/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.ws.dbsources;\r
\r
* @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
* (non-Javadoc)\r
* \r
* @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *\r
- * this doesn't work - DbSource is key for the hash of DbSourceProxy\r
- * instances - 1:many mapping for DbSource to proxy will be lost. *\r
- * suggest : PFAM is an 'alignment' source - means proxy is higher level\r
- * than a sequence source. return jalview.datamodel.DBRefSource.PFAM; }\r
+ * this doesn't work - DbSource is key for the hash of DbSourceProxy instances\r
+ * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an\r
+ * 'alignment' source - means proxy is higher level than a sequence source.\r
+ * return jalview.datamodel.DBRefSource.PFAM; }\r
*/\r
\r
/*\r
* (non-Javadoc)\r
* \r
* @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable\r
- * getDbSourceProperties() {\r
+ * getDbSourceProperties() {\r
* \r
* return null; }\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