-/*\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 java.util.Hashtable;\r
-\r
-import com.stevesoft.pat.Regex;\r
-\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.ws.seqfetcher.DbSourceProxy;\r
-\r
-public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy\r
-{\r
-\r
- public EmblCdsSouce()\r
- {\r
- super();\r
- addDbSourceProperty(DBRefSource.CODINGSEQDB);\r
- }\r
-\r
- public String getAccessionSeparator()\r
- {\r
- return null;\r
- }\r
-\r
- public Regex getAccessionValidator()\r
- {\r
- // TODO Auto-generated method stub\r
- return null;\r
- }\r
-\r
- public String getDbSource()\r
- {\r
- return DBRefSource.EMBLCDS;\r
- }\r
-\r
- public String getDbVersion()\r
- {\r
- return "0"; // TODO : this is dynamically set for a returned record - not\r
- // tied to proxy\r
- }\r
-\r
- public AlignmentI getSequenceRecords(String queries) throws Exception\r
- {\r
- if (queries.indexOf(".") > -1)\r
- {\r
- queries = queries.substring(0, queries.indexOf("."));\r
- }\r
- return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);\r
- }\r
-\r
- public boolean isValidReference(String accession)\r
- {\r
- // TODO Auto-generated method stub\r
- return true;\r
- }\r
-\r
- /**\r
- * cDNA for LDHA_CHICK swissprot sequence\r
- */\r
- public String getTestQuery()\r
- {\r
- return "CAA37824";\r
- }\r
-\r
- public String getDbName()\r
- {\r
- return "EMBL (CDS)";\r
- }\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 com.stevesoft.pat.Regex;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
+{
+
+ public EmblCdsSouce()
+ {
+ super();
+ addDbSourceProperty(DBRefSource.CODINGSEQDB);
+ }
+
+ public String getAccessionSeparator()
+ {
+ return null;
+ }
+
+ public Regex getAccessionValidator()
+ {
+ return new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+");
+ }
+
+ public String getDbSource()
+ {
+ return DBRefSource.EMBLCDS;
+ }
+
+ public String getDbVersion()
+ {
+ return "0"; // TODO : this is dynamically set for a returned record - not
+ // tied to proxy
+ }
+
+ public AlignmentI getSequenceRecords(String queries) throws Exception
+ {
+ if (queries.indexOf(".") > -1)
+ {
+ queries = queries.substring(0, queries.indexOf("."));
+ }
+ return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
+ }
+
+ public boolean isValidReference(String accession)
+ {
+ // most embl CDS refs look like ..
+ // TODO: improve EMBLCDS regex
+ return (accession == null || accession.length() < 2) ? false
+ : getAccessionValidator().search(accession);
+ }
+
+ /**
+ * cDNA for LDHA_CHICK swissprot sequence
+ */
+ public String getTestQuery()
+ {
+ return "CAA37824";
+ }
+
+ public String getDbName()
+ {
+ return "EMBL (CDS)";
+ }
+
+ @Override
+ public int getTier()
+ {
+ return 0;
+ }
+
+}