src/jalview/ws/SequenceFetcher.java

   1 package jalview.ws;\r
   2 \r
   3 import java.util.Enumeration;\r
   4 import java.util.Vector;\r
   5 \r
   6 import jalview.datamodel.Alignment;\r
   7 import jalview.datamodel.AlignmentI;\r
   8 import jalview.datamodel.DBRefSource;\r
   9 import jalview.datamodel.SequenceI;\r
  10 import jalview.ws.seqfetcher.ASequenceFetcher;\r
  11 import jalview.ws.seqfetcher.DbSourceProxy;\r
  12 \r
  13 /**\r
  14  * This is the the concrete implementation of the sequence retrieval interface\r
  15  * and abstract class in jalview.ws.seqfetcher. This implements the discovery \r
  16  * \r
  17  */\r
  18 public class SequenceFetcher extends ASequenceFetcher\r
  19 {\r
  20   /**\r
  21    * Thread safe construction of database proxies TODO: extend to a configurable\r
  22    * database plugin mechanism where classes are instantiated by reflection and\r
  23    * queried for their DbRefSource and version association.\r
  24    * \r
  25    */\r
  26   public SequenceFetcher()\r
  27   {\r
  28     addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);\r
  29     addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);\r
  30     addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);\r
  31     addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);\r
  32     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);\r
  33     addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);\r
  34   };\r
  35 \r
  36   public static void main(String[] argv)\r
  37   {\r
  38     AlignmentI ds = null;\r
  39     Vector noProds = new Vector();\r
  40     if (argv != null && argv.length > 0)\r
  41     {\r
  42       System.out\r
  43               .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");\r
  44     }\r
  45     ASequenceFetcher sfetcher = new SequenceFetcher();\r
  46     String[] dbSources = sfetcher.getSupportedDb();\r
  47     for (int dbsource=0; dbsource<dbSources.length;dbsource++)\r
  48     {\r
  49       String db = dbSources[dbsource];\r
  50       // skip me\r
  51       if (db.equals(DBRefSource.PDB))\r
  52         continue;\r
  53       DbSourceProxy sp = sfetcher.getSourceProxy(db);\r
  54       System.out\r
  55               .println("" + db + ": retrieving test:" + sp.getTestQuery());\r
  56       AlignmentI al = null;\r
  57       try\r
  58       {\r
  59         al = sp.getSequenceRecords(sp.getTestQuery());\r
  60         if (al != null && al.getHeight() > 0)\r
  61         {\r
  62           boolean dna = sp.getDbSourceProperties().containsKey(\r
  63                   DBRefSource.DNACODINGSEQDB)\r
  64                   || sp.getDbSourceProperties().containsKey(\r
  65                           DBRefSource.DNASEQDB)\r
  66                   || sp.getDbSourceProperties().containsKey(\r
  67                           DBRefSource.CODINGSEQDB);\r
  68           // try and find products\r
  69           String types[] = jalview.analysis.CrossRef.findSequenceXrefTypes(\r
  70                   dna, al.getSequencesArray());\r
  71           if (types != null)\r
  72           {\r
  73             System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));\r
  74             for (int t = 0; t < types.length; t++)\r
  75             {\r
  76               System.out.println("Type: " + types[t]);\r
  77               SequenceI[] prod = jalview.analysis.CrossRef\r
  78                       .findXrefSequences(al.getSequencesArray(), dna,\r
  79                               types[t]).getSequencesArray();\r
  80               System.out.println("Found "\r
  81                       + ((prod == null) ? "no" : "" + prod.length)\r
  82                       + " products");\r
  83               if (prod != null)\r
  84               {\r
  85                 for (int p = 0; p < prod.length; p++)\r
  86                 {\r
  87                   System.out.println("Prod " + p + ": "\r
  88                           + prod[p].getDisplayId(true));\r
  89                 }\r
  90               }\r
  91             }\r
  92           }\r
  93           else\r
  94           {\r
  95             noProds.addElement((dna ? new Object[]\r
  96             { al, al } : new Object[]\r
  97             { al }));\r
  98           }\r
  99 \r
 100         }\r
 101       } catch (Exception ex)\r
 102       {\r
 103         System.out.println("ERROR:Failed to retrieve test query.");\r
 104         ex.printStackTrace(System.out);\r
 105       }\r
 106       if (al == null)\r
 107       {\r
 108         System.out.println("ERROR:No alignment retrieved.");\r
 109         StringBuffer raw = sp.getRawRecords();\r
 110         if (raw != null)\r
 111           System.out.println(raw.toString());\r
 112         else\r
 113           System.out.println("ERROR:No Raw results.");\r
 114       }\r
 115       else\r
 116       {\r
 117         System.out.println("Retrieved " + al.getHeight() + " sequences.");\r
 118         for (int s = 0; s < al.getHeight(); s++)\r
 119         {\r
 120           SequenceI sq = al.getSequenceAt(s);\r
 121           while (sq.getDatasetSequence() != null)\r
 122           {\r
 123             sq = sq.getDatasetSequence();\r
 124 \r
 125           }\r
 126           if (ds == null)\r
 127           {\r
 128             ds = new Alignment(new SequenceI[]\r
 129             { sq });\r
 130 \r
 131           }\r
 132           else\r
 133           {\r
 134             ds.addSequence(sq);\r
 135           }\r
 136         }\r
 137       }\r
 138       System.out.flush();\r
 139       System.err.flush();\r
 140 \r
 141     }\r
 142     if (noProds.size() > 0)\r
 143     {\r
 144       Enumeration ts = noProds.elements();\r
 145       while (ts.hasMoreElements())\r
 146 \r
 147       {\r
 148         Object[] typeSq = (Object[]) ts.nextElement();\r
 149         boolean dna = (typeSq.length > 1);\r
 150         AlignmentI al = (AlignmentI) typeSq[0];\r
 151         System.out.println("Trying getProducts for "\r
 152                 + al.getSequenceAt(0).getDisplayId(true));\r
 153         System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));\r
 154         // have a bash at finding the products amongst all the retrieved\r
 155         // sequences.\r
 156         SequenceI[] seqs = al.getSequencesArray();\r
 157         Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(\r
 158                 seqs, dna, null, ds);\r
 159         System.out.println("Found "\r
 160                 + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");\r
 161         if (prodal != null)\r
 162         {\r
 163           SequenceI[] prod = prodal.getSequencesArray(); // note\r
 164           // should\r
 165           // test\r
 166           // rather\r
 167           // than\r
 168           // throw\r
 169           // away\r
 170           // codon\r
 171           // mapping\r
 172           // (if\r
 173           // present)\r
 174             for (int p = 0; p < prod.length; p++)\r
 175           {\r
 176             System.out.println("Prod " + p + ": "\r
 177                     + prod[p].getDisplayId(true));\r
 178           }\r
 179         }\r
 180       }\r
 181 \r
 182     }\r
 183   }\r
 184 }\r