4 package jalview.ws.dbsources;
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7 import java.util.Hashtable;
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8 import java.util.Iterator;
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9 import java.util.StringTokenizer;
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11 import com.stevesoft.pat.Regex;
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13 import jalview.datamodel.Alignment;
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14 import jalview.datamodel.AlignmentI;
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15 import jalview.datamodel.DBRefSource;
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16 import jalview.datamodel.SequenceI;
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17 import jalview.datamodel.xdb.embl.EmblEntry;
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18 import jalview.ws.DbSourceProxy;
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19 import jalview.ws.DbSourceProxyImpl;
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20 import jalview.ws.EBIFetchClient;
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26 public class EmblSource extends EmblXmlSource implements DbSourceProxy
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29 public EmblSource() {
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30 addDbSourceProperty(DBRefSource.DNASEQDB);
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31 addDbSourceProperty(DBRefSource.CODINGSEQDB);
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35 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
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37 public String getAccessionSeparator()
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39 // TODO Auto-generated method stub
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44 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
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46 public Regex getAccessionValidator()
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48 // TODO Auto-generated method stub
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53 * @see jalview.ws.DbSourceProxy#getDbSource()
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55 public String getDbSource()
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57 return DBRefSource.EMBL;
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60 * @see jalview.ws.DbSourceProxy#getDbVersion()
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62 public String getDbVersion()
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64 // TODO Auto-generated method stub
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69 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
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71 public AlignmentI getSequenceRecords(String queries) throws Exception
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73 return getEmblSequenceRecords(DBRefSource.EMBL, queries);
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76 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
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78 public boolean isValidReference(String accession)
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80 // TODO Auto-generated method stub
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85 * return LHD_CHICK coding gene
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87 public String getTestQuery()
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