JAL-1569 remove stdout on parsing RNA

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2845122..dc26a36 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -372,12 +372,12 @@ public class PopupMenu extends JPopupMenu
       {
         AlignmentAnnotation[] aa = ap.av.getAlignment()
                 .getAlignmentAnnotation();
-        for (int i = 0; i < aa.length; i++)
+        for (int i = 0; aa != null && i < aa.length; i++)
         {
-          if (aa[i].getRNAStruc() != null)
+          if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
           {
             final String rnastruc = aa[i].getRNAStruc();
-            final String structureLine = aa[i].label;
+            final String structureLine = aa[i].label + " (alignment)";
             menuItem = new JMenuItem();
             menuItem.setText(MessageManager.formatMessage(
                     "label.2d_rna_structure_line", new String[]
@@ -387,15 +387,15 @@ public class PopupMenu extends JPopupMenu
               @Override
               public void actionPerformed(ActionEvent e)
               {
-                // System.out.println("1:"+structureLine);
-                System.out.println("1:sname" + seq.getName());
-                System.out.println("2:seq" + seq);
-
-                // System.out.println("3:"+seq.getSequenceAsString());
-                System.out.println("3:strucseq" + rnastruc);
-                // System.out.println("4:struc"+seq.getRNA());
-                System.out.println("5:name" + seq.getName());
-                System.out.println("6:ap" + ap);
+                // // System.out.println("1:"+structureLine);
+                // System.out.println("1:sname" + seq.getName());
+                // System.out.println("2:seq" + seq);
+                //
+                // // System.out.println("3:"+seq.getSequenceAsString());
+                // System.out.println("3:strucseq" + rnastruc);
+                // // System.out.println("4:struc"+seq.getRNA());
+                // System.out.println("5:name" + seq.getName());
+                // System.out.println("6:ap" + ap);
                 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
                         rnastruc, seq.getName(), ap);
                 // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
@@ -414,7 +414,7 @@ public class PopupMenu extends JPopupMenu
           AlignmentAnnotation seqAnno[] = seq.getAnnotation();
           for (int i = 0; i < seqAnno.length; i++)
           {
-            if (seqAnno[i].getRNAStruc() != null)
+            if (seqAnno[i].isValidStruc())
             {
               final String rnastruc = seqAnno[i].getRNAStruc();
 
@@ -1875,7 +1875,6 @@ public class PopupMenu extends JPopupMenu
      * Add annotations at the top of the annotation, in the same order as their
      * related sequences.
      */
-    int insertPosition = 0;
     for (SequenceI seq : candidates.keySet())
     {
       for (AlignmentAnnotation ann : candidates.get(seq))
@@ -1896,7 +1895,7 @@ public class PopupMenu extends JPopupMenu
         // adjust for gaps
         copyAnn.adjustForAlignment();
         // add to the alignment and set visible
-        this.ap.getAlignment().addAnnotation(copyAnn, insertPosition++);
+        this.ap.getAlignment().addAnnotation(copyAnn);
         copyAnn.visible = true;
       }
     }