+++ /dev/null
-package jalview.datamodel.xdb.embl;
-
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.FeatureProperties;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-
-public class EmblEntry
-{
- String accession;
-
- String version;
-
- String taxDivision;
-
- String desc;
-
- String rCreated;
-
- String rLastUpdated;
-
- String lastUpdated;
-
- Vector keywords;
-
- Vector refs;
-
- Vector dbRefs;
-
- Vector features;
-
- EmblSequence sequence;
-
- /**
- * @return the accession
- */
- public String getAccession()
- {
- return accession;
- }
-
- /**
- * @param accession
- * the accession to set
- */
- public void setAccession(String accession)
- {
- this.accession = accession;
- }
-
- /**
- * @return the dbRefs
- */
- public Vector getDbRefs()
- {
- return dbRefs;
- }
-
- /**
- * @param dbRefs
- * the dbRefs to set
- */
- public void setDbRefs(Vector dbRefs)
- {
- this.dbRefs = dbRefs;
- }
-
- /**
- * @return the desc
- */
- public String getDesc()
- {
- return desc;
- }
-
- /**
- * @param desc
- * the desc to set
- */
- public void setDesc(String desc)
- {
- this.desc = desc;
- }
-
- /**
- * @return the features
- */
- public Vector getFeatures()
- {
- return features;
- }
-
- /**
- * @param features
- * the features to set
- */
- public void setFeatures(Vector features)
- {
- this.features = features;
- }
-
- /**
- * @return the keywords
- */
- public Vector getKeywords()
- {
- return keywords;
- }
-
- /**
- * @param keywords
- * the keywords to set
- */
- public void setKeywords(Vector keywords)
- {
- this.keywords = keywords;
- }
-
- /**
- * @return the lastUpdated
- */
- public String getLastUpdated()
- {
- return lastUpdated;
- }
-
- /**
- * @param lastUpdated
- * the lastUpdated to set
- */
- public void setLastUpdated(String lastUpdated)
- {
- this.lastUpdated = lastUpdated;
- }
-
- /**
- * @return the refs
- */
- public Vector getRefs()
- {
- return refs;
- }
-
- /**
- * @param refs
- * the refs to set
- */
- public void setRefs(Vector refs)
- {
- this.refs = refs;
- }
-
- /**
- * @return the releaseCreated
- */
- public String getRCreated()
- {
- return rCreated;
- }
-
- /**
- * @param releaseCreated
- * the releaseCreated to set
- */
- public void setRcreated(String releaseCreated)
- {
- this.rCreated = releaseCreated;
- }
-
- /**
- * @return the releaseLastUpdated
- */
- public String getRLastUpdated()
- {
- return rLastUpdated;
- }
-
- /**
- * @param releaseLastUpdated
- * the releaseLastUpdated to set
- */
- public void setRLastUpdated(String releaseLastUpdated)
- {
- this.rLastUpdated = releaseLastUpdated;
- }
-
- /**
- * @return the sequence
- */
- public EmblSequence getSequence()
- {
- return sequence;
- }
-
- /**
- * @param sequence
- * the sequence to set
- */
- public void setSequence(EmblSequence sequence)
- {
- this.sequence = sequence;
- }
-
- /**
- * @return the taxDivision
- */
- public String getTaxDivision()
- {
- return taxDivision;
- }
-
- /**
- * @param taxDivision
- * the taxDivision to set
- */
- public void setTaxDivision(String taxDivision)
- {
- this.taxDivision = taxDivision;
- }
-
- /**
- * @return the version
- */
- public String getVersion()
- {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- */
- public void setVersion(String version)
- {
- this.version = version;
- }
-
- /*
- * EMBL Feature support is limited. The text below is included for the benefit
- * of any developer working on improving EMBL feature import in Jalview.
- * Extract from EMBL feature specification see
- * http://www.embl-ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
- * 3.5 Location 3.5.1 Purpose
- *
- * The location indicates the region of the presented sequence which
- * corresponds to a feature.
- *
- * 3.5.2 Format and conventions The location contains at least one sequence
- * location descriptor and may contain one or more operators with one or more
- * sequence location descriptors. Base numbers refer to the numbering in the
- * entry. This numbering designates the first base (5' end) of the presented
- * sequence as base 1. Base locations beyond the range of the presented
- * sequence may not be used in location descriptors, the only exception being
- * location in a remote entry (see 3.5.2.1, e).
- *
- * Location operators and descriptors are discussed in more detail below.
