4 package jalview.ws.dbsources;
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6 import jalview.datamodel.Alignment;
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7 import jalview.datamodel.DBRefEntry;
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8 import jalview.datamodel.DBRefSource;
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9 import jalview.datamodel.SequenceI;
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11 import java.io.BufferedInputStream;
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12 import java.io.InputStream;
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13 import java.io.InputStreamReader;
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14 import java.util.Hashtable;
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15 import java.util.Vector;
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17 import MCview.PDBChain;
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18 import MCview.PDBfile;
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20 import com.stevesoft.pat.Regex;
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22 import jalview.datamodel.AlignmentI;
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23 import jalview.io.FileParse;
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24 import jalview.ws.ebi.EBIFetchClient;
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25 import jalview.ws.seqfetcher.DbSourceProxy;
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26 import jalview.ws.seqfetcher.DbSourceProxyImpl;
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32 public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
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36 addDbSourceProperty(DBRefSource.PROTSEQDB);
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40 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
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42 public String getAccessionSeparator()
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44 // TODO Auto-generated method stub
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49 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
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51 public Regex getAccessionValidator()
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53 return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
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57 * @see jalview.ws.DbSourceProxy#getDbSource()
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59 public String getDbSource()
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61 return DBRefSource.PDB;
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65 * @see jalview.ws.DbSourceProxy#getDbVersion()
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67 public String getDbVersion()
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72 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
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74 public AlignmentI getSequenceRecords(String queries) throws Exception
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77 Vector result = new Vector();
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78 String chain = null;
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80 if (queries.indexOf(":") > -1)
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82 chain = queries.substring(queries.indexOf(":") + 1);
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83 id = queries.substring(0, queries.indexOf(":"));
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89 if (queries.length() > 4 && chain == null)
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91 chain = queries.substring(4,5);
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92 id = queries.substring(0, 4);
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94 if (!isValidReference(id))
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96 System.err.println("Ignoring invalid pdb query: '"+id+"'");
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100 EBIFetchClient ebi = new EBIFetchClient();
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101 file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw")
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102 .getAbsolutePath();
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111 PDBfile pdbfile = new PDBfile(file,
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112 jalview.io.AppletFormatAdapter.FILE);
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113 for (int i = 0; i < pdbfile.chains.size(); i++)
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116 || ((PDBChain) pdbfile.chains.elementAt(i)).id
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117 .toUpperCase().equals(chain))
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119 PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
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120 // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
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121 SequenceI sq = pdbchain.sequence;
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122 // Specially formatted name for the PDB chain sequences retrieved from the PDB
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123 sq.setName(jalview.datamodel.DBRefSource.PDB+"|" + id + "|" + sq.getName());
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124 // Might need to add more metadata to the PDBEntry object
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127 * PDBEntry entry = new PDBEntry();
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128 // Construct the PDBEntry
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130 if (entry.getProperty() == null)
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131 entry.setProperty(new Hashtable());
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132 entry.getProperty().put("chains",
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134 + "=" + sq.getStart()
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135 + "-" + sq.getEnd());
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136 sq.getDatasetSequence().addPDBId(entry);
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139 // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
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140 // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
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141 DBRefEntry dbentry = new DBRefEntry(getDbSource(),
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142 getDbVersion(), id + pdbchain.id);
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143 sq.addDBRef(dbentry);
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144 // and add seuqence to the retrieved set
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145 result.addElement(sq.deriveSequence());
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149 if (result.size() < 1)
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151 throw new Exception("No PDB Records for " + id + " chain "
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152 + ((chain == null) ? "' '" : chain));
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154 } catch (Exception ex) // Problem parsing PDB file
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160 SequenceI[] results = new SequenceI[result.size()];
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161 for (int i = 0, j = result.size(); i < j; i++)
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163 results[i] = (SequenceI) result.elementAt(i);
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164 result.setElementAt(null, i);
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166 return new Alignment(results);
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170 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
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172 public boolean isValidReference(String accession)
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174 Regex r = getAccessionValidator();
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175 return r.search(accession.trim());
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179 * obtain human glyoxalase chain A sequence
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181 public String getTestQuery()
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186 public String getDbName()
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188 return "PDB"; // getDbSource();
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