X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=ef5cd9151eddb43b8fddc35bc47cc6543c42ced0;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b20ebbb5f2d611b1a6d20f3e31fcc958cd525d13;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index b20ebbb..ef5cd91 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.ws;
 
@@ -31,6 +30,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.ws.dbsources.DasSequenceSource;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -58,9 +58,11 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
     addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
     addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
-                                                              // alignment is
-                                                              // 'default' for
-                                                              // PFAM
+    // alignment is
+    // 'default' for
+    // PFAM
+    addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
     registerDasSequenceSources();
   }
 
@@ -319,58 +321,89 @@ public class SequenceFetcher extends ASequenceFetcher
   {
     DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher
             .getDASSources();
-    for (int s = 0; s < sources.length; s++)
+    if (sources != null)
     {
-      Das1Source d1s = null;
-      if (sources[s].hasCapability("sequence"))
+      for (int s = 0; sources != null && s < sources.length; s++)
       {
-        if (sources[s] instanceof Das2Source)
-        {
-          if (((Das2Source) sources[s]).hasDas1Capabilities())
-          {
-            try
-            {
-              d1s = org.biojava.dasobert.das2.DasSourceConverter
-                      .toDas1Source((Das2Source) sources[s]);
-            } catch (Exception e)
-            {
-              System.err.println("Ignoring DAS2 sequence source "
-                      + sources[s].getNickname()
-                      + " - couldn't map to Das1Source.\n");
-              e.printStackTrace();
-            }
-          }
-        }
-        else
-        {
-          if (sources[s] instanceof Das1Source)
-          {
-            d1s = (Das1Source) sources[s];
-          }
-        }
+        addDasSequenceSource(sources[s]);
       }
-      if (d1s != null)
+    }
+
+    Vector localsources = jalview.bin.Cache.getLocalDasSources();
+    if (localsources != null)
+    {
+      for (Enumeration ls = localsources.elements(); ls.hasMoreElements();)
       {
-        DasCoordinateSystem[] css = d1s.getCoordinateSystem();
-        for (int c = 0; c < css.length; c++)
+        addDasSequenceSource((DasSource) ls.nextElement());
+      }
+    }
+  }
+
+  /**
+   * Try to create and add a DasSequenceSource to the list of sources.
+   * 
+   * @param source
+   * @return null if no source was added, or the new DasSequenceSource created
+   */
+  DasSequenceSource addDasSequenceSource(DasSource source)
+  {
+    DasSequenceSource ds = null;
+    Das1Source d1s = null;
+    if (source.hasCapability("sequence"))
+    {
+      if (source instanceof Das2Source)
+      {
+        if (((Das2Source) source).hasDas1Capabilities())
         {
           try
           {
-            addDbRefSourceImpl(new jalview.ws.dbsources.DasSequenceSource(
-                    "das:" + d1s.getNickname() + " (" + css[c].getName()
-                            + ")", css[c].getName(), d1s, css[c]));
+            d1s = org.biojava.dasobert.das2.DasSourceConverter
+                    .toDas1Source((Das2Source) source);
           } catch (Exception e)
           {
-            System.err.println("Ignoring sequence coord system " + c + " ("
-                    + css[c].getName() + ") for source "
-                    + d1s.getNickname()
-                    + "- threw exception when constructing fetcher.\n");
+            System.err.println("Ignoring DAS2 sequence source "
+                    + source.getNickname()
+                    + " - couldn't map to Das1Source.\n");
             e.printStackTrace();
           }
         }
       }
-
+      else
+      {
+        if (source instanceof Das1Source)
+        {
+          d1s = (Das1Source) source;
+        }
+      }
+    }
+    if (d1s != null)
+    {
+      DasCoordinateSystem[] css = d1s.getCoordinateSystem();
+      if (css == null || css.length == 0)
+      {
+        // TODO: query das source directly to identify coordinate system... or
+        // have to make up a coordinate system
+        css = new DasCoordinateSystem[]
+        { new DasCoordinateSystem() };
+        css[0].setName(d1s.getNickname());
+        css[0].setUniqueId(d1s.getNickname());
+      }
+      for (int c = 0; c < css.length; c++)
+      {
+        try
+        {
+          addDbRefSourceImpl(ds = new DasSequenceSource("das:"
+                  + d1s.getNickname() + " (" + css[c].getName() + ")",
+                  css[c].getName(), d1s, css[c]));
+        } catch (Exception e)
+        {
+          System.err.println("Ignoring sequence coord system " + c + " ("
+                  + css[c].getName() + ") for source " + d1s.getNickname()
+                  + "- threw exception when constructing fetcher.\n");
+          e.printStackTrace();
+        }
+      }
     }
+    return ds;
   }
-
 }