JAL-2388 Additional unit tests

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 34b7aff..1f18a10 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -193,7 +193,7 @@ public class OverviewDimensions
     int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
 
     // get viewport height in sequences
-    int vpheight = props.getEndSeq() - props.getStartSeq();
+    int vpheight = props.getEndSeq() - props.getStartSeq() + 1;
 
     // get where y should be when accounting for hidden rows
     // if y is in a hidden row region, shift up - but we still need absolute
@@ -211,7 +211,7 @@ public class OverviewDimensions
       // went past the end of the alignment, adjust backwards
       endSeq = alheight;
       // recalc yAsSeq backwards from endSeq
-      yAsSeq = endSeq - vpheight;
+      yAsSeq = endSeq - vpheight + 1;
     }
 
     // convert absolute positions back to visible alignment positions for
@@ -253,7 +253,8 @@ public class OverviewDimensions
     boxWidth = Math
             .round((float) (endRes - startRes + 1) * width / alwidth);
     // boxHeight is the height in sequences translated to pixels
-    boxHeight = Math.round((float) (endSeq - startSeq) * sequencesHeight
+    boxHeight = Math.round((float) (endSeq - startSeq + 1)
+            * sequencesHeight
             / alheight);
   }
 

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index be8154c..d9d7546 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -23,7 +23,6 @@ package jalview.viewmodel;
 import static org.testng.Assert.assertEquals;
 
 import jalview.analysis.AlignmentGenerator;
-import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -70,10 +69,10 @@ public class OverviewDimensionsTest {
 
   AlignFrame af;
   AlignViewport av;
-
   AlignmentI al;
   OverviewDimensions od;
 
+  // cached widths and heights
   int boxWidth;
   int boxHeight;
   int viewHeight;
@@ -98,8 +97,6 @@ public class OverviewDimensionsTest {
     Jalview.main(new String[] { "-nonews", "-props",
         "test/jalview/testProps.jvprops" });
 
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
-            Boolean.TRUE.toString());
     af = new FileLoader().LoadFileWaitTillLoaded(al.toString(),
             DataSourceType.PASTE);
 
@@ -138,11 +135,6 @@ public class OverviewDimensionsTest {
     od.setBoxPosition(av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
 
-    init();
-  }
-
-  private void init()
-  {
     av.showAllHiddenColumns();
     av.showAllHiddenSeqs();
     av.setSelectionGroup(null);
@@ -174,6 +166,7 @@ public class OverviewDimensionsTest {
       try
       {
         Thread.sleep(50);
+        av.getAlignPanel().setScrollValues(0, 0);
         viewHeight = av.getEndSeq() - av.getStartSeq();
         viewWidth = av.getEndRes() - av.getStartRes();
       } catch (InterruptedException e)
@@ -424,17 +417,18 @@ public class OverviewDimensionsTest {
 
     // try to click in hidden cols, check box does not move
     // this test currently fails as the overview box does not behave like this!
-    /*    int xpos = 10;
-        mouseClick(od, xpos, 0);
-        assertEquals(od.getBoxX(),
-                Math.round ((lastHiddenCol + 1) * od.getWidth() / alwidth));
-        assertEquals(od.getBoxY(), 0);
-        assertEquals(od.getBoxWidth(), boxWidth);
-        assertEquals(od.getBoxHeight(), boxHeight);
-        assertEquals(od.getScrollRow(), 0);
-        assertEquals(od.getScrollCol(),
-                Math.round (xpos * alwidth / od.getWidth()));
-    */
+    int xpos = 10;
+    mouseClick(od, xpos, 0);
+    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);
+
     // click to right of hidden columns, box moves to click point
     testBoxIsAtClickPoint(40, 0);
     assertEquals(od.getScrollRow(), 0);
@@ -446,7 +440,7 @@ public class OverviewDimensionsTest {
     // of alignment
     // box position is adjusted away from the edge
     // overly large boxX value reset to width-boxWidth
-    int xpos = 100;
+    xpos = 100;
     mouseClick(od, xpos, 5);
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxY(), 5);
@@ -476,7 +470,7 @@ public class OverviewDimensionsTest {
     assertEquals(od.getScrollCol(), 0);
     assertEquals(od.getScrollRow(), 0);
     
-    // hide columns 60-68, no change to box position or dimensions
+    // hide columns 63-73, no change to box position or dimensions
     int firstHidden = 63;
     int lastHidden = 73;
     hideColumns(firstHidden, lastHidden);
@@ -521,35 +515,31 @@ public class OverviewDimensionsTest {
     assertEquals(od.getScrollRow(), 0);
 
     // move box so boxX is in hidden cols, box overhangs at right
-    // box width back to normal, boxX and scrollCol move to right of hidden area
-    // TODO currently this test fails in the Jalview GUI, there is a gap between
-    // the rhs of the hidden area and the box
-    /*    xpos = 50;
-        mouseClick(od, xpos, 0);
-        assertEquals(od.getBoxX(),
-                (lastHidden + 1) * scalew * av.getCharWidth());
-        assertEquals(od.getBoxY(), 0);
-        assertEquals(od.getBoxWidth(), boxWidth);
-        assertEquals(od.getBoxHeight(), boxHeight);
-        assertEquals(od.getScrollCol(),
-                Math.round(xpos * alwidth / od.getWidth()));
-        assertEquals(od.getScrollRow(), 0);*/
+    // 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);
 
     // 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
-    // TODO currently this test fails in the Jalview GUI because boxX is
-    // calculated
-    // based on the current boxWidth, which includes hidden columns, thereby
-    // pushing
-    // the box off the end of the alignment. So boxX is adjusted backwards
-    // unnecessarily.
-    /*   xpos = 72;
-       testBoxIsAtClickPoint(xpos, 0);
-       assertEquals(od.getScrollRow(), 0);
-       assertEquals(od.getScrollCol(),
-               Math.round(xpos * alwidth / od.getWidth())
-               - lastHidden);*/
+    xpos = 75;
+    testBoxIsAtClickPoint(xpos, 0);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getScrollCol(),
+            Math.round(xpos * alwidth / od.getWidth())
+                    - (lastHidden - firstHidden + 1));
     
     // move box so it goes beyond full width of alignment
     // boxX, scrollCol adjusted back, box width normal
@@ -584,9 +574,9 @@ public class OverviewDimensionsTest {
     assertEquals(od.getScrollCol(), 0);
     assertEquals(od.getScrollRow(), 0);
 
-    // hide columns 140-157, no change to box position or dimensions
+    // hide columns 140-164, no change to box position or dimensions
     int firstHidden = 140;
-    int lastHidden = 157;
+    int lastHidden = 164;
     hideColumns(firstHidden, lastHidden);
     od.setBoxPosition(av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
@@ -606,21 +596,19 @@ public class OverviewDimensionsTest {
 
     // click to left of hidden cols, with overlap
     // boxX and scrollCol adjusted for hidden cols, width normal
-    // TODO this fails because setBoxPosition screws up the hidden cols calc
-    // only works in GUI because of AlignmentPanel::setScrollValues
-    /*xpos = 115 - boxWidth;
-    mouseClick(od, xpos, 0);
-    assertEquals(
-            od.getBoxX(),
-            Math.round((firstHidden - 1) * scalew * av.getCharWidth())
-                    - od.getBoxWidth());
-    assertEquals(od.getBoxY(), 0);
-    assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(od.getScrollCol(),
-            Math.round(od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getScrollRow(), 0);*/
-
+    /*    xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
+        mouseClick(od, xpos, 0);
+        assertEquals(
+                od.getBoxX(),
+                Math.round((firstHidden - 1) * od.getWidth() / alwidth)
+                        - boxWidth);
+        assertEquals(od.getBoxY(), 0);
+        assertEquals(od.getBoxWidth(), boxWidth);
+        assertEquals(od.getBoxHeight(), boxHeight);
+        assertEquals(od.getScrollCol(),
+                Math.round(od.getBoxX() * alwidth / od.getWidth()));
+        assertEquals(od.getScrollRow(), 0);
+    */
     // click in hidden cols
     // boxX and scrollCol adjusted for hidden cols, width normal
     // TODO breaks as above test
@@ -830,22 +818,15 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
-    // move viewport to end of alignment, need to account for hidden rows
-    // because of how alignment panel/overview panel are implemented
-
-    // AlignViewport adjusts endSeq using Alignment height which excludes hidden
-    // rows if we happen to be at the bottom of the alignment
-    // od.setBoxPosition adjusts endSeq to include hidden rows
-    // od.checkValid adjusts scroll position to exclude hidden rows
-    // TODO this test fails because of the above!
-
-    /*    moveViewport(0, 525 - viewHeight - lastHidden - 1);
-        assertEquals(od.getBoxX(), 0);
-        assertEquals(od.getBoxY(),
-                (525 - viewHeight) * scaleh
-                * av.getCharHeight());
-        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.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
   }
 
   /**
@@ -861,23 +842,22 @@ public class OverviewDimensionsTest {
 
     // move viewport to start of alignment:
     // box, height etc as in non-hidden case
-    // TODO fails with boxy=12 because that's what setBoxPosition sets it to!
-    /*moveViewport(0, 0);
+    moveViewport(0, 0);
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
-    assertEquals(od.getBoxHeight(), boxHeight);*/
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to straddle hidden rows
-    // TODO also fails with boxY out by 12
-    /*moveViewport(0, 198);
+    moveViewport(0, 198);
     assertEquals(od.getBoxX(), 0);
-    assertEquals(od.getBoxY(), Math.round (198 * scaleh * av.getCharHeight()),
-            1.5);
+    assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
+            / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight
-            + ((lastHidden - firstHidden) * scaleh * av.getCharHeight()),
-            1.5);*/
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getSequencesHeight()
+ / alheight));
   }
 
   /**
@@ -900,18 +880,15 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxHeight(), boxHeight);
 
     // move viewport to end of alignment
-    // TODO fails with wrong boxHeight who knows why
-    /*moveViewport(0, firstHidden - viewHeight - 1);
-        assertEquals(od.getBoxX(), 0);
-        assertEquals(od.getBoxY(),
-     Math.round ((firstHidden - viewHeight - 1)
-                * scaleh * av.getCharHeight()));
-        assertEquals(od.getBoxWidth(), boxWidth);
-        assertEquals(
-                od.getBoxHeight(),
-                boxHeight
-                        + Math.round ((lastHidden - firstHidden + 1) * scaleh * av
-                                .getCharHeight()));*/
+    // viewport sits above hidden rows and does not include them
+    moveViewport(0, firstHidden - viewHeight - 1);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (firstHidden - viewHeight - 1)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
   }
 
@@ -946,15 +923,15 @@ public class OverviewDimensionsTest {
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
 
-    // click in hidden rows
-    // TODO fails because boxHeight is 27 not 25 (possible rounding issue)
-    /*    mouseClick(od, 0, 0);
-        assertEquals(od.getBoxX(), 0);
-        assertEquals(od.getBoxY(), 0);
-        assertEquals(od.getBoxWidth(), boxWidth);
-        assertEquals(od.getBoxHeight(), boxHeight
-                + Math.round ((lastHiddenRow + 1) * scaleh * av.getCharHeight()),
-                1.5);*/
+    // 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.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
 
     // click below hidden rows
     mouseClick(od, 0, 150);