-package jalview.analysis;\r
-\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import java.util.Hashtable;\r
-\r
-import jalview.datamodel.AlignedCodonFrame;\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.Sequence;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.ws.SequenceFetcher;\r
-import jalview.ws.seqfetcher.ASequenceFetcher;\r
-\r
-/**\r
- * Functions for cross-referencing sequence databases. user must first specify\r
- * if cross-referencing from protein or dna (set dna==true)\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public class CrossRef\r
-{\r
- /**\r
- * get the DNA or protein references for a protein or dna sequence\r
- * \r
- * @param dna\r
- * @param rfs\r
- * @return\r
- */\r
- public static DBRefEntry[] findXDbRefs(boolean dna, DBRefEntry[] rfs)\r
- {\r
- if (dna)\r
- {\r
- rfs = jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS);\r
- }\r
- else\r
- {\r
- rfs = jalview.util.DBRefUtils.selectRefs(rfs,\r
- DBRefSource.DNACODINGDBS); // could attempt to find other cross\r
- // refs and return here - ie PDB xrefs\r
- // (not dna, not protein seq)\r
- }\r
- return rfs;\r
- }\r
-\r
- public static Hashtable classifyDbRefs(DBRefEntry[] rfs)\r
- {\r
- Hashtable classes = new Hashtable();\r
- classes.put(DBRefSource.PROTEINDBS, jalview.util.DBRefUtils.selectRefs(\r
- rfs, DBRefSource.PROTEINDBS));\r
- classes.put(DBRefSource.DNACODINGDBS, jalview.util.DBRefUtils\r
- .selectRefs(rfs, DBRefSource.DNACODINGDBS));\r
- classes.put(DBRefSource.DOMAINDBS, jalview.util.DBRefUtils.selectRefs(\r
- rfs, DBRefSource.DOMAINDBS));\r
- // classes.put(OTHER, )\r
- return classes;\r
- }\r
-\r
- /**\r
- * @param dna\r
- * true if seqs are DNA seqs\r
- * @param seqs\r
- * @return a list of sequence database cross reference source types\r
- */\r
- public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs)\r
- {\r
- return findSequenceXrefTypes(dna, seqs, null);\r
- }\r
-\r
- /**\r
- * Indirect references are references from other sequences from the dataset to\r
- * any of the direct DBRefEntrys on the given sequences.\r
- * \r
- * @param dna\r
- * true if seqs are DNA seqs\r
- * @param seqs\r
- * @return a list of sequence database cross reference source types\r
- */\r
- public static String[] findSequenceXrefTypes(boolean dna,\r
- SequenceI[] seqs, AlignmentI dataset)\r
- {\r
- String[] dbrefs = null;\r
- Vector refs = new Vector();\r
- for (int s = 0; s < seqs.length; s++)\r
- {\r
- SequenceI dss = seqs[s];\r
- while (dss.getDatasetSequence() != null)\r
- {\r
- dss = dss.getDatasetSequence();\r
- }\r
- DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());\r
- for (int r = 0; rfs != null && r < rfs.length; r++)\r
- {\r
- if (!refs.contains(rfs[r].getSource()))\r
- {\r
- refs.addElement(rfs[r].getSource());\r
- }\r
- }\r
- if (dataset != null)\r
- {\r
- // search for references to this sequence's direct references.\r
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());\r
- Vector rseqs = new Vector();\r
- CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,\r
- null); // don't need to specify codon frame for mapping here\r
- Enumeration lr = rseqs.elements();\r
- while (lr.hasMoreElements())\r
- {\r
- SequenceI rs = (SequenceI) lr.nextElement();\r
- DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());\r
- for (int r = 0; rfs != null && r < rfs.length; r++)\r
- {\r
- if (!refs.contains(rfs[r].getSource()))\r
- {\r
- refs.addElement(rfs[r].getSource());\r
- }\r
- }\r
- }\r
- }\r
- }\r
- if (refs.size() > 0)\r
- {\r
- dbrefs = new String[refs.size()];\r
- refs.copyInto(dbrefs);\r
- }\r
- return dbrefs;\r
- }\r
-\r
- /*\r
- * if (dna) { if (rfs[r].hasMap()) { // most likely this is a protein cross\r
- * reference if (!refs.contains(rfs[r].getSource())) {\r
- * refs.addElement(rfs[r].getSource()); } } }\r
- */\r
- public static boolean hasCdnaMap(SequenceI[] seqs)\r
- {\r
- String[] reftypes = findSequenceXrefTypes(false, seqs);\r
- for (int s = 0; s < reftypes.length; s++)\r
- {\r
- if (reftypes.equals(DBRefSource.EMBLCDS))\r
- {\r
- return true;\r
- // no map\r
- }\r
- }\r
- return false;\r
- }\r
-\r
- public static SequenceI[] getCdnaMap(SequenceI[] seqs)\r
- {\r
- Vector cseqs = new Vector();\r
- for (int s = 0; s < seqs.length; s++)\r
- {\r
- DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());\r
- for (int c = 0; c < cdna.length; c++)\r
- {\r
- if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))\r
- {\r
- System.err.println("TODO: unimplemented sequence retrieval for coding region sequence.");\r
- // TODO: retrieve CDS dataset sequences\r
- // need global dataset sequence retriever/resolver to reuse refs\r
- // and construct Mapping entry.\r
- // insert gaps in CDS according to peptide gaps.\r
- // add gapped sequence to cseqs\r
- }\r
- }\r
- }\r
- if (cseqs.size() > 0)\r
- {\r
- SequenceI[] rsqs = new SequenceI[cseqs.size()];\r
- cseqs.copyInto(rsqs);\r
- return rsqs;\r
- }\r
- return null;\r
-\r
- }\r
-\r
- /**\r
- * \r
- * @param dna\r
- * @param seqs\r
- * @return\r
- */\r
- public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,\r
- String source)\r
- {\r
- return findXrefSequences(seqs, dna, source, null);\r
- }\r
-\r
- /**\r
- * \r
- * @param seqs\r
- * @param dna\r
- * @param source\r
- * @param dataset\r
- * alignment to search for product sequences.\r
- * @return products (as dataset sequences)\r
- */\r
- public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,\r
- String source, AlignmentI dataset)\r
- {\r
- Vector rseqs = new Vector();\r
