X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=0d93cb82902834cbec7e09fbc49efd48235ff556;hb=3d1147ffae5fbc5bdb7c80caa9655df656b8e67b;hp=e6fc3856ec3b916d5040c7d098efb5bcc1f27a9b;hpb=5d88ae6bbf1ea113cefcb43b7918b5baf560a76e;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index e6fc385..0d93cb8 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,16 +1,25 @@
 package jalview.ws;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
-import java.util.Hashtable;
 import java.util.Vector;
 
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasSource;
+
 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
@@ -23,44 +32,123 @@ 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
+    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
+   */
   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)
     {
+      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("Ignoring arguments. Future Usage = dbname:query1;query2;...");
+              .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());
+              .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)
@@ -73,25 +161,31 @@ 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 }));
           }
 
         }
@@ -136,32 +230,96 @@ 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));
           }
         }
       }
 
     }
   }
+  /**
+   * 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() {
+    DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();
+    for (int s=0;s<sources.length; s++)
+    {
+      Das1Source d1s=null;
+      if (sources[s].hasCapability("sequence"))
+      {
+        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];
+          }
+        }
+      }
+      if (d1s!=null)
+      {
+        DasCoordinateSystem[] css = d1s.getCoordinateSystem();
+        for (int c=0;c<css.length;c++)
+        {
+          try {
+            addDbRefSourceImpl(
+                    new jalview.ws.dbsources.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();
+          }
+        }
+      }
+          
+    }
+  }
+
 }