JAL-2388 Corrected overview panel behaviour, updated tests

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 0d3f058..0bb9392 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -75,7 +75,15 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    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);
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -123,23 +131,24 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
-    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
-    ap.paintAlignment(false);
+    mouseAction(evt);
   }
 
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    od.setBoxPositionByMouse(evt.getX(), evt.getY());
+    mouseAction(evt);
+  }
+
+  private void mouseAction(MouseEvent evt)
+  {
+    od.updateViewportFromMouse(evt.getX(), evt.getY());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
@@ -197,11 +206,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
     Graphics mg = miniMe.getGraphics();
 
-    od.updateScales();
+    // od.updateScales();
 
     int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
+    int alheight = av.getAlignment().getAbsoluteHeight();
     float sampleCol = alwidth / (float) od.getWidth();
     float sampleRow = alheight / (float) od.getSequencesHeight();
 
@@ -244,7 +252,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int sameCol = 0;
 
     jalview.datamodel.SequenceI seq = null;
-    final boolean hasHiddenRows = av.hasHiddenRows();
+
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
 
@@ -256,33 +264,10 @@ public class OverviewPanel extends Panel implements Runnable,
       }
       else
       {
-        // this should largely be a method in Alignment
-        hiddenRow = false;
-        if (hasHiddenRows)
-        {
-          // look for sequence in hidden rows
-          seq = av.getAlignment().getHiddenSequences()
-                  .getHiddenSequence(lastrow);
-          if (seq == null)
-          {
-            // didn't find in hidden rows, adjust the index and retrieve from
-            // full row set
-            int index = av.getAlignment().getHiddenSequences()
-                    .findIndexWithoutHiddenSeqs(lastrow);
-
-            seq = av.getAlignment().getSequenceAt(index);
-          }
-          else
-          {
-            // found in hidden rows, ergo this row is hidden
-            hiddenRow = true;
-          }
-        }
-        else
-        {
-          seq = av.getAlignment().getSequenceAt(lastrow);
-        }
-        // end of Alignment method
+        // 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);
 
         for (int col = 0; col < od.getWidth(); col++)
         {