JAL-1705 DbSourceProxy properties converted to methods, tidy/format code

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

diff --git a/src/jalview/ws/dbsources/EmblCdsSource.java b/src/jalview/ws/dbsources/EmblCdsSource.java
new file mode 100644 (file)
index 0000000..a73af61
--- /dev/null
+++ b/src/jalview/ws/dbsources/EmblCdsSource.java
@@ -0,0 +1,101 @@
+/*
+ * 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.datamodel.AlignmentI;
+import jalview.datamodel.DBRefSource;
+
+import com.stevesoft.pat.Regex;
+
+public class EmblCdsSource extends EmblXmlSource
+{
+
+  public EmblCdsSource()
+  {
+    super();
+  }
+
+  @Override
+  public String getAccessionSeparator()
+  {
+    return null;
+  }
+
+  @Override
+  public Regex getAccessionValidator()
+  {
+    return new Regex("^[A-Z]+[0-9]+");
+  }
+
+  @Override
+  public String getDbSource()
+  {
+    return DBRefSource.EMBLCDS;
+  }
+
+  @Override
+  public String getDbVersion()
+  {
+    return "0"; // TODO : this is dynamically set for a returned record - not
+    // tied to proxy
+  }
+
+  @Override
+  public AlignmentI getSequenceRecords(String queries) throws Exception
+  {
+    if (queries.indexOf(".") > -1)
+    {
+      queries = queries.substring(0, queries.indexOf("."));
+    }
+    return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
+  }
+
+  @Override
+  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
+   */
+  @Override
+  public String getTestQuery()
+  {
+    return "CAA37824";
+  }
+
+  @Override
+  public String getDbName()
+  {
+    return "EMBL (CDS)";
+  }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+
+}