JAL-842: some bugfixes;

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index bc83400..81ea76c 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -106,9 +106,10 @@ public class AppVarna extends JInternalFrame implements InterfaceVARNAListener//
          StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
          StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
          for(int i=0;i<rnaTrim.getSeq().length();i++){
+                 //TODO: Jalview utility for gap detection java.utils.isGap()
+                 //TODO: Switch to jalview rna datamodel
                  if(seq.substring(i, i+1).compareTo("-")==0 || seq.substring(i, i+1).compareTo(".")==0){
                          if(!rnaTrim.findPair(i).isEmpty()){
-                                 System.out.println(rnaTrim.findPair(i));
                                  int m=rnaTrim.findPair(i).get(1);
                                  int l=rnaTrim.findPair(i).get(0);