Merge branch 'develop' into features/JAL-892varnaToProject

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2aa8675..37082aa 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,6 +20,27 @@
  */
 package jalview.gui;
 
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
@@ -59,27 +80,6 @@ import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
 /**
  * DOCUMENT ME!
  * 
@@ -322,49 +322,54 @@ public class PopupMenu extends JPopupMenu
         makeReferenceSeq.setText("Mark as representative");
       }
 
-      if (ap.av.getAlignment().isNucleotide() == false)
+      if (!ap.av.getAlignment().isNucleotide())
       {
         remove(rnaStructureMenu);
       }
-
-      if (ap.av.getAlignment().isNucleotide() == true)
+      else
       {
-        AlignmentAnnotation[] aa = ap.av.getAlignment()
+        /*
+         * add menu items to 2D-render any alignment or sequence secondary
+         * structure annotation
+         */
+        AlignmentAnnotation[] aas = ap.av.getAlignment()
                 .getAlignmentAnnotation();
-        for (int i = 0; aa != null && i < aa.length; i++)
+        if (aas != null)
         {
-          if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
+          for (final AlignmentAnnotation aa : aas)
           {
-            final String rnastruc = aa[i].getRNAStruc();
-            final String structureLine = aa[i].label + " (alignment)";
-            menuItem = new JMenuItem();
-            menuItem.setText(MessageManager.formatMessage(
-                    "label.2d_rna_structure_line", new Object[]
-                    { structureLine }));
-            menuItem.addActionListener(new java.awt.event.ActionListener()
+            if (aa.isValidStruc() && aa.sequenceRef == null)
             {
-              @Override
-              public void actionPerformed(ActionEvent e)
+              /*
+               * valid alignment RNA secondary structure annotation
+               */
+              menuItem = new JMenuItem();
+              menuItem.setText(MessageManager.formatMessage(
+                      "label.2d_rna_structure_line", new Object[]
+                      { aa.label }));
+              menuItem.addActionListener(new java.awt.event.ActionListener()
               {
-                new AppVarna(structureLine, seq, seq.getSequenceAsString(),
-                        rnastruc, seq.getName(), ap);
-                System.out.println("end");
-              }
-            });
-            rnaStructureMenu.add(menuItem);
+                @Override
+                public void actionPerformed(ActionEvent e)
+                {
+                  new AppVarna(seq, aa, ap);
+                }
+              });
+              rnaStructureMenu.add(menuItem);
+            }
           }
         }
 
-
         if (seq.getAnnotation() != null)
         {
-          AlignmentAnnotation seqAnno[] = seq.getAnnotation();
-          for (int i = 0; i < seqAnno.length; i++)
+          AlignmentAnnotation seqAnns[] = seq.getAnnotation();
+          for (final AlignmentAnnotation aa : seqAnns)
           {
-            if (seqAnno[i].isValidStruc())
+            if (aa.isValidStruc())
             {
-              final String rnastruc = seqAnno[i].getRNAStruc();
-
+              /*
+               * valid sequence RNA secondary structure annotation
+               */
               // TODO: make rnastrucF a bit more nice
               menuItem = new JMenuItem();
               menuItem.setText(MessageManager.formatMessage(
@@ -376,10 +381,7 @@ public class PopupMenu extends JPopupMenu
                 public void actionPerformed(ActionEvent e)
                 {
                   // TODO: VARNA does'nt print gaps in the sequence
-
-                  new AppVarna(seq.getName() + " structure", seq, seq
-                          .getSequenceAsString(), rnastruc, seq.getName(),
-                          ap);
+                  new AppVarna(seq, aa, ap);
                 }
               });
               rnaStructureMenu.add(menuItem);