- Alignment ral = null;\r
- AlignedCodonFrame cf = new AlignedCodonFrame(0); // nominal width\r
- for (int s = 0; s < seqs.length; s++)\r
- {\r
- SequenceI dss = seqs[s];\r
- while (dss.getDatasetSequence() != null)\r
- {\r
- dss = dss.getDatasetSequence();\r
- }\r
- boolean found = false;\r
- DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());\r
- if ((xrfs == null || xrfs.length == 0) && dataset != null)\r
- {\r
- System.out.println("Attempting to find ds Xrefs refs.");\r
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less\r
- // ambiguous\r
- // would\r
- // be a\r
- // 'find\r
- // primary\r
- // dbRefEntry'\r
- // method.\r
- // filter for desired source xref here\r
- found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,\r
- rseqs, cf);\r
- }\r
- for (int r = 0; xrfs != null && r < xrfs.length; r++)\r
- {\r
- if (source != null && !source.equals(xrfs[r].getSource()))\r
- continue;\r
- if (xrfs[r].hasMap())\r
- {\r
- if (xrfs[r].getMap().getTo() != null)\r
- {\r
- Sequence rsq = new Sequence(xrfs[r].getMap().getTo());\r
- rseqs.addElement(rsq);\r
- if (xrfs[r].getMap().getMap().getFromRatio() != xrfs[r]\r
- .getMap().getMap().getToRatio())\r
- {\r
- // get sense of map correct for adding to product alignment.\r
- if (dna)\r
- {\r
- // map is from dna seq to a protein product\r
- cf.addMap(dss, rsq, xrfs[r].getMap().getMap());\r
- }\r
- else\r
- {\r
- // map should be from protein seq to its coding dna\r
- cf.addMap(rsq, dss, xrfs[r].getMap().getMap().getInverse());\r
- }\r
- }\r
- found = true;\r
- }\r
- }\r
- if (!found)\r
- {\r
- // do a bit more work - search for sequences with references matching\r
- // xrefs on this sequence.\r
- if (dataset != null)\r
- {\r
- found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf);\r
- if (found)\r
- xrfs[r] = null; // we've recovered seqs for this one.\r
- }\r
- }\r
- }\r
- if (!found)\r
- {\r
- if (xrfs != null && xrfs.length > 0)\r
- {\r
- // Try and get the sequence reference...\r
- /*\r
- * Ideal world - we ask for a sequence fetcher implementation here if\r
- * (jalview.io.RunTimeEnvironment.getSequenceFetcher()) (\r
- */\r
- ASequenceFetcher sftch = new SequenceFetcher();\r
- SequenceI[] retrieved = null;\r
- int l = xrfs.length;\r
- for (int r = 0; r < xrfs.length; r++)\r
- {\r
- // filter out any irrelevant or irretrievable references\r
- if (xrfs[r] == null\r
- || ((source != null && !source.equals(xrfs[r]\r
- .getSource())) || !sftch.isFetchable(xrfs[r]\r
- .getSource())))\r
- {\r
- l--;\r
- xrfs[r] = null;\r
- }\r
- }\r
- if (l > 0)\r
- {\r
- System.out\r
- .println("Attempting to retrieve cross referenced sequences.");\r
- DBRefEntry[] t = new DBRefEntry[l];\r
- l = 0;\r
- for (int r = 0; r < xrfs.length; r++)\r
- {\r
- if (xrfs[r] != null)\r
- t[l++] = xrfs[r];\r
- }\r
- xrfs = t;\r
- try\r
- {\r
- retrieved = sftch.getSequences(xrfs); // problem here is we don't know which of xrfs resulted in which retrieved element\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Problem whilst retrieving cross references for Sequence : "\r
- + seqs[s].getName());\r
- e.printStackTrace();\r
- }\r
- if (retrieved != null)\r
- {\r
- for (int rs = 0; rs < retrieved.length; rs++)\r
- {\r
- // TODO: examine each sequence for 'redundancy'\r
- jalview.datamodel.DBRefEntry[] dbr = retrieved[rs].getDBRef();\r
- if (dbr != null && dbr.length > 0)\r
- {\r
- for (int di = 0; di < dbr.length; di++)\r
- {\r
- // find any entry where we should put in the sequence being cross-referenced into the map\r
- jalview.datamodel.Mapping map = dbr[di].getMap();\r
- if (map != null)\r
- {\r
- if (map.getTo() != null && map.getMap() != null)\r
- {\r
- // should search the local dataset to find any existing candidates for To !\r
- try\r
- {\r
- // compare ms with dss and replace with dss in mapping if map is congruent\r
- SequenceI ms = map.getTo();\r
- int sf = map.getMap().getToLowest();\r
- int st = map.getMap().getToHighest();\r
- SequenceI mappedrg = ms.getSubSequence(sf, st);\r
- SequenceI loc = dss.getSubSequence(sf, st);\r
- if (mappedrg.getLength()>0 && mappedrg.getSequenceAsString().equals(\r
- loc.getSequenceAsString()))\r
- {\r
- System.err\r
- .println("Mapping updated for retrieved crossreference");\r
- // method to update all refs of existing To on retrieved sequence with dss and merge any props on To onto dss.\r
- map.setTo(dss);\r
- }\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Exception when consolidating Mapped sequence set...");\r
- e.printStackTrace(System.err);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- retrieved[rs].updatePDBIds();\r
- rseqs.addElement(retrieved[rs]);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
- if (rseqs.size() > 0)\r
- {\r
- SequenceI[] rsqs = new SequenceI[rseqs.size()];\r
- rseqs.copyInto(rsqs);\r
- ral = new Alignment(rsqs);\r
- if (cf != null && cf.getProtMappings() != null)\r
- {\r
- ral.addCodonFrame(cf);\r
- }\r
- }\r
- return ral;\r
- }\r
-\r
- /**\r
- * find references to lrfs in the cross-reference set of each sequence in\r
- * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry\r
- * based on source and accession string only - Map and Version are nulled.\r
- * \r
- * @param sequenceI\r
- * @param lrfs\r
- * @param dataset\r
- * @param rseqs\r
- * @return true if matches were found.\r
- */\r
- private static boolean searchDatasetXrefs(SequenceI sequenceI,\r
- boolean dna, DBRefEntry[] lrfs, AlignmentI dataset, Vector rseqs,\r
- AlignedCodonFrame cf)\r
- {\r
- boolean found = false;\r
- if (lrfs == null)\r
