1 package jalview.analysis;
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3 import java.util.Enumeration;
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4 import java.util.Vector;
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5 import java.util.Hashtable;
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7 import jalview.datamodel.AlignedCodonFrame;
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8 import jalview.datamodel.Alignment;
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9 import jalview.datamodel.AlignmentI;
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10 import jalview.datamodel.DBRefSource;
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11 import jalview.datamodel.DBRefEntry;
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12 import jalview.datamodel.Sequence;
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13 import jalview.datamodel.SequenceI;
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14 import jalview.ws.ASequenceFetcher;
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15 import jalview.ws.SequenceFetcher;
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18 * Functions for cross-referencing sequence databases. user must first specify
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19 * if cross-referencing from protein or dna (set dna==true)
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24 public class CrossRef
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27 * get the DNA or protein references for a protein or dna sequence
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33 public static DBRefEntry[] findXDbRefs(boolean dna, DBRefEntry[] rfs)
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37 rfs = jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS);
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41 rfs = jalview.util.DBRefUtils.selectRefs(rfs,
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42 DBRefSource.DNACODINGDBS); // could attempt to find other cross refs and return here - ie PDB xrefs (not dna, not protein seq)
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48 public static Hashtable classifyDbRefs(DBRefEntry[] rfs)
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50 Hashtable classes = new Hashtable();
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51 classes.put(DBRefSource.PROTEINDBS, jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS));
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52 classes.put(DBRefSource.DNACODINGDBS, jalview.util.DBRefUtils.selectRefs(rfs,
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53 DBRefSource.DNACODINGDBS));
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54 classes.put(DBRefSource.DOMAINDBS, jalview.util.DBRefUtils.selectRefs(rfs,
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55 DBRefSource.DOMAINDBS));
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56 // classes.put(OTHER, )
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62 * true if seqs are DNA seqs
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64 * @return a list of sequence database cross reference source types
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66 public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs)
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68 return findSequenceXrefTypes(dna, seqs, null);
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71 * Indirect references are references from other sequences from the dataset to any of the direct
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72 * DBRefEntrys on the given sequences.
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74 * true if seqs are DNA seqs
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76 * @return a list of sequence database cross reference source types
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78 public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs, AlignmentI dataset)
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80 String[] dbrefs = null;
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81 Vector refs = new Vector();
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82 for (int s = 0; s < seqs.length; s++)
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84 SequenceI dss = seqs[s];
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85 while (dss.getDatasetSequence()!=null)
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87 dss = dss.getDatasetSequence();
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89 DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
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90 for (int r = 0; rfs != null && r < rfs.length; r++)
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92 if (!refs.contains(rfs[r].getSource()))
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94 refs.addElement(rfs[r].getSource());
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99 // search for references to this sequence's direct references.
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100 DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
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101 Vector rseqs = new Vector();
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102 CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs, null); // don't need to specify codon frame for mapping here
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103 Enumeration lr = rseqs.elements();
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104 while (lr.hasMoreElements())
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106 SequenceI rs = (SequenceI) lr.nextElement();
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107 DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
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108 for (int r=0; rfs != null && r < rfs.length; r++)
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110 if (!refs.contains(rfs[r].getSource()))
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112 refs.addElement(rfs[r].getSource());
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118 if (refs.size() > 0)
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120 dbrefs = new String[refs.size()];
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121 refs.copyInto(dbrefs);
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127 * if (dna) { if (rfs[r].hasMap()) { // most likely this is a protein cross
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128 * reference if (!refs.contains(rfs[r].getSource())) {
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129 * refs.addElement(rfs[r].getSource()); } } }
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131 public static boolean hasCdnaMap(SequenceI[] seqs)
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133 String[] reftypes = findSequenceXrefTypes(false, seqs);
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134 for (int s = 0; s < reftypes.length; s++)
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136 if (reftypes.equals(DBRefSource.EMBLCDS))
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145 public static SequenceI[] getCdnaMap(SequenceI[] seqs)
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147 Vector cseqs = new Vector();
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148 for (int s = 0; s < seqs.length; s++)
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150 DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());
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151 for (int c = 0; c < cdna.length; c++)
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153 if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
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155 // retrieve CDS dataset sequences
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156 // need global dataset sequence retriever/resolver to reuse refs
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157 // and construct Mapping entry.
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158 // insert gaps in CDS according to peptide gaps.
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159 // add gapped sequence to cseqs
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163 if (cseqs.size() > 0)
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165 SequenceI[] rsqs = new SequenceI[cseqs.size()];
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166 cseqs.copyInto(rsqs);
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179 public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
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182 return findXrefSequences(seqs, dna, source, null);
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191 * alignment to search for product sequences.
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192 * @return products (as dataset sequences)
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194 public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
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195 String source, AlignmentI dataset)
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197 Vector rseqs = new Vector();
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198 Alignment ral = null;
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199 AlignedCodonFrame cf=new AlignedCodonFrame(dataset.getWidth()); // nominal width
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200 for (int s = 0; s < seqs.length; s++)
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202 SequenceI dss = seqs[s];
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203 while (dss.getDatasetSequence()!=null)
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205 dss = dss.getDatasetSequence();
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207 boolean found = false;
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208 DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());
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209 if ((xrfs == null || xrfs.length == 0) && dataset!=null)
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211 System.out.println("Attempting to find ds Xrefs refs.");
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212 DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less ambiguous would be a 'find primary dbRefEntry' method.
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213 found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset, rseqs, cf);
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215 for (int r = 0; xrfs!=null && r < xrfs.length; r++)
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217 if (source != null && !source.equals(xrfs[r].getSource()))
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219 if (xrfs[r].hasMap())
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221 if (xrfs[r].getMap().getTo() != null)
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223 Sequence rsq = new Sequence(xrfs[r].getMap().getTo());
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224 rseqs.addElement(rsq);
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225 if (xrfs[r].getMap().getMap().getFromRatio()!=xrfs[r].getMap().getMap().getToRatio())
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227 // get sense of map correct for adding to product alignment.
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230 // map is from dna seq to a protein product
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231 cf.addMap(dss, rsq, xrfs[r].getMap().getMap());
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233 // map should be from protein seq to its coding dna
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234 cf.addMap(rsq, dss, xrfs[r].getMap().getMap().getInverse());
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242 // do a bit more work - search for sequences with references matching
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243 // xrefs on this sequence.
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244 if (dataset != null)
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246 found = searchDataset(dss, xrfs[r], dataset, rseqs, cf);
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252 if (xrfs != null && xrfs.length > 0)
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254 // Try and get the sequence reference...
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256 * Ideal world - we ask for a sequence fetcher implementation here if
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257 * (jalview.io.RunTimeEnvironment.getSequenceFetcher()) (
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259 ASequenceFetcher sftch = new SequenceFetcher();
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260 SequenceI[] retrieved = null;
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261 int l = xrfs.length;
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262 for (int r = 0; r < xrfs.length; r++)
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264 // filter out any irrelevant or irretrievable references
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265 if ((source != null && !source.equals(xrfs[r].getSource()))
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266 || !sftch.isFetchable(xrfs[r].getSource()))
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275 .println("Attempting to retrieve cross referenced sequences.");
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276 DBRefEntry[] t = new DBRefEntry[l];
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278 for (int r = 0; r < xrfs.length; r++)
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280 if (xrfs[r] != null)
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286 retrieved = sftch.getSequences(xrfs);
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287 } catch (Exception e)
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290 .println("Problem whilst retrieving cross references for Sequence : "
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291 + seqs[s].getName());
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292 e.printStackTrace();
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294 if (retrieved != null)
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296 for (int rs = 0; rs < retrieved.length; rs++)
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298 rseqs.addElement(retrieved[rs]);
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305 if (rseqs.size() > 0)
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307 SequenceI[] rsqs = new SequenceI[rseqs.size()];
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308 rseqs.copyInto(rsqs);
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309 ral = new Alignment(rsqs);
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310 if (cf!=null && cf.getProtMappings()!=null)
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312 ral.addCodonFrame(cf);
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319 * find references to lrfs in the cross-reference set of each sequence in dataset (that is not equal to sequenceI)
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320 * Identifies matching DBRefEntry based on source and accession string only - Map and Version are nulled.
