X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblCdsSouce.java;h=3a9ebe9e6c43b964be1588d00cae7c534ae03652;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=9912c9ca44e501caab3ead6f723f32b1f71fb9d6;hpb=5d88ae6bbf1ea113cefcb43b7918b5baf560a76e;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 9912c9c..3a9ebe9 100644
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -1,62 +1,95 @@
-package jalview.ws.dbsources;
-
-import java.util.Hashtable;
-
-import com.stevesoft.pat.Regex;
-
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.ws.DbSourceProxy;
-
-public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
-{
-
-  public EmblCdsSouce() {
-    super();
-    addDbSourceProperty(DBRefSource.CODINGSEQDB); 
-  }
-  
-  public String getAccessionSeparator()
-  {
-   return null;
-  }
-
-  public Regex getAccessionValidator()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  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)
-  {
-    // TODO Auto-generated method stub
-    return true;
-  }
-  /**
-   * cDNA for LDHA_CHICK swissprot sequence
-   */
-  public String getTestQuery()
-  {
-    return "CAA37824";
-  }
-
-}
+/*
+ * 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;
+  }
+
+}