- return false;\r
- for (int i = 0; i < lrfs.length; i++)\r
- {\r
- DBRefEntry xref = new DBRefEntry(lrfs[i]);\r
- // add in wildcards\r
- xref.setVersion(null);\r
- xref.setMap(null);\r
- found = searchDataset(sequenceI, xref, dataset, rseqs, cf, false, dna);\r
- }\r
- return found;\r
- }\r
-\r
- /**\r
- * search a given sequence dataset for references matching cross-references to\r
- * the given sequence\r
- * \r
- * @param sequenceI\r
- * @param xrf\r
- * @param dataset\r
- * @param rseqs\r
- * set of unique sequences\r
- * @param cf\r
- * @return true if one or more unique sequences were found and added\r
- */\r
- public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,\r
- AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf)\r
- {\r
- return searchDataset(sequenceI, xrf, dataset, rseqs, cf, true, false);\r
- }\r
-\r
- /**\r
- * TODO: generalise to different protein classifications Search dataset for\r
- * DBRefEntrys matching the given one (xrf) and add the associated sequence to\r
- * rseq.\r
- * \r
- * @param sequenceI\r
- * @param xrf\r
- * @param dataset\r
- * @param rseqs\r
- * @param direct -\r
- * search all references or only subset\r
- * @param dna\r
- * search dna or protein xrefs (if direct=false)\r
- * @return true if relationship found and sequence added.\r
- */\r
- public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,\r
- AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf,\r
- boolean direct, boolean dna)\r
- {\r
- boolean found = false;\r
- SequenceI[] typer=new SequenceI[1];\r
- if (dataset == null)\r
- return false;\r
- if (dataset.getSequences() == null)\r
- {\r
- System.err.println("Empty dataset sequence set - NO VECTOR");\r
- return false;\r
- }\r
- Enumeration e = dataset.getSequences().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceI nxt = (SequenceI) e.nextElement();\r
- if (nxt != null)\r
- {\r
- if (nxt.getDatasetSequence() != null)\r
- {\r
- System.err\r
- .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");\r
- }\r
- if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())\r
- {\r
- // check if this is the correct sequence type\r
- {\r
- typer[0] = nxt;\r
- boolean isDna = jalview.util.Comparison.isNucleotide(typer);\r
- if ((direct && isDna == dna) || (!direct && isDna!=dna))\r
- {\r
- // skip this sequence because it is same molecule type\r
- continue;\r
- }\r
- }\r
-\r
- // look for direct or indirect references in common\r
- DBRefEntry[] poss = null, cands = null;\r
- if (direct)\r
- {\r
- cands = jalview.util.DBRefUtils.searchRefs(poss = nxt\r
- .getDBRef(), xrf);\r
- }\r
- else\r
- {\r
- cands = jalview.util.DBRefUtils.searchRefs(poss = CrossRef\r
- .findXDbRefs(dna, nxt.getDBRef()), xrf);\r
- }\r
- if (cands != null)\r
- {\r
- if (!rseqs.contains(nxt))\r
- {\r
- rseqs.addElement(nxt);\r
- boolean foundmap = cf != null; // don't search if we aren't given\r
- // a codon map object\r
- for (int r = 0; foundmap && r < cands.length; r++)\r
- {\r
- if (cands[r].hasMap())\r
- {\r
- if (cands[r].getMap().getTo() != null\r
- && cands[r].getMap().getMap().getFromRatio() != cands[r]\r
- .getMap().getMap().getToRatio())\r
- {\r
- foundmap = true;\r
- // get sense of map correct for adding to product alignment.\r
- if (dna)\r
- {\r
- // map is from dna seq to a protein product\r
- cf.addMap(sequenceI, nxt, cands[r].getMap().getMap());\r
- }\r
- else\r
- {\r
- // map should be from protein seq to its coding dna\r
- cf.addMap(nxt, sequenceI, cands[r].getMap().getMap()\r
- .getInverse());\r
- }\r
- }\r
- }\r
- }\r
- // TODO: add mapping between sequences if necessary\r
- found = true;\r
- }\r
- }\r
-\r
- }\r
- }\r
- }\r
- return found;\r
- }\r
-\r
- /**\r
- * precalculate different products that can be found for seqs in dataset and\r
- * return them.\r
- * \r
- * @param dna\r
- * @param seqs\r
- * @param dataset\r
- * @param fake -\r
- * don't actually build lists - just get types\r
- * @return public static Object[] buildXProductsList(boolean dna, SequenceI[]\r
- * seqs, AlignmentI dataset, boolean fake) { String types[] =\r
- * jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,\r
- * dataset); if (types != null) { System.out.println("Xref Types for:\r
- * "+(dna ? "dna" : "prot")); for (int t = 0; t < types.length; t++) {\r
- * System.out.println("Type: " + types[t]); SequenceI[] prod =\r
- * jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);\r
- * System.out.println("Found " + ((prod == null) ? "no" : "" +\r
- * prod.length) + " products"); if (prod!=null) { for (int p=0; p<prod.length;\r
- * p++) { System.out.println("Prod "+p+":\r
- * "+prod[p].getDisplayId(true)); } } }\r
- * } else { System.out.println("Trying getProducts for\r
- * "+al.getSequenceAt(0).getDisplayId(true)); System.out.println("Search DS\r
- * Xref for: "+(dna ? "dna" : "prot")); // have a bash at finding the products\r
- * amongst all the retrieved sequences. SequenceI[] prod =\r
- * jalview.analysis.CrossRef.findXrefSequences(al .getSequencesArray(), dna,\r
- * null, ds); System.out.println("Found " + ((prod == null) ? "no" : "" +\r
- * prod.length) + " products"); if (prod!=null) { // select non-equivalent\r
- * sequences from dataset list for (int p=0; p<prod.length; p++) {\r
- * System.out.println("Prod "+p+": "+prod[p].getDisplayId(true)); } }\r
- * } }\r
- */\r
-}
\ No newline at end of file
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.ws.SequenceFetcherFactory;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * Functions for cross-referencing sequence databases.
