X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=518e7c6025ca2f57f65829e248cf9a3f1c626911;hb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;hp=0d93cb82902834cbec7e09fbc49efd48235ff556;hpb=2de36153a84ca246643cd28b2ce05e9f4159dd89;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 0d93cb8..518e7c6 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,325 +1,99 @@
-package jalview.ws;
-
-import java.util.ArrayList;
-import java.util.Enumeration;
-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;
-
-/**
- * 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
-{
-  /**
-   * 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()
-  {
-    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(usage);
-    }
-    ASequenceFetcher sfetcher = new SequenceFetcher();
-    String[] dbSources = sfetcher.getSupportedDb();
-    for (int dbsource=0; dbsource<dbSources.length;dbsource++)
-    {
-      String db = dbSources[dbsource];
-      // skip me
-      if (db.equals(DBRefSource.PDB))
-        continue;
-      DbSourceProxy sp = sfetcher.getSourceProxy(db);
-      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 && sp.getDbSourceProperties()!=null)
-        {
-          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[] seqs = al.getSequencesArray();
-        Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
-                seqs, dna, null, ds);
-        System.out.println("Found "
-                + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");
-        if (prodal != null)
-        {
-          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));
-          }
-        }
-      }
-
-    }
-  }
-  /**
-   * 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();
-          }
-        }
-      }
-          
-    }
-  }
-
-}
+/*
+ * 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.ext.ensembl.EnsemblGene;
+import jalview.ws.dbsources.EBIAlfaFold;
+import jalview.ws.dbsources.EmblCdsSource;
+import jalview.ws.dbsources.EmblSource;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.PfamFull;
+import jalview.ws.dbsources.PfamSeed;
+import jalview.ws.dbsources.RfamSeed;
+import jalview.ws.dbsources.TDBeacons;
+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;
+
+/**
+ * This implements the run-time discovery of sequence database clients.
+ * 
+ */
+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()
+  {
+    addDBRefSourceImpl(EnsemblGene.class);
+    // addDBRefSourceImpl(EnsemblGenomes.class);
+    addDBRefSourceImpl(EmblSource.class);
+    addDBRefSourceImpl(EmblCdsSource.class);
+    addDBRefSourceImpl(Uniprot.class);
+    // not a sequence source yet
+    // addDBRefSourceImpl(TDBeacons.class);
+    addDBRefSourceImpl(Pdb.class);
+    addDBRefSourceImpl(PfamFull.class);
+    addDBRefSourceImpl(PfamSeed.class);
+    addDBRefSourceImpl(RfamSeed.class);
+    addDBRefSourceImpl(EBIAlfaFold.class);
+  }
+
+  /**
+   * return an ordered list of database sources excluding alignment only
+   * databases
+   */
+  public String[] getNonAlignmentSources()
+  {
+    String[] srcs = this.getSupportedDb();
+    List<String> src = new ArrayList<>();
+
+    for (int i = 0; i < srcs.length; i++)
+    {
+      boolean accept = true;
+      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())
+        {
+          accept = false;
+          break;
+        }
+      }
+      if (accept)
+      {
+        src.add(srcs[i]);
+      }
+    }
+
+    Collections.sort(src, String.CASE_INSENSITIVE_ORDER);
+    return src.toArray(new String[src.size()]);
+  }
+}