some print statements to test things

Change-Id: I0730499d395e8f84b9cfd9ec2aaaa7283fc4b1fa

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 82ce835..9de51ea 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -264,14 +264,14 @@ public class PopupMenu extends JPopupMenu
          AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
          String rnastruc=new String();
          for(int i=0; i<aa.length;i++){
-                 if(aa[i]._rnasecstr != null){
+                 if(aa[i].getRNAStruc() != null){
                          rnastruc=aa[i].getRNAStruc();
                          break;
                  }
          }
-         
-         SequenceGroup a = aa[0].groupRef;
 
+         AlignmentAnnotation a[] = seq.getAnnotation();
+         
          //TODO: make rnastrucF a bit more nice
          final String rnastrucF=rnastruc;
          menuItem = new JMenuItem();
@@ -280,8 +280,9 @@ public class PopupMenu extends JPopupMenu
          {
                  public void actionPerformed(ActionEvent e)
                  {
-                         System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
+                         //System.out.println("Call Varna "+seq.getSequenceAsString()+" "+seq.getName());
                          //TODO: VARNA does'nt print gaps in the sequence
+                         
                          new AppVarna(seq.getSequenceAsString(),rnastrucF,seq.getName(),ap);
                  }
                        });       

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index e9574fc..fc1d870 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -67,7 +67,7 @@ public class AppletFormatAdapter
    */
   public static final String[] READABLE_EXTENSIONS = new String[]
   { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
-      "stk" }; // ,
+      "sto,stk" }; // ,
 
   // ".blast"
   // };