+ *
+ * @author JimP
+ *
+ */
+public class CrossRef
+{
+ /*
+ * the dataset of the alignment for which we are searching for
+ * cross-references; in some cases we may resolve xrefs by
+ * searching in the dataset
+ */
+ private AlignmentI dataset;
+
+ /*
+ * the sequences for which we are seeking cross-references
+ */
+ private SequenceI[] fromSeqs;
+
+ /**
+ * matcher built from dataset
+ */
+ SequenceIdMatcher matcher;
+
+ /**
+ * sequences found by cross-ref searches to fromSeqs
+ */
+ List<SequenceI> rseqs;
+
+ /**
+ * Constructor
+ *
+ * @param seqs
+ * the sequences for which we are seeking cross-references
+ * @param ds
+ * the containing alignment dataset (may be searched to resolve
+ * cross-references)
+ */
+ public CrossRef(SequenceI[] seqs, AlignmentI ds)
+ {
+ fromSeqs = seqs;
+ dataset = ds.getDataset() == null ? ds : ds.getDataset();
+ }
+
+ /**
+ * Returns a list of distinct database sources for which sequences have either
+ * <ul>
+ * <li>a (dna-to-protein or protein-to-dna) cross-reference</li>
+ * <li>an indirect cross-reference - a (dna-to-protein or protein-to-dna)
+ * reference from another sequence in the dataset which has a cross-reference
+ * to a direct DBRefEntry on the given sequence</li>
+ * </ul>
+ *
+ * @param dna
+ * - when true, cross-references *from* dna returned. When false,
+ * cross-references *from* protein are returned
+ * @return
+ */
+ public List<String> findXrefSourcesForSequences(boolean dna)
+ {
+ List<String> sources = new ArrayList<>();
+ for (SequenceI seq : fromSeqs)
+ {
+ if (seq != null)
+ {
+ findXrefSourcesForSequence(seq, dna, sources);
+ }
+ }
+ sources.remove(DBRefSource.EMBL); // hack to prevent EMBL xrefs resulting in
+ // redundant datasets
+ if (dna)
+ {
+ sources.remove(DBRefSource.ENSEMBL); // hack to prevent Ensembl and
+ // EnsemblGenomes xref option shown
+ // from cdna panel
+ sources.remove(DBRefSource.ENSEMBLGENOMES);
+ }
+ // redundant datasets
+ return sources;
+ }
+
+ /**
+ * Returns a list of distinct database sources for which a sequence has either
+ * <ul>
+ * <li>a (dna-to-protein or protein-to-dna) cross-reference</li>
+ * <li>an indirect cross-reference - a (dna-to-protein or protein-to-dna)
+ * reference from another sequence in the dataset which has a cross-reference
+ * to a direct DBRefEntry on the given sequence</li>
+ * </ul>
+ *
+ * @param seq
+ * the sequence whose dbrefs we are searching against
+ * @param fromDna
+ * when true, context is DNA - so sources identifying protein
+ * products will be returned.
+ * @param sources
+ * a list of sources to add matches to
+ */
+ void findXrefSourcesForSequence(SequenceI seq, boolean fromDna,
+ List<String> sources)
+ {
+ /*
+ * first find seq's xrefs (dna-to-peptide or peptide-to-dna)
+ */
+ DBRefEntry[] rfs = DBRefUtils.selectDbRefs(!fromDna, seq.getDBRefs());
+ addXrefsToSources(rfs, sources);
+ if (dataset != null)
+ {
+ /*
+ * find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
+ */
+ DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
+ List<SequenceI> foundSeqs = new ArrayList<>();
+
+ /*
+ * find sequences in the alignment which xref one of these DBRefs
+ * i.e. is xref-ed to a common sequence identifier
+ */
+ searchDatasetXrefs(fromDna, seq, lrfs, foundSeqs, null);
+
+ /*
+ * add those sequences' (dna-to-peptide or peptide-to-dna) dbref sources
+ */
+ for (SequenceI rs : foundSeqs)
+ {
+ DBRefEntry[] xrs = DBRefUtils.selectDbRefs(!fromDna,
+ rs.getDBRefs());
+ addXrefsToSources(xrs, sources);
+ }
+ }
+ }
+
+ /**
+ * Helper method that adds the source identifiers of some cross-references to
+ * a (non-redundant) list of database sources
+ *
+ * @param xrefs
+ * @param sources
+ */
+ void addXrefsToSources(DBRefEntry[] xrefs, List<String> sources)
+ {
+ if (xrefs != null)
+ {
+ for (DBRefEntry ref : xrefs)
+ {
+ /*
+ * avoid duplication e.g. ENSEMBL and Ensembl
+ */
+ String source = DBRefUtils.getCanonicalName(ref.getSource());
+ if (!sources.contains(source))
+ {
+ sources.add(source);
+ }
+ }
+ }
+ }
+
+ /**
+ * Attempts to find cross-references from the sequences provided in the
+ * constructor to the given source database. Cross-references may be found
+ * <ul>
+ * <li>in dbrefs on the sequence which hold a mapping to a sequence
+ * <ul>
+ * <li>provided with a fetched sequence (e.g. ENA translation), or</li>
+ * <li>populated previously after getting cross-references</li>
+ * </ul>
+ * <li>as other sequences in the alignment which share a dbref identifier with
+ * the sequence</li>
+ * <li>by fetching from the remote database</li>
+ * </ul>
+ * The cross-referenced sequences, and mappings to them, are added to the
+ * alignment dataset.
+ *
+ * @param source
+ * @return cross-referenced sequences (as dataset sequences)
+ */
+ public Alignment findXrefSequences(String source, boolean fromDna)
+ {
+
+ rseqs = new ArrayList<>();
+ AlignedCodonFrame cf = new AlignedCodonFrame();
+ matcher = new SequenceIdMatcher(dataset.getSequences());
+
+ for (SequenceI seq : fromSeqs)
+ {
+ SequenceI dss = seq;
+ while (dss.getDatasetSequence() != null)
+ {
+ dss = dss.getDatasetSequence();
+ }
+ boolean found = false;
+ DBRefEntry[] xrfs = DBRefUtils.selectDbRefs(!fromDna,
+ dss.getDBRefs());
+ // ENST & ENSP comes in to both Protein and nucleotide, so we need to
+ // filter them
+ // out later.
+ if ((xrfs == null || xrfs.length == 0) && dataset != null)
+ {
+ /*
+ * found no suitable dbrefs on sequence - look for sequences in the
+ * alignment which share a dbref with this one
+ */
+ DBRefEntry[] lrfs = DBRefUtils.selectDbRefs(fromDna,
+ seq.getDBRefs());
+
+ /*
+ * find sequences (except this one!), of complementary type,
+ * which have a dbref to an accession id for this sequence,
+ * and add them to the results
+ */
+ found = searchDatasetXrefs(fromDna, dss, lrfs, rseqs, cf);
+ }
+ if (xrfs == null && !found)
+ {
+ /*
+ * no dbref to source on this sequence or matched
+ * complementary sequence in the dataset
+ */
+ continue;
+ }
+ List<DBRefEntry> sourceRefs = DBRefUtils.searchRefsForSource(xrfs,
+ source);
+ Iterator<DBRefEntry> refIterator = sourceRefs.iterator();
+ // At this point, if we are retrieving Ensembl, we still don't filter out
+ // ENST when looking for protein crossrefs.
