X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FASequenceFetcher.java;h=09a7a95f3d3fdf8ea04e86d9378ccc1e2da3cf74;hb=d904a499f1863e96cd699e0c5f7f0f81710e8ad9;hp=c63e148a3293b4afafd74fb1f46d9f64130559f6;hpb=994985c6ff0ea1ebadb8e184e8090dbb780e3c10;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index c63e148..09a7a95 100644
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -23,11 +23,13 @@ import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.Stack;
 import java.util.Vector;
 
@@ -37,7 +39,7 @@ public class ASequenceFetcher
   /**
    * set of databases we can retrieve entries from
    */
-  protected Hashtable<String, List<DbSourceProxy>> FETCHABLEDBS;
+  protected Hashtable<String, Map<String, DbSourceProxy>> FETCHABLEDBS;
 
   public ASequenceFetcher()
   {
@@ -259,7 +261,26 @@ public class ASequenceFetcher
    */
   public List<DbSourceProxy> getSourceProxy(String db)
   {
-    List<DbSourceProxy> dbs = FETCHABLEDBS.get(db);
+    List<DbSourceProxy> dbs;
+    Map<String,DbSourceProxy> dblist = FETCHABLEDBS.get(db);
+    if (dblist==null) {return new ArrayList<DbSourceProxy>();};
+    if (dblist.size()>1) {
+      DbSourceProxy[] l=dblist.values().toArray(new DbSourceProxy[0]);
+      int i=0;
+      String[] nm=new String[l.length];
+      for (DbSourceProxy s:l)
+      {
+        nm[i++]=s.getDbName().toLowerCase();
+      }
+      jalview.util.QuickSort.sort(nm,l);
+      dbs = new ArrayList<DbSourceProxy>();
+      for (i=l.length-1;i>=0; i--)
+      {
+        dbs.add(l[i]);
+      }
+    } else {
+      dbs = new ArrayList<DbSourceProxy>(dblist.values());
+    }
     return dbs;
   }
 
@@ -311,15 +332,15 @@ public class ASequenceFetcher
     {
       if (FETCHABLEDBS == null)
       {
-        FETCHABLEDBS = new Hashtable<String, List<DbSourceProxy>>();
+        FETCHABLEDBS = new Hashtable<String, Map<String,DbSourceProxy>>();
       }
-      List<DbSourceProxy> slist = FETCHABLEDBS.get(proxy.getDbSource());
+      Map<String,DbSourceProxy> slist = FETCHABLEDBS.get(proxy.getDbSource());
       if (slist == null)
       {
         FETCHABLEDBS.put(proxy.getDbSource(),
-                slist = new ArrayList<DbSourceProxy>());
+                slist = new Hashtable<String,DbSourceProxy>());
       }
-      slist.add(proxy);
+      slist.put(proxy.getDbName(),proxy);
     }
   }
 
@@ -373,7 +394,7 @@ public class ASequenceFetcher
     while (dbs.hasMoreElements())
     {
       String dbn = (String) dbs.nextElement();
-      for (DbSourceProxy dbp : FETCHABLEDBS.get(dbn))
+      for (DbSourceProxy dbp : FETCHABLEDBS.get(dbn).values())
       {
         if (class1.isAssignableFrom(dbp.getClass()))
         {
@@ -387,4 +408,20 @@ public class ASequenceFetcher
     }
     return sources;
   }
+  public DbSourceProxy[] getDbSourceProxyInstances(
+          Class class1)
+  {
+    ArrayList<DbSourceProxy> prlist=new ArrayList<DbSourceProxy>();
+    for (String fetchable:getSupportedDb())
+    for (DbSourceProxy pr:getSourceProxy(fetchable))
+    {
+      if (class1.isInstance(pr)) {prlist.add(pr);}
+    }
+    if (prlist.size()==0)
+    {
+      return null;
+    }
+    return prlist.toArray(new DbSourceProxy[0]);
+  }
+
 }