JAL-1432 updated copyright notices

[jalview.git] / src / jalview / ws / dbsources / EmblCdsSouce.java

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index b3242ad..02e7f29 100644 (file)
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,89 +1,93 @@
-/*\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
-    // most embl CDS refs look like ..\r
-    // TODO: improve EMBLCDS regex\r
-    return (accession==null || accession.length()<2) ? false : new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+").search(accession);\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 2.8.0b1)
+ * Copyright (C) 2014 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;
+  }
+
+}