X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=10a2b282ddaefeefa447880c2f494ede691cf325;hb=6f2c3b8cb30d8ccf7ff9ab949a7b244f0c415bc1;hp=e6fc3856ec3b916d5040c7d098efb5bcc1f27a9b;hpb=5d88ae6bbf1ea113cefcb43b7918b5baf560a76e;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index e6fc385..10a2b28 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,167 +1,135 @@
-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;
-
-/**
- * prototype of abstract sequence retrieval interface
- * 
- */
-public class SequenceFetcher extends ASequenceFetcher
-{
-  /**
-   * Thread safe construction of database proxies TODO: extend to a configurable
-   * database plugin mechanism where classes are instantiated by reflection and
-   * queried for their DbRefSource and version association.
-   * 
-   */
-  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());
-  };
-
-  public static void main(String[] argv)
-  {
-    AlignmentI ds = null;
-    Vector noProds = new Vector();
-    if (argv != null && argv.length > 0)
-    {
-      System.out
-              .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");
-    }
-    SequenceFetcher sfetcher = new SequenceFetcher();
-    Enumeration e = sfetcher.FETCHABLEDBS.keys();
-    while (e.hasMoreElements())
-    {
-      String db = (String) e.nextElement();
-      // skip me
-      if (db.equals(DBRefSource.PDB))
-        continue;
-      DbSourceProxy sp = sfetcher.getSourceProxy(db);
-      System.out
-              .println("" + db + ": retrieving test:" + sp.getTestQuery());
-      AlignmentI al = null;
-      try
-      {
-        al = sp.getSequenceRecords(sp.getTestQuery());
-        if (al != null && al.getHeight() > 0)
-        {
-          boolean dna = sp.getDbSourceProperties().containsKey(
-                  DBRefSource.DNACODINGSEQDB)
-                  || sp.getDbSourceProperties().containsKey(
-                          DBRefSource.DNASEQDB)
-                  || sp.getDbSourceProperties().containsKey(
-                          DBRefSource.CODINGSEQDB);
-          // try and find products
-          String types[] = jalview.analysis.CrossRef.findSequenceXrefTypes(
-                  dna, al.getSequencesArray());
-          if (types != null)
-          {
-            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();
-              System.out.println("Found "
-                      + ((prod == null) ? "no" : "" + prod.length)
-                      + " products");
-              if (prod!=null)
-              {
-                for (int p=0; p<prod.length; p++)
-                {
-                  System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
-                }
-              }
-            }
-          } else {
-            noProds.addElement((dna ? new Object[] { al, al } : new Object[] { al }) ); 
-          }
-
-        }
-      } catch (Exception ex)
-      {
-        System.out.println("ERROR:Failed to retrieve test query.");
-        ex.printStackTrace(System.out);
-      }
-      if (al == null)
-      {
-        System.out.println("ERROR:No alignment retrieved.");
-        StringBuffer raw = sp.getRawRecords();
-        if (raw != null)
-          System.out.println(raw.toString());
-        else
-          System.out.println("ERROR:No Raw results.");
-      }
-      else
-      {
-        System.out.println("Retrieved " + al.getHeight() + " sequences.");
-        for (int s = 0; s < al.getHeight(); s++)
-        {
-          SequenceI sq = al.getSequenceAt(s);
-          while (sq.getDatasetSequence() != null)
-          {
-            sq = sq.getDatasetSequence();
-
-          }
-          if (ds == null)
-          {
-            ds = new Alignment(new SequenceI[]
-            { sq });
-
-          }
-          else
-          {
-            ds.addSequence(sq);
-          }
-        }
-      }
-      System.out.flush();
-      System.err.flush();
-
-    }
-    if (noProds.size()>0)
-    {
-      Enumeration ts = noProds.elements();
-      while (ts.hasMoreElements())
-        
-      {
-        Object[] typeSq = (Object[]) ts.nextElement();
-        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("Found "
-                + ((prod == null) ? "no" : "" + prod.length)
-                + " products");
-        if (prod!=null)
-        {
-          for (int p=0; p<prod.length; p++)
-          {
-            System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
-          }
-        }
-      }
-
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws;
+
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.DBRefSource;
+import jalview.ext.ensembl.EnsemblGene;
+import jalview.ws.dbsources.Uniprot;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+/**
+ * Thread safe construction of database proxies. This implements the run-time
+ * discovery of sequence database clients.
