import jalview.datamodel.DBRefEntry;\r
import jalview.datamodel.Sequence;\r
import jalview.datamodel.SequenceI;\r
-import jalview.ws.ASequenceFetcher;\r
import jalview.ws.SequenceFetcher;\r
+import jalview.ws.seqfetcher.ASequenceFetcher;\r
\r
/**\r
* Functions for cross-referencing sequence databases. user must first specify\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.DBRefSource;\r
import jalview.datamodel.SequenceI;\r
+import jalview.ws.seqfetcher.ASequenceFetcher;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
\r
/**\r
* prototype of abstract sequence retrieval interface\r
FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb());\r
FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam());\r
};\r
-\r
+ \r
public static void main(String[] argv)\r
{\r
AlignmentI ds = null;\r
import com.stevesoft.pat.Regex;\r
\r
import jalview.datamodel.AlignmentI;\r
-import jalview.ws.DbSourceProxyImpl;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
\r
public abstract class EbiFileRetrievedProxy extends DbSourceProxyImpl\r
{\r
\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.DBRefSource;\r
-import jalview.ws.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
\r
public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy\r
{\r
import jalview.datamodel.DBRefSource;\r
import jalview.datamodel.SequenceI;\r
import jalview.datamodel.xdb.embl.EmblEntry;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
import jalview.ws.EBIFetchClient;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
\r
/**\r
* @author JimP\r
\r
import jalview.datamodel.AlignmentI;\r
import jalview.io.FileParse;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
import jalview.ws.EBIFetchClient;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
\r
/**\r
* @author JimP\r
import com.stevesoft.pat.Regex;\r
\r
import jalview.datamodel.AlignmentI;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
/**\r
* TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment.\r
* TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment\r
import jalview.io.FormatAdapter;\r
import jalview.io.IdentifyFile;\r
import jalview.ws.DBRefFetcher;\r
-import jalview.ws.DbSourceProxy;\r
-import jalview.ws.DbSourceProxyImpl;\r
import jalview.ws.EBIFetchClient;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
\r
/**\r
* @author JimP\r
-package jalview.ws;\r
+package jalview.ws.seqfetcher;\r
\r
import jalview.datamodel.AlignmentI;\r
import jalview.datamodel.SequenceI;\r
-package jalview.ws;\r
+package jalview.ws.seqfetcher;\r
\r
import jalview.datamodel.AlignmentI;\r
\r
-package jalview.ws;\r
+package jalview.ws.seqfetcher;\r
\r
import jalview.datamodel.Alignment;\r
import jalview.datamodel.DBRefSource;\r