+ while (refIterator.hasNext())
+ {
+ DBRefEntry xref = refIterator.next();
+ found = false;
+ // we're only interested in coding cross-references, not
+ // locus->transcript
+ if (xref.hasMap() && xref.getMap().getMap().isTripletMap())
+ {
+ SequenceI mappedTo = xref.getMap().getTo();
+ if (mappedTo != null)
+ {
+ /*
+ * dbref contains the sequence it maps to; add it to the
+ * results unless we have done so already (could happen if
+ * fetching xrefs for sequences which have xrefs in common)
+ * for example: UNIPROT {P0CE19, P0CE20} -> EMBL {J03321, X06707}
+ */
+ found = true;
+ /*
+ * problem: matcher.findIdMatch() is lenient - returns a sequence
+ * with a dbref to the search arg e.g. ENST for ENSP - wrong
+ * but findInDataset() matches ENSP when looking for Uniprot...
+ */
+ SequenceI matchInDataset = findInDataset(xref);
+ if (matchInDataset != null && xref.getMap().getTo() != null
+ && matchInDataset != xref.getMap().getTo())
+ {
+ System.err.println(
+ "Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
+ + "Found:" + matchInDataset + "\nExpected:"
+ + xref.getMap().getTo() + "\nFor xref:"
+ + xref);
+ }
+ /*matcher.findIdMatch(mappedTo);*/
+ if (matchInDataset != null)
+ {
+ if (!rseqs.contains(matchInDataset))
+ {
+ rseqs.add(matchInDataset);
+ }
+ // even if rseqs contained matchInDataset - check mappings between
+ // these seqs are added
+ // need to try harder to only add unique mappings
+ if (xref.getMap().getMap().isTripletMap()
+ && dataset.getMapping(seq, matchInDataset) == null
+ && cf.getMappingBetween(seq, matchInDataset) == null)
+ {
+ // materialise a mapping for highlighting between these
+ // sequences
+ if (fromDna)
+ {
+ cf.addMap(dss, matchInDataset, xref.getMap().getMap(),
+ xref.getMap().getMappedFromId());
+ }
+ else
+ {
+ cf.addMap(matchInDataset, dss,
+ xref.getMap().getMap().getInverse(),
+ xref.getMap().getMappedFromId());
+ }
+ }
+
+ refIterator.remove();
+ continue;
+ }
+ // TODO: need to determine if this should be a deriveSequence
+ SequenceI rsq = new Sequence(mappedTo);
+ rseqs.add(rsq);
+ if (xref.getMap().getMap().isTripletMap())
+ {
+ // get sense of map correct for adding to product alignment.
+ if (fromDna)
+ {
+ // map is from dna seq to a protein product
+ cf.addMap(dss, rsq, xref.getMap().getMap(),
+ xref.getMap().getMappedFromId());
+ }
+ else
+ {
+ // map should be from protein seq to its coding dna
+ cf.addMap(rsq, dss, xref.getMap().getMap().getInverse(),
+ xref.getMap().getMappedFromId());
+ }
+ }
+ }
+ }
+
+ if (!found)
+ {
+ SequenceI matchedSeq = matcher.findIdMatch(
+ xref.getSource() + "|" + xref.getAccessionId());
+ // if there was a match, check it's at least the right type of
+ // molecule!
+ if (matchedSeq != null && matchedSeq.isProtein() == fromDna)
+ {
+ if (constructMapping(seq, matchedSeq, xref, cf, fromDna))
+ {
+ found = true;
+ }
+ }
+ }
+
+ if (!found)
+ {
+ // do a bit more work - search for sequences with references matching
+ // xrefs on this sequence.
+ found = searchDataset(fromDna, dss, xref, rseqs, cf, false);
+ }
+ if (found)
+ {
+ refIterator.remove();
+ }
+ }
+
+ /*
+ * fetch from source database any dbrefs we haven't resolved up to here
+ */
+ if (!sourceRefs.isEmpty())
+ {
+ retrieveCrossRef(sourceRefs, seq, xrfs, fromDna, cf);
+ }
+ }
+
+ Alignment ral = null;
+ if (rseqs.size() > 0)
+ {
+ ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
+ if (!cf.isEmpty())
+ {
+ dataset.addCodonFrame(cf);
+ }
+ }
+ return ral;
+ }
+
+ private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
+ DBRefEntry[] xrfs, boolean fromDna, AlignedCodonFrame cf)
+ {
+ ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
+ SequenceI[] retrieved = null;
+ SequenceI dss = seq.getDatasetSequence() == null ? seq
+ : seq.getDatasetSequence();
+ // first filter in case we are retrieving crossrefs that have already been
+ // retrieved. this happens for cases where a database record doesn't yield
+ // protein products for CDS
+ removeAlreadyRetrievedSeqs(sourceRefs, fromDna);
+ if (sourceRefs.size() == 0)
+ {
+ // no more work to do! We already had all requested sequence records in
+ // the dataset.
+ return;
+ }
+ try
+ {
+ retrieved = sftch.getSequences(sourceRefs, !fromDna);
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Problem whilst retrieving cross references for Sequence : "
+ + seq.getName());
+ e.printStackTrace();
+ }
+
+ if (retrieved != null)
+ {
+ boolean addedXref = false;
+ List<SequenceI> newDsSeqs = new ArrayList<>(),
+ doNotAdd = new ArrayList<>();
+
+ for (SequenceI retrievedSequence : retrieved)
+ {
+ // dataset gets contaminated ccwith non-ds sequences. why ??!
+ // try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
+ SequenceI retrievedDss = retrievedSequence
+ .getDatasetSequence() == null ? retrievedSequence
+ : retrievedSequence.getDatasetSequence();
+ addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
+ retrievedDss);
+ }
+ if (!addedXref)
+ {
+ // try again, after looking for matching IDs
+ // shouldn't need to do this unless the dbref mechanism has broken.
+ updateDbrefMappings(seq, xrfs, retrieved, cf, fromDna);
+ for (SequenceI retrievedSequence : retrieved)
+ {
+ // dataset gets contaminated ccwith non-ds sequences. why ??!
+ // try: Ensembl -> Nuc->Ensembl, Nuc->Uniprot-->Protein->EMBL->
+ SequenceI retrievedDss = retrievedSequence
+ .getDatasetSequence() == null ? retrievedSequence
+ : retrievedSequence.getDatasetSequence();
+ addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
+ retrievedDss);
+ }
+ }
+ for (SequenceI newToSeq : newDsSeqs)
+ {
+ if (!doNotAdd.contains(newToSeq)
+ && dataset.findIndex(newToSeq) == -1)
+ {
+ dataset.addSequence(newToSeq);
+ matcher.add(newToSeq);
+ }
+ }
+ }
+ }
+
+ /**
+ * Search dataset for sequences with a primary reference contained in
+ * sourceRefs.
