2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.ws.dbsources;
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20 import java.io.File;
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21 import java.util.Hashtable;
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22 import java.util.Iterator;
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23 import java.util.StringTokenizer;
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25 import com.stevesoft.pat.Regex;
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27 import jalview.datamodel.Alignment;
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28 import jalview.datamodel.AlignmentI;
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29 import jalview.datamodel.DBRefSource;
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30 import jalview.datamodel.SequenceI;
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31 import jalview.datamodel.xdb.embl.EmblEntry;
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32 import jalview.ws.ebi.EBIFetchClient;
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33 import jalview.ws.seqfetcher.DbSourceProxy;
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34 import jalview.ws.seqfetcher.DbSourceProxyImpl;
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37 * Test class for accessing GeneDB - not yet finished.
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42 public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
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45 public GeneDbSource()
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47 addDbSourceProperty(DBRefSource.DNASEQDB);
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48 addDbSourceProperty(DBRefSource.CODINGSEQDB);
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54 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
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56 public String getAccessionSeparator()
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58 // TODO Auto-generated method stub
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65 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
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67 public Regex getAccessionValidator()
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69 // TODO Auto-generated method stub
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76 * @see jalview.ws.DbSourceProxy#getDbSource()
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78 public String getDbSource()
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80 return DBRefSource.GENEDB;
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86 * @see jalview.ws.DbSourceProxy#getDbVersion()
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88 public String getDbVersion()
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90 // TODO Auto-generated method stub
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97 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
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99 public AlignmentI getSequenceRecords(String queries) throws Exception
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102 // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
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104 return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
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110 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
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112 public boolean isValidReference(String accession)
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114 // TODO Auto-generated method stub
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119 * return T.Brucei Mannosyl-Transferase TbPIG-M
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121 public String getTestQuery()
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123 return "Tb927.6.3300";
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126 public String getDbName()
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128 return "GeneDB"; // getDbSource();
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