X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FCrossRef.java;h=7e77fc1e0903799660db67205966ddcf768a1897;hb=0ebcd487f08f9873987d9a32edce7df47aa27927;hp=159d96a2a9a2a76fc3198dd95384cbf3ed38dcd6;hpb=5ab495cf0873d14455eaab904823838563620064;p=jalview.git
diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 159d96a..7e77fc1 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -1,565 +1,740 @@
-package jalview.analysis;
-
-import java.util.Enumeration;
-import java.util.Vector;
-import java.util.Hashtable;
-
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.ws.SequenceFetcher;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-
-/**
- * Functions for cross-referencing sequence databases. user must first specify
- * if cross-referencing from protein or dna (set dna==true)
- *
- * @author JimP
- *
- */
-public class CrossRef
-{
- /**
- * get the DNA or protein references for a protein or dna sequence
- *
- * @param dna
- * @param rfs
- * @return
- */
- public static DBRefEntry[] findXDbRefs(boolean dna, DBRefEntry[] rfs)
- {
- if (dna)
- {
- rfs = jalview.util.DBRefUtils.selectRefs(rfs, DBRefSource.PROTEINDBS);
- }
- else
- {
- rfs = jalview.util.DBRefUtils.selectRefs(rfs,
- DBRefSource.DNACODINGDBS); // could attempt to find other cross
- // refs and return here - ie PDB xrefs
- // (not dna, not protein seq)
- }
- return rfs;
- }
-
- public static Hashtable classifyDbRefs(DBRefEntry[] rfs)
- {
- Hashtable classes = new Hashtable();
- classes.put(DBRefSource.PROTEINDBS, jalview.util.DBRefUtils.selectRefs(
- rfs, DBRefSource.PROTEINDBS));
- classes.put(DBRefSource.DNACODINGDBS, jalview.util.DBRefUtils
- .selectRefs(rfs, DBRefSource.DNACODINGDBS));
- classes.put(DBRefSource.DOMAINDBS, jalview.util.DBRefUtils.selectRefs(
- rfs, DBRefSource.DOMAINDBS));
- // classes.put(OTHER, )
- return classes;
- }
-
- /**
- * @param dna
- * true if seqs are DNA seqs
- * @param seqs
- * @return a list of sequence database cross reference source types
- */
- public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs)
- {
- return findSequenceXrefTypes(dna, seqs, null);
- }
-
- /**
- * Indirect references are references from other sequences from the dataset to
- * any of the direct DBRefEntrys on the given sequences.
- *
- * @param dna
- * true if seqs are DNA seqs
- * @param seqs
- * @return a list of sequence database cross reference source types
- */
- public static String[] findSequenceXrefTypes(boolean dna,
- SequenceI[] seqs, AlignmentI dataset)
- {
- String[] dbrefs = null;
- Vector refs = new Vector();
- for (int s = 0; s < seqs.length; s++)
- {
- SequenceI dss = seqs[s];
- while (dss.getDatasetSequence() != null)
- {
- dss = dss.getDatasetSequence();
- }
- DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
- for (int r = 0; rfs != null && r < rfs.length; r++)
- {
- if (!refs.contains(rfs[r].getSource()))
- {
- refs.addElement(rfs[r].getSource());
- }
- }
- if (dataset != null)
- {
- // search for references to this sequence's direct references.
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
- Vector rseqs = new Vector();
- CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
- null); // don't need to specify codon frame for mapping here
- Enumeration lr = rseqs.elements();
- while (lr.hasMoreElements())
- {
- SequenceI rs = (SequenceI) lr.nextElement();
- DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef());
- for (int r = 0; rfs != null && r < rfs.length; r++)
- {
- if (!refs.contains(rfs[r].getSource()))
- {
- refs.addElement(rfs[r].getSource());
- }
- }
- }
- }
- }
- if (refs.size() > 0)
- {
- dbrefs = new String[refs.size()];
- refs.copyInto(dbrefs);
- }
- return dbrefs;
- }
-
- /*
- * if (dna) { if (rfs[r].hasMap()) { // most likely this is a protein cross
- * reference if (!refs.contains(rfs[r].getSource())) {
- * refs.addElement(rfs[r].getSource()); } } }
- */
- public static boolean hasCdnaMap(SequenceI[] seqs)
- {
- String[] reftypes = findSequenceXrefTypes(false, seqs);
- for (int s = 0; s < reftypes.length; s++)
- {
- if (reftypes.equals(DBRefSource.EMBLCDS))
- {
- return true;
- // no map
- }
- }
- return false;
- }
-
- public static SequenceI[] getCdnaMap(SequenceI[] seqs)
- {
- Vector cseqs = new Vector();
- for (int s = 0; s < seqs.length; s++)
- {
- DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());
- for (int c = 0; c < cdna.length; c++)
- {
- if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
- {
- System.err.println("TODO: unimplemented sequence retrieval for coding region sequence.");
- // TODO: retrieve CDS dataset sequences
- // need global dataset sequence retriever/resolver to reuse refs
- // and construct Mapping entry.