+ *
+ * @param sourceRefs
+ * - list of references to filter.
+ * @param fromDna
+ * - type of sequence to search for matching primary reference.
+ */
+ private void removeAlreadyRetrievedSeqs(List<DBRefEntry> sourceRefs,
+ boolean fromDna)
+ {
+ DBRefEntry[] dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+ for (SequenceI sq : dataset.getSequences())
+ {
+ boolean dupeFound = false;
+ // !fromDna means we are looking only for nucleotide sequences, not
+ // protein
+ if (sq.isProtein() == fromDna)
+ {
+ for (DBRefEntry dbr : sq.getPrimaryDBRefs())
+ {
+ for (DBRefEntry found : DBRefUtils.searchRefs(dbrSourceSet, dbr))
+ {
+ sourceRefs.remove(found);
+ dupeFound = true;
+ }
+ }
+ }
+ if (dupeFound)
+ {
+ // rebuild the search array from the filtered sourceRefs list
+ dbrSourceSet = sourceRefs.toArray(new DBRefEntry[0]);
+ }
+ }
+ }
+
+ /**
+ * process sequence retrieved via a dbref on source sequence to resolve and
+ * transfer data
+ *
+ * @param cf
+ * @param sourceSequence
+ * @param retrievedSequence
+ * @return true if retrieveSequence was imported
+ */
+ private boolean importCrossRefSeq(AlignedCodonFrame cf,
+ List<SequenceI> newDsSeqs, List<SequenceI> doNotAdd,
+ SequenceI sourceSequence, SequenceI retrievedSequence)
+ {
+ /**
+ * set when retrievedSequence has been verified as a crossreference for
+ * sourceSequence
+ */
+ boolean imported = false;
+ DBRefEntry[] dbr = retrievedSequence.getDBRefs();
+ if (dbr != null)
+ {
+ for (DBRefEntry dbref : dbr)
+ {
+ SequenceI matched = findInDataset(dbref);
+ if (matched == sourceSequence)
+ {
+ // verified retrieved and source sequence cross-reference each other
+ imported = true;
+ }
+ // find any entry where we should put in the sequence being
+ // cross-referenced into the map
+ Mapping map = dbref.getMap();
+ if (map != null)
+ {
+ if (map.getTo() != null && map.getMap() != null)
+ {
+ if (map.getTo() == sourceSequence)
+ {
+ // already called to import once, and most likely this sequence
+ // already imported !
+ continue;
+ }
+ if (matched == null)
+ {
+ /*
+ * sequence is new to dataset, so save a reference so it can be added.
+ */
+ newDsSeqs.add(map.getTo());
+ continue;
+ }
+
+ /*
+ * there was a matching sequence in dataset, so now, check to see if we can update the map.getTo() sequence to the existing one.
+ */
+
+ try
+ {
+ // compare ms with dss and replace with dss in mapping
+ // if map is congruent
+ SequenceI ms = map.getTo();
+ // TODO findInDataset requires exact sequence match but
+ // 'congruent' test is only for the mapped part
+ // maybe not a problem in practice since only ENA provide a
+ // mapping and it is to the full protein translation of CDS
+ // matcher.findIdMatch(map.getTo());
+ // TODO addendum: if matched is shorter than getTo, this will fail
+ // - when it should really succeed.
+ int sf = map.getMap().getToLowest();
+ int st = map.getMap().getToHighest();
+ SequenceI mappedrg = ms.getSubSequence(sf, st);
+ if (mappedrg.getLength() > 0 && ms.getSequenceAsString()
+ .equals(matched.getSequenceAsString()))
+ {
+ /*
+ * sequences were a match,
+ */
+ String msg = "Mapping updated from " + ms.getName()
+ + " to retrieved crossreference "
+ + matched.getName();
+ System.out.println(msg);
+
+ DBRefEntry[] toRefs = map.getTo().getDBRefs();
+ if (toRefs != null)
+ {
+ /*
+ * transfer database refs
+ */
+ for (DBRefEntry ref : toRefs)
+ {
+ if (dbref.getSrcAccString()
+ .equals(ref.getSrcAccString()))
+ {
+ continue; // avoid overwriting the ref on source sequence
+ }
+ matched.addDBRef(ref); // add or update mapping
+ }
+ }
+ doNotAdd.add(map.getTo());
+ map.setTo(matched);
+
+ /*
+ * give the reverse reference the inverse mapping
+ * (if it doesn't have one already)
+ */
+ setReverseMapping(matched, dbref, cf);
+
+ /*
+ * copy sequence features as well, avoiding
+ * duplication (e.g. same variation from two
+ * transcripts)
+ */
+ List<SequenceFeature> sfs = ms.getFeatures()
+ .getAllFeatures();
+ for (SequenceFeature feat : sfs)
+ {
+ /*
+ * make a flyweight feature object which ignores Parent
+ * attribute in equality test; this avoids creating many
+ * otherwise duplicate exon features on genomic sequence
+ */
+ SequenceFeature newFeature = new SequenceFeature(feat)
+ {
+ @Override
+ public boolean equals(Object o)
+ {
+ return super.equals(o, true);
+ }
+ };
+ matched.addSequenceFeature(newFeature);
+ }
+ }
+ cf.addMap(retrievedSequence, map.getTo(), map.getMap());
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Exception when consolidating Mapped sequence set...");
+ e.printStackTrace(System.err);
+ }
+ }
+ }
+ }
+ }
+ if (imported)
+ {
+ retrievedSequence.updatePDBIds();
+ rseqs.add(retrievedSequence);
+ if (dataset.findIndex(retrievedSequence) == -1)
+ {
+ dataset.addSequence(retrievedSequence);
+ matcher.add(retrievedSequence);
+ }
+ }
+ return imported;
+ }
+
+ /**
+ * Sets the inverse sequence mapping in the corresponding dbref of the mapped
+ * to sequence (if any). This is used after fetching a cross-referenced
+ * sequence, if the fetched sequence has a mapping to the original sequence,
+ * to set the mapping in the original sequence's dbref.
