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<Object[]> noProds = new Vector<Object[]>();
  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], null)
 120                         .getSequencesArray();
 121                 System.out.println("Found "
 122                         + ((prod == null) ? "no" : "" + prod.length)
 123                         + " products");
 124                 if (prod != null)
 125                 {
 126                   for (int p = 0; p < prod.length; p++)
 127                   {
 128                     System.out.println("Prod " + p + ": "
 129                             + prod[p].getDisplayId(true));
 130                   }
 131                 }
 132               }
 133             }
 134             else
 135             {
 136               noProds.addElement((dna ? new Object[] { al, al }
 137                       : new Object[] { al }));
 138             }
 139
 140           }
 141         } catch (Exception ex)
 142         {
 143           System.out.println("ERROR:Failed to retrieve test query.");
 144           ex.printStackTrace(System.out);
 145         }
 146
 147         if (al == null)
 148         {
 149           System.out.println("ERROR:No alignment retrieved.");
 150           StringBuffer raw = sp.getRawRecords();
 151           if (raw != null)
 152           {
 153             System.out.println(raw.toString());
 154           }
 155           else
 156           {
 157             System.out.println("ERROR:No Raw results.");
 158           }
 159         }
 160         else
 161         {
 162           System.out.println("Retrieved " + al.getHeight() + " sequences.");
 163           for (int s = 0; s < al.getHeight(); s++)
 164           {
 165             SequenceI sq = al.getSequenceAt(s);
 166             while (sq.getDatasetSequence() != null)
 167             {
 168               sq = sq.getDatasetSequence();
 169
 170             }
 171             if (ds == null)
 172             {
 173               ds = new Alignment(new SequenceI[] { sq });
 174
 175             }
 176             else
 177             {
 178               ds.addSequence(sq);
 179             }
 180           }
 181         }
 182         System.out.flush();
 183         System.err.flush();
 184
 185       }
 186       if (noProds.size() > 0)
 187       {
 188         Enumeration<Object[]> ts = noProds.elements();
 189         while (ts.hasMoreElements())
 190
 191         {
 192           Object[] typeSq = ts.nextElement();
 193           boolean dna = (typeSq.length > 1);
 194           AlignmentI al = (AlignmentI) typeSq[0];
 195           System.out.println("Trying getProducts for "
 196                   + al.getSequenceAt(0).getDisplayId(true));
 197           System.out.println("Search DS Xref for: "
 198                   + (dna ? "dna" : "prot"));
 199           // have a bash at finding the products amongst all the retrieved
 200           // sequences.
 201           SequenceI[] seqs = al.getSequencesArray();
 202           Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
 203                   seqs, dna, null, ds);
 204           System.out.println("Found "
 205                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
 206                   + " products");
 207           if (prodal != null)
 208           {
 209             SequenceI[] prod = prodal.getSequencesArray(); // note
 210             // should
 211             // test
 212             // rather
 213             // than
 214             // throw
 215             // away
 216             // codon
 217             // mapping
 218             // (if
 219             // present)
 220             for (int p = 0; p < prod.length; p++)
 221             {
 222               System.out.println("Prod " + p + ": "
 223                       + prod[p].getDisplayId(true));
 224             }
 225           }
 226         }
 227
 228       }
 229
 230     }
 231   }
 232
 233 }