- // insert gaps in CDS according to peptide gaps.
- // add gapped sequence to cseqs
- }
- }
- }
- if (cseqs.size() > 0)
- {
- SequenceI[] rsqs = new SequenceI[cseqs.size()];
- cseqs.copyInto(rsqs);
- return rsqs;
- }
- return null;
-
- }
-
- /**
- *
- * @param dna
- * @param seqs
- * @return
- */
- public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
- String source)
- {
- return findXrefSequences(seqs, dna, source, null);
- }
-
- /**
- *
- * @param seqs
- * @param dna
- * @param source
- * @param dataset
- * alignment to search for product sequences.
- * @return products (as dataset sequences)
- */
- public static Alignment findXrefSequences(SequenceI[] seqs, boolean dna,
- String source, AlignmentI dataset)
- {
- Vector rseqs = new Vector();
- Alignment ral = null;
- AlignedCodonFrame cf = new AlignedCodonFrame(0); // nominal width
- for (int s = 0; s < seqs.length; s++)
- {
- SequenceI dss = seqs[s];
- while (dss.getDatasetSequence() != null)
- {
- dss = dss.getDatasetSequence();
- }
- boolean found = false;
- DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());
- if ((xrfs == null || xrfs.length == 0) && dataset != null)
- {
- System.out.println("Attempting to find ds Xrefs refs.");
- DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less
- // ambiguous
- // would
- // be a
- // 'find
- // primary
- // dbRefEntry'
- // method.
- // filter for desired source xref here
- found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
- rseqs, cf);
- }
- for (int r = 0; xrfs != null && r < xrfs.length; r++)
- {
- if (source != null && !source.equals(xrfs[r].getSource()))
- continue;
- if (xrfs[r].hasMap())
- {
- if (xrfs[r].getMap().getTo() != null)
- {
- Sequence rsq = new Sequence(xrfs[r].getMap().getTo());
- rseqs.addElement(rsq);
- if (xrfs[r].getMap().getMap().getFromRatio() != xrfs[r]
- .getMap().getMap().getToRatio())
- {
- // get sense of map correct for adding to product alignment.
- if (dna)
- {
- // map is from dna seq to a protein product
- cf.addMap(dss, rsq, xrfs[r].getMap().getMap());
- }
- else
- {
- // map should be from protein seq to its coding dna
- cf.addMap(rsq, dss, xrfs[r].getMap().getMap().getInverse());
- }
- }
- found = true;
- }
- }
- if (!found)
- {
- // do a bit more work - search for sequences with references matching
- // xrefs on this sequence.
- if (dataset != null)
- {
- found |= searchDataset(dss, xrfs[r], dataset, rseqs, cf);
- if (found)
- xrfs[r] = null; // we've recovered seqs for this one.
- }
- }
- }
- if (!found)
- {
- if (xrfs != null && xrfs.length > 0)
- {
- // Try and get the sequence reference...