+ *
+ * @param mapFrom
+ * the sequence mapped from
+ * @param dbref
+ * @param mappings
+ */
+ void setReverseMapping(SequenceI mapFrom, DBRefEntry dbref,
+ AlignedCodonFrame mappings)
+ {
+ SequenceI mapTo = dbref.getMap().getTo();
+ if (mapTo == null)
+ {
+ return;
+ }
+ DBRefEntry[] dbrefs = mapTo.getDBRefs();
+ if (dbrefs == null)
+ {
+ return;
+ }
+ for (DBRefEntry toRef : dbrefs)
+ {
+ if (toRef.hasMap() && mapFrom == toRef.getMap().getTo())
+ {
+ /*
+ * found the reverse dbref; update its mapping if null
+ */
+ if (toRef.getMap().getMap() == null)
+ {
+ MapList inverse = dbref.getMap().getMap().getInverse();
+ toRef.getMap().setMap(inverse);
+ mappings.addMap(mapTo, mapFrom, inverse);
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns null or the first sequence in the dataset which is identical to
+ * xref.mapTo, and has a) a primary dbref matching xref, or if none found, the
+ * first one with an ID source|xrefacc
+ *
+ * @param xref
+ * with map and mapped-to sequence
+ * @return
+ */
+ SequenceI findInDataset(DBRefEntry xref)
+ {
+ if (xref == null || !xref.hasMap() || xref.getMap().getTo() == null)
+ {
+ return null;
+ }
+ SequenceI mapsTo = xref.getMap().getTo();
+ String name = xref.getAccessionId();
+ String name2 = xref.getSource() + "|" + name;
+ SequenceI dss = mapsTo.getDatasetSequence() == null ? mapsTo
+ : mapsTo.getDatasetSequence();
+ // first check ds if ds is directly referenced
+ if (dataset.findIndex(dss) > -1)
+ {
+ return dss;
+ }
+ DBRefEntry template = new DBRefEntry(xref.getSource(), null,
+ xref.getAccessionId());
+ /**
+ * remember the first ID match - in case we don't find a match to template
+ */
+ SequenceI firstIdMatch = null;
+ for (SequenceI seq : dataset.getSequences())
+ {
+ // first check primary refs.
+ List<DBRefEntry> match = DBRefUtils.searchRefs(
+ seq.getPrimaryDBRefs().toArray(new DBRefEntry[0]), template);
+ if (match != null && match.size() == 1 && sameSequence(seq, dss))
+ {
+ return seq;
+ }
+ /*
+ * clumsy alternative to using SequenceIdMatcher which currently
+ * returns sequences with a dbref to the matched accession id
+ * which we don't want
+ */
+ if (firstIdMatch == null && (name.equals(seq.getName())
+ || seq.getName().startsWith(name2)))
+ {
+ if (sameSequence(seq, dss))
+ {
+ firstIdMatch = seq;
+ }
+ }
+ }
+ return firstIdMatch;
+ }
+
+ /**
+ * Answers true if seq1 and seq2 contain exactly the same characters (ignoring
+ * case), else false. This method compares the lengths, then each character in
+ * turn, in order to 'fail fast'. For case-sensitive comparison, it would be
+ * possible to use Arrays.equals(seq1.getSequence(), seq2.getSequence()).
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ // TODO move to Sequence / SequenceI
+ static boolean sameSequence(SequenceI seq1, SequenceI seq2)
+ {
+ if (seq1 == seq2)
+ {
+ return true;
+ }
+ if (seq1 == null || seq2 == null)
+ {
+ return false;
+ }
+
+ if (seq1.getLength() != seq2.getLength())
+ {
+ return false;
+ }
+ int length = seq1.getLength();
+ for (int i = 0; i < length; i++)
+ {
+ int diff = seq1.getCharAt(i) - seq2.getCharAt(i);
+ /*
+ * same char or differ in case only ('a'-'A' == 32)
+ */
+ if (diff != 0 && diff != 32 && diff != -32)
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Updates any empty mappings in the cross-references with one to a compatible
+ * retrieved sequence if found, and adds any new mappings to the
+ * AlignedCodonFrame
+ *
+ * @param mapFrom
+ * @param xrefs
+ * @param retrieved
+ * @param acf
+ */
+ void updateDbrefMappings(SequenceI mapFrom, DBRefEntry[] xrefs,
+ SequenceI[] retrieved, AlignedCodonFrame acf, boolean fromDna)
+ {
+ SequenceIdMatcher idMatcher = new SequenceIdMatcher(retrieved);
+ for (DBRefEntry xref : xrefs)
+ {
+ if (!xref.hasMap())
+ {
+ String targetSeqName = xref.getSource() + "|"
+ + xref.getAccessionId();
+ SequenceI[] matches = idMatcher.findAllIdMatches(targetSeqName);
+ if (matches == null)
+ {
+ return;
+ }
+ for (SequenceI seq : matches)
+ {
+ constructMapping(mapFrom, seq, xref, acf, fromDna);
+ }
+ }
+ }
+ }
+
+ /**
+ * Tries to make a mapping between sequences. If successful, adds the mapping
+ * to the dbref and the mappings collection and answers true, otherwise
+ * answers false. The following methods of making are mapping are tried in
+ * turn:
+ * <ul>
+ * <li>if 'mapTo' holds a mapping to 'mapFrom', take the inverse; this is, for
+ * example, the case after fetching EMBL cross-references for a Uniprot
+ * sequence</li>
+ * <li>else check if the dna translates exactly to the protein (give or take
+ * start and stop codons></li>
+ * <li>else try to map based on CDS features on the dna sequence</li>
+ * </ul>
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @param xref
+ * @param mappings
+ * @return
+ */
+ boolean constructMapping(SequenceI mapFrom, SequenceI mapTo,
+ DBRefEntry xref, AlignedCodonFrame mappings, boolean fromDna)
+ {
+ MapList mapping = null;
+ SequenceI dsmapFrom = mapFrom.getDatasetSequence() == null ? mapFrom
+ : mapFrom.getDatasetSequence();
+ SequenceI dsmapTo = mapTo.getDatasetSequence() == null ? mapTo
+ : mapTo.getDatasetSequence();
+ /*
+ * look for a reverse mapping, if found make its inverse.
+ * Note - we do this on dataset sequences only.
