Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

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

diff --git a/src/jalview/ws/dbsources/EmblCdsSource.java b/src/jalview/ws/dbsources/EmblCdsSource.java
index a73af61..d02910c 100644 (file)
--- a/src/jalview/ws/dbsources/EmblCdsSource.java
+++ b/src/jalview/ws/dbsources/EmblCdsSource.java
@@ -23,9 +23,7 @@ package jalview.ws.dbsources;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 
-import com.stevesoft.pat.Regex;
-
-public class EmblCdsSource extends EmblXmlSource
+public class EmblCdsSource extends EmblFlatfileSource // was EmblXmlSource
 {
 
   public EmblCdsSource()
@@ -34,31 +32,12 @@ public class EmblCdsSource extends EmblXmlSource
   }
 
   @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)
@@ -68,15 +47,6 @@ public class EmblCdsSource extends EmblXmlSource
     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
    */
@@ -92,10 +62,4 @@ public class EmblCdsSource extends EmblXmlSource
     return "EMBL (CDS)";
   }
 
-  @Override
-  public int getTier()
-  {
-    return 0;
-  }
-
 }