-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 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 java.util.Hashtable;\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 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
-abstract public class Pfam extends DbSourceProxyImpl implements\r
- 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
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
- */\r
- public String getAccessionSeparator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
- */\r
- public Regex getAccessionValidator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\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
- */\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable\r
- * getDbSourceProperties() {\r
- * \r
- * return null; }\r
- */\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getDbVersion()\r
- */\r
- public String getDbVersion()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- /**\r
- * \r
- * @return PFAM URL stub for this DbSource\r
- */\r
- protected abstract String getPFAMURL();\r
-\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
- // 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(getPFAMURL()\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
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
- */\r
- public boolean isValidReference(String accession)\r
- {\r
- return accession.indexOf("PF") == 0;\r
- }\r
-\r
- /*\r
- * public String getDbName() { return "PFAM"; // getDbSource(); }\r
- */\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.bin.Cache;
+import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
+
+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
+{
+ /*
+ * append to URLs to retrieve as a gzipped file
+ */
+ protected static final String GZIPPED = "/gzipped";
+
+ static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
+
+ private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
+ static {
+ Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
+ }
+
+ public Pfam()
+ {
+ super();
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
+ */
+ @Override
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getAccessionValidator()
+ */
+ @Override
+ public Regex getAccessionValidator()
+ {
+ 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()
+ {
+ return null;
+ }
+
+ @Override
+ protected String getURLPrefix()
+ {
+ return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
+ */
+ @Override
+ public boolean isValidReference(String accession)
+ {
+ return accession.indexOf("PF") == 0;
+ }
+
+ /*
+ * public String getDbName() { return "PFAM"; // getDbSource(); }
+ */
+
+ @Override
+ public String getXfamSource()
+ {
+ return DBRefSource.PFAM;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff