1 package jalview.ws.seqfetcher;
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3 import jalview.datamodel.AlignmentI;
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4 import jalview.datamodel.SequenceI;
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6 import java.util.Enumeration;
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7 import java.util.Hashtable;
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8 import java.util.Vector;
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10 public class ASequenceFetcher
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14 * set of databases we can retrieve entries from
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16 protected Hashtable FETCHABLEDBS;
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18 public ASequenceFetcher()
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24 * get list of supported Databases
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26 * @return database source string for each database - only the latest version
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27 * of a source db is bound to each source.
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29 public String[] getSupportedDb()
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31 if (FETCHABLEDBS == null)
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33 String[] sf = new String[FETCHABLEDBS.size()];
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34 Enumeration e = FETCHABLEDBS.keys();
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36 while (e.hasMoreElements())
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38 sf[i++] = (String) e.nextElement();
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44 public boolean isFetchable(String source)
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46 Enumeration e = FETCHABLEDBS.keys();
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47 while (e.hasMoreElements())
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49 String db = (String) e.nextElement();
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50 if (source.compareToIgnoreCase(db) == 0)
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53 jalview.bin.Cache.log.warn("isFetchable doesn't know about '" + source
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58 public SequenceI[] getSequences(jalview.datamodel.DBRefEntry[] refs)
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60 SequenceI[] ret = null;
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61 Vector rseqs = new Vector();
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62 Hashtable queries = new Hashtable();
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63 for (int r = 0; r < refs.length; r++)
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65 if (!queries.containsKey(refs[r].getSource()))
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67 queries.put(refs[r].getSource(), new Vector());
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69 Vector qset = (Vector) queries.get(refs[r].getSource());
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70 if (!qset.contains(refs[r].getAccessionId()))
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72 qset.addElement(refs[r].getAccessionId());
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75 Enumeration e = queries.keys();
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76 while (e.hasMoreElements())
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78 Vector query = null;
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82 db = (String) e.nextElement();
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83 query = (Vector) queries.get(db);
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84 if (!isFetchable(db))
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85 throw new Exception(
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86 "Don't know how to fetch from this database :" + db);
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87 DbSourceProxy fetcher = getSourceProxy(db);
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88 boolean doMultiple = fetcher.getAccessionSeparator() != null; // No
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93 Enumeration qs = query.elements();
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94 while (qs.hasMoreElements())
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96 StringBuffer qsb = new StringBuffer();
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99 qsb.append((String) qs.nextElement());
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100 if (qs.hasMoreElements() && doMultiple) // and not reached limit for
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101 // multiple queries at one
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102 // time for this source
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104 qsb.append(fetcher.getAccessionSeparator());
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106 } while (doMultiple && qs.hasMoreElements());
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108 AlignmentI seqset=null;
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110 // create a fetcher and go to it
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111 seqset = fetcher.getSequenceRecords(qsb.toString());
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112 } catch (Exception ex)
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114 System.err.println("Failed to retrieve the following from "+db);
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115 System.err.println(qsb);
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116 ex.printStackTrace(System.err);
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118 // TODO: Merge alignment together - perhaps
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119 if (seqset != null)
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121 SequenceI seqs[] = seqset.getSequencesArray();
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124 for (int is = 0; is < seqs.length; is++)
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126 rseqs.addElement(seqs[is]);
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132 if (fetcher.getRawRecords() != null)
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134 System.out.println("# Retrieved from " + db + ":"
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136 StringBuffer rrb = fetcher.getRawRecords();
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138 * for (int rr = 0; rr<rrb.length; rr++) {
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141 // if (rr<qs.length)
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143 hdr = "# " + db + ":" + qsb.toString();
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145 * } else { hdr = "# part "+rr; }
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147 System.out.println(hdr);
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149 System.out.println(rrb);
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150 System.out.println("# end of " + hdr);
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155 } catch (Exception ex)
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158 .println("Failed to retrieve the following references from "
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160 Enumeration qv = query.elements();
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162 while (qv.hasMoreElements())
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164 System.err.print(" " + qv.nextElement() + ";");
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167 System.err.println();
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171 System.err.println();
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172 ex.printStackTrace();
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175 if (rseqs.size() > 0)
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177 ret = new SequenceI[rseqs.size()];
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178 Enumeration sqs = rseqs.elements();
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180 while (sqs.hasMoreElements())
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182 SequenceI s = (SequenceI) sqs.nextElement();
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191 * Retrieve an instance of the proxy for the given source
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194 * database source string TODO: add version string/wildcard for
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195 * retrieval of specific DB source/version combinations.
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196 * @return an instance of DbSourceProxy for that db.
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198 public DbSourceProxy getSourceProxy(String db)
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200 DbSourceProxy dbs = (DbSourceProxy) FETCHABLEDBS.get(db);
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205 * constructs and instance of the proxy and registers it as a valid
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208 * @param dbSourceProxy
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209 * reference for class implementing
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210 * jalview.ws.seqfetcher.DbSourceProxy
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211 * @throws java.lang.IllegalArgumentException
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212 * if class does not implement
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213 * jalview.ws.seqfetcher.DbSourceProxy
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215 protected void addDBRefSourceImpl(Class dbSourceProxy)
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216 throws java.lang.IllegalArgumentException
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220 Object proxyObj = dbSourceProxy.getConstructor(
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221 null).newInstance(null);
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222 if (!DbSourceProxy.class.isInstance(proxyObj))
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224 throw new IllegalArgumentException(
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225 dbSourceProxy.toString()
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226 + " does not implement the jalview.ws.seqfetcher.DbSourceProxy");
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228 DbSourceProxy proxy = (DbSourceProxy) proxyObj;
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231 if (FETCHABLEDBS == null)
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233 FETCHABLEDBS = new Hashtable();
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235 FETCHABLEDBS.put(proxy.getDbSource(), proxy);
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238 catch (IllegalArgumentException e)
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242 catch (Exception e)
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244 // Serious problems if this happens.
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245 throw new Error("DBRefSource Implementation Exception", e);
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