From 6d9cb59a547de8c4d73e1ba365fe8b91f91063c6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 30 Mar 2010 17:46:55 +0000
Subject: [PATCH] bugfix for redraw when AlignPanel partially constructed.
 group autoannotation and consensus display settings

---
 src/jalview/gui/AnnotationPanel.java |   36 +++++++++++++++++++++++++++-------
 1 file changed, 29 insertions(+), 7 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 281d5dc..b196444 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -141,6 +141,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     {
       for (int i = 0; i < aa.length; i++)
       {
+        if (aa[i]==null)
+        {
+          System.err.println("Null annotation row: ignoring.");
+          continue;
+        }
         if (!aa[i].visible)
         {
           continue;
@@ -177,7 +182,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     }
 
     this.setPreferredSize(new Dimension(1, height));
-    ap.alabels.validate();
+    if (ap!=null)
+    {
+      // revalidate only when the alignment panel is fully constructed
+      ap.validate();
+    }
 
     return height;
   }
@@ -1300,7 +1309,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
     int column;
     int aaMax = aa.annotations.length - 1;
-
+    boolean renderHistogram = true, renderProfile = true;
+    if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
+      // TODO: generalise this to have render styles for consensus/profile data 
+      if (aa.groupRef!=null)
+      {
+        renderHistogram = aa.groupRef.isShowConsensusHistogram();
+        renderProfile = aa.groupRef.isIncludeAllConsSymbols();
+      } else {
+        renderHistogram = av.isShowConsensusHistogram();
+        renderProfile = av.isShowConsensusProfile();
+      }
+    }
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -1319,7 +1339,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         x++;
         continue;
       }
-
       if (aa.annotations[column].colour == null)
         g.setColor(Color.black);
       else
@@ -1328,7 +1347,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       y1 = y
               - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
-      if (y1 - y2 > 0)
+      if (renderHistogram)
+      {      
+        if (y1 - y2 > 0)
       {
         g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
       }
@@ -1336,8 +1357,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       {
         g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
       }
+      }
       // draw profile if available
-      if (aa.annotations[column].value!=0)
+      if (aa.annotations[column].value!=0 && renderProfile)
       {
         int profl[] = getProfileFor(aa,column);
         int ht = y1,htn=y2-y1;//aa.graphHeight;
@@ -1391,11 +1413,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
   private int[] getProfileFor(AlignmentAnnotation aa, int column)
   {
     if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
-    if (aa.groupRef!=null && aa.groupRef.consensusData!=null) {
+    if (aa.groupRef!=null && aa.groupRef.consensusData!=null && aa.groupRef.isIncludeAllConsSymbols()) {
       return AAFrequency.extractProfile(aa.groupRef.consensusData[column],aa.groupRef.getIgnoreGapsConsensus());
     }
     // TODO extend annotation row to enable dynamic and static profile data to be stored  
-    if (aa.groupRef==null && aa.sequenceRef==null)
+    if (aa.groupRef==null && aa.sequenceRef==null && av.isShowConsensusProfile())
     {
       return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
     }
-- 
1.7.10.2