- *
- * 3.5.2.1 Location descriptors
- *
- * The location descriptor can be one of the following: (a) a single base
- * number (b) a site between two indicated adjoining bases (c) a single base
- * chosen from within a specified range of bases (not allowed for new entries)
- * (d) the base numbers delimiting a sequence span (e) a remote entry
- * identifier followed by a local location descriptor (i.e., a-d)
- *
- * A site between two adjoining nucleotides, such as endonucleolytic cleavage
- * site, is indicated by listing the two points separated by a carat (^). The
- * permitted formats for this descriptor are n^n+1 (for example 55^56), or,
- * for circular molecules, n^1, where "n" is the full length of the molecule,
- * ie 1000^1 for circular molecule with length 1000.
- *
- * A single base chosen from a range of bases is indicated by the first base
- * number and the last base number of the range separated by a single period
- * (e.g., '12.21' indicates a single base taken from between the indicated
- * points). From October 2006 the usage of this descriptor is restricted : it
- * is illegal to use "a single base from a range" (c) either on its own or in
- * combination with the "sequence span" (d) descriptor for newly created
- * entries. The existing entries where such descriptors exist are going to be
- * retrofitted.
- *
- * Sequence spans are indicated by the starting base number and the ending
- * base number separated by two periods (e.g., '34..456'). The '<' and '>'
- * symbols may be used with the starting and ending base numbers to indicate
- * that an end point is beyond the specified base number. The starting and
- * ending base positions can be represented as distinct base numbers
- * ('34..456') or a site between two indicated adjoining bases.
- *
- * A location in a remote entry (not the entry to which the feature table
- * belongs) can be specified by giving the accession-number and sequence
- * version of the remote entry, followed by a colon ":", followed by a
- * location descriptor which applies to that entry's sequence (i.e.
- * J12345.1:1..15, see also examples below)
- *
- * 3.5.2.2 Operators
- *
- * The location operator is a prefix that specifies what must be done to the
- * indicated sequence to find or construct the location corresponding to the
- * feature. A list of operators is given below with their definitions and most
- * common format.
- *
- * complement(location) Find the complement of the presented sequence in the
- * span specified by " location" (i.e., read the complement of the presented
- * strand in its 5'-to-3' direction)
- *
- * join(location,location, ... location) The indicated elements should be
- * joined (placed end-to-end) to form one contiguous sequence
- *
- * order(location,location, ... location) The elements can be found in the
- * specified order (5' to 3' direction), but nothing is implied about the
- * reasonableness about joining them
- *
- * Note : location operator "complement" can be used in combination with
- * either " join" or "order" within the same location; combinations of "join"
- * and "order" within the same location (nested operators) are illegal.
- *
- *
- *
- * 3.5.3 Location examples
- *
- * The following is a list of common location descriptors with their meanings:
- *
- * Location Description
- *
- * 467 Points to a single base in the presented sequence
- *
- * 340..565 Points to a continuous range of bases bounded by and including the
- * starting and ending bases
- *
- * <345..500 Indicates that the exact lower boundary point of a feature is
- * unknown. The location begins at some base previous to the first base
- * specified (which need not be contained in the presented sequence) and
- * continues to and includes the ending base
- *
- * <1..888 The feature starts before the first sequenced base and continues to
- * and includes base 888
- *
- * 1..>888 The feature starts at the first sequenced base and continues beyond
- * base 888
- *
- * 102.110 Indicates that the exact location is unknown but that it is one of
- * the bases between bases 102 and 110, inclusive
- *
- * 123^124 Points to a site between bases 123 and 124
- *
- * join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to
- * form one contiguous sequence
- *
- *
- * complement(34..126) Start at the base complementary to 126 and finish at
- * the base complementary to base 34 (the feature is on the strand
- * complementary to the presented strand)
- *
- *
- * complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918
- * to 5163, then complements the joined segments (the feature is on the strand
- * complementary to the presented strand)
- *
- * join(complement(4918..5163),complement(2691..4571)) Complements regions
- * 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the
- * feature is on the strand complementary to the presented strand)
- *
- * J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in
- * this database) with primary accession number 'J00194'
- *
- * join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry
- * with the region 100..202 of remote entry J00194
- *
- */
- /**
- * Recover annotated sequences from EMBL file
- *
- * @param noNa
- * don't return nucleic acid sequences
- * @param sourceDb
- * TODO
- * @param noProtein
- * don't return any translated protein sequences marked in features
- * @return dataset sequences with DBRefs and features - DNA always comes first
- */
- public jalview.datamodel.SequenceI[] getSequences(boolean noNa,
- boolean noPeptide, String sourceDb)
- { //TODO: ensure emblEntry.getSequences behaves correctly for returning all cases of noNa and noPeptide
- Vector seqs = new Vector();
- Sequence dna = null;
- if (!noNa)
- {
- // In theory we still need to create this if noNa is set to avoid a null pointer exception
- dna = new Sequence(sourceDb + "|" + accession, sequence.getSequence());
- dna.setDescription(desc);
- dna.addDBRef(new DBRefEntry(sourceDb, version, accession));
- // TODO: add mapping for parentAccession attribute
- // TODO: transform EMBL Database refs to canonical form
- if (dbRefs != null)
- for (Iterator i = dbRefs.iterator(); i.hasNext(); dna
- .addDBRef((DBRefEntry) i.next()))
- ;
- }
- try
- {
- for (Iterator i = features.iterator(); i.hasNext();)
- {
- EmblFeature feature = (EmblFeature) i.next();
- if (!noNa)
- {
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
- {
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
- }
- }
- if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
- {
- parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide);
- }
- else
- {
- // General feature type.