- /*
- * Ideal world - we ask for a sequence fetcher implementation here if
- * (jalview.io.RunTimeEnvironment.getSequenceFetcher()) (
- */
- ASequenceFetcher sftch = new SequenceFetcher();
- SequenceI[] retrieved = null;
- int l = xrfs.length;
- for (int r = 0; r < xrfs.length; r++)
- {
- // filter out any irrelevant or irretrievable references
- if (xrfs[r] == null
- || ((source != null && !source.equals(xrfs[r]
- .getSource())) || !sftch.isFetchable(xrfs[r]
- .getSource())))
- {
- l--;
- xrfs[r] = null;
- }
- }
- if (l > 0)
- {
- System.out
- .println("Attempting to retrieve cross referenced sequences.");
- DBRefEntry[] t = new DBRefEntry[l];
- l = 0;
- for (int r = 0; r < xrfs.length; r++)
- {
- if (xrfs[r] != null)
- t[l++] = xrfs[r];
- }
- xrfs = t;
- try
- {
- retrieved = sftch.getSequences(xrfs); // problem here is we don't know which of xrfs resulted in which retrieved element
- } catch (Exception e)
- {
- System.err
- .println("Problem whilst retrieving cross references for Sequence : "
- + seqs[s].getName());
- e.printStackTrace();
- }
- if (retrieved != null)
- {
- for (int rs = 0; rs < retrieved.length; rs++)
- {
- // TODO: examine each sequence for 'redundancy'
- jalview.datamodel.DBRefEntry[] dbr = retrieved[rs].getDBRef();
- if (dbr != null && dbr.length > 0)
- {
- for (int di = 0; di < dbr.length; di++)
- {
- // find any entry where we should put in the sequence being cross-referenced into the map
- jalview.datamodel.Mapping map = dbr[di].getMap();
- if (map != null)
- {
- if (map.getTo() != null && map.getMap() != null)
- {
- // should search the local dataset to find any existing candidates for To !
- try
- {
- // compare ms with dss and replace with dss in mapping if map is congruent
- SequenceI ms = map.getTo();
- int sf = map.getMap().getToLowest();
- int st = map.getMap().getToHighest();
- SequenceI mappedrg = ms.getSubSequence(sf, st);
- SequenceI loc = dss.getSubSequence(sf, st);
- if (mappedrg.getLength()>0 && mappedrg.getSequenceAsString().equals(
- loc.getSequenceAsString()))
- {
- System.err
- .println("Mapping updated for retrieved crossreference");
- // method to update all refs of existing To on retrieved sequence with dss and merge any props on To onto dss.
- map.setTo(dss);
- }
- } catch (Exception e)
- {
- System.err
- .println("Exception when consolidating Mapped sequence set...");
- e.printStackTrace(System.err);
- }
- }
- }
- }
- }
- retrieved[rs].updatePDBIds();
- rseqs.addElement(retrieved[rs]);
- }
- }
- }
- }
- }
- }
- if (rseqs.size() > 0)
- {
- SequenceI[] rsqs = new SequenceI[rseqs.size()];
- rseqs.copyInto(rsqs);
- ral = new Alignment(rsqs);
- if (cf != null && cf.getProtMappings() != null)
- {
- ral.addCodonFrame(cf);
- }
- }
- return ral;
- }
-
- /**
- * 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 sequenceI
- * @param lrfs
- * @param dataset
- * @param rseqs
- * @return true if matches were found.
- */
- private static boolean searchDatasetXrefs(SequenceI sequenceI,
- boolean dna, DBRefEntry[] lrfs, AlignmentI dataset, Vector rseqs,
- 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(sequenceI, xref, dataset, rseqs, cf, false, dna);
- }
- return found;
- }
-
- /**
- * search a given sequence dataset for references matching cross-references to
- * the given sequence
- *
- * @param sequenceI
- * @param xrf
- * @param dataset
- * @param rseqs
- * set of unique sequences
- * @param cf
- * @return true if one or more unique sequences were found and added
- */
- public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
- AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf)
- {
- return searchDataset(sequenceI, xrf, dataset, rseqs, cf, true, false);
- }
-
- /**
- * TODO: generalise to different protein classifications Search dataset for
- * DBRefEntrys matching the given one (xrf) and add the associated sequence to
- * rseq.
- *
- * @param sequenceI
- * @param xrf
- * @param dataset
- * @param rseqs
- * @param direct -
- * search all references or only subset
- * @param dna
- * search dna or protein xrefs (if direct=false)
- * @return true if relationship found and sequence added.
