JAL-2388 Moving some alignment panel logic into overview (in progress)

diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 4a2dd29..4af4175 100644 (file)
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -138,19 +138,11 @@ public class OverviewDimensions
     {
       x = 0;
     }
-    else if (x >= width)
-    {
-      x = alwidth - 1;
-    }
 
     if (y < 0)
     {
       y = 0;
     }
-    else if (y >= sequencesHeight)
-    {
-      y = alheight - 1;
-    }
 
     //
     // Convert x value to residue position
@@ -178,13 +170,14 @@ public class OverviewDimensions
     int endRes = xAsRes + vpwidth - 1;
 
     // check in case we went off the edge of the alignment
-    if (endRes > alwidth)
+    int visAlignWidth = hiddenCols.findColumnPosition(alwidth);
+    if (endRes > visAlignWidth - 1)
     {
       // went past the end of the alignment, adjust backwards
-      endRes = alwidth;
+      endRes = visAlignWidth - 1;
       // recalc xAsRes backwards from endRes
       // add 1 because width includes xAsRes
-      xAsRes = endRes - vpwidth + 1;
+      xAsRes = hiddenCols.adjustForHiddenColumns(endRes - vpwidth + 1);
     }
 
     //
@@ -209,10 +202,11 @@ public class OverviewDimensions
     int endSeq = yAsSeq + vpheight - 1;
 
     // check in case we went off the edge of the alignment
-    if (endSeq > alheight)
+    int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
+    if (hiddenSeqs.findIndexWithoutHiddenSeqs(endSeq) > visAlignHeight - 1)
     {
       // went past the end of the alignment, adjust backwards
-      endSeq = alheight;
+      endSeq = visAlignHeight - 1;
       // recalc yAsSeq backwards from endSeq
       yAsSeq = endSeq - vpheight + 1;
     }

diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
index e86f41b..8ceadba 100644 (file)
--- a/test/jalview/viewmodel/OverviewDimensionsTest.java
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -39,28 +39,8 @@ import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 @Test(singleThreaded = true)
-public class OverviewDimensionsTest {
-
-  SequenceI seq1 = new Sequence(
-          "Seq1",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq2 = new Sequence(
-          "Seq2",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq3 = new Sequence(
-          "Seq3",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq4 = new Sequence(
-          "Seq4",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
-  SequenceI seq5 = new Sequence(
-          "Seq5",
-          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
+public class OverviewDimensionsTest
+{
   AlignmentI al;
   OverviewDimensions od;
 
@@ -509,19 +489,18 @@ public class OverviewDimensionsTest {
 
     // 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);
-        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);
-    */
+    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