* @author JimP\r
* \r
*/\r
-abstract public class Pfam extends DbSourceProxyImpl implements\r
+abstract public class Pfam extends Xfam implements\r
DbSourceProxy\r
{\r
\r
super();\r
// all extensions of this PFAM source base class are DOMAINDB sources\r
addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);\r
+ addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);\r
}\r
\r
/*\r
* \r
* @see jalview.ws.DbSourceProxy#getDbVersion()\r
*/\r
- public String getDbVersion()\r
+ @Override\r
+public String getDbVersion()\r
{\r
// TODO Auto-generated method stub\r
return null;\r
}\r
\r
- /**\r
+ /**Returns base URL for selected Pfam alignment type\r
* \r
* @return PFAM URL stub for this DbSource\r
*/\r
- protected abstract String getPFAMURL();\r
+ @Override\r
+protected abstract String getXFAMURL();\r
\r
/*\r
* (non-Javadoc)\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
+ AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()\r
+ queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,\r
"STH");\r
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)\r
/*\r
* public String getDbName() { return "PFAM"; // getDbSource(); }\r
*/\r
+ \r
+ \r
+ public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }\r
+ \r
+ \r
}\r