- */
- public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
- AlignmentI dataset, Vector rseqs, AlignedCodonFrame cf,
- boolean direct, boolean dna)
- {
- boolean found = false;
- SequenceI[] typer=new SequenceI[1];
- if (dataset == null)
- return false;
- if (dataset.getSequences() == null)
- {
- System.err.println("Empty dataset sequence set - NO VECTOR");
- return false;
- }
- Enumeration e = dataset.getSequences().elements();
- while (e.hasMoreElements())
- {
- SequenceI nxt = (SequenceI) e.nextElement();
- if (nxt != null)
- {
- if (nxt.getDatasetSequence() != null)
- {
- System.err
- .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
- }
- if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
- {
- // check if this is the correct sequence type
- {
- typer[0] = nxt;
- boolean isDna = jalview.util.Comparison.isNucleotide(typer);
- if ((direct && isDna == dna) || (!direct && isDna!=dna))
- {
- // skip this sequence because it is same molecule type
- continue;
- }
- }
-
- // look for direct or indirect references in common
- DBRefEntry[] poss = null, cands = null;
- if (direct)
- {
- cands = jalview.util.DBRefUtils.searchRefs(poss = nxt
- .getDBRef(), xrf);
- }
- else
- {
- cands = jalview.util.DBRefUtils.searchRefs(poss = CrossRef
- .findXDbRefs(dna, nxt.getDBRef()), xrf);
- }
- if (cands != null)
- {
- if (!rseqs.contains(nxt))
- {
- rseqs.addElement(nxt);
- boolean foundmap = cf != null; // don't search if we aren't given
- // a codon map object
- for (int r = 0; foundmap && r < cands.length; r++)
- {
- if (cands[r].hasMap())
- {
- if (cands[r].getMap().getTo() != null
- && cands[r].getMap().getMap().getFromRatio() != cands[r]
- .getMap().getMap().getToRatio())
- {
- foundmap = true;
- // get sense of map correct for adding to product alignment.
- if (dna)
- {
- // map is from dna seq to a protein product
- cf.addMap(sequenceI, nxt, cands[r].getMap().getMap());
- }
- else
- {
- // map should be from protein seq to its coding dna
- cf.addMap(nxt, sequenceI, cands[r].getMap().getMap()
- .getInverse());
- }
- }
- }
- }
- // TODO: add mapping between sequences if necessary
- found = true;
- }
- }
-
- }
- }
- }
- return found;
- }
-
- /**
- * precalculate different products that can be found for seqs in dataset and
- * return them.
- *
- * @param dna
- * @param seqs
- * @param dataset
- * @param fake -
- * don't actually build lists - just get types
- * @return public static Object[] buildXProductsList(boolean dna, SequenceI[]
- * seqs, AlignmentI dataset, boolean fake) { String types[] =
- * jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,
- * dataset); if (types != null) { System.out.println("Xref Types for:
- * "+(dna ? "dna" : "prot")); for (int t = 0; t < types.length; t++) {
- * System.out.println("Type: " + types[t]); SequenceI[] prod =
- * jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);
- * System.out.println("Found " + ((prod == null) ? "no" : "" +
- * prod.length) + " products"); if (prod!=null) { for (int p=0; p.
+ * 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.SequenceFetcher;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+/**
+ * Functions for cross-referencing sequence databases. user must first specify
+ * if cross-referencing from protein or dna (set dna==true)
+ *
+ * @author JimP
+ *
+ */
+public class CrossRef
+{
+ /*
+ * A sub-class that ignores Parent attribute when comparing sequence
+ * features. This avoids 'duplicate' CDS features that only
+ * differ in their parent Transcript ids.
+ */
+ class MySequenceFeature extends SequenceFeature
+ {
+ private SequenceFeature feat;
+
+ MySequenceFeature(SequenceFeature sf)
+ {
+ this.feat = sf;
+ }
+
+ @Override
+ public boolean equals(Object o)
+ {
+ return feat.equals(o, true);
+ }
+ }
+
+ /**
+ * Select just the DNA or protein references for a protein or dna sequence
+ *
+ * @param fromDna
+ * if true, select references from DNA (i.e. Protein databases), else
+ * DNA database references
+ * @param refs
+ * a set of references to select from
+ * @return
+ */
+ public static DBRefEntry[] findXDbRefs(boolean fromDna, DBRefEntry[] refs)
+ {
+ return DBRefUtils.selectRefs(refs, fromDna ? DBRefSource.PROTEINDBS
+ : DBRefSource.DNACODINGDBS);
+ // could attempt to find other cross
+ // refs here - ie PDB xrefs
+ // (not dna, not protein seq)
+ }
+
+ /**
+ * @param dna
+ * true if seqs are DNA seqs
+ * @param seqs
+ * @return a list of sequence database cross reference source types
+ */
+ public static String[] findSequenceXrefTypes(boolean dna, SequenceI[] seqs)
+ {
+ return findSequenceXrefTypes(dna, seqs, null);
+ }
+
+ /**
+ * Indirect references are references from other sequences from the dataset to
+ * any of the direct DBRefEntrys on the given sequences.
