X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=d5b3d11e8ce5816d6c92d6708c64643745ac4fc6;hb=2a5cbe264ec842c1a0f93e6bd78294607a94e686;hp=524311192bff927d2568d1d29f71fb59744e73c2;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 5243111..d5b3d11 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,18 +1,40 @@
+/*
+ * 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 file is part of Jalview.
+ * 
+ * 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.
+ * 
+ * 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;
 
-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.dbsources.das.api.jalviewSourceI;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+
 /**
- * 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
@@ -25,44 +47,142 @@ 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.PfamFull.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
+    // alignment is
+    // 'default' for
+    // PFAM
+    addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
+    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.das.datamodel.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
+   */
   public static void main(String[] argv)
   {
     AlignmentI ds = null;
     Vector noProds = new Vector();
+    String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"
+            + "With no arguments, all DbSources will be queried with their test Accession number.\n"
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
     if (argv != null && argv.length > 0)
     {
-      System.out
-              .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");
+      DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);
+      if (sp != null)
+      {
+        AlignmentI al = null;
+        try
+        {
+          al = sp.getSequenceRecords(argv[1]);
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+          System.err.println("Error when retrieving " + argv[1] + " from "
+                  + argv[0] + "\nUsage: " + usage);
+        }
+        SequenceI[] prod = al.getSequencesArray();
+        if (al != null)
+        {
+          for (int p = 0; p < prod.length; p++)
+          {
+            System.out.println("Prod " + p + ": "
+                    + prod[p].getDisplayId(true) + " : "
+                    + prod[p].getDescription());
+          }
+        }
+        return;
+      }
+      else
+      {
+        System.err.println("Can't resolve " + argv[0]
+                + " as a database name. Allowed values are :\n"
+                + new SequenceFetcher().getSupportedDb());
+      }
+      System.out.println(usage);
     }
-    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;
       DbSourceProxy sp = sfetcher.getSourceProxy(db);
-      System.out
-              .println("" + db + ": retrieving test:" + sp.getTestQuery());
+      System.out.println("Source: " + sp.getDbName() + " (" + db
+              + "): retrieving test:" + sp.getTestQuery());
       AlignmentI al = null;
       try
       {
         al = sp.getSequenceRecords(sp.getTestQuery());
-        if (al != null && al.getHeight() > 0)
+        if (al != null && al.getHeight() > 0
+                && sp.getDbSourceProperties() != null)
         {
           boolean dna = sp.getDbSourceProperties().containsKey(
                   DBRefSource.DNACODINGSEQDB)
@@ -75,25 +195,31 @@ 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 }));
           }
 
         }
@@ -138,32 +264,69 @@ 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)
+                + ((prodal == null) ? "no" : "" + prodal.getHeight())
                 + " products");
-        if (prod!=null)
+        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));
           }
         }
       }
 
     }
   }
+
+  /**
+   * query the currently defined DAS source registry for sequence sources and
+   * add a DasSequenceSource instance for each source to the SequenceFetcher
+   * source list.
+   */
+  public void registerDasSequenceSources()
+  {
+    // TODO: define a context as a registry provider (either desktop,
+    // jalview.bin.cache, or something else).
+    for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry().getSources())
+    {
+      if (source.isSequenceSource())
+      {
+        List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
+        for (DbSourceProxy seqsrc : dassources)
+        {
+          addDbRefSourceImpl(seqsrc);
+        }
+      }
+    }
+  }
 }