShowHiddenTest
     // viewport can't actually extend into hidden cols,
     // so move to the far right edge of the viewport
     moveViewport(firstHidden - viewWidth, 0);
-    assertEquals(od.getBoxX(),
-            Math.round((float) (firstHidden - viewWidth)
-                    * od.getWidth() / alwidth));
+    assertEquals(od.getBoxX(), Math.round(
+            (float) (firstHidden - viewWidth) * od.getWidth() / alwidth));
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
@@ -699,19 +681,16 @@ public class OverviewDimensionsShowHiddenTest
     // box moves to below hidden rows, height remains same
     moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(),
-            Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
-                    / alheight));
+    assertEquals(od.getBoxY(), Math.round(
+            (float) (lastHidden + 1) * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to end of alignment
     moveViewport(0, 525 - viewHeight - lastHidden - 1);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(
-            od.getBoxY(),
-            Math.round((float) (525 - viewHeight) * od.getSequencesHeight()
-                    / alheight));
+    assertEquals(od.getBoxY(), Math.round((float) (525 - viewHeight)
+            * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
   }
@@ -738,11 +717,10 @@ public class OverviewDimensionsShowHiddenTest
     // move viewport to straddle hidden rows
     moveViewport(0, 198);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
-            / alheight));
+    assertEquals(od.getBoxY(),
+            Math.round((float) 198 * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(
-            od.getBoxHeight(),
+    assertEquals(od.getBoxHeight(),
             Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
                     * od.getSequencesHeight() / alheight));
   }
@@ -770,8 +748,7 @@ public class OverviewDimensionsShowHiddenTest
     // viewport sits above hidden rows and does not include them
     moveViewport(0, firstHidden - viewHeight - 1);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(
-            od.getBoxY(),
+    assertEquals(od.getBoxY(),
             Math.round((float) (firstHidden - viewHeight - 1)
                     * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -791,8 +768,8 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide rows at start and check updated box position is correct
     // changes boxY but not boxheight
@@ -801,24 +778,21 @@ public class OverviewDimensionsShowHiddenTest
 
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(),
-            Math.round((float) (lastHiddenRow + 1)
-                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
+            * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // click in hidden rows - same result
     mouseClick(od, 0, 0);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(
-            od.getBoxY(),
-            Math.round((float) (lastHiddenRow + 1)
-                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
+            * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // click below hidden rows
-    mouseClick(od, 0, 150);
+    mouseClick(od, 0, 150 + boxHeight / 2);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 150);
     assertEquals(od.getBoxWidth(), boxWidth);
@@ -838,8 +812,8 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide rows in middle and check updated box position is correct
     // no changes
@@ -855,31 +829,17 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // click above hidden rows, so that box overlaps
-    int ypos = 35; // column value in residues
-    mouseClick(od, 0,
-            Math.round((float) ypos * od.getSequencesHeight() / alheight));
-    assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(),
-            Math.round((float) ypos * od.getSequencesHeight() / alheight));
-    assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(
-            od.getBoxHeight(),
-            boxHeight
-                    + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
-                            * od.getSequencesHeight() / alheight));
-
-    // click so that box straddles hidden rows
-    ypos = 44; // column value in residues
-    mouseClick(od, 0,
-            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    int rowpos = 35; // row value in residues
+    int centrepos = 43; // centre row
+    mouseClick(od, 0, Math
+            .round((float) centrepos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(),
-            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxY(), Math
+            .round((float) rowpos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(
-            od.getBoxHeight(),
-            boxHeight
-                    + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+    assertEquals(od.getBoxHeight(),
+            boxHeight + Math
+                    .round((float) (lastHiddenRow - firstHiddenRow + 1)
                             * od.getSequencesHeight() / alheight));
   }
 
@@ -895,8 +855,8 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(), 0);
-    assertEquals(od.getScrollRow(), 0);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
 