+ */
+ if (dsmapTo.getDBRefs() != null)
+ {
+ for (DBRefEntry dbref : dsmapTo.getDBRefs())
+ {
+ String name = dbref.getSource() + "|" + dbref.getAccessionId();
+ if (dbref.hasMap() && dsmapFrom.getName().startsWith(name))
+ {
+ /*
+ * looks like we've found a map from 'mapTo' to 'mapFrom'
+ * - invert it to make the mapping the other way
+ */
+ MapList reverse = dbref.getMap().getMap().getInverse();
+ xref.setMap(new Mapping(dsmapTo, reverse));
+ mappings.addMap(mapFrom, dsmapTo, reverse);
+ return true;
+ }
+ }
+ }
+
+ if (fromDna)
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(mapTo, mapFrom);
+ }
+ else
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(mapFrom, mapTo);
+ if (mapping != null)
+ {
+ mapping = mapping.getInverse();
+ }
+ }
+ if (mapping == null)
+ {
+ return false;
+ }
+ xref.setMap(new Mapping(mapTo, mapping));
+
+ /*
+ * and add a reverse DbRef with the inverse mapping
+ */
+ if (mapFrom.getDatasetSequence() != null && false)
+ // && mapFrom.getDatasetSequence().getSourceDBRef() != null)
+ {
+ // possible need to search primary references... except, why doesn't xref
+ // == getSourceDBRef ??
+ // DBRefEntry dbref = new DBRefEntry(mapFrom.getDatasetSequence()
+ // .getSourceDBRef());
+ // dbref.setMap(new Mapping(mapFrom.getDatasetSequence(), mapping
+ // .getInverse()));
+ // mapTo.addDBRef(dbref);
+ }
+
+ if (fromDna)
+ {
+ // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+ mappings.addMap(mapFrom, mapTo, mapping);
+ }
+ else
+ {
+ mappings.addMap(mapTo, mapFrom, mapping.getInverse());
+ }
+
+ return true;
+ }
+
+ /**
+ * find references to lrfs in the cross-reference set of each sequence in
+ * dataset (that is not equal to sequenceI) Identifies matching DBRefEntry
+ * based on source and accession string only - Map and Version are nulled.
+ *
+ * @param fromDna
+ * - true if context was searching from Dna sequences, false if
+ * context was searching from Protein sequences
+ * @param sequenceI
+ * @param lrfs
+ * @param foundSeqs
+ * @return true if matches were found.
+ */
+ private boolean searchDatasetXrefs(boolean fromDna, SequenceI sequenceI,
+ DBRefEntry[] lrfs, List<SequenceI> foundSeqs,
+ AlignedCodonFrame cf)
+ {
+ boolean found = false;
+ if (lrfs == null)
+ {
+ return false;
+ }
+ for (int i = 0; i < lrfs.length; i++)
+ {
+ DBRefEntry xref = new DBRefEntry(lrfs[i]);
+ // add in wildcards
+ xref.setVersion(null);
+ xref.setMap(null);
+ found |= searchDataset(fromDna, sequenceI, xref, foundSeqs, cf,
+ false);
+ }
+ return found;
+ }
+
+ /**
+ * Searches dataset for DBRefEntrys matching the given one (xrf) and adds the
+ * associated sequence to rseqs
+ *
+ * @param fromDna
+ * true if context was searching for refs *from* dna sequence, false
+ * if context was searching for refs *from* protein sequence
+ * @param fromSeq
+ * a sequence to ignore (start point of search)
+ * @param xrf
+ * a cross-reference to try to match
+ * @param foundSeqs
+ * result list to add to
+ * @param mappings
+ * a set of sequence mappings to add to
+ * @param direct
+ * - indicates the type of relationship between returned sequences,
+ * xrf, and sequenceI that is required.
+ * <ul>
+ * <li>direct implies xrf is a primary reference for sequenceI AND
+ * the sequences to be located (eg a uniprot ID for a protein
+ * sequence, and a uniprot ref on a transcript sequence).</li>
+ * <li>indirect means xrf is a cross reference with respect to
+ * sequenceI or all the returned sequences (eg a genomic reference
+ * associated with a locus and one or more transcripts)</li>
+ * </ul>
+ * @return true if relationship found and sequence added.
+ */
+ boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,
+ List<SequenceI> foundSeqs, AlignedCodonFrame mappings,
+ boolean direct)
+ {
+ boolean found = false;
+ if (dataset == null)
+ {
+ return false;
+ }
+ if (dataset.getSequences() == null)
+ {
+ System.err.println("Empty dataset sequence set - NO VECTOR");
+ return false;
+ }
+ List<SequenceI> ds;
+ synchronized (ds = dataset.getSequences())
+ {
+ for (SequenceI nxt : ds)
+ {
+ if (nxt != null)
+ {
+ if (nxt.getDatasetSequence() != null)
+ {
+ System.err.println(
+ "Implementation warning: CrossRef initialised with a dataset alignment with non-dataset sequences in it! ("
+ + nxt.getDisplayId(true) + " has ds reference "
+ + nxt.getDatasetSequence().getDisplayId(true)
+ + ")");
+ }
+ if (nxt == fromSeq || nxt == fromSeq.getDatasetSequence())
+ {
+ continue;
+ }
+ /*
+ * only look at same molecule type if 'direct', or
+ * complementary type if !direct
+ */
+ {
+ boolean isDna = !nxt.isProtein();
+ if (direct ? (isDna != fromDna) : (isDna == fromDna))
+ {
+ // skip this sequence because it is wrong molecule type
+ continue;
+ }
+ }
+
+ // look for direct or indirect references in common
+ DBRefEntry[] poss = nxt.getDBRefs();
+ List<DBRefEntry> cands = null;
+
+ // todo: indirect specifies we select either direct references to nxt
+ // that match xrf which is indirect to sequenceI, or indirect
+ // references to nxt that match xrf which is direct to sequenceI
+ cands = DBRefUtils.searchRefs(poss, xrf);
+ // else
+ // {
+ // poss = DBRefUtils.selectDbRefs(nxt.isProtein()!fromDna, poss);
+ // cands = DBRefUtils.searchRefs(poss, xrf);
+ // }
+ if (!cands.isEmpty())
+ {
+ if (foundSeqs.contains(nxt))
+ {
+ continue;
+ }
+ found = true;
+ foundSeqs.add(nxt);
+ if (mappings != null && !direct)
+ {
+ /*
+ * if the matched sequence has mapped dbrefs to
+ * protein product / cdna, add equivalent mappings to
+ * our source sequence
+ */
+ for (DBRefEntry candidate : cands)
+ {
+ Mapping mapping = candidate.getMap();
+ if (mapping != null)
+ {
+ MapList map = mapping.getMap();
+ if (mapping.getTo() != null
+ && map.getFromRatio() != map.getToRatio())
+ {
+ /*
+ * add a mapping, as from dna to peptide sequence
+ */
+ if (map.getFromRatio() == 3)
+ {
+ mappings.addMap(nxt, fromSeq, map);
+ }
+ else
+ {
+ mappings.addMap(nxt, fromSeq, map.getInverse());
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ return found;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff