JAL-2388 Reinstated original overview checks for annotation display

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 836a800..3ef2936 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -20,6 +20,8 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
@@ -61,10 +63,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
   private Frame nullFrame;
 
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
     nullFrame = new Frame();
     nullFrame.addNotify();
@@ -75,15 +77,8 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    boolean showAnnotation = true;
-    // TODO: in applet this was getSequenceConsensusHash()
-    // check if it makes any functional difference: hconsensus or conservation
-    if (av.getAlignmentConservationAnnotation() == null)
-    {
-      showAnnotation = false;
-    }
-
-    od = new OverviewDimensions(av.getPosProps(), showAnnotation);
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
@@ -150,13 +145,13 @@ public class OverviewPanel extends Panel implements Runnable,
   {
     od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
             .getHiddenSequences(), av.getColumnSelection(), av
-            .getPosProps());
+            .getRanges());
     ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
 
   /**
-   * DOCUMENT ME!
+   * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
   {
@@ -173,10 +168,10 @@ public class OverviewPanel extends Panel implements Runnable,
 
     resizing = true;
 
-    if ((getWidth() > 0) && (getHeight() > 0))
+    if ((getSize().width > 0) && (getSize().height > 0))
     {
-      od.setWidth(getWidth()); // width = getWidth();
-      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getSize().width);
+      od.setHeight(getSize().height);
     }
     setSize(new Dimension(od.getWidth(), od.getHeight()));
 
@@ -198,7 +193,7 @@ public class OverviewPanel extends Panel implements Runnable,
     if (getSize().width > 0 && getSize().height > 0)
     {
       od.setWidth(getSize().width);
-      od.setHeight(getSize().height - od.getGraphHeight());
+      od.setHeight(getSize().height);
     }
 
     setSize(new Dimension(od.getWidth(), od.getHeight()));
@@ -208,8 +203,6 @@ public class OverviewPanel extends Panel implements Runnable,
 
     Graphics mg = miniMe.getGraphics();
 
-    // od.updateScales();
-
     int alwidth = av.getAlignment().getWidth();
     int alheight = av.getAlignment().getAbsoluteHeight();
     float sampleCol = alwidth / (float) od.getWidth();
@@ -217,7 +210,9 @@ public class OverviewPanel extends Panel implements Runnable,
 
     buildImage(sampleRow, sampleCol, mg);
 
-    if (av.getAlignmentConservationAnnotation() != null)
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
     {
       for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
@@ -243,6 +238,9 @@ public class OverviewPanel extends Panel implements Runnable,
     }
   }
 
+  /*
+   * Build the overview panel image
+   */
   private void buildImage(float sampleRow, float sampleCol, Graphics mg)
   {
     int lastcol = 0;
@@ -253,7 +251,8 @@ public class OverviewPanel extends Panel implements Runnable,
     int sameRow = 0;
     int sameCol = 0;
 
-    jalview.datamodel.SequenceI seq = null;
+    SequenceI seq = null;
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
     final boolean hasHiddenCols = av.hasHiddenColumns();
     boolean hiddenRow = false;
@@ -283,7 +282,7 @@ public class OverviewPanel extends Panel implements Runnable,
             lastcol = (int) (col * sampleCol);
 
             color = getColumnColourFromSequence(seq, hiddenRow,
-                    hasHiddenCols, lastcol);
+                    hasHiddenCols, lastcol, finder);
 
             mg.setColor(color);
             if (sameCol == 1 && sameRow == 1)
@@ -304,7 +303,6 @@ public class OverviewPanel extends Panel implements Runnable,
         sameRow = 1;
       }
     }
-
   }
 
   /*
@@ -312,21 +310,12 @@ public class OverviewPanel extends Panel implements Runnable,
    */
   private Color getColumnColourFromSequence(
           jalview.datamodel.SequenceI seq, boolean hiddenRow,
-          boolean hasHiddenCols, int lastcol)
+          boolean hasHiddenCols, int lastcol, FeatureColourFinder finder)
   {
-    Color color;
+    Color color = Color.white;
     if (seq.getLength() > lastcol)
     {
-      color = sr.getResidueBoxColour(seq, lastcol);
-
-      if (av.isShowSequenceFeatures())
-      {
-        color = fr.findFeatureColour(color, seq, lastcol);
-      }
-    }
-    else
-    {
-      color = Color.white; // White
+      color = sr.getResidueColour(seq, lastcol, finder);
     }
 
     if (hiddenRow
@@ -346,7 +335,7 @@ public class OverviewPanel extends Panel implements Runnable,
   public void setBoxPosition()
   {
     od.setBoxPosition(av.getAlignment()
-            .getHiddenSequences(), av.getColumnSelection(), av.getPosProps());
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
     repaint();
   }