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.ArrayList;
  11 import java.util.Enumeration;
  12 import java.util.List;
  13 import java.util.Vector;
  14
  15 public class SequenceFetcherTest
  16 {
  17
  18   /**
  19    * simple run method to test dbsources.
  20    *
  21    * @param argv
  22    */
  23   public static void main(String[] argv)
  24   {
  25     // TODO: extracted from SequenceFetcher - convert to proper unit test with
  26     // assertions
  27
  28     AlignmentI ds = null;
  29     Vector noProds = new Vector();
  30     String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
  31             + "With no arguments, all DbSources will be queried with their test Accession number.\n"
  32             + "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"
  33             + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
  34             + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
  35     boolean withDas = true;
  36     if (argv != null && argv.length > 0
  37             && argv[0].toLowerCase().startsWith("-nodas"))
  38     {
  39       withDas = false;
  40       String targs[] = new String[argv.length - 1];
  41       System.arraycopy(argv, 1, targs, 0, targs.length);
  42       argv = targs;
  43     }
  44     if (argv != null && argv.length > 0)
  45     {
  46       List<DbSourceProxy> sps = new SequenceFetcher(withDas)
  47               .getSourceProxy(argv[0]);
  48
  49       if (sps != null)
  50       {
  51         for (DbSourceProxy sp : sps)
  52         {
  53           AlignmentI al = null;
  54           try
  55           {
  56             al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
  57                     .getTestQuery());
  58           } catch (Exception e)
  59           {
  60             e.printStackTrace();
  61             System.err.println("Error when retrieving "
  62                     + (argv.length > 1 ? argv[1] : sp.getTestQuery())
  63                     + " from " + argv[0] + "\nUsage: " + usage);
  64           }
  65           SequenceI[] prod = al.getSequencesArray();
  66           if (al != null)
  67           {
  68             for (int p = 0; p < prod.length; p++)
  69             {
  70               System.out.println("Prod " + p + ": "
  71                       + prod[p].getDisplayId(true) + " : "
  72                       + prod[p].getDescription());
  73             }
  74           }
  75         }
  76         return;
  77       }
  78       else
  79       {
  80         System.err.println("Can't resolve " + argv[0]
  81                 + " as a database name. Allowed values are :\n"
  82                 + new SequenceFetcher().getSupportedDb());
  83       }
  84       System.out.println(usage);
  85       return;
  86     }
  87     ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
  88     String[] dbSources = sfetcher.getSupportedDb();
  89     for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
  90     {
  91       String db = dbSources[dbsource];
  92       // skip me
  93       if (db.equals(DBRefSource.PDB))
  94       {
  95         continue;
  96       }
  97       for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
  98       {
  99         System.out.println("Source: " + sp.getDbName() + " (" + db
 100                 + "): retrieving test:" + sp.getTestQuery());
 101         AlignmentI al = null;
 102         try
 103         {
 104           al = sp.getSequenceRecords(sp.getTestQuery());
 105           if (al != null && al.getHeight() > 0)
 106           {
 107             boolean dna = sp.isDnaCoding();
 108             // try and find products
 109             String types[] = jalview.analysis.CrossRef
 110                     .findSequenceXrefTypes(dna, al.getSequencesArray());
 111             if (types != null)
 112             {
 113               System.out.println("Xref Types for: "
 114                       + (dna ? "dna" : "prot"));
 115               for (int t = 0; t < types.length; t++)
 116               {
 117                 System.out.println("Type: " + types[t]);
 118                 SequenceI[] prod = jalview.analysis.CrossRef
 119                         .findXrefSequences(al.getSequencesArray(), dna,
 120                                 types[t], null, new ArrayList<SequenceI>())
 121                         .getSequencesArray();
 122                 System.out.println("Found "
 123                         + ((prod == null) ? "no" : "" + prod.length)
 124                         + " products");
 125                 if (prod != null)
 126                 {
 127                   for (int p = 0; p < prod.length; p++)
 128                   {
 129                     System.out.println("Prod " + p + ": "
 130                             + prod[p].getDisplayId(true));
 131                   }
 132                 }
 133               }
 134             }
 135             else
 136             {
 137               noProds.addElement((dna ? new Object[] { al, al }
 138                       : new Object[] { al }));
 139             }
 140
 141           }
 142         } catch (Exception ex)
 143         {
 144           System.out.println("ERROR:Failed to retrieve test query.");
 145           ex.printStackTrace(System.out);
 146         }
 147
 148         if (al == null)
 149         {
 150           System.out.println("ERROR:No alignment retrieved.");
 151           StringBuffer raw = sp.getRawRecords();
 152           if (raw != null)
 153           {
 154             System.out.println(raw.toString());
 155           }
 156           else
 157           {
 158             System.out.println("ERROR:No Raw results.");
 159           }
 160         }
 161         else
 162         {
 163           System.out.println("Retrieved " + al.getHeight() + " sequences.");
 164           for (int s = 0; s < al.getHeight(); s++)
 165           {
 166             SequenceI sq = al.getSequenceAt(s);
 167             while (sq.getDatasetSequence() != null)
 168             {
 169               sq = sq.getDatasetSequence();
 170
 171             }
 172             if (ds == null)
 173             {
 174               ds = new Alignment(new SequenceI[] { sq });
 175
 176             }
 177             else
 178             {
 179               ds.addSequence(sq);
 180             }
 181           }
 182         }
 183         System.out.flush();
 184         System.err.flush();
 185
 186       }
 187       if (noProds.size() > 0)
 188       {
 189         Enumeration ts = noProds.elements();
 190         while (ts.hasMoreElements())
 191
 192         {
 193           Object[] typeSq = (Object[]) ts.nextElement();
 194           boolean dna = (typeSq.length > 1);
 195           AlignmentI al = (AlignmentI) typeSq[0];
 196           System.out.println("Trying getProducts for "
 197                   + al.getSequenceAt(0).getDisplayId(true));
 198           System.out.println("Search DS Xref for: "
 199                   + (dna ? "dna" : "prot"));
 200           // have a bash at finding the products amongst all the retrieved
 201           // sequences.
 202           SequenceI[] seqs = al.getSequencesArray();
 203           Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
 204                   seqs, dna, null, ds, new ArrayList<SequenceI>());
 205           System.out.println("Found "
 206                   + ((prodal == null) ? "no" : "" + prodal.getHeight())
 207                   + " products");
 208           if (prodal != null)
 209           {
 210             SequenceI[] prod = prodal.getSequencesArray(); // note
 211             // should
 212             // test
 213             // rather
 214             // than
 215             // throw
 216             // away
 217             // codon
 218             // mapping
 219             // (if
 220             // present)
 221             for (int p = 0; p < prod.length; p++)
 222             {
 223               System.out.println("Prod " + p + ": "
 224                       + prod[p].getDisplayId(true));
 225             }
 226           }
 227         }
 228
 229       }
 230
 231     }
 232   }
 233
 234 }