2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
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3 * Copyright (C) 2008 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.io.File;
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22 import java.util.Hashtable;
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23 import java.util.Iterator;
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24 import java.util.StringTokenizer;
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26 import com.stevesoft.pat.Regex;
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28 import jalview.datamodel.Alignment;
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29 import jalview.datamodel.AlignmentI;
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30 import jalview.datamodel.DBRefSource;
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31 import jalview.datamodel.SequenceI;
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32 import jalview.datamodel.xdb.embl.EmblEntry;
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33 import jalview.ws.ebi.EBIFetchClient;
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34 import jalview.ws.seqfetcher.DbSourceProxy;
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35 import jalview.ws.seqfetcher.DbSourceProxyImpl;
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41 public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
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44 public GeneDbSource()
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46 addDbSourceProperty(DBRefSource.DNASEQDB);
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47 addDbSourceProperty(DBRefSource.CODINGSEQDB);
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53 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
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55 public String getAccessionSeparator()
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57 // TODO Auto-generated method stub
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64 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
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66 public Regex getAccessionValidator()
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68 // TODO Auto-generated method stub
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75 * @see jalview.ws.DbSourceProxy#getDbSource()
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77 public String getDbSource()
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79 return DBRefSource.GENEDB;
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85 * @see jalview.ws.DbSourceProxy#getDbVersion()
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87 public String getDbVersion()
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89 // TODO Auto-generated method stub
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96 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
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98 public AlignmentI getSequenceRecords(String queries) throws Exception
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101 // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
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103 return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
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109 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
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111 public boolean isValidReference(String accession)
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113 // TODO Auto-generated method stub
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118 * return T.Brucei Mannosyl-Transferase TbPIG-M
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120 public String getTestQuery()
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122 return "Tb927.6.3300";
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125 public String getDbName()
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127 return getDbSource();
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