JAL-2388 Corrected overview panel behaviour, updated tests

[jalview.git] / src / jalview / gui / OverviewPanel.java

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index d87285c..d15ec40 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -88,7 +88,14 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(alPanel);
 
-    od = new OverviewDimensions(av);
+    boolean showAnnotation = false;
+    // TODO: in applet this was getSequenceConsensusHash()
+    // check if it makes any functional difference: hconsensus or conservation
+    if (av.getAlignmentConservationAnnotation() == null)
+    {
+      showAnnotation = true;
+    }
+    od = new OverviewDimensions(av, showAnnotation);
 
     addComponentListener(new ComponentAdapter()
     {
@@ -112,7 +119,7 @@ public class OverviewPanel extends JPanel implements Runnable
         {
           // TODO: feature: jv2.5 detect shift drag and update selection from
           // it.
-          od.setBoxPositionByMouse(evt.getX(), evt.getY());
+          od.updateViewportFromMouse(evt.getX(), evt.getY());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -125,7 +132,7 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          od.setBoxPositionByMouse(evt.getX(), evt.getY());
+          od.updateViewportFromMouse(evt.getX(), evt.getY());
           ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
@@ -181,15 +188,11 @@ public class OverviewPanel extends JPanel implements Runnable
     mg.setColor(Color.orange);
     mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
 
-    // calculate scale based on current alignment width and height
-    od.updateScales();
-
     // calculate sampleCol and sampleRow
     // alignment width is max number of residues/bases
     // alignment height is number of sequences
     int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
+    int alheight = av.getAlignment().getAbsoluteHeight();
 
     // sampleCol or sampleRow is the width/height allocated to each residue
     // in particular, sometimes we may need more than one row/col of the
@@ -239,7 +242,7 @@ public class OverviewPanel extends JPanel implements Runnable
     int color = Color.white.getRGB();
 
     jalview.datamodel.SequenceI seq = null;
-    final boolean hasHiddenRows = av.hasHiddenRows();
+
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
     // get hidden row and hidden column map once at beginning.
@@ -255,29 +258,10 @@ public class OverviewPanel extends JPanel implements Runnable
 
         lastrow = currentrow;
 
-        hiddenRow = false;
-        // should be method(s) in Alignment
-        if (hasHiddenRows)
-        {
-          seq = av.getAlignment().getHiddenSequences()
-                  .getHiddenSequence(lastrow);
-          if (seq == null)
-          {
-            int index = av.getAlignment().getHiddenSequences()
-                    .findIndexWithoutHiddenSeqs(lastrow);
-
-            seq = av.getAlignment().getSequenceAt(index);
-          }
-          else
-          {
-            hiddenRow = true;
-          }
-        }
-        else
-        {
-          seq = av.getAlignment().getSequenceAt(lastrow);
-        }
-        // end of Alignment method(s)
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // columns were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
       }
 
       if (seq == null)