test/jalview/ws/SequenceFetcherTest.java

   1 package jalview.ws;
   2
   3 import jalview.datamodel.Alignment;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.DBRefSource;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.ws.seqfetcher.ASequenceFetcher;
   8 import jalview.ws.seqfetcher.DbSourceProxy;
   9
  10 import java.util.Enumeration;
  11 import java.util.List;
  12 import java.util.Vector;
  13
  14 public class SequenceFetcherTest
  15 {
  16
  17   /**
  18    * simple run method to test dbsources.
  19    *
  20    * @param argv
  21    */
  22   public static void main(String[] argv)
  23   {
  24     // TODO: extracted from SequenceFetcher - convert to proper unit test with
  25     // assertions
  26
  27     AlignmentI ds = null;
  28     Vector noProds = new Vector();
  29     String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
  30             + "With no arguments, all DbSources will be queried with their test Accession number.\n"
  31             + "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"
  32             + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
  33             + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
  34     boolean withDas = true;
  35     if (argv != null && argv.length > 0
  36             && argv[0].toLowerCase().startsWith("-nodas"))
  37     {
  38       withDas = false;
  39       String targs[] = new String[argv.length - 1];
  40       System.arraycopy(argv, 1, targs, 0, targs.length);
  41       argv = targs;
  42     }
  43     if (argv != null && argv.length > 0)
  44     {
  45       List<DbSourceProxy> sps = new SequenceFetcher(withDas)
  46               .getSourceProxy(argv[0]);
  47
  48       if (sps != null)
  49       {
  50         for (DbSourceProxy sp : sps)
  51         {
  52           AlignmentI al = null;
  53           try
  54           {
  55             al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
  56                     .getTestQuery());
  57           } catch (Exception e)
  58           {
  59             e.printStackTrace();
  60             System.err.println("Error when retrieving "
  61                     + (argv.length > 1 ? argv[1] : sp.getTestQuery())
  62                     + " from " + argv[0] + "\nUsage: " + usage);
  63           }
  64           SequenceI[] prod = al.getSequencesArray();
  65           if (al != null)
  66           {
  67             for (int p = 0; p < prod.length; p++)
  68             {
  69               System.out.println("Prod " + p + ": "
  70                       + prod[p].getDisplayId(true) + " : "
  71                       + prod[p].getDescription());
  72             }
  73           }
  74         }
  75         return;
  76       }
  77       else
  78       {
  79         System.err.println("Can't resolve " + argv[0]
  80                 + " as a database name. Allowed values are :\n"
  81                 + new SequenceFetcher().getSupportedDb());
  82       }
  83       System.out.println(usage);
  84       return;
  85     }
  86     ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
  87     String[] dbSources = sfetcher.getSupportedDb();
  88     for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
  89     {
  90       String db = dbSources[dbsource];
  91       // skip me
  92       if (db.equals(DBRefSource.PDB))
  93       {
  94         continue;
  95       }
  96       for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
  97       {
  98         System.out.println("Source: " + sp.getDbName() + " (" + db
  99                 + "): retrieving test:" + sp.getTestQuery());
 100         AlignmentI al = null;
 101         try
 102         {
 103           al = sp.getSequenceRecords(sp.getTestQuery());
 104           if (al != null && al.getHeight() > 0)
 105           {
 106             boolean dna = sp.isDnaCoding();
 107             // try and find products
 108             String types[] = jalview.analysis.CrossRef
 109                     .findSequenceXrefTypes(dna, al.getSequencesArray());
 110             if (types != null)
 111             {
 112               System.out.println("Xref Types for: "
 113                       + (dna ? "dna" : "prot"));
 114               for (int t = 0; t < types.length; t++)
 115               {
 116                 System.out.println("Type: " + types[t]);
 117                 SequenceI[] prod = jalview.analysis.CrossRef
 118                         .findXrefSequences(al.getSequencesArray(), dna,
 119                                 types[t]).getSequencesArray();
 120                 System.out.println("Found "
 121                         + ((prod == null) ? "no" : "" + prod.length)
 122                         + " products");
 123                 if (prod != null)
 124                 {
 125                   for (int p = 0; p < prod.length; p++)
 126                   {
 127                     System.out.println("Prod " + p + ": "
 128                             + prod[p].getDisplayId(true));
 129                   }
 130                 }
 131               }
 132             }
 133             else
 134             {
 135               noProds.addElement((dna ? new Object[] { al, al }
 136                       : new Object[] { al }));
 137             }
 138
 139           }
 140         } catch (Exception ex)
 141         {
 142           System.out.println("ERROR:Failed to retrieve test query.");
 143           ex.printStackTrace(System.out);
 144         }
 145
 146         if (al == null)
 147         {
 148           System.out.println("ERROR:No alignment retrieved.");
 149           StringBuffer raw = sp.getRawRecords();
 150           if (raw != null)
 151           {
 152             System.out.println(raw.toString());
 153           }
 154           else
 155           {
 156             System.out.println("ERROR:No Raw results.");
 157           }
 158         }
 159         else
 160         {
 161           System.out.println("Retrieved " + al.getHeight() + " sequences.");
 162           for (int s = 0; s < al.getHeight(); s++)
 163           {
 164             SequenceI sq = al.getSequenceAt(s);
 165             while (sq.getDatasetSequence() != null)
 166             {
 167               sq = sq.getDatasetSequence();
 168
 169             }
 170             if (ds == null)
 171             {
 172               ds = new Alignment(new SequenceI[] { sq });
 173
 174             }
 175             else
 176             {
 177               ds.addSequence(sq);
 178             }
 179           }
 180         }
 181         System.out.flush();
 182         System.err.flush();
 183
 184       }
 185       if (noProds.size() > 0)
 186       {
 187         Enumeration ts = noProds.elements();
 188         while (ts.hasMoreElements())
 189
 190         {
 191           Object[] typeSq = (Object[]) ts.nextElement();
 192           boolean dna = (typeSq.length > 1);
 193           AlignmentI al = (AlignmentI) typeSq[0];
 194           System.out.println("Trying getProducts for "
 195                   + al.getSequenceAt(0).getDisplayId(true));
 196           System.out.println("Search DS Xref for: "
 197                   + (dna ? "dna" : "prot"));
 198           // have a bash at finding the products amongst all the retrieved
 199           // sequences.
 200           SequenceI[] seqs = al.getSequencesArray();
 201           Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
 202                   seqs, dna, null, ds);
 203           System.out.println("Found "
 204                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
 205                   + " products");
 206           if (prodal != null)
 207           {
 208             SequenceI[] prod = prodal.getSequencesArray(); // note
 209             // should
 210             // test
 211             // rather
 212             // than
 213             // throw
 214             // away
 215             // codon
 216             // mapping
 217             // (if
 218             // present)
 219             for (int p = 0; p < prod.length; p++)
 220             {
 221               System.out.println("Prod " + p + ": "
 222                       + prod[p].getDisplayId(true));
 223             }
 224           }
 225         }
 226
 227       }
 228
 229     }
 230   }
 231
 232 }