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325 * @return true if matches were found.
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327 private static boolean searchDatasetXrefs(SequenceI sequenceI, boolean dna, DBRefEntry[] lrfs, AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf)
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329 boolean found=false;
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332 for (int i=0;i<lrfs.length; i++)
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334 DBRefEntry xref = new DBRefEntry(lrfs[i]);
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335 // add in wildcards
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336 xref.setVersion(null);
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338 found = searchDataset(sequenceI, xref, dataset, rseqs, cf, false, dna);
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345 * search a given sequence dataset for references matching cross-references to
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346 * the given sequence
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354 * @return true if sequences were found and added
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356 public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
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357 AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf)
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359 return searchDataset(sequenceI, xrf,
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360 dataset, rseqs, cf, true, false);
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363 * TODO: generalise to different protein classifications
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364 * Search dataset for DBRefEntrys matching the given one (xrf) and add
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365 * the associated sequence to rseq.
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370 * @param direct - search all references or only subset
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371 * @param dna search dna or protein xrefs (if direct=false)
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372 * @return true if relationship found and sequence added.
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374 public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
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375 AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf, boolean direct, boolean dna)
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377 boolean found = false;
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380 Enumeration e = dataset.getSequences().elements();
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381 while (e.hasMoreElements())
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383 SequenceI nxt = (SequenceI) e.nextElement();
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386 if (nxt.getDatasetSequence() != null)
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389 .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
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391 if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
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393 DBRefEntry[] poss=null, cands=null;
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396 cands = jalview.util.DBRefUtils.searchRefs(poss=nxt
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399 cands = jalview.util.DBRefUtils.searchRefs(
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400 poss=CrossRef.findXDbRefs(dna, nxt.getDBRef()), xrf);
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404 rseqs.addElement(nxt);
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405 boolean foundmap= cf!=null; // don't search if we aren't given a codon map object
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406 for (int r=0; foundmap && r<cands.length; r++)
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408 if (cands[r].hasMap())
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410 if (cands[r].getMap().getTo()!=null && cands[r].getMap().getMap().getFromRatio()!=cands[r].getMap().getMap().getToRatio())
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413 // get sense of map correct for adding to product alignment.
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416 // map is from dna seq to a protein product
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417 cf.addMap(sequenceI, nxt, cands[r].getMap().getMap());
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419 // map should be from protein seq to its coding dna
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420 cf.addMap(nxt, sequenceI, cands[r].getMap().getMap().getInverse());
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427 // TODO: add mapping between sequences if necessary
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436 * precalculate different products that can be found for seqs in dataset
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441 * @param fake - don't actually build lists - just get types
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443 public static Object[] buildXProductsList(boolean dna, SequenceI[] seqs, AlignmentI dataset, boolean fake)
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445 String types[] = jalview.analysis.CrossRef.findSequenceXrefTypes(
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446 dna, seqs, dataset);
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449 System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));
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450 for (int t = 0; t < types.length; t++)
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452 System.out.println("Type: " + types[t]);
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453 SequenceI[] prod =
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454 jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);
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455 System.out.println("Found "
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456 + ((prod == null) ? "no" : "" + prod.length)
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460 for (int p=0; p<prod.length; p++)
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462 System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
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468 System.out.println("Trying getProducts for "+al.getSequenceAt(0).getDisplayId(true));
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469 System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));
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470 // have a bash at finding the products amongst all the retrieved sequences.
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471 SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al
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472 .getSequencesArray(), dna, null, ds);
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473 System.out.println("Found "
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474 + ((prod == null) ? "no" : "" + prod.length)
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478 // select non-equivalent sequences from dataset list
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479 for (int p=0; p<prod.length; p++)
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481 System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));
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