X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=aba3c6f793685a12141f5439cdce10b82c3c703b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=da2dab6c00682d60dcf0f23cb3d2fad443733392;hpb=b7885c2f1d36f515354ede5793f5b3cddbc9db04;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index da2dab6..aba3c6f 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,216 +1,452 @@
-package jalview.ws;
-
-import java.util.Enumeration;
-import java.util.Vector;
-
-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.Pfam.class);
-  };
-  /**
-   * 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("" + 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[] 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));
-          }
-        }
-      }
-
-    }
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.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;
+
+/**
+ * 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()
+  {
+    this(true);
+  }
+
+  public SequenceFetcher(boolean addDas)
+  {
+    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);
+    if (addDas)
+    {
+      registerDasSequenceSources();
+    }
+  }
+
+  /**
+   * return an ordered list of database sources where non-das database classes
+   * appear before das database classes
+   */
+  public String[] getOrderedSupportedSources()
+  {
+    String[] srcs = this.getSupportedDb();
+    ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+    for (int i = 0; i < srcs.length; i++)
+    {
+      boolean das = false, skip = false;
+      String nm;
+      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.isA(DBRefSource.ALIGNMENTDB))
+        {
+          skip = true;
+        }
+        else
+        {
+          nm = dbs.getDbName();
+          if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+          {
+            if (nm.startsWith("das:"))
+            {
+              nm = nm.substring(4);
+              das = true;
+            }
+            break;
+          }
+        }
+      }
+      if (skip)
+      {
+        continue;
+      }
+      if (das)
+      {
+        dassrc.add(srcs[i]);
+      }
+      else
+      {
+        nondas.add(srcs[i]);
+      }
+    }
+    String[] tosort = nondas.toArray(new String[0]), sorted = nondas
+            .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
+
+    srcs = new String[sorted.length + dassrc.size()];
+    int i = 0;
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
+    {
+      srcs[i] = sorted[j];
+      sorted[j] = null;
+    }
+
+    sorted = dassrc.toArray(new String[0]);
+    tosort = dassrc.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);
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
+    {
+      srcs[i] = sorted[j];
+    }
+    return srcs;
+  }
+
+  /**
+   * return plaintext databse list 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++)
+    {
+      for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
+      {
+        String nm = dbs.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;
+    // construct array with all sources listed
+    srcs = new String[sorted.length + dassrc.size()];
+    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 [-nodas] [<DBNAME> [<ACCNO>]]\n"
+            + "With no arguments, all DbSources will be queried with their test Accession number.\n"
+            + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
+            + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
+    boolean withDas = true;
+    if (argv != null && argv.length > 0
+            && argv[0].toLowerCase().startsWith("-nodas"))
+    {
+      withDas = false;
+      String targs[] = new String[argv.length - 1];
+      System.arraycopy(argv, 1, targs, 0, targs.length);
+      argv = targs;
+    }
+    if (argv != null && argv.length > 0)
+    {
+      List<DbSourceProxy> sps = new SequenceFetcher(withDas)
+              .getSourceProxy(argv[0]);
+
+      if (sps != null)
+      {
+        for (DbSourceProxy sp : sps)
+        {
+          AlignmentI al = null;
+          try
+          {
+            al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
+                    .getTestQuery());
+          } catch (Exception e)
+          {
+            e.printStackTrace();
+            System.err.println("Error when retrieving "
+                    + (argv.length > 1 ? argv[1] : sp.getTestQuery())
+                    + " 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);
+      return;
+    }
+    ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
+    String[] dbSources = sfetcher.getSupportedDb();
+    for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
+    {
+      String db = dbSources[dbsource];
+      // skip me
+      if (db.equals(DBRefSource.PDB))
+      {
+        continue;
+      }
+      for (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()
+  {
+    // 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);
+        }
+      }
+    }
+  }
+
+}