+ *
+ * @param dna
+ * true if seqs are DNA seqs
+ * @param seqs
+ * @return a list of sequence database cross reference source types
+ */
+ public static String[] findSequenceXrefTypes(boolean dna,
+ SequenceI[] seqs, AlignmentI dataset)
+ {
+ String[] dbrefs = null;
+ List refs = new ArrayList();
+ for (SequenceI seq : seqs)
+ {
+ if (seq != null)
+ {
+ SequenceI dss = seq;
+ while (dss.getDatasetSequence() != null)
+ {
+ dss = dss.getDatasetSequence();
+ }
+ DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRefs());
+ if (rfs != null)
+ {
+ for (DBRefEntry ref : rfs)
+ {
+ if (!refs.contains(ref.getSource()))
+ {
+ refs.add(ref.getSource());
+ }
+ }
+ }
+ if (dataset != null)
+ {
+ // search for references to this sequence's direct references.
+ DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
+ List rseqs = new ArrayList();
+ CrossRef.searchDatasetXrefs(seq, !dna, lrfs, dataset, rseqs,
+ null); // don't need to specify codon frame for mapping here
+ for (SequenceI rs : rseqs)
+ {
+ DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRefs());
+ if (xrs != null)
+ {
+ for (DBRefEntry ref : xrs)
+ {
+ if (!refs.contains(ref.getSource()))
+ {
+ refs.add(ref.getSource());
+ }
+ }
+ }
+ // looks like copy and paste - change rfs to xrs?
+ // for (int r = 0; rfs != null && r < rfs.length; r++)
+ // {
+ // if (!refs.contains(rfs[r].getSource()))
+ // {
+ // refs.add(rfs[r].getSource());
+ // }
+ // }
+ }
+ }
+ }
+ }
+ if (refs.size() > 0)
+ {
+ dbrefs = new String[refs.size()];
+ refs.toArray(dbrefs);
+ }
+ return dbrefs;
+ }
+
+ public static boolean hasCdnaMap(SequenceI[] seqs)
+ {
+ // TODO unused - remove?
+ String[] reftypes = findSequenceXrefTypes(false, seqs);
+ for (int s = 0; s < reftypes.length; s++)
+ {
+ if (reftypes.equals(DBRefSource.EMBLCDS))
+ {
+ return true;
+ // no map
+ }
+ }
+ return false;
+ }
+
+ public static SequenceI[] getCdnaMap(SequenceI[] seqs)
+ {
+ // TODO unused - remove?
+ Vector cseqs = new Vector();
+ for (int s = 0; s < seqs.length; s++)
+ {
+ DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRefs());
+ for (int c = 0; c < cdna.length; c++)
+ {
+ if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
+ {
+ System.err
+ .println("TODO: unimplemented sequence retrieval for coding region sequence.");
+ // TODO: retrieve CDS dataset sequences
+ // need global dataset sequence retriever/resolver to reuse refs
+ // and construct Mapping entry.
+ // insert gaps in CDS according to peptide gaps.
+ // add gapped sequence to cseqs
+ }
+ }
+ }
+ if (cseqs.size() > 0)
+ {
+ SequenceI[] rsqs = new SequenceI[cseqs.size()];
+ cseqs.copyInto(rsqs);
+ return rsqs;
+ }
+ return null;
+
+ }
+
+ /**
+ *
+ * @param seqs
+ * sequences whose xrefs are being retrieved
+ * @param dna
+ * true if sequences are nucleotide
+ * @param source
+ * @param al
+ * alignment to search for cross-referenced sequences (and possibly
+ * add to)
+ * @return products (as dataset sequences)
+ */
+ public static Alignment findXrefSequences(SequenceI[] seqs,
+ final boolean dna, final String source, AlignmentI al)
+ {
+ AlignmentI dataset = al.getDataset() == null ? al : al.getDataset();
+ List rseqs = new ArrayList();
+ AlignedCodonFrame cf = new AlignedCodonFrame();
+ for (SequenceI seq : seqs)
+ {
+ SequenceI dss = seq;
+ while (dss.getDatasetSequence() != null)
+ {
+ dss = dss.getDatasetSequence();
+ }
+ boolean found = false;
+ DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRefs());
+ if ((xrfs == null || xrfs.length == 0) && dataset != null)
+ {
+ System.out.println("Attempting to find ds Xrefs refs.");
+ // FIXME should be dss not seq here?
+ DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seq.getDBRefs());
+ // less ambiguous would be a 'find primary dbRefEntry' method.
