*/\r
public SequenceFetcher()\r
{\r
+ this(true);\r
+ }\r
+ public SequenceFetcher(boolean addDas)\r
+ {\r
addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);\r
// PFAM\r
addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);\r
addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);\r
- registerDasSequenceSources();\r
+ if (addDas) {\r
+ registerDasSequenceSources();\r
+ }\r
}\r
\r
/**\r
{\r
AlignmentI ds = null;\r
Vector noProds = new Vector();\r
- String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"\r
+ String usage = "SequenceFetcher.main [-nodas] [<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
+ + "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"\r
+ + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"\r
+ + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";\r
+ boolean withDas=true;\r
+ if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))\r
+ {\r
+ withDas=false;\r
+ String targs[] = new String[argv.length-1];\r
+ System.arraycopy(argv, 1, targs, 0, targs.length);\r
+ argv=targs;\r
+ }\r
if (argv != null && argv.length > 0)\r
{\r
- List<DbSourceProxy> sps = new SequenceFetcher()\r
+ List<DbSourceProxy> sps = new SequenceFetcher(withDas)\r
.getSourceProxy(argv[0]);\r
\r
if (sps != null)\r
AlignmentI al = null;\r
try\r
{\r
- al = sp.getSequenceRecords(argv[1]);\r
+ al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());\r
} catch (Exception e)\r
{\r
e.printStackTrace();\r
- System.err.println("Error when retrieving " + argv[1]\r
+ System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())\r
+ " from " + argv[0] + "\nUsage: " + usage);\r
}\r
SequenceI[] prod = al.getSequencesArray();\r
System.out.println(usage);\r
return;\r
}\r
- ASequenceFetcher sfetcher = new SequenceFetcher();\r
+ ASequenceFetcher sfetcher = new SequenceFetcher(withDas);\r
String[] dbSources = sfetcher.getSupportedDb();\r
for (int dbsource = 0; dbsource < dbSources.length; dbsource++)\r
{\r