X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=184ffeb58ba6d1c9f0fbcde5ef8bdd73542c1bd5;hb=ef887ebe817cd6595b6275f5f51001677c377214;hp=5654c540868079cd60d61c934268a1af85a0ac42;hpb=1d9ed8ea1705fd5ed1cdc569fa1574363ad0a749;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5654c54..184ffeb 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -53,6 +53,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
@@ -61,9 +62,10 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.AptxInit;
-import jalview.ext.archaeopteryx.JalviewBinding;
 import jalview.ext.forester.io.SupportedTreeFileFilter;
 import jalview.ext.forester.io.TreeParser;
+import jalview.ext.treeviewer.ExternalTreeFrame;
+import jalview.ext.treeviewer.ExternalTreeViewerBindingI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
@@ -90,6 +92,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
@@ -139,6 +142,7 @@ import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -154,7 +158,8 @@ import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
-import org.forester.archaeopteryx.MainFrame;
+import org.forester.archaeopteryx.webservices.PhylogeniesWebserviceClient;
+import org.forester.archaeopteryx.webservices.WebservicesManager;
 
 /**
  * DOCUMENT ME!
@@ -3760,7 +3765,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .get(viewport.getSequenceSetId());
     List<TreePanel> treePanels = new ArrayList<>();
 
-    Map<MainFrame, JalviewBinding> aptxFrames = AptxInit.getAllAptxFrames();
+    Map<ExternalTreeFrame, ExternalTreeViewerBindingI> aptxFrames = AptxInit
+            .getAllAptxFrames();
 
     for (Component comp : comps)
     {
@@ -3780,19 +3786,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     sortByTreeMenu.setVisible(true);
 
-    for (Map.Entry<MainFrame, JalviewBinding> aptxFrameWithBinding : aptxFrames
+    for (Entry<ExternalTreeFrame, ExternalTreeViewerBindingI> aptxFrameWithBinding : aptxFrames
             .entrySet())
     {
-      MainFrame aptxFrame = aptxFrameWithBinding.getKey();
-      JalviewBinding binding = aptxFrameWithBinding.getValue();
+      ExternalTreeFrame aptxFrame = aptxFrameWithBinding.getKey();
+      ExternalTreeViewerBindingI binding = aptxFrameWithBinding.getValue();
 
       // future support for multiple tabs
       // for (org.forester.archaeopteryx.TreePanel aptxTree : aptxFrame
       // .getMainPanel().getTreePanels())
       {
         final JMenuItem item = new JMenuItem(
-                aptxFrame.getMainPanel().getCurrentTreePanel()
-                        .getPhylogeny().getName());
+                aptxFrame.getTree().getTreeName());
 
           item.addActionListener(new ActionListener()
           {
@@ -3946,33 +3951,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void loadTreeBaseStudy_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb(0);
+    chooseTreeDb(0, null);
 
   }
 
   @Override
   protected void loadTreeBase_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb(1);
+    chooseTreeDb(1, null);
 
   }
   @Override
   protected void loadTreePfam_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb(2);
+
+    // only DBRefs of first sequence are checked for matching DB for now,
+    // iterating through them all seems excessive
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+    String dbId = null;
+    for (DBRefEntry pfamRef : DBRefUtils
+            .searchRefsForSource(seq.getDBRefs(), "pfam"))
+    {
+      if (pfamRef.getAccessionId().startsWith("PF"))
+      {
+        dbId = pfamRef.getAccessionId().replaceAll("[A-Za-z]", "");
+      }
+
+    }
+    chooseTreeDb(2, dbId);
 
   }
   @Override
   protected void loadTreeFam_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb(3);
+    chooseTreeDb(3, null);
 
   }
 
   @Override
   protected void loadTreeOfLife_actionPerformed(ActionEvent e)
   {
-    chooseTreeDb(4);
+    chooseTreeDb(4, null);
 
   }
 
@@ -4082,9 +4101,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param databaseIndex
    */
-  public void chooseTreeDb(int databaseIndex)
-  {
-    AptxInit.createInstancesFromDb(databaseIndex, viewport);
+  public void chooseTreeDb(int databaseIndex, String defaultIdentifier)
+  {
+    final WebservicesManager webservices_manager = WebservicesManager
+            .getInstance();
+    final PhylogeniesWebserviceClient client = webservices_manager
+            .getAvailablePhylogeniesWebserviceClient(databaseIndex);
+    String identifier = JvOptionPane
+            .showInternalInputDialog(Desktop.desktop,
+                    client.getInstructions() + "\n(Reference: "
+                            + client.getReference() + ")",
+                    client.getDescription(), JvOptionPane.QUESTION_MESSAGE,
+                    null, null, defaultIdentifier)
+            .toString();
+
+    AptxInit.createInstancesFromDb(client, identifier, viewport);
   }
 
   public TreePanel showNewickTree(NewickFile nf, String treeTitle)