JAL-3070 TODO for mateusz

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3f74327..a9fd70c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3476,6 +3476,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 alignPanel.setOverviewPanel(null);
               };
             });
+    if (getKeyListeners().length > 0)
+    {
+      frame.addKeyListener(getKeyListeners()[0]);
+    }
 
     alignPanel.setOverviewPanel(overview);
   }
@@ -4308,7 +4312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       jws2servs.attachWSMenuEntry(webService, me);
                       for (Jws2Instance sv : jws2servs.getServices())
                       {
-                        if (sv.description.toLowerCase().contains("jpred"))
+                        if (sv.getName().toLowerCase().contains("jpred"))
                         {
                           for (JMenuItem jmi : legacyItems)
                           {
@@ -4328,6 +4332,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                 }
                 build_urlServiceMenu(me.webService);
+
+                // TODO Mateusz - follow pattern for adding web service
+                // JMenuItems for slivka-based services
+
                 build_fetchdbmenu(webService);
                 for (JMenu item : wsmenu)
                 {
@@ -4674,17 +4682,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             int assocfiles = 0;
             if (filesmatched.size() > 0)
             {
-              if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false)
-                      || JvOptionPane.showConfirmDialog(thisaf,
-                              MessageManager.formatMessage(
-                                      "label.automatically_associate_structure_files_with_sequences_same_name",
-                                      new Object[]
-                                      { Integer.valueOf(filesmatched.size())
-                                              .toString() }),
-                              MessageManager.getString(
-                                      "label.automatically_associate_structure_files_by_name"),
-                              JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)
-
+              boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+              if (!autoAssociate)
+              {
+                String msg = MessageManager.formatMessage(
+                        "label.automatically_associate_structure_files_with_sequences_same_name",
+                        new Object[]
+                        { Integer.valueOf(filesmatched.size())
+                                .toString() });
+                String ttl = MessageManager.getString(
+                        "label.automatically_associate_structure_files_by_name");
+                int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
+                        ttl, JvOptionPane.YES_NO_OPTION);
+                autoAssociate = choice == JvOptionPane.YES_OPTION;
+              }
+              if (autoAssociate)
               {
                 for (Object[] fm : filesmatched)
                 {
@@ -4710,6 +4722,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   alignPanel.paintAlignment(true, false);
                 }
               }
+              else
+              {
+                /*
+                 * add declined structures as sequences
+                 */
+                for (Object[] o : filesmatched)
+                {
+                  filesnotmatched.add((String) o[0]);
+                }
+              }
             }
             if (filesnotmatched.size() > 0)
             {
@@ -5796,22 +5818,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
-  public void hmmerMenu_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup grp = getViewport().getSelectionGroup();
-    if (grp != null)
-    {
-      hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
-              + grp.getName());
-    }
-    else
-    {
-      hmmBuild.setText(MessageManager.getString("label.hmmbuild")
-              + " from Alignment");
-    }
-  }
-
-  @Override
   protected void loadVcf_actionPerformed()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(