fetch database references for all EBI db + selected das sequence sources or a specifi...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f5a1494..8f1aa46 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3642,30 +3642,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   private void resetWebServiceMenu()
   {
     webService.removeAll();
-    // Temporary hack - DBRef Fetcher always top level ws entry.
-    JMenuItem rfetch = new JMenuItem("Fetch DB References");
-    rfetch
-            .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
-    webService.add(rfetch);
-    rfetch.addActionListener(new ActionListener()
-    {
-
-      public void actionPerformed(ActionEvent e)
-      {
-        new Thread(new Runnable()
-        {
-
-          public void run()
-          {
-            new jalview.ws.DBRefFetcher(alignPanel.av
-                    .getSequenceSelection(), alignPanel.alignFrame)
-                    .fetchDBRefs(false);
-          }
-        }).start();
-
-      }
-
-    });
+    build_fetchdbmenu(webService);
   }
 
   /*
@@ -4184,6 +4161,86 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     return false;
   }
+  protected void build_fetchdbmenu(JMenu webService) {
+    // Temporary hack - DBRef Fetcher always top level ws entry.
+    // TODO We probably want to store a sequence database checklist in preferences and have checkboxes.. rather than individual sources selected here
+    JMenu rfetch = new JMenu("Fetch DB References");
+    rfetch
+            .setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
+    webService.add(rfetch);
+
+    JMenuItem fetchr = new JMenuItem("Standard Databases");
+    fetchr.setToolTipText("Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources");
+    fetchr.addActionListener(new ActionListener()
+    {
+
+      public void actionPerformed(ActionEvent e)
+      {
+        new Thread(new Runnable()
+        {
+
+          public void run()
+          {
+            new jalview.ws.DBRefFetcher(alignPanel.av
+                    .getSequenceSelection(), alignPanel.alignFrame)
+                    .fetchDBRefs(false);
+          }
+        }).start();
+
+      }
+
+    });
+    rfetch.add(fetchr);
+    JMenu dfetch = new JMenu();
+    rfetch.add(dfetch);
+    jalview.ws.SequenceFetcher sf = SequenceFetcher.getSequenceFetcherSingleton(this);
+    String[] otherdb = sf.getOrderedSupportedSources(); 
+    // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+    // jalview.util.QuickSort.sort(otherdb, otherdb);
+    int comp=0,mcomp=15;
+    String mname=null;
+    if (otherdb!=null && otherdb.length>0)
+    {
+      for (int i=0; i<otherdb.length; i++)
+      {
+        String dbname =sf.getSourceProxy(otherdb[i]).getDbName();
+        if (mname == null)
+        {
+          mname = "from '"+dbname+"'";
+        }
+        fetchr = new JMenuItem(otherdb[i]);
+        final String[] dassource = new String[] { otherdb[i] };
+        fetchr.addActionListener(new ActionListener()
+        {
+
+          public void actionPerformed(ActionEvent e)
+          {
+            new Thread(new Runnable()
+            {
+
+              public void run()
+              {
+                new jalview.ws.DBRefFetcher(alignPanel.av
+                        .getSequenceSelection(), alignPanel.alignFrame, dassource)
+                        .fetchDBRefs(false);
+              }
+            }).start();
+          }
+          
+        });
+        fetchr.setToolTipText("Retrieve from "+dbname);
+        dfetch.add(fetchr);
+        if (comp++==mcomp || i==(otherdb.length-1))
+        {
+          dfetch.setText(mname+" to '"+dbname+"'");
+          rfetch.add(dfetch);
+          dfetch = new JMenu();
+          mname = null;
+          comp=0;
+        }
+      }
+    }
+  }
 }
 
 class PrintThread extends Thread