-/**\r
- * \r
- */\r
-package jalview.ws.dbsources;\r
-\r
-import java.util.Hashtable;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.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
- * @author JimP\r
- *\r
- */\r
-public class Pfam extends DbSourceProxyImpl implements DbSourceProxy\r
-{\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
- */\r
- public String getAccessionSeparator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
- */\r
- public Regex getAccessionValidator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\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
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbSourceProperties()\r
- */\r
- public Hashtable getDbSourceProperties()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see jalview.ws.DbSourceProxy#getDbVersion()\r
- */\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
- */\r
- public StringBuffer getRawRecords()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\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
- }\r
-\r
- /* (non-Javadoc)\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
- }\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
- {\r
- return "PF00535";\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * TODO: later PFAM is a complex datasource - it could return a tree in addition
+ * to an alignment TODO: create interface to pass alignment properties and tree
+ * back to sequence fetcher
+ *
+ * @author JimP
+ *
+ */
+abstract public class Pfam extends Xfam implements DbSourceProxy
+{
+
+ public Pfam()
+ {
+ super();
+ // all extensions of this PFAM source base class are DOMAINDB sources
+ addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
+ addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ public String getAccessionSeparator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ public Regex getAccessionValidator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
+ * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
+ * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
+ * 'alignment' source - means proxy is higher level than a sequence source.
+ * return jalview.datamodel.DBRefSource.PFAM; }
+ */
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
+ * getDbSourceProperties() {
+ *
+ * return null; }
+ */
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getDbVersion()
+ */
+ @Override
+ public String getDbVersion()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /**
+ * Returns base URL for selected Pfam alignment type
+ *
+ * @return PFAM URL stub for this DbSource
+ */
+ @Override
+ protected abstract String getXFAMURL();
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
+ */
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ // 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.
+ startQuery();
+ AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
+ + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
+ "STH");
+ for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
+ {
+ rcds.getSequenceAt(s).addDBRef(
+ new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
+ // getDbSource(),
+ getDbVersion(), queries.trim().toUpperCase()));
+ if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
+ { // add the specific ref too
+ rcds.getSequenceAt(s).addDBRef(
+ new DBRefEntry(getDbSource(), getDbVersion(), queries
+ .trim().toUpperCase()));
+ }
+ }
+ stopQuery();
+ return rcds;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ public boolean isValidReference(String accession)
+ {
+ return accession.indexOf("PF") == 0;
+ }
+
+ /*
+ * public String getDbName() { return "PFAM"; // getDbSource(); }
+ */
+
+ public String getXfamSource()
+ {
+ return jalview.datamodel.DBRefSource.PFAM;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff