package jalview.ws;\r
\r
import java.util.Enumeration;\r
-import java.util.Hashtable;\r
import java.util.Vector;\r
\r
+import org.biojava.dasobert.das2.Das2Source;\r
+import org.biojava.dasobert.dasregistry.Das1Source;\r
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
+import org.biojava.dasobert.dasregistry.DasSource;\r
+\r
import jalview.datamodel.Alignment;\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.DBRefSource;\r
import jalview.datamodel.SequenceI;\r
+import jalview.ws.seqfetcher.ASequenceFetcher;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
\r
/**\r
- * prototype of abstract sequence retrieval interface\r
+ * This is the the concrete implementation of the sequence retrieval interface\r
+ * and abstract class in jalview.ws.seqfetcher. This implements the run-time\r
+ * discovery of sequence database clients, and provides a hardwired main for testing all registered handlers. \r
* \r
*/\r
public class SequenceFetcher extends ASequenceFetcher\r
*/\r
public SequenceFetcher()\r
{\r
- FETCHABLEDBS = new Hashtable();\r
- FETCHABLEDBS.put(DBRefSource.EMBL,\r
- new jalview.ws.dbsources.EmblSource());\r
- FETCHABLEDBS.put(DBRefSource.EMBLCDS,\r
- new jalview.ws.dbsources.EmblCdsSouce());\r
- FETCHABLEDBS.put(DBRefSource.UNIPROT,\r
- new jalview.ws.dbsources.Uniprot());\r
- FETCHABLEDBS.put(DBRefSource.UP_NAME,\r
- new jalview.ws.dbsources.Uniprot());\r
- FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb());\r
- FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam());\r
- };\r
-\r
+ addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);\r
+ addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);\r
+ addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);\r
+ addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);\r
+ addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);\r
+ addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);\r
+ registerDasSequenceSources();\r
+ }\r
+ /**\r
+ * simple run method to test dbsources.\r
+ * @param argv\r
+ */\r
public static void main(String[] argv)\r
{\r
AlignmentI ds = null;\r
Vector noProds = new Vector();\r
+ String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"\r
+ +"With no arguments, all DbSources will be queried with their test Accession number.\n"\r
+ +"If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";\r
if (argv != null && argv.length > 0)\r
{\r
+ DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);\r
+ if (sp!=null)\r
+ {\r
+ AlignmentI al = null;\r
+ try\r
+ {\r
+ al = sp.getSequenceRecords(argv[1]);\r
+ } catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ System.err.println("Error when retrieving "+argv[1]+" from "+argv[0]+"\nUsage: "+usage);\r
+ }\r
+ SequenceI[] prod = al.getSequencesArray();\r
+ if (al!=null)\r
+ {\r
+ for (int p = 0; p < prod.length; p++)\r
+ {\r
+ System.out.println("Prod " + p + ": "\r
+ + prod[p].getDisplayId(true) + " : "+prod[p].getDescription());\r
+ }\r
+ }\r
+ return;\r
+ } else {\r
+ System.err.println("Can't resolve "+argv[0]+" as a database name. Allowed values are :\n"+new SequenceFetcher().getSupportedDb());\r
+ }\r
System.out\r
- .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");\r
+ .println(usage);\r
}\r
- SequenceFetcher sfetcher = new SequenceFetcher();\r
- Enumeration e = sfetcher.FETCHABLEDBS.keys();\r
- while (e.hasMoreElements())\r
+ ASequenceFetcher sfetcher = new SequenceFetcher();\r
+ String[] dbSources = sfetcher.getSupportedDb();\r
+ for (int dbsource=0; dbsource<dbSources.length;dbsource++)\r
{\r
- String db = (String) e.nextElement();\r
+ String db = dbSources[dbsource];\r
// skip me\r
if (db.equals(DBRefSource.PDB))\r
continue;\r
DbSourceProxy sp = sfetcher.getSourceProxy(db);\r
System.out\r
- .println("" + db + ": retrieving test:" + sp.getTestQuery());\r
+ .println("Source: "+sp.getDbName()+" (" + db + "): retrieving test:" + sp.getTestQuery());\r
AlignmentI al = null;\r
try\r
{\r
al = sp.getSequenceRecords(sp.getTestQuery());\r
- if (al != null && al.getHeight() > 0)\r
+ if (al != null && al.getHeight() > 0 && sp.getDbSourceProperties()!=null)\r
{\r
boolean dna = sp.getDbSourceProperties().containsKey(\r
DBRefSource.DNACODINGSEQDB)\r
dna, al.getSequencesArray());\r
if (types != null)\r
{\r
- System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));\r
