1 package jalview.ws.dbsources;
3 import java.util.Locale;
6 import java.io.IOException;
8 import com.stevesoft.pat.Regex;
10 import jalview.bin.Console;
11 import jalview.datamodel.Alignment;
12 import jalview.datamodel.AlignmentI;
13 import jalview.datamodel.SequenceI;
14 import jalview.io.DataSourceType;
15 import jalview.io.EmblFlatFile;
16 import jalview.io.FileParse;
17 import jalview.ws.ebi.EBIFetchClient;
20 * A class that does partial parsing of an EMBL flatfile.
25 public abstract class EmblFlatfileSource extends EbiFileRetrievedProxy
27 private static final Regex ACCESSION_REGEX = new Regex("^[A-Z]+[0-9]+");
30 public String getDbVersion()
36 public String getAccessionSeparator()
42 public Regex getAccessionValidator()
44 return ACCESSION_REGEX;
48 public boolean isValidReference(String accession)
50 if (accession == null || accession.length() < 2)
54 return getAccessionValidator().search(accession);
58 public AlignmentI getSequenceRecords(String queries) throws Exception
69 protected AlignmentI getEmblSequenceRecords(String dbName, String query)
73 EBIFetchClient dbFetch = new EBIFetchClient();
77 reply = dbFetch.fetchDataAsFile(
78 dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null,
84 String.format("EBI EMBL retrieval failed for %s:%s",
85 dbName.toLowerCase(Locale.ROOT), query.trim()),
88 return getEmblSequenceRecords(dbName, query, reply);
91 private AlignmentI getEmblSequenceRecords(String dbName, String query,
92 File reply) throws IOException
96 if (reply != null && reply.exists())
98 file = reply.getAbsolutePath();
99 FileParse fp = new FileParse(file, DataSourceType.FILE);
100 EmblFlatFile emblParser = new EmblFlatFile(fp, getDbSource());
101 SequenceI[] seqs = emblParser.getSeqsAsArray();
104 al = new Alignment(seqs);
109 Console.error("No record found for '" + dbName + ":" + query + "'");
118 public boolean isDnaCoding()