- if (!noNa)
- {
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
- {
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
- .addDBRef((DBRefEntry) dbr.next()))
- ;
- }
- }
- }
- }
- }
- catch (Exception e)
- {
- System.err.println("EMBL Record Features parsing error!");
- System.err
- .println("Please report the following to help@jalview.org :");
- System.err.println("EMBL Record " + accession);
- System.err.println("Resulted in exception: " + e.getMessage());
- e.printStackTrace(System.err);
- }
- if (!noNa && dna != null)
- {
- seqs.add(dna);
- }
- SequenceI[] sqs = new SequenceI[seqs.size()];
- for (int i = 0, j = seqs.size(); i < j; i++)
- {
- sqs[i] = (SequenceI) seqs.elementAt(i);
- seqs.set(i, null);
- }
- return sqs;
- }
-
- /**
- * attempt to extract coding region and product from a feature and properly decorate it with annotations.
- * @param feature coding feature
- * @param sourceDb source database for the EMBLXML
- * @param seqs place where sequences go
- * @param dna parent dna sequence for this record
- * @param noPeptide flag for generation of Peptide sequence objects
- */
- private void parseCodingFeature(EmblFeature feature, String sourceDb, Vector seqs, Sequence dna, boolean noPeptide)
- {
- boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
- // extract coding region(s)
- jalview.datamodel.Mapping map = null;
- int[] exon = null;
- if (feature.locations != null && feature.locations.size() > 0)
- {
- for (Enumeration locs = feature.locations.elements(); locs
- .hasMoreElements();)
- {
- EmblFeatureLocations loc = (EmblFeatureLocations) locs
- .nextElement();
- int[] se = loc.getElementRanges(accession);
- if (exon == null)
- {
- exon = se;
- }
- else
- {
- int[] t = new int[exon.length + se.length];
- System.arraycopy(exon, 0, t, 0, exon.length);
- System.arraycopy(se, 0, t, exon.length, se.length);
- exon = t;
- }
- }
- }
- String prseq = null;
- String prname = new String();
- String prid = null;
- Hashtable vals = new Hashtable();
- int prstart = 1;
- // get qualifiers
- if (feature.getQualifiers() != null
- && feature.getQualifiers().size() > 0)
- {
- for (Iterator quals = feature.getQualifiers().iterator(); quals
- .hasNext();)
- {
- Qualifier q = (Qualifier) quals.next();
- if (q.getName().equals("translation"))
- {
- StringBuffer prsq = new StringBuffer(q.getValues()[0]);
- int p = prsq.indexOf(" ");
- while (p > -1)
- {
- prsq.deleteCharAt(p);
- p = prsq.indexOf(" ", p);
- }
- prseq = prsq.toString();
- prsq = null;
-
- }
- else if (q.getName().equals("protein_id"))
- {
- prid = q.getValues()[0];
- }
- else if (q.getName().equals("codon_start"))
- {
- prstart = Integer.parseInt(q.getValues()[0]);
- }
- else if (q.getName().equals("product"))
- {
- prname = q.getValues()[0];
- }
- else
- {
- // throw anything else into the additional properties hash
- String[] s= q.getValues();
- StringBuffer sb = new StringBuffer();
- if (s!=null)
- {
- for (int i=0; i<s.length; i++)
- {
- sb.append(s[i]);
- sb.append("\n");
- }
- }
- vals.put(q.getName(), sb.toString());
- }
- }
- }
- Sequence product = null;
- if (prseq != null && prname != null && prid != null)
- {
- // extract proteins.
