2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
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3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.ws.dbsources;
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21 import java.util.Hashtable;
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23 import com.stevesoft.pat.Regex;
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25 import jalview.datamodel.AlignmentI;
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26 import jalview.datamodel.DBRefSource;
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27 import jalview.ws.seqfetcher.DbSourceProxy;
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29 public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
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32 public EmblCdsSouce()
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35 addDbSourceProperty(DBRefSource.CODINGSEQDB);
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38 public String getAccessionSeparator()
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43 public Regex getAccessionValidator()
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45 // TODO Auto-generated method stub
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49 public String getDbSource()
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51 return DBRefSource.EMBLCDS;
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54 public String getDbVersion()
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56 return "0"; // TODO : this is dynamically set for a returned record - not
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60 public AlignmentI getSequenceRecords(String queries) throws Exception
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62 if (queries.indexOf(".") > -1)
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64 queries = queries.substring(0, queries.indexOf("."));
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66 return getEmblSequenceRecords(DBRefSource.EMBLCDS, queries);
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69 public boolean isValidReference(String accession)
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71 // most embl CDS refs look like ..
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72 // TODO: improve EMBLCDS regex
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73 return (accession==null || accession.length()<2) ? false : new com.stevesoft.pat.Regex("^[A-Z]+[0-9]+").search(accession);
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78 * cDNA for LDHA_CHICK swissprot sequence
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80 public String getTestQuery()
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85 public String getDbName()
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87 return "EMBL (CDS)";
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