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 8e0e6e3..dc26a36 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
-import jalview.analysis.AnnotationSorter;
 import jalview.analysis.Conservation;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
@@ -373,12 +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[]
@@ -388,15 +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(),
@@ -415,7 +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();
 
@@ -1900,11 +1899,6 @@ public class PopupMenu extends JPopupMenu
         copyAnn.visible = true;
       }
     }
-    // TODO: save annotation sort order on AlignViewport
-    // do sorting from AlignmentPanel.updateAnnotation()
-    new AnnotationSorter(this.ap.getAlignment())
-            .sortBySequenceAndType(this.ap.getAlignment()
-                    .getAlignmentAnnotation());
     refresh();
   }
 
@@ -2572,7 +2566,8 @@ public class PopupMenu extends JPopupMenu
       String choice = chooser.getSelectedFile().getPath();
       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
-              jalview.io.AppletFormatAdapter.FILE, sequence, true);
+              jalview.io.AppletFormatAdapter.FILE, sequence, true,
+              Desktop.instance);
     }
 
   }