     // hide rows at end and check updated box position is correct
     // no changes
@@ -910,49 +870,143 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
-    // click above hidden rows
-    int ypos = 40; // row 40
+    // click above hidden rows, no overlap
+    int ypos = 40 + viewHeight / 2; // top is row 40
     mouseClick(od, 0,
             Math.round((float) ypos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
-            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+            Math.round((float) 40 * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // click above hidden rows so box overlaps
     // boxY moved upwards, boxHeight remains same
-    ypos = 497; // row 497
+    ypos = 497 + viewHeight / 2; // row 497
     mouseClick(od, 0,
             Math.round((float) ypos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxX(), 0);
-    assertEquals(
-            od.getBoxY(),
-            Math.round((float) (firstHidden - viewHeight)
-                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxY(), Math.round((float) (firstHidden - viewHeight)
+            * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // click within hidden rows
-    ypos = 505;
+    ypos = 505 + boxHeight / 2;
     mouseClick(od, 0,
             Math.round((float) ypos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxX(), 0);
-    assertEquals(
-            od.getBoxY(),
-            Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
-                    / alheight));
+    assertEquals(od.getBoxY(), Math.round((firstHidden - viewHeight)
+            * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
   }
 
+  /**
+   * Test the function to determine if a point is in the overview's box or not
+   */
+  @Test(groups = { "Functional" })
+  public void testPositionInBox()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+
+    assertFalse(od.isPositionInBox(0, 0));
+    assertTrue(od.isPositionInBox(10, 9));
+    assertFalse(od.isPositionInBox(0, 9));
+    assertFalse(od.isPositionInBox(9, 0));
+    assertFalse(od.isPositionInBox(75, 20));
+
+    assertTrue(od.isPositionInBox(47, 6));
+    assertFalse(od.isPositionInBox(48, 6));
+    assertTrue(od.isPositionInBox(47, 9));
+    assertFalse(od.isPositionInBox(47, 10));
+
+    // hide columns in the box area
+    // extends area where a point is considered to be in the box
+    hiddenCols.hideColumns(1, 4);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+    assertFalse(od.isPositionInBox(0, 0));
+    assertTrue(od.isPositionInBox(10, 9));
+    assertFalse(od.isPositionInBox(0, 9));
+    assertFalse(od.isPositionInBox(9, 0));
+    assertFalse(od.isPositionInBox(75, 20));
+
+    assertTrue(od.isPositionInBox(47, 6));
+    assertTrue(od.isPositionInBox(48, 6));
+    assertTrue(od.isPositionInBox(47, 9));
+    assertFalse(od.isPositionInBox(47, 10));
+
+    // hide sequences in box area
+    // extends area where a point is considered to be in the box
+    hideSequences(1, 3);
+    ColumnSelection cs = new ColumnSelection();
+    hiddenCols.revealAllHiddenColumns(cs);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+    assertFalse(od.isPositionInBox(0, 0));
+    assertTrue(od.isPositionInBox(10, 9));
+    assertFalse(od.isPositionInBox(0, 9));
+    assertFalse(od.isPositionInBox(9, 0));
+    assertFalse(od.isPositionInBox(75, 20));
+
+    assertTrue(od.isPositionInBox(47, 6));
+    assertFalse(od.isPositionInBox(48, 6));
+    assertTrue(od.isPositionInBox(47, 9));
+    assertTrue(od.isPositionInBox(47, 10));
+  }
+
+  /**
+   * Test the dragging functionality
+   */
+  @Test(groups = { "Functional" })
+  public void testDragging()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+    od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+    od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+
+    // updates require an OverviewPanel to exist which it doesn't here
+    // so call setBoxPosition() as it would be called by the AlignmentPanel
+    // normally
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+    // corner moves 16 (20-4) right and 6 (22-16) up
+    assertEquals(od.getBoxX(), 16);
+    assertEquals(od.getBoxY(), 6);
+
+    // hide columns - box moves drag distance + hidden cols, vertically makes no
+    // difference
+    hiddenCols.hideColumns(1, 4);
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+    od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+    od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+    // corner moves 16 (20-4) + hiddenCols right and 6 (22-16) down
+    assertEquals(od.getBoxX(),
+            16 + Math.round((float) 4 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 6);
+
+    // hide sequences in box area
+    // makes absolutely no difference
+    hideSequences(1, 3);
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+    od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+    od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+
+    // corner moves 16 (20-4) + hiddenCols right and 6 (22-16) + hiddenRows down
+    assertEquals(od.getBoxX(),
+            16 + Math.round((float) 4 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(),
+            6 + Math.round((float) 3 * od.getHeight() / alheight));
+  }
+
   /*
    * Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
    */
   private void moveViewportH(int startRes)
   {
-    vpranges.setStartRes(startRes);
-    vpranges.setEndRes(startRes + viewWidth - 1);
+    vpranges.setViewportStartAndWidth(startRes, viewWidth);
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
   }
 