+ // filter for desired source xref here
+ found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
+ rseqs, cf);
+ }
+ for (int r = 0; xrfs != null && r < xrfs.length; r++)
+ {
+ DBRefEntry xref = xrfs[r];
+ if (source != null && !source.equals(xref.getSource()))
+ {
+ continue;
+ }
+ if (xref.hasMap())
+ {
+ if (xref.getMap().getTo() != null)
+ {
+ SequenceI rsq = new Sequence(xref.getMap().getTo());
+ rseqs.add(rsq);
+ if (xref.getMap().getMap().getFromRatio() != xref
+ .getMap().getMap().getToRatio())
+ {
+ // get sense of map correct for adding to product alignment.
+ if (dna)
+ {
+ // map is from dna seq to a protein product
+ cf.addMap(dss, rsq, xref.getMap().getMap());
+ }
+ else
+ {
+ // map should be from protein seq to its coding dna
+ cf.addMap(rsq, dss, xref.getMap().getMap().getInverse());
+ }
+ }
+ found = true;
+ }
+ }
+ if (!found)
+ {
+ // do a bit more work - search for sequences with references matching
+ // xrefs on this sequence.
+ if (dataset != null)
+ {
+ found |= searchDataset(dss, xref, dataset, rseqs, cf, false,
+ !dna);
+ if (found)
+ {
+ xrfs[r] = null; // we've recovered seqs for this one.
+ }
+ }
+ }
+ }
+ if (!found)
+ {
+ if (xrfs != null && xrfs.length > 0)
+ {
+ // Try and get the sequence reference...
+ /*
+ * Ideal world - we ask for a sequence fetcher implementation here if
+ * (jalview.io.RunTimeEnvironment.getSequenceFetcher()) (
+ */
+ ASequenceFetcher sftch = new SequenceFetcher();
+ SequenceI[] retrieved = null;
+ int l = xrfs.length;
+ for (int r = 0; r < xrfs.length; r++)
+ {
+ // filter out any irrelevant or irretrievable references
+ if (xrfs[r] == null
+ || ((source != null && !source.equals(xrfs[r]
+ .getSource())) || !sftch.isFetchable(xrfs[r]
+ .getSource())))
+ {
+ l--;
+ xrfs[r] = null;
+ }
+ }
+ if (l > 0)
+ {
+ // System.out
+ // .println("Attempting to retrieve cross referenced sequences.");
+ DBRefEntry[] t = new DBRefEntry[l];
+ l = 0;
+ for (int r = 0; r < xrfs.length; r++)
+ {
+ if (xrfs[r] != null)
+ {
+ t[l++] = xrfs[r];
+ }
+ }
+ xrfs = t;
+ try
+ {
+ retrieved = sftch.getSequences(xrfs, !dna);
+ // problem here is we don't know which of xrfs resulted in which
+ // retrieved element
+ } catch (Exception e)
+ {
+ System.err
+ .println("Problem whilst retrieving cross references for Sequence : "
+ + seq.getName());
+ e.printStackTrace();
+ }
+
+ if (retrieved != null)
+ {
+ updateDbrefMappings(dna, seq, xrfs, retrieved, cf);
+
+ SequenceIdMatcher matcher = new SequenceIdMatcher(
+ dataset.getSequences());
+ List copiedFeatures = new ArrayList();
+ CrossRef me = new CrossRef();
+ for (int rs = 0; rs < retrieved.length; rs++)
+ {
+ // TODO: examine each sequence for 'redundancy'
+ DBRefEntry[] dbr = retrieved[rs].getDBRefs();
+ if (dbr != null && dbr.length > 0)
+ {
+ for (int di = 0; di < dbr.length; di++)
+ {
+ // find any entry where we should put in the sequence being
+ // cross-referenced into the map
+ Mapping map = dbr[di].getMap();
+ if (map != null)
+ {
+ if (map.getTo() != null && map.getMap() != null)
+ {
+ SequenceI matched = matcher
+ .findIdMatch(map.getTo());
+ if (matched != null)
+ {
+ /*
+ * already got an xref to this sequence; update this
+ * map to point to the same sequence, and add
+ * any new dbrefs to it
+ */
+ for (DBRefEntry ref : map.getTo().getDBRefs())
+ {
+ matched.addDBRef(ref); // add or update mapping
+ }
+ map.setTo(matched);
+ }
+ else
+ {
+ matcher.add(map.getTo());
+ }
+ try
+ {
+ // compare ms with dss and replace with dss in mapping
+ // if map is congruent
+ SequenceI ms = map.getTo();
+ int sf = map.getMap().getToLowest();
+ int st = map.getMap().getToHighest();
+ SequenceI mappedrg = ms.getSubSequence(sf, st);
+ // SequenceI loc = dss.getSubSequence(sf, st);
+ if (mappedrg.getLength() > 0
+ && ms.getSequenceAsString().equals(
+ dss.getSequenceAsString()))
+ // && mappedrg.getSequenceAsString().equals(
+ // loc.getSequenceAsString()))
+ {
+ String msg = "Mapping updated from "
+ + ms.getName()
+ + " to retrieved crossreference "
+ + dss.getName();
+ System.out.println(msg);
+ // method to update all refs of existing To on
+ // retrieved sequence with dss and merge any props
+ // on To onto dss.
