JAL-891; base-pair logos can now be activated for structure

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 1acc0ca..ca9b95f 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1572,12 +1572,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           char[] dc;
 
           /**
-           * profl.length == 11 indicates that the profile of a secondary
+           * profl.length == 51 indicates that the profile of a secondary
            * structure conservation row was accesed.
            * Therefore dc gets length 2, to have space for a basepair instead of
            * just a single nucleotide
            */
-          if (profl.length == 22)
+          if (profl.length == 51)
           {
             dc = new char[2];
           }
@@ -1593,7 +1593,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
             if (aa.label.startsWith("StrucConsensus"))
             {
-              dc[1] = 'A';
+              dc[1] = (char) profl[c++];
             }
             
             wdth = av.charWidth;