profile visualizations are now logos

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 9c2cbdd..9626e80 100755 (executable)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,6 +20,7 @@ package jalview.gui;
 
 import java.beans.*;
 import java.io.*;
+import java.util.Hashtable;
 import java.util.Vector;
 
 import java.awt.*;
@@ -400,6 +401,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), height));
     annotationScroller.validate();// repaint();
+    addNotify();
     repaint();
   }
 
@@ -1320,9 +1322,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void updateAnnotation()
   {
+    updateAnnotation(false);
+  }
+  public void updateAnnotation(boolean applyGlobalSettings)
+  {
     boolean updateCalcs = false;
     boolean conv = av.isShowGroupConservation();
     boolean cons = av.isShowGroupConsensus();
+    boolean showprf = av.isShowSequenceLogo();
+    boolean showConsHist = av.isShowConsensusHistogram();
+    
     boolean sortg = true;
 
     // remove old automatic annotation
@@ -1332,10 +1341,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     // intersect alignment annotation with alignment groups
 
     AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+    Hashtable oldrfs = new Hashtable();
     for (int an = 0; an < aan.length; an++)
     {
       if (aan[an].autoCalculated && aan[an].groupRef != null)
       {
+        oldrfs.put(aan[an].groupRef, aan[an].groupRef);
         av.alignment.deleteAnnotation(aan[an]);
         aan[an] = null;
       }
@@ -1345,7 +1356,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       updateCalcs = false;
       sg = (SequenceGroup) gr.elementAt(g);
-
+      if (applyGlobalSettings || !oldrfs.containsKey(sg))
+      {
+        // set defaults for this group's conservation/consensus
+        sg.setIncludeAllConsSymbols(showprf);
+        sg.setShowConsensusHistogram(showConsHist);
+      }
       if (conv)
       {
         updateCalcs = true;
@@ -1362,6 +1378,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         sg.recalcConservation();
       }
     }
+    oldrfs.clear();
     adjustAnnotationHeight();
   }
 }