X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=208eb887dc787bb41085a2bc598989d2bc8fc840;hb=77e9dc41516acc93470931bcc5f344c67e819e70;hp=e6fc3856ec3b916d5040c7d098efb5bcc1f27a9b;hpb=5d88ae6bbf1ea113cefcb43b7918b5baf560a76e;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index e6fc385..208eb88 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,16 +1,19 @@
 package jalview.ws;
 
 import java.util.Enumeration;
-import java.util.Hashtable;
 import java.util.Vector;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
 
 /**
- * prototype of abstract sequence retrieval interface
+ * This is the the concrete implementation of the sequence retrieval interface
+ * and abstract class in jalview.ws.seqfetcher. This implements the run-time
+ * discovery of sequence database clients, and provides a hardwired main for testing all registered handlers. 
  * 
  */
 public class SequenceFetcher extends ASequenceFetcher
@@ -23,17 +26,12 @@ public class SequenceFetcher extends ASequenceFetcher
    */
   public SequenceFetcher()
   {
-    FETCHABLEDBS = new Hashtable();
-    FETCHABLEDBS.put(DBRefSource.EMBL,
-            new jalview.ws.dbsources.EmblSource());
-    FETCHABLEDBS.put(DBRefSource.EMBLCDS,
-            new jalview.ws.dbsources.EmblCdsSouce());
-    FETCHABLEDBS.put(DBRefSource.UNIPROT,
-            new jalview.ws.dbsources.Uniprot());
-    FETCHABLEDBS.put(DBRefSource.UP_NAME,
-            new jalview.ws.dbsources.Uniprot());
-    FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb());
-    FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam());
+    addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);
   };
 
   public static void main(String[] argv)
@@ -45,11 +43,11 @@ public class SequenceFetcher extends ASequenceFetcher
       System.out
               .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");
     }
-    SequenceFetcher sfetcher = new SequenceFetcher();
-    Enumeration e = sfetcher.FETCHABLEDBS.keys();
-    while (e.hasMoreElements())
+    ASequenceFetcher sfetcher = new SequenceFetcher();
+    String[] dbSources = sfetcher.getSupportedDb();
+    for (int dbsource=0; dbsource<dbSources.length;dbsource++)
     {
-      String db = (String) e.nextElement();
+      String db = dbSources[dbsource];
       // skip me
       if (db.equals(DBRefSource.PDB))
         continue;
@@ -73,25 +71,31 @@ public class SequenceFetcher extends ASequenceFetcher
                   dna, al.getSequencesArray());
           if (types != null)
           {
-            System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));
+            System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));
             for (int t = 0; t < types.length; t++)
             {
               System.out.println("Type: " + types[t]);
-              SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al
-                      .getSequencesArray(), dna, types[t]).getSequencesArray();
+              SequenceI[] prod = jalview.analysis.CrossRef
+                      .findXrefSequences(al.getSequencesArray(), dna,
+                              types[t]).getSequencesArray();
               System.out.println("Found "
                       + ((prod == null) ? "no" : "" + prod.length)
                       + " products");
-              if (prod!=null)
+              if (prod != null)
               {
-                for (int p=0; p<prod.length; p++)
+                for (int p = 0; p < prod.length; p++)
                 {
-                  System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
+                  System.out.println("Prod " + p + ": "
+                          + prod[p].getDisplayId(true));
                 }
               }
             }
-          } else {
-            noProds.addElement((dna ? new Object[] { al, al } : new Object[] { al }) ); 
+          }
+          else
+          {
+            noProds.addElement((dna ? new Object[]
+            { al, al } : new Object[]
+            { al }));
           }
 
         }
@@ -136,28 +140,42 @@ public class SequenceFetcher extends ASequenceFetcher
       System.err.flush();
 
     }
-    if (noProds.size()>0)
+    if (noProds.size() > 0)
     {
       Enumeration ts = noProds.elements();
       while (ts.hasMoreElements())
-        
+
       {
         Object[] typeSq = (Object[]) ts.nextElement();
-        boolean dna = (typeSq.length>1);
+        boolean dna = (typeSq.length > 1);
         AlignmentI al = (AlignmentI) typeSq[0];
-        System.out.println("Trying getProducts for "+al.getSequenceAt(0).getDisplayId(true));
-        System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));
-        // have a bash at finding the products amongst all the retrieved sequences.
-        SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al
-              .getSequencesArray(), dna, null, ds).getSequencesArray(); // note should test rather than throw away codon mapping (if present)
+        System.out.println("Trying getProducts for "
+                + al.getSequenceAt(0).getDisplayId(true));
+        System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));
+        // have a bash at finding the products amongst all the retrieved
+        // sequences.
+        SequenceI[] seqs = al.getSequencesArray();
+        Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
+                seqs, dna, null, ds);
         System.out.println("Found "
-                + ((prod == null) ? "no" : "" + prod.length)
-                + " products");
-        if (prod!=null)
+                + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");
+        if (prodal != null)
         {
-          for (int p=0; p<prod.length; p++)
+          SequenceI[] prod = prodal.getSequencesArray(); // note
+          // should
+          // test
+          // rather
+          // than
+          // throw
+          // away
+          // codon
+          // mapping
+          // (if
+          // present)
+            for (int p = 0; p < prod.length; p++)
           {
-            System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
+            System.out.println("Prod " + p + ": "
+                    + prod[p].getDisplayId(true));
           }
         }
       }