-/**\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \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
+ * 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
import com.stevesoft.pat.Regex;\r
\r
import jalview.datamodel.AlignmentI;\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
/**\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: later PFAM is a complex datasource - it could return a tree in addition\r
+ * to an alignment TODO: create interface to pass alignment properties and tree\r
+ * back to sequence fetcher\r
+ * \r
* @author JimP\r
- *\r
+ * \r
*/\r
-public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
+abstract public class Pfam extends Xfam implements\r
+ DbSourceProxy\r
{\r
\r
- /* (non-Javadoc)\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
+ addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
*/\r
public String getAccessionSeparator()\r
return null;\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
*/\r
public Regex getAccessionValidator()\r
return null;\r
}\r
\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbSource()\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 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
- public String getDbSource()\r
- {\r
- // TODO Auto-generated method stub\r
- return jalview.datamodel.DBRefSource.PFAM;\r
- }\r
\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbSourceProperties()\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable\r
+ * getDbSourceProperties() {\r
+ * \r
+ * return null; }\r
*/\r
- public Hashtable getDbSourceProperties()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\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
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getRawRecords()\r
+ /**Returns base URL for selected Pfam alignment type\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
+ @Override\r
+protected abstract String getXFAMURL();\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \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\r
+ // individual references to each sequence in each family alignment that's\r
+ // retrieved.\r
+ startQuery();\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
+ 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
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\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 String getDbName() { return "PFAM"; // getDbSource(); }\r
*/\r
- public boolean queryInProgress()\r
- {\r
- // TODO Auto-generated method stub\r
- return false;\r
- }\r
-\r
- public String getTestQuery()\r
- {\r
- return "PF00535";\r
- }\r
-\r
+ \r
+ \r
+ public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }\r
+ \r
+ \r
}\r
git://source.jalview.org / jalview.git / blobdiff