/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ws.dbsources;
+import com.stevesoft.pat.Regex;
+
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
-import com.stevesoft.pat.Regex;
-
-public class EmblCdsSource extends EmblXmlSource
+public class EmblCdsSource extends /*EmblXmlSource */ EmblFlatfileSource
{
public EmblCdsSource()
}
@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)
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
*/
return "EMBL (CDS)";
}
- @Override
- public int getTier()
- {
- return 0;
- }
-
}