+ System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));\r
for (int t = 0; t < types.length; t++)\r
{\r
System.out.println("Type: " + types[t]);\r
- SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al\r
- .getSequencesArray(), dna, types[t]).getSequencesArray();\r
+ SequenceI[] prod = jalview.analysis.CrossRef\r
+ .findXrefSequences(al.getSequencesArray(), dna,\r
+ types[t]).getSequencesArray();\r
System.out.println("Found "\r
+ ((prod == null) ? "no" : "" + prod.length)\r
+ " products");\r
- if (prod!=null)\r
+ if (prod != null)\r
{\r
- for (int p=0; p<prod.length; p++)\r
+ for (int p = 0; p < prod.length; p++)\r
{\r
- System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
+ System.out.println("Prod " + p + ": "\r
+ + prod[p].getDisplayId(true));\r
}\r
}\r
}\r
- } else {\r
- noProds.addElement((dna ? new Object[] { al, al } : new Object[] { al }) ); \r
+ }\r
+ else\r
+ {\r
+ noProds.addElement((dna ? new Object[]\r
+ { al, al } : new Object[]\r
+ { al }));\r
}\r
\r
}\r
System.err.flush();\r
\r
}\r
- if (noProds.size()>0)\r
+ if (noProds.size() > 0)\r
{\r
Enumeration ts = noProds.elements();\r
while (ts.hasMoreElements())\r
- \r
+\r
{\r
Object[] typeSq = (Object[]) ts.nextElement();\r
- boolean dna = (typeSq.length>1);\r
+ boolean dna = (typeSq.length > 1);\r
AlignmentI al = (AlignmentI) typeSq[0];\r
- System.out.println("Trying getProducts for "+al.getSequenceAt(0).getDisplayId(true));\r
- System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));\r
- // have a bash at finding the products amongst all the retrieved sequences.\r
- SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al\r
- .getSequencesArray(), dna, null, ds).getSequencesArray(); // note should test rather than throw away codon mapping (if present)\r
+ System.out.println("Trying getProducts for "\r
+ + al.getSequenceAt(0).getDisplayId(true));\r
+ System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));\r
+ // have a bash at finding the products amongst all the retrieved\r
+ // sequences.\r
+ SequenceI[] seqs = al.getSequencesArray();\r
+ Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(\r
+ seqs, dna, null, ds);\r
System.out.println("Found "\r
- + ((prod == null) ? "no" : "" + prod.length)\r
- + " products");\r
- if (prod!=null)\r
+ + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");\r
+ if (prodal != null)\r
{\r
- for (int p=0; p<prod.length; p++)\r
+ SequenceI[] prod = prodal.getSequencesArray(); // note\r
+ // should\r
+ // test\r
+ // rather\r
+ // than\r
+ // throw\r
+ // away\r
+ // codon\r
+ // mapping\r
+ // (if\r
+ // present)\r
+ for (int p = 0; p < prod.length; p++)\r
{\r
- System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
+ System.out.println("Prod " + p + ": "\r
+ + prod[p].getDisplayId(true));\r
}\r
}\r
}\r
\r
}\r
}\r
+ /**\r
+ * query the currently defined DAS source registry for sequence sources and add a DasSequenceSource instance for each source to the SequenceFetcher source list.\r
+ */\r
+ public void registerDasSequenceSources() {\r
+ DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher.getDASSources();\r
+ for (int s=0;s<sources.length; s++)\r
+ {\r
+ Das1Source d1s=null;\r
+ if (sources[s].hasCapability("sequence"))\r
+ {\r
+ if (sources[s] instanceof Das2Source)\r
+ {\r
+ if (((Das2Source)sources[s]).hasDas1Capabilities()) {\r
+ try {\r
+ d1s = org.biojava.dasobert.das2.DasSourceConverter.toDas1Source((Das2Source) sources[s]);\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Ignoring DAS2 sequence source "+sources[s].getNickname()+" - couldn't map to Das1Source.\n");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ } else {\r
+ if (sources[s] instanceof Das1Source)\r
+ { \r
+ d1s = (Das1Source) sources[s];\r
+ }\r
+ }\r
+ }\r
+ if (d1s!=null)\r
+ {\r
+ DasCoordinateSystem[] css = d1s.getCoordinateSystem();\r
+ for (int c=0;c<css.length;c++)\r
+ {\r
+ try {\r
+ addDbRefSourceImpl(\r
+ new jalview.ws.dbsources.DasSequenceSource("das:"+d1s.getNickname()+" ("+css[c].getName()+")",\r
+ css[c].getName(),d1s, css[c]));\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Ignoring sequence coord system "+c+" ("+\r
+ css[c].getName()+") for source "+d1s.getNickname()\r
+ + "- threw exception when constructing fetcher.\n");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ \r
+ }\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff