X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=0d93cb82902834cbec7e09fbc49efd48235ff556;hb=2de36153a84ca246643cd28b2ce05e9f4159dd89;hp=073d448e3ffb7c9ff9bd5208fceb538ec6224c08;hpb=c0c5cf49bdc063815641e28d51aa0e77873f80fe;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 073d448..0d93cb8 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,5 +1,6 @@
 package jalview.ws;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Vector;
 
@@ -36,10 +37,62 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
     addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed alignment is 'default' for PFAM
     registerDasSequenceSources();
   }
   /**
+   * return an ordered list of database sources suitable for using in a GUI element
+   */
+  public String[] getOrderedSupportedSources() {
+    String[] srcs = this.getSupportedDb();
+    ArrayList dassrc = new ArrayList(),
+      nondas=new ArrayList();
+    for (int i=0;i<srcs.length;i++)
+    {
+      String nm = getSourceProxy(srcs[i]).getDbName();
+      if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.DasSequenceSource)
+      {
+        if (nm.startsWith("das:"))
+        {
+          nm = nm.substring(4);
+        }
+        dassrc.add(new String[] { srcs[i], nm.toUpperCase()} );
+      } else {
+        nondas.add(new String[] { srcs[i], nm.toUpperCase()} );
+      }
+    }
+    Object[] sorted = nondas.toArray();
+    String[] tosort = new String[sorted.length];
+    nondas.clear();
+    for (int j=0;j<sorted.length;j++)
+    {
+      tosort[j] = ((String[]) sorted[j])[1];
+    }
+    jalview.util.QuickSort.sort(tosort, sorted);
+    int i=0;
+    for (int j=sorted.length-1;j>=0; j--,i++)
+    {
+      srcs[i] = ((String[]) sorted[j])[0];
+      sorted[j] = null;
+    }
+
+    sorted = dassrc.toArray();
+    tosort = new String[sorted.length];
+    dassrc.clear();
+    for (int j=0;j<sorted.length;j++)
+    {
+      tosort[j] = ((String[]) sorted[j])[1];
+    }
+    jalview.util.QuickSort.sort(tosort, sorted);
+    for (int j=sorted.length-1;j>=0; j--,i++)
+    {
+      srcs[i] = ((String[]) sorted[j])[0];
+      sorted[j] = null;
+    }
+    return srcs;
+  }
+  /**
    * simple run method to test dbsources.
    * @param argv
    */