+ // 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
+ results = new StringBuffer();\r
+ // split queries into many little ones.\r
+ results.append(new FastaFile(\r
+ PFAMURL+queries.trim().toUpperCase(), "URL").print());\r
+ stopQuery();\r
+ AlignmentI rcds = parseResult(results.toString());\r
+ for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)\r
+ {\r
+ rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(), getDbVersion(), queries.trim().toUpperCase()));\r
+ }\r
+ return rcds;\r