- product = new Sequence(prid
- , prseq, prstart, prstart
- + prseq.length() - 1);
- product.setDescription(((prname.length()==0) ? "Protein Product from " + sourceDb : prname));
-
- if (!noPeptide)
- {
- // Protein is also added to vector of sequences returned
- seqs.add(product);
- }
- // we have everything - create the mapping and perhaps the protein
- // sequence
- if (exon == null || exon.length == 0)
- {
- System.err
- .println("Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
- + sourceDb + ":" + getAccession() + ")");
- if (prseq.length() * 3 == dna.getSequence().length)
- {
- // this might occur for CDS sequences where no features are
- // marked.
- exon = new int[]
- { dna.getStart(), dna.getEnd() };
- map = new jalview.datamodel.Mapping(product, exon,
- new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
- }
- if ((prseq.length() + 1) * 3 == dna.getSequence().length)
- {
- exon = new int[]
- { dna.getStart(), dna.getEnd() - 3 };
- map = new jalview.datamodel.Mapping(product, exon,
- new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
- }
- }
- else
- {
- if (isEmblCdna)
- {
- // TODO: Add a DbRef back to the parent EMBL sequence with the exon
- // map
- // if given a dataset reference, search dataset for parent EMBL sequence if it exists and set its map
- // make a new feature annotating the coding contig
- }
- else
- {
- map = new jalview.datamodel.Mapping(product, exon,
- new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
- // reconstruct the EMBLCDS entry
- DBRefEntry pcdnaref = new DBRefEntry();
- pcdnaref.setAccessionId(prid);
- pcdnaref.setSource(DBRefSource.EMBLCDS);
- pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
- jalview.util.MapList mp = new jalview.util.MapList(new int[]
- { 1+(prstart-1)*3, 1+(prstart-1)*3 + (prseq.length()-1)*3 }, new int[] { prstart, prstart+prseq.length() - 1 }, 3, 1);
- pcdnaref.setMap(new Mapping(mp));
- if (product!=null)
- product.addDBRef(pcdnaref);
-
- }
- }
- // add cds feature to dna seq - this may include the stop codon
- for (int xint = 0; exon != null && xint < exon.length; xint += 2)
- {
- SequenceFeature sf = new SequenceFeature();
- sf.setBegin(exon[xint]);
- sf.setEnd(exon[xint + 1]);
- sf.setType(feature.getName());
- sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + xint) + " for protein '"
- + prname + "' EMBLCDS:" + prid);
- sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint));
- sf.setValue(FeatureProperties.EXONPRODUCT, prname);
- if (vals != null && vals.size() > 0)
- {
- Enumeration kv = vals.elements();
- while (kv.hasMoreElements())
- {
- Object key = kv.nextElement();
- if (key != null)
- sf.setValue(key.toString(), vals.get(key));
- }
- }
- dna.addSequenceFeature(sf);
- }
- }
- // add dbRefs to sequence
- if (feature.dbRefs != null && feature.dbRefs.size() > 0)
- {
- for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();)
- {
- DBRefEntry ref = (DBRefEntry) dbr.next();
- ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref
- .getSource()));
- // Hard code the kind of protein product accessions that EMBL cite
- if (ref.getSource().equals(
- jalview.datamodel.DBRefSource.UNIPROT))
- {
- ref.setMap(map);
- if (map!=null && map.getTo()!=null)
- {
- map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
- if (map.getTo().getName().indexOf(prid)==0)
- {
- map.getTo().setName(jalview.datamodel.DBRefSource.UNIPROT+"|"+ref.getAccessionId());
- }
- }
- }
- if (product != null)
- {
- DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
- .getVersion(), ref.getAccessionId());
- pref.setMap(null); // reference is direct
- product.addDBRef(pref);
- // Add converse mapping reference
- if (map != null)
- {
- Mapping pmap = new Mapping(dna, map.getMap().getInverse());
- pref = new DBRefEntry(sourceDb, getVersion(), this
- .getAccession());
- pref.setMap(pmap);
- if (map.getTo()!=null)
- {
- map.getTo().addDBRef(pref);
- }
- }
- }
- dna.addDBRef(ref);
- }
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff