+ // TODO: this is not a perfect implementation. We need to be able to add individual references to each sequence in each family alignment that's retrieved. \r
+ startQuery();\r
+ AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()+queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,"STH");\r
+ for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)\r
+ {\r
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,\r
+ // getDbSource(), \r
+ getDbVersion(), queries.trim().toUpperCase()));\r
+ if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))\r
+ { // add the specific ref too\r
+ rcds.getSequenceAt(s).addDBRef(\r
+ new DBRefEntry( getDbSource(), \r
+ getDbVersion(), queries.trim().toUpperCase()));\r
+ }\r
+ }\r
+ stopQuery();\r
+ return rcds;\r