+ map.setTo(dss);
+ /*
+ * copy sequence features as well, avoiding
+ * duplication (e.g. same variation from 2
+ * transcripts)
+ */
+ SequenceFeature[] sfs = ms
+ .getSequenceFeatures();
+ if (sfs != null)
+ {
+ for (SequenceFeature feat : sfs)
+ {
+ /*
+ * we override SequenceFeature.equals here (but
+ * not elsewhere) to ignore Parent attribute
+ * TODO not quite working yet!
+ */
+ if (!copiedFeatures
+ .contains(me.new MySequenceFeature(
+ feat)))
+ {
+ dss.addSequenceFeature(feat);
+ copiedFeatures.add(feat);
+ }
+ }
+ }
+ cf.addMap(retrieved[rs].getDatasetSequence(),
+ dss, map.getMap());
+ }
+ else
+ {
+ cf.addMap(retrieved[rs].getDatasetSequence(),
+ map.getTo(), map.getMap());
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Exception when consolidating Mapped sequence set...");
+ e.printStackTrace(System.err);
+ }
+ }
+ }
+ }
+ }
+ retrieved[rs].updatePDBIds();
+ rseqs.add(retrieved[rs]);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ Alignment ral = null;
+ if (rseqs.size() > 0)
+ {
+ ral = new Alignment(rseqs.toArray(new SequenceI[rseqs.size()]));
+ if (cf != null && !cf.isEmpty())
+ {
+ ral.addCodonFrame(cf);
+ }
+ }
+ return ral;
+ }
+
+ /**
+ * 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 dna
+ * @param mapFrom
+ * @param xrefs
+ * @param retrieved
+ * @param acf
+ */
+ static void updateDbrefMappings(boolean dna, SequenceI mapFrom,
+ DBRefEntry[] xrefs, SequenceI[] retrieved, AlignedCodonFrame acf)
+ {
+ SequenceIdMatcher matcher = new SequenceIdMatcher(retrieved);
+ for (DBRefEntry xref : xrefs)
+ {
+ if (!xref.hasMap())
+ {
+ String targetSeqName = xref.getSource() + "|"
+ + xref.getAccessionId();
+ SequenceI[] matches = matcher.findAllIdMatches(targetSeqName);
+ if (matches == null)
+ {
+ return;
+ }
+ for (SequenceI seq : matches)
+ {
+ MapList mapping = null;
+ if (dna)
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(seq, mapFrom);
+ }
+ else
+ {
+ mapping = AlignmentUtils.mapCdnaToProtein(mapFrom, seq);
+ if (mapping != null)
+ {
+ mapping = mapping.getInverse();
+ }
+ }
+ if (mapping != null)
+ {
+ xref.setMap(new Mapping(seq, mapping));
+ if (dna)
+ {
+ AlignmentUtils.computeProteinFeatures(mapFrom, seq, mapping);
+ }
+ if (dna)
+ {
+ acf.addMap(mapFrom, seq, mapping);
+ }
+ else
+ {
+ acf.addMap(seq, mapFrom, mapping.getInverse());
+ }
+ continue;
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * 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 sequenceI
+ * @param lrfs
+ * @param dataset
+ * @param rseqs
+ * @return true if matches were found.
+ */
+ private static boolean searchDatasetXrefs(SequenceI sequenceI,
+ boolean dna, DBRefEntry[] lrfs, AlignmentI dataset,
+ List rseqs, 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(sequenceI, xref, dataset, rseqs, cf, false, dna);
+ }
+ return found;
+ }
+
+ /**
+ * search a given sequence dataset for references matching cross-references to
+ * the given sequence
+ *
+ * @param sequenceI
+ * @param xrf
+ * @param dataset
+ * @param rseqs
+ * set of unique sequences
+ * @param cf
+ * @return true if one or more unique sequences were found and added
+ */
+ public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
+ AlignmentI dataset, List rseqs, AlignedCodonFrame cf)
+ {
+ return searchDataset(sequenceI, xrf, dataset, rseqs, cf, true, false);
+ }
+
+ /**
+ * TODO: generalise to different protein classifications Search dataset for
+ * DBRefEntrys matching the given one (xrf) and add the associated sequence to
+ * rseq.
