profile visualizations are now logos

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index b196444..695eced 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1315,10 +1315,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if (aa.groupRef!=null)
       {
         renderHistogram = aa.groupRef.isShowConsensusHistogram();
-        renderProfile = aa.groupRef.isIncludeAllConsSymbols();
+        renderProfile = aa.groupRef.isShowSequenceLogo();
       } else {
         renderHistogram = av.isShowConsensusHistogram();
-        renderProfile = av.isShowConsensusProfile();
+        renderProfile = av.isShowSequenceLogo();
       }
     }
     while (x < eRes - sRes)
@@ -1413,11 +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 && aa.groupRef.isIncludeAllConsSymbols()) {
+    if (aa.groupRef!=null && aa.groupRef.consensusData!=null && aa.groupRef.isShowSequenceLogo()) {
       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 && av.isShowConsensusProfile())
+    if (aa.groupRef==null && aa.sequenceRef==null && av.isShowSequenceLogo())
     {
       return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
     }