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.datamodel.DBRefEntry;
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12 import jalview.io.AppletFormatAdapter;
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13 import jalview.io.FastaFile;
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14 import jalview.io.StockholmFile;
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15 import jalview.ws.seqfetcher.DbSourceProxy;
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16 import jalview.ws.seqfetcher.DbSourceProxyImpl;
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18 * TODO: later PFAM is a complex datasource - it could return a tree in addition to an alignment
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19 * TODO: create interface to pass alignment properties and tree back to sequence fetcher
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23 abstract public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
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29 // all extensions of this PFAM source base class are DOMAINDB sources
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30 addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
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34 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
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36 public String getAccessionSeparator()
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38 // TODO Auto-generated method stub
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43 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
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45 public Regex getAccessionValidator()
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47 // TODO Auto-generated method stub
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52 * @see jalview.ws.DbSourceProxy#getDbSource()
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53 public String getDbSource()
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55 ** this doesn't work - DbSource is key for the hash of DbSourceProxy instances - 1:many mapping for DbSource to proxy will be lost.
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56 ** suggest : PFAM is an 'alignment' source - means proxy is higher level than a sequence source.
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57 return jalview.datamodel.DBRefSource.PFAM;
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63 * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
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64 public Hashtable getDbSourceProperties()
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72 * @see jalview.ws.DbSourceProxy#getDbVersion()
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74 public String getDbVersion()
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76 // TODO Auto-generated method stub
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81 * @return PFAM URL stub for this DbSource
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83 protected abstract String getPFAMURL();
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85 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
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87 public AlignmentI getSequenceRecords(String queries) throws Exception
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89 // TODO: this is not a perfect implementation. We need to be able to add individual references to each sequence in each family alignment that's retrieved.
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91 AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getPFAMURL()+queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,"STH");
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92 for (int s=0,sNum=rcds.getHeight(); s<sNum;s++)
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94 rcds.getSequenceAt(s).addDBRef(new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
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96 getDbVersion(), queries.trim().toUpperCase()));
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97 if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
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98 { // add the specific ref too
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99 rcds.getSequenceAt(s).addDBRef(
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100 new DBRefEntry( getDbSource(),
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101 getDbVersion(), queries.trim().toUpperCase()));
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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 return accession.indexOf("PF")==0;
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117 /*public String getDbName()
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119 return "PFAM"; // getDbSource();
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