@@ -961,8 +1015,7 @@ public class OverviewDimensionsShowHiddenTest
    */
   private void moveViewportV(int startSeq)
   {
-    vpranges.setStartSeq(startSeq);
-    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    vpranges.setViewportStartAndHeight(startSeq, viewHeight);
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
   }
 
@@ -971,40 +1024,33 @@ public class OverviewDimensionsShowHiddenTest
    */
   private void moveViewport(int startRes, int startSeq)
   {
-    vpranges.setStartRes(startRes);
-    vpranges.setEndRes(startRes + viewWidth - 1);
-    vpranges.setStartSeq(startSeq);
-    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    vpranges.setViewportStartAndWidth(startRes, viewWidth);
+    vpranges.setViewportStartAndHeight(startSeq, viewHeight);
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
   }
 
   /*
    * Mouse click as position x,y in overview window
    */
-  private void mouseClick(OverviewDimensionsShowHidden od, int x, int y)
+  private void mouseClick(OverviewDimensions od, int x, int y)
   {
     od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols);
 
     // updates require an OverviewPanel to exist which it doesn't here
     // so call setBoxPosition() as it would be called by the AlignmentPanel
     // normally
-
-    vpranges.setStartRes(od.getScrollCol());
-    vpranges.setEndRes(od.getScrollCol() + viewWidth - 1);
-    vpranges.setStartSeq(od.getScrollRow());
-    vpranges.setEndSeq(od.getScrollRow() + viewHeight - 1);
     od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
   }
-  
+
   /*
-   * Test that the box is positioned with the top left corner at xpos, ypos
+   * Test that the box is positioned with the centre at xpos, ypos
    * and with the original width and height
    */
   private void testBoxIsAtClickPoint(int xpos, int ypos)
   {
     mouseClick(od, xpos, ypos);
-    assertEquals(od.getBoxX(), xpos);
-    assertEquals(od.getBoxY(), ypos);
+    assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
+    assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
@@ -1017,7 +1063,7 @@ public class OverviewDimensionsShowHiddenTest
   {
     SequenceI[] allseqs = al.getSequencesArray();
     SequenceGroup theseSeqs = new SequenceGroup();
-    
+
     for (int i = start; i <= end; i++)
     {
       theseSeqs.addSequence(allseqs[i], false);
@@ -1026,4 +1072,50 @@ public class OverviewDimensionsShowHiddenTest
 
     hiddenRepSequences.put(allseqs[start], theseSeqs);
   }
+
+  /**
+   * Test setting of the box position, when there are hidden rows at the start
+   * of the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenRowsAtStartWrapped()
+  {
+    vpranges.setWrappedMode(true);
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(vpranges.getStartRes(), 0);
+    assertEquals(vpranges.getStartSeq(), 0);
+
+    // hide rows at start and check updated box position is correct
+    // changes boxY but not boxheight
+    int lastHiddenRow = 30;
+    hideSequences(0, lastHiddenRow);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
+            * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click in hidden rows - same result
+    mouseClick(od, 0, 0);
+    assertEquals(od.getBoxX(), 0);
+    int boxY = od.getBoxY();
+    assertEquals(boxY, Math.round((float) (lastHiddenRow + 1)
+            * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click below hidden rows
+    // vertical move of overview box is suppressed in wrapped mode
+    mouseClick(od, 0, 150);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), boxY); // unchanged
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
 }