JAL-1486 fix: pass selected region to jalview.io via alignment view and align viewpor...

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ace4762..25cad0a 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -256,9 +256,12 @@ public class PopupMenu extends JPopupMenu
             {
               // TODO re JAL-860: optionally open dialog or provide a menu entry
               // allowing user to open just one structure per sequence
-              new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
-              { pdb })[0], null, ap);
-              // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+              //new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
+              //{ pdb })[0], null, ap);
+              new StructureViewer(ap.getStructureSelectionManager())
+                      .viewStructures(pdb,
+                              ap.av.collateForPDB(new PDBEntry[]
+                              { pdb })[0], null, ap);
             }
 
           });
@@ -558,7 +561,7 @@ public class PopupMenu extends JPopupMenu
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            new AppJmol(ap, pe, ap.av.collateForPDB(pe));
+            new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pe, ap.av.collateForPDB(pe));
           }
         });
         if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
@@ -576,7 +579,7 @@ public class PopupMenu extends JPopupMenu
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+              new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr));
             }
           });
         }
@@ -2068,23 +2071,21 @@ public class PopupMenu extends JPopupMenu
     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
     // or we simply trust the user wants
     // wysiwig behaviour
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
-    omitHidden = ap.av.getViewAsString(true);
-    Alignment oal = new Alignment(ap.av.getSequenceSelection());
-    AlignmentAnnotation[] nala = ap.av.getAlignment()
-            .getAlignmentAnnotation();
-    if (nala != null)
+
+    AlignmentView selvew = ap.av.getAlignmentView(true, false);
+    AlignmentI aselview = selvew.getVisibleAlignment(ap.av
+            .getGapCharacter());
+    List<AlignmentAnnotation> ala = (ap.av
+            .getVisibleAlignmentAnnotation(true));
+    if (ala != null)
     {
-      for (int i = 0; i < nala.length; i++)
+      for (AlignmentAnnotation aa : ala)
       {
-        AlignmentAnnotation na = nala[i];
-        oal.addAnnotation(na);
+        aselview.addAnnotation(aa);
       }
     }
     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-            oal, omitHidden, csel, sg));
-    oal = null;
+            aselview, null, null, null));
   }
 
   public void pdbFromFile_actionPerformed()