+ *
+ * @param sequenceI
+ * @param xrf
+ * @param dataset
+ * @param rseqs
+ * @param direct
+ * - search all references or only subset
+ * @param dna
+ * search dna or protein xrefs (if direct=false)
+ * @return true if relationship found and sequence added.
+ */
+ public static boolean searchDataset(SequenceI sequenceI, DBRefEntry xrf,
+ AlignmentI dataset, List rseqs, AlignedCodonFrame cf,
+ boolean direct, boolean dna)
+ {
+ boolean found = false;
+ SequenceI[] typer = new SequenceI[1];
+ if (dataset == null)
+ {
+ return false;
+ }
+ if (dataset.getSequences() == null)
+ {
+ System.err.println("Empty dataset sequence set - NO VECTOR");
+ return false;
+ }
+ List ds;
+ synchronized (ds = dataset.getSequences())
+ {
+ for (SequenceI nxt : ds)
+ {
+ if (nxt != null)
+ {
+ if (nxt.getDatasetSequence() != null)
+ {
+ System.err
+ .println("Implementation warning: getProducts passed a dataset alignment without dataset sequences in it!");
+ }
+ if (nxt != sequenceI && nxt != sequenceI.getDatasetSequence())
+ {
+ // check if this is the correct sequence type
+ {
+ typer[0] = nxt;
+ boolean isDna = jalview.util.Comparison.isNucleotide(typer);
+ if ((direct && isDna == dna) || (!direct && isDna != dna))
+ {
+ // skip this sequence because it is same molecule type
+ continue;
+ }
+ }
+
+ // look for direct or indirect references in common
+ DBRefEntry[] poss = nxt.getDBRefs(), cands = null;
+ if (direct)
+ {
+ cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+ }
+ else
+ {
+ poss = CrossRef.findXDbRefs(dna, poss); //
+ cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);
+ }
+ if (cands != null)
+ {
+ if (!rseqs.contains(nxt))
+ {
+ rseqs.add(nxt);
+ boolean foundmap = cf != null;
+ // don't search if we aren't given a codon map object
+ for (int r = 0; foundmap && r < cands.length; r++)
+ {
+ if (cands[r].hasMap())
+ {
+ if (cands[r].getMap().getTo() != null
+ && cands[r].getMap().getMap().getFromRatio() != cands[r]
+ .getMap().getMap().getToRatio())
+ {
+ foundmap = true;
+ // get sense of map correct for adding to product
+ // alignment.
+ if (dna)
+ {
+ // map is from dna seq to a protein product
+ cf.addMap(sequenceI, nxt, cands[r].getMap()
+ .getMap());
+ }
+ else
+ {
+ // map should be from protein seq to its coding dna
+ cf.addMap(nxt, sequenceI, cands[r].getMap()
+ .getMap().getInverse());
+ }
+ }
+ }
+ }
+ // TODO: add mapping between sequences if necessary
+ found = true;
+ }
+ }
+
+ }
+ }
+ }
+ }
+ return found;
+ }
+
+ /**
+ * precalculate different products that can be found for seqs in dataset and
+ * return them.
+ *
+ * @param dna
+ * @param seqs
+ * @param dataset
+ * @param fake
+ * - don't actually build lists - just get types
+ * @return public static Object[] buildXProductsList(boolean dna, SequenceI[]
+ * seqs, AlignmentI dataset, boolean fake) { String types[] =
+ * jalview.analysis.CrossRef.findSequenceXrefTypes( dna, seqs,
+ * dataset); if (types != null) { System.out.println("Xref Types for:
+ * "+(dna ? "dna" : "prot")); for (int t = 0; t < types.length; t++) {
+ * System.out.println("Type: " + types[t]); SequenceI[] prod =
+ * jalview.analysis.CrossRef.findXrefSequences(seqs, dna, types[t]);
+ * System.out.println("Found " + ((prod == null) ? "no" : "" +
+ * prod.length) + " products"); if (prod!=null) { for (int p=0;
+ * p