src/jalview/ws/SequenceFetcher.java

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