X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=15cbf01120e7eebd8a857cb6558fadf4f81a519d;hb=942de34caf73a7d61104783c8d278c32eaf6b65d;hp=f53638234f3579da27b8edd81759cba378f60a59;hpb=fd29e047719a470cf304c5a41abfff5c1eac3ee8;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f536382..15cbf01 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3270,7 +3270,7 @@ public class AlignFrame
    * or just the selected set will be submitted for multiple alignment.
    *
    */
-  private jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+  public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
     // Now, check we have enough sequences
     AlignmentView msa = null;
@@ -3308,12 +3308,14 @@ public class AlignFrame
   }
 
   /**
-   * Decides what is submitted to a secondary structure prediction service,
-   * the currently selected sequence, or the currently selected alignment
+   * Decides what is submitted to a secondary structure prediction service:
+   * the first sequence in the alignment, or in the current selection,
+   * or, if the alignment is 'aligned' (ie padded with gaps), then the
+   * currently selected region or the whole alignment.
    * (where the first sequence in the set is the one that the prediction
    * will be for).
    */
-  AlignmentView gatherSeqOrMsaForSecStrPrediction()
+  public AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
    AlignmentView seqs = null;
 
@@ -3475,43 +3477,9 @@ public class AlignFrame
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.
               get(i);
-          final JMenuItem method = new JMenuItem(sh.getName());
-          method.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              AlignmentView msa = gatherSequencesForAlignment();
-              new jalview.ws.MsaWSClient(sh, title, msa,
-                                         false, true,
-                                         viewport.getAlignment().getDataset(),
-                                         af);
-
-            }
-
-          });
-          msawsmenu.add(method);
-          // Deal with services that we know accept partial alignments.
-          // TODO: this should be a service property - ie sh.getProperty("submitGaps")==Boolean.true
-          if (sh.getName().indexOf("lustal") > -1)
-          {
-            // We know that ClustalWS can accept partial alignments for refinement.
-            final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");
-            methodR.addActionListener(new ActionListener()
-            {
-              public void actionPerformed(ActionEvent e)
-              {
-                AlignmentView msa = gatherSequencesForAlignment();
-                new jalview.ws.MsaWSClient(sh, title, msa,
-                                           true, true,
-                                           viewport.getAlignment().getDataset(),
-                                           af);
-
-              }
-
-            });
-            msawsmenu.add(methodR);
-
-          }
+          jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+          impl.attachWSMenuEntry(msawsmenu, this);
+        
         }
         wsmenu.add(msawsmenu);
       }
@@ -3523,105 +3491,24 @@ public class AlignFrame
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
               secstrpr.get(i);
-          final JMenuItem method = new JMenuItem(sh.getName());
-          method.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
-              if (msa.getSequences().length == 1)
-              {
-                // Single Sequence prediction
-                new jalview.ws.JPredClient(sh, title, false, msa, af, true);
-              }
-              else
-              {
-                if (msa.getSequences().length > 1)
-                {
-                  // Sequence profile based prediction
-                  new jalview.ws.JPredClient(sh,
-                      title, true, msa, af, true);
-                }
-              }
-            }
-          });
-          secstrmenu.add(method);
+          jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+          impl.attachWSMenuEntry(secstrmenu, this);
         }
         wsmenu.add(secstrmenu);
-/*      }
+      }
       if (seqsrch!=null)
       {
-        // Add any secondary structure prediction services
+        // Add any sequence search services
         final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
-        Hashtable dbsrchs = new Hashtable();
-        JMenu defmenu;
-        dbsrchs.put("<default>", defmenu = new JMenu("Default Database"));
         for (int i = 0, j = seqsrch.size(); i < j; i++)
         {
           final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)
               seqsrch.elementAt(i);
-          
-          String dbs[] = null;
-          try {
-            dbs = new jalview.ws.SeqSearchWSClient(sh).getSupportedDatabases();
-          } catch (Exception e)
-          {
-            jalview.bin.Cache.log.warn("Database list request failed, so disabling SeqSearch Service client "+sh.getName()+" at "+sh.getEndpointURL(), e);
-            continue;
-          }
-          JMenuItem method;
-          // do default entry
-          defmenu.add(method = new JMenuItem(sh.getName()));
-          method.addActionListener(new ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              // use same input gatherer as for secondary structure prediction
-              // we could actually parameterise the gatherer method here...
-              AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
-              new jalview.ws.SeqSearchWSClient(sh, title, msa, null, 
-                      viewport.getAlignment().getDataset(),
-                      af);
-              }
-            }
-          );
-          // add entry for each database the service supports
-          for (int db=0; dbs!=null && db<dbs.length; db++)
-          {
-            JMenu dbmenu = (JMenu) dbsrchs.get(dbs[db]);
-            if (dbmenu==null)
-            {
-              dbsrchs.put(dbs[db], dbmenu = new JMenu(dbs[db]));
-            }
-            // add the client handler code for this service
-            dbmenu.add(method = new JMenuItem(sh.getName()));
-            final String searchdb = dbs[db];
-            method.addActionListener(new ActionListener()
-            {
-              public void actionPerformed(ActionEvent e)
-              {
-                AlignmentView msa = gatherSeqOrMsaForSecStrPrediction();
-                new jalview.ws.SeqSearchWSClient(sh, title, msa, searchdb, 
-                          viewport.getAlignment().getDataset(),
-                          af);
-              }
-            });
-          }
-        }
-        // add the databases onto the seqsearch menu
-        Enumeration e = dbsrchs.elements();
-        while (e.hasMoreElements())
-        {
-          Object el = e.nextElement();
-          if (el instanceof JMenu)
-          {
-            seqsrchmenu.add((JMenu) el);
-          } else {
-            seqsrchmenu.add((JMenuItem) el);
-          }
+          jalview.ws.WSClient impl = jalview.ws.Discoverer.getServiceClient(sh);
+          impl.attachWSMenuEntry(seqsrchmenu, this);
         }
         // finally, add the whole shebang onto the webservices menu
-        wsmenu.add(seqsrchmenu); */
+        wsmenu.add(seqsrchmenu); 
       }
       resetWebServiceMenu();
       for (int i = 0, j = wsmenu.size(); i < j; i++)
@@ -4024,6 +3911,7 @@ public void drop(DropTargetDropEvent evt)
       {
         
         alignPanel.adjustAnnotationHeight();
+        viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
         alignPanel.paintAlignment(true);
       }