JAL-2847 if pfam id is detected in first sequence its shown in db query

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5654c54..c76ce56 100644 (file)
--- 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;
@@ -90,6 +91,7 @@ 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;
@@ -3946,33 +3948,46 @@ 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
+    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 +4097,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param databaseIndex
    */
-  public void chooseTreeDb(int databaseIndex)
+  public void chooseTreeDb(int databaseIndex, String defaultIdentifier)
   {
-    AptxInit.createInstancesFromDb(databaseIndex, viewport);
+    AptxInit.createInstancesFromDb(databaseIndex, viewport,
+            defaultIdentifier);
   }
 
   public TreePanel showNewickTree(NewickFile nf, String treeTitle)