4 package jalview.ws.dbsources;
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6 import java.util.Hashtable;
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8 import com.stevesoft.pat.Regex;
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10 import jalview.datamodel.AlignmentI;
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11 import jalview.ws.DbSourceProxy;
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12 import jalview.ws.DbSourceProxyImpl;
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14 * TODO: later PFAM is a complex datasource - it currently returns a seed alignment, but could optionally return a full alignment.
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15 * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment
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16 * TODO: HP: Incorporate jalview.gui.SequenceFetcher retrieval code here.
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20 public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
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24 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
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26 public String getAccessionSeparator()
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28 // TODO Auto-generated method stub
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33 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
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35 public Regex getAccessionValidator()
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37 // TODO Auto-generated method stub
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42 * @see jalview.ws.DbSourceProxy#getDbSource()
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44 public String getDbSource()
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46 // TODO Auto-generated method stub
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51 * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
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53 public Hashtable getDbSourceProperties()
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55 // TODO Auto-generated method stub
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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#getRawRecords()
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71 public StringBuffer getRawRecords()
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73 // TODO Auto-generated method stub
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78 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
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80 public AlignmentI getSequenceRecords(String queries) throws Exception
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82 throw new Exception("PFAM Retrieval not yet implemented - see jalview.gui.SequenceFetcher for current implementation");
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86 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
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88 public boolean isValidReference(String accession)
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90 // TODO Auto-generated method stub
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95 * @see jalview.ws.DbSourceProxy#queryInProgress()
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97 public boolean queryInProgress()
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99 // TODO Auto-generated method stub
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103 public String getTestQuery()
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