+ * 
+ * TODO: extend to a configurable database plugin mechanism where classes are
+ * instantiated by reflection and queried for their DbRefSource and version
+ * association.
+ */
+public class SequenceFetcher extends ASequenceFetcher implements ApplicationSingletonI
+{
+  /*
+   * set a mock fetcher here for testing only - reset to null afterwards
+   */
+  private static SequenceFetcher mockFetcher;
+
+  /**
+   * Returns a new SequenceFetcher singleton, or a mock object if one has been
+   * set.
+   * 
+   * @return
+   */
+  public static SequenceFetcher getInstance()
+  {
+    return mockFetcher != null ? mockFetcher
+            : (SequenceFetcher) ApplicationSingletonProvider
+                    .getInstance(SequenceFetcher.class);
+  }
+
+  /**
+   * Set the instance object to use (intended for unit testing with mock
+   * objects).
+   * 
+   * Be sure to reset to null in the tearDown method of any tests!
+   * 
+   * @param sf
+   */
+  public static void setSequenceFetcher(SequenceFetcher sf)
+  {
+    mockFetcher = sf;
+  }
+
+  /**
+   * 
+   * This public constructor is only is for use by testng to anonymously
+   * subclass SequenceFetcher.
+   * 
+   * 
+   */
+  public SequenceFetcher()
+  {
+    addAllDatabases();
+  }
+
+  public void addAllDatabases()
+  {
+    addDBRefSourceImpl(EnsemblGene.class); // includes EnsemblGenomes.class
+    addDBRefSourceImpl(Uniprot.class); // includes UniprotName.class
+    // addDBRefSourceImpl(EmblSource.class);
+    // addDBRefSourceImpl(EmblCdsSource.class);
+    // addDBRefSourceImpl(Pdb.class);
+    // addDBRefSourceImpl(PfamFull.class);
+    // addDBRefSourceImpl(PfamSeed.class);
+    // addDBRefSourceImpl(RfamSeed.class);
+    addDBRefSourceImpl(DBRefSource.EMBL,
+            "jalview.ws.dbsources.EmblSource");
+    addDBRefSourceImpl(DBRefSource.EMBLCDS,
+            "jalview.ws.dbsources.EmblCdsSource");
+    addDBRefSourceImpl(DBRefSource.PDB, "jalview.ws.dbsources.Pdb");
+    addDBRefSourceImpl(DBRefSource.PFAM_FULL,
+            "jalview.ws.dbsources.PfamFull");
+    addDBRefSourceImpl(DBRefSource.PFAM_SEED,
+            "jalview.ws.dbsources.PfamSeed");
+    addDBRefSourceImpl(DBRefSource.RFAM_SEED,
+            "jalview.ws.dbsources.RfamSeed");
+  }
+
+  /**
+   * return an ordered list of database sources excluding alignment only
+   * databases
+   */
+  public String[] getNonAlignmentSources()
+  {
+    String[] srcs = this.getSupportedDb();
+    List<String> src = new ArrayList<>();
+    outer: for (int i = 0; i < srcs.length; i++)
+    {
+      for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
+      {
+        // Skip the alignment databases for the moment - they're not useful for
+        // verifying a single sequence against its reference source
+        if (dbs.isAlignmentSource())
+        {
+          continue outer;
+        }
+      }
+      src.add(srcs[i]);
+    }
+    Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+    return src.toArray(new String[src.size()]);
+  }
+}