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