import java.util.Enumeration;\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
addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);\r
- };\r
+ registerDasSequenceSources();\r
+ }\r
/**\r
* simple run method to test dbsources.\r
* @param argv\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
\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