JAL-2613 Unit tests and a fix. Phew.

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index a98b10e..ed07290 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -310,7 +310,7 @@ public class HiddenSequences
       return startRow - visibleDistance;
     }
 
-    int index = startRow;
+    int index = Math.min(startRow, hiddenSequences.length - 1);
     int count = 0;
     while ((index > -1) && (count < visibleDistance))
     {

diff --git a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
index fe20195..c5ce19b 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
@@ -73,9 +73,6 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
     // Convert y value to sequence position
     //
 
-    // convert y to residues
-    // int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
-
     // get viewport height in sequences
     // add 1 because height includes both endSeq and startSeq
     int vpheight = ranges.getViewportHeight();

diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index be69db9..1bd96ab 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -212,15 +212,14 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
   {
     int vpx = Math.round((float) mousex * alwidth / width);
-    return hidden.findColumnPosition(hidden.subtractVisibleColumns(
-            ranges.getViewportWidth() / 2, vpx));
+    return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
+            vpx);
   }
 
   @Override
   protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
   {
     int vpy = Math.round((float) mousey * alheight / sequencesHeight);
-    return hidden.findIndexWithoutHiddenSeqs(hidden.subtractVisibleRows(
-            ranges.getViewportHeight() / 2, vpy));
+    return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
   }
 }

diff --git a/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java b/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
index fef7548..7b4c65c 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsShowHiddenTest.java
@@ -236,18 +236,18 @@ public class OverviewDimensionsShowHiddenTest
 
     // 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(vpranges.getStartRes() + vpranges.getViewportWidth() / 2,
+    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(
-            vpranges.getStartSeq() + vpranges.getViewportWidth() / 2,
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()) - 1);
 
@@ -256,28 +256,29 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
-    assertEquals(vpranges.getStartRes() + vpranges.getViewportWidth() / 2,
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
     assertEquals(
-            vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
+            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(vpranges.getStartRes() + vpranges.getViewportWidth() / 2,
+    assertEquals(vpranges.getStartRes(),
             Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
-    assertEquals(od.getBoxY(), oldboxy + 2);
+    assertEquals(od.getBoxY(), oldboxy + 3);
     assertEquals(
-            vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
+            vpranges.getStartSeq(),
             Math.round((float) od.getBoxY() * alheight
                     / od.getSequencesHeight()));
 
@@ -331,10 +332,15 @@ public class OverviewDimensionsShowHiddenTest
     assertEquals(vpranges.getStartRes(), 0);
 
     // click to right of hidden columns, box moves to click point
-    testBoxIsAtClickPoint(40, 0);
+    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) 40 * alwidth / od.getWidth())
+            Math.round(
+                    (float) 60 * alwidth / od.getWidth())
                     - (lastHiddenCol + 1));
 
     // click to right of hidden columns such that box runs over right hand side
@@ -342,7 +348,7 @@ 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);
@@ -384,10 +390,10 @@ public class OverviewDimensionsShowHiddenTest
 
     // 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
+    int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
                               // between cols 60 and 70
-    mouseClick(od, xpos, 0);
-    assertEquals(od.getBoxX(), xpos);
+    mouseClick(od, xpos, boxHeight / 2);
+    assertEquals(od.getBoxX(), xpos - boxWidth / 2);
     assertEquals(od.getBoxY(), 0);
     assertEquals(
             od.getBoxWidth(),
@@ -395,14 +401,15 @@ public class OverviewDimensionsShowHiddenTest
                     * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(vpranges.getStartRes(),
-            Math.round(xpos * alwidth / od.getWidth()));
+            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(),
@@ -410,42 +417,28 @@ public class OverviewDimensionsShowHiddenTest
                     * od.getWidth() / alwidth));
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(vpranges.getStartRes(),
-            Math.round((float) xpos * alwidth / od.getWidth()));
-    assertEquals(vpranges.getStartSeq(), 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(vpranges.getStartRes(), firstHidden - 1);
+            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);
+    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(),
-            Math.round(xpos * alwidth / od.getWidth())
-                    - (lastHidden - firstHidden + 1));
+            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(
@@ -486,24 +479,29 @@ public class OverviewDimensionsShowHiddenTest
 
     // click to left of hidden cols, without overlapping
     // boxX, scrollCol and width as normal
-    int xpos = 5;
-    testBoxIsAtClickPoint(xpos, 0);
-    assertEquals(vpranges.getStartSeq(), 0);
-    assertEquals(vpranges.getStartRes(),
-            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)
+            Math.round((float) (firstHidden - 1)
+                    * od.getWidth() / alwidth)
                     - boxWidth + 1);
     assertEquals(od.getBoxY(), 0);
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(od.getBoxHeight(), boxHeight);
     assertEquals(vpranges.getStartRes(),
-            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+            Math.round((float) (od.getBoxX()) * alwidth
+                    / od.getWidth()));
     assertEquals(vpranges.getStartSeq(), 0);
 
     // click in hidden cols
@@ -822,7 +820,7 @@ public class OverviewDimensionsShowHiddenTest
     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);
@@ -859,26 +857,15 @@ 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
+    int rowpos = 35; // row value in residues
+    int centrepos = 43; // centre row
     mouseClick(od, 0,
-            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+            Math.round((float) centrepos * od.getSequencesHeight()
+                    / alheight));
     assertEquals(od.getBoxX(), 0);
     assertEquals(od.getBoxY(),
-            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+            Math.round(
+                    (float) rowpos * od.getSequencesHeight() / alheight));
     assertEquals(od.getBoxWidth(), boxWidth);
     assertEquals(
             od.getBoxHeight(),
@@ -914,19 +901,19 @@ 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);
@@ -938,7 +925,7 @@ public class OverviewDimensionsShowHiddenTest
     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);
@@ -992,14 +979,14 @@ public class OverviewDimensionsShowHiddenTest
   }
   
   /*
-   * 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);