X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=1a7235fa1f87f64d66cd81b3869fe78bbbf91af2;hb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;hp=3da449446b684cf6df1a02e032bbf56083f1b9e4;hpb=c46ac1bbccd595dfeb504220b465023d38815223;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3da4494..1a7235f 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -25,6 +25,7 @@ import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.Conservation;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
@@ -372,12 +373,12 @@ 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 +388,15 @@ 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 +415,7 @@ 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 +1876,6 @@ 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 +1896,7 @@ 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;
       }
     }
@@ -1933,7 +1933,7 @@ public class PopupMenu extends JPopupMenu
                       true,
                       true,
                       false,
-                      (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+                      (ap.getSeqPanel().seqCanvas.fr != null) ? ap.getSeqPanel().seqCanvas.fr.minmax
                               : null);
       contents.append("</p>");
     }
@@ -2567,7 +2567,8 @@ 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);
     }
 
   }
@@ -2649,7 +2650,7 @@ public class PopupMenu extends JPopupMenu
     System.arraycopy(features, 0, tfeatures, 0, rsize);
     features = tfeatures;
     seqs = rseqs;
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
             features, true, ap))
     {
       ap.alignFrame.setShowSeqFeatures(true);
@@ -2707,7 +2708,7 @@ public class PopupMenu extends JPopupMenu
       {
         EditCommand editCommand = new EditCommand(
                 MessageManager.getString("label.edit_sequences"),
-                EditCommand.REPLACE, dialog.getName().replace(' ',
+                Action.REPLACE, dialog.getName().replace(' ',
                         ap.av.getGapCharacter()),
                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());