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.util.Hashtable;
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22 import com.stevesoft.pat.Regex;
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24 import jalview.datamodel.AlignmentI;
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25 import jalview.datamodel.DBRefEntry;
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26 import jalview.io.AppletFormatAdapter;
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27 import jalview.io.FastaFile;
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28 import jalview.io.StockholmFile;
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29 import jalview.ws.seqfetcher.DbSourceProxy;
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30 import jalview.ws.seqfetcher.DbSourceProxyImpl;
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33 * TODO: later PFAM is a complex datasource - it could return a tree in addition
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34 * to an alignment TODO: create interface to pass alignment properties and tree
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35 * back to sequence fetcher
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40 abstract public class Pfam extends Xfam implements
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47 // all extensions of this PFAM source base class are DOMAINDB sources
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48 addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
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49 addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
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55 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
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57 public String getAccessionSeparator()
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59 // TODO Auto-generated method stub
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66 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
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68 public Regex getAccessionValidator()
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70 // TODO Auto-generated method stub
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77 * @see jalview.ws.DbSourceProxy#getDbSource() public String getDbSource() { *
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78 * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
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79 * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
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80 * 'alignment' source - means proxy is higher level than a sequence source.
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81 * return jalview.datamodel.DBRefSource.PFAM; }
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87 * @see jalview.ws.DbSourceProxy#getDbSourceProperties() public Hashtable
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88 * getDbSourceProperties() {
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96 * @see jalview.ws.DbSourceProxy#getDbVersion()
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99 public String getDbVersion()
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101 // TODO Auto-generated method stub
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105 /**Returns base URL for selected Pfam alignment type
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107 * @return PFAM URL stub for this DbSource
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110 protected abstract String getXFAMURL();
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115 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
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117 public AlignmentI getSequenceRecords(String queries) throws Exception
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119 // TODO: this is not a perfect implementation. We need to be able to add
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120 // individual references to each sequence in each family alignment that's
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123 AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
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124 + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
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126 for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
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128 rcds.getSequenceAt(s).addDBRef(
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129 new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
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131 getDbVersion(), queries.trim().toUpperCase()));
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132 if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
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133 { // add the specific ref too
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134 rcds.getSequenceAt(s).addDBRef(
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135 new DBRefEntry(getDbSource(), getDbVersion(), queries
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136 .trim().toUpperCase()));
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146 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
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148 public boolean isValidReference(String accession)
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150 return accession.indexOf("PF") == 0;
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154 * public String getDbName() { return "PFAM"; // getDbSource(); }
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158 public String getXfamSource() { return jalview.datamodel.DBRefSource.PFAM; }
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