-/**\r
+/*\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
+ * \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
* \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
+ * \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
*/\r
package jalview.ws.dbsources;\r
\r
import com.stevesoft.pat.Regex;\r
\r
import jalview.datamodel.AlignmentI;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
+import jalview.datamodel.DBRefEntry;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FastaFile;\r
+import jalview.io.StockholmFile;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
/**\r
- * TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment.\r
* TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment\r
- * TODO: HP: Incorporate jalview.gui.SequenceFetcher retrieval code here.\r
+ * TODO: create interface to pass alignment properties and tree back to sequence fetcher\r
* @author JimP\r
*\r
*/\r
-public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
+abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
{\r
\r
+ public Pfam()\r
+ {\r
+ super();\r
+ // all extensions of this PFAM source base class are DOMAINDB sources \r
+ addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);\r
+ }\r
+\r
/* (non-Javadoc)\r
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
*/\r
\r
/* (non-Javadoc)\r
* @see jalview.ws.DbSourceProxy#getDbSource()\r
- */\r
public String getDbSource()\r
{\r
- // TODO Auto-generated method stub\r
- return null;\r
+ ** this doesn't work - DbSource is key for the hash of DbSourceProxy instances - 1:many mapping for DbSource to proxy will be lost.\r
+ ** suggest : PFAM is an 'alignment' source - means proxy is higher level than a sequence source.\r
+ return jalview.datamodel.DBRefSource.PFAM;\r
}\r
+ */\r
\r
+ \r
/* (non-Javadoc)\r
* @see jalview.ws.DbSourceProxy#getDbSourceProperties()\r
- */\r
public Hashtable getDbSourceProperties()\r
{\r
- // TODO Auto-generated method stub\r
+ \r
return null;\r
}\r
-\r
+ */\r
+ \r
/* (non-Javadoc)\r
* @see jalview.ws.DbSourceProxy#getDbVersion()\r
*/\r
// TODO Auto-generated method stub\r
return null;\r
}\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getRawRecords()\r
+ /**\r
+ * \r
+ * @return PFAM URL stub for this DbSource\r
*/\r
- public StringBuffer getRawRecords()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
+ protected abstract String getPFAMURL();\r
/* (non-Javadoc)\r
* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
*/\r
public AlignmentI getSequenceRecords(String queries) throws Exception\r
{\r
- throw new Exception("PFAM Retrieval not yet implemented - see jalview.gui.SequenceFetcher for current implementation");\r
+ // 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
}\r
\r
/* (non-Javadoc)\r
*/\r
public boolean isValidReference(String accession)\r
{\r
- // TODO Auto-generated method stub\r
- return false;\r
+ return accession.indexOf("PF")==0;\r
}\r
\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#queryInProgress()\r
- */\r
- public boolean queryInProgress()\r
- {\r
- // TODO Auto-generated method stub\r
- return false;\r
- }\r
\r
- public String getTestQuery()\r
+ /*public String getDbName()\r
{\r
- return "PF00535";\r
- }\r
-\r
+ return "PFAM"; // getDbSource();\r
+ } */\r
}\r
git://source.jalview.org / jalview.git / blobdiff