X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=29d4ec790de4508477b4d0325d7dd2d5b5c1e98c;hb=20a4d7ddb86ee996f2b6617a0470922b83354c35;hp=adf386c7b9c1f21cc7e4b3201afcfa36ad5aeebc;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index adf386c..29d4ec7 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,405 +1,105 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- * 
- * This program 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 2
- * of the License, or (at your option) any later version.
- * 
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-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.dbsources.DasSequenceSource;
-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();
-    if (sources!=null)
-    {
-      for (int s=0; sources!=null && s<sources.length; s++)
-      {
-        addDasSequenceSource(sources[s]);
-      }
-    }
-    
-    Vector localsources = jalview.bin.Cache.getLocalDasSources();
-    if (localsources!=null)
-    {   
-      for (Enumeration ls = localsources.elements(); ls.hasMoreElements(); )
-      {
-        addDasSequenceSource((DasSource) ls.nextElement());
-      }
-    } 
-  }
-  /**
-   * Try to create and add a DasSequenceSource to the list of sources.
-   * @param source
-   * @return null if no source was added, or the new DasSequenceSource created
-   */
-  DasSequenceSource addDasSequenceSource(DasSource source) {
-    DasSequenceSource ds=null;
-    Das1Source d1s = null;
-    if (source.hasCapability("sequence"))
-    {
-      if (source instanceof Das2Source)
-      {
-          if (((Das2Source) source).hasDas1Capabilities())
-          {
-            try
-            {
-              d1s = org.biojava.dasobert.das2.DasSourceConverter
-                      .toDas1Source((Das2Source) source);
-            } catch (Exception e)
-            {
-              System.err.println("Ignoring DAS2 sequence source "
-                      + source.getNickname()
-                      + " - couldn't map to Das1Source.\n");
-              e.printStackTrace();
-            }
-          }
-        }
-        else
-        {
-          if (source instanceof Das1Source)
-          {
-            d1s = (Das1Source) source;
-          }
-        }
-      }
-      if (d1s != null)
-      {
-        DasCoordinateSystem[] css = d1s.getCoordinateSystem();
-        if (css==null || css.length==0)
-        {
-          // TODO: query das source directly to identify coordinate system... or
-          // have to make up a coordinate system
-          css = new DasCoordinateSystem[] { new DasCoordinateSystem()};
-          css[0].setName(d1s.getNickname());
-          css[0].setUniqueId(d1s.getNickname());
-        }
-        for (int c = 0; c < css.length; c++)
-        {
-          try
-          {
-            addDbRefSourceImpl(ds=new 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();
-          }
-        }
-      }
-      return ds;
-  }
-}
+/*
+ * 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.ext.ensembl.EnsemblGenomes;
+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.Uniprot;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.util.ArrayList;
+
+/**
+ * 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);
+    addDBRefSourceImpl(Pdb.class);
+    addDBRefSourceImpl(PfamFull.class);
+    addDBRefSourceImpl(PfamSeed.class);
+    addDBRefSourceImpl(RfamSeed.class);
+  }
+
+  /**
+   * return an ordered list of database sources excluding alignment only databases
+   */
+  public String[] getOrderedSupportedSources()
+  {
+    String[] srcs = this.getSupportedDb();
+    ArrayList<String> src = new ArrayList<>();
+
+    for (int i = 0; i < srcs.length; i++)
+    {
+      boolean skip = false;
+      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())
+        {
+          skip = true;
+        }
+      }
+      if (skip)
+      {
+        continue;
+      }
+      {
+        src.add(srcs[i]);
+      }
+    }
+    String[] tosort = src.toArray(new String[0]),
+            sorted = src.toArray(new String[0]);
+    for (int j = 0, jSize = sorted.length; j < jSize; j++)
+    {
+      tosort[j] = tosort[j].toLowerCase();
+    }
+    jalview.util.QuickSort.sort(tosort, sorted);
+    // construct array with all sources listed
+    int i = 0;
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
+    {
+      srcs[i] = sorted[j];
+    }
+    return srcs;
+  }
+}