X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=27aee2412eb9f6560621d01ef44b0f2f855c210b;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=e6c7197e22c76962063a405e32287194ef00118d;hpb=3f89c3afc646bf1d83607110e538f20f9c01c3b2;p=jalview.git diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index e6c7197..27aee24 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -1,15 +1,45 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ 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.Map.Entry; import java.util.Vector; +/** + * Data model for one entry returned from an EMBL query, as marshalled by a + * Castor binding file + * + * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml + * + * @see embl_mapping.xml + */ public class EmblEntry { String accession; @@ -26,13 +56,11 @@ public class EmblEntry String lastUpdated; - Vector keywords; + Vector keywords; - Vector refs; + Vector dbRefs; - Vector dbRefs; - - Vector features; + Vector features; EmblSequence sequence; @@ -56,7 +84,7 @@ public class EmblEntry /** * @return the dbRefs */ - public Vector getDbRefs() + public Vector getDbRefs() { return dbRefs; } @@ -65,7 +93,7 @@ public class EmblEntry * @param dbRefs * the dbRefs to set */ - public void setDbRefs(Vector dbRefs) + public void setDbRefs(Vector dbRefs) { this.dbRefs = dbRefs; } @@ -90,7 +118,7 @@ public class EmblEntry /** * @return the features */ - public Vector getFeatures() + public Vector getFeatures() { return features; } @@ -99,7 +127,7 @@ public class EmblEntry * @param features * the features to set */ - public void setFeatures(Vector features) + public void setFeatures(Vector features) { this.features = features; } @@ -107,7 +135,7 @@ public class EmblEntry /** * @return the keywords */ - public Vector getKeywords() + public Vector getKeywords() { return keywords; } @@ -116,7 +144,7 @@ public class EmblEntry * @param keywords * the keywords to set */ - public void setKeywords(Vector keywords) + public void setKeywords(Vector keywords) { this.keywords = keywords; } @@ -139,23 +167,6 @@ public class EmblEntry } /** - * @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() @@ -167,7 +178,7 @@ public class EmblEntry * @param releaseCreated * the releaseCreated to set */ - public void setRcreated(String releaseCreated) + public void setRCreated(String releaseCreated) { this.rCreated = releaseCreated; } @@ -244,8 +255,8 @@ public class EmblEntry * 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 + * 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. @@ -369,7 +380,6 @@ public class EmblEntry * * 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 @@ -384,193 +394,452 @@ public class EmblEntry */ public jalview.datamodel.SequenceI[] getSequences(boolean noNa, boolean noPeptide, String sourceDb) - { - Vector seqs = new Vector(); + { // 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 + DBRefEntry retrievedref = new DBRefEntry(sourceDb, version, accession); + dna.addDBRef(retrievedref); + // add map to indicate the sequence is a valid coordinate frame for the + // dbref + retrievedref.setMap(new Mapping(null, + new int[] { 1, dna.getLength() }, new int[] { 1, + dna.getLength() }, 1, 1)); // TODO: transform EMBL Database refs to canonical form if (dbRefs != null) - for (Iterator i = dbRefs.iterator(); i.hasNext(); dna - .addDBRef((DBRefEntry) i.next())) - ; + { + for (DBRefEntry dbref : dbRefs) + { + dna.addDBRef(dbref); + } + } } try { - for (Iterator i = features.iterator(); i.hasNext();) + for (EmblFeature feature : features) { - boolean nextFeature=false; - EmblFeature feature = (EmblFeature) i.next(); if (!noNa) { - if (feature.dbRefs != null && feature.dbRefs.size() > 0) + if (feature.dbRefs != null) { - for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna - .addDBRef((DBRefEntry) dbr.next())) - ; + for (DBRefEntry dbref : feature.dbRefs) + { + dna.addDBRef(dbref); + } } } - if (feature.getName().equalsIgnoreCase("CDS")) + if (FeatureProperties.isCodingFeature(sourceDb, feature.getName())) + { + parseCodingFeature(feature, sourceDb, seqs, dna, noPeptide); + } + else { - // extract coding region(s) - jalview.datamodel.Mapping map = null; - int[] exon = null; - if (feature.locations != null && feature.locations.size() > 0) + // General feature type. + // TODO this is just duplicated code ?? + if (!noNa) { - for (Enumeration locs = feature.locations.elements(); locs - .hasMoreElements();) + if (feature.dbRefs != null) { - EmblFeatureLocations loc = (EmblFeatureLocations) locs - .nextElement(); - int[] se = loc.getElementRanges(accession); - if (exon == null) - { - exon = se; - } - else + for (DBRefEntry dbref : feature.dbRefs) { - 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; + dna.addDBRef(dbref); } } } - 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) + } + } + } 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] = 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) + { + for (EmblFeatureLocations loc : feature.locations) + { + 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) + { + for (Qualifier q : feature.getQualifiers()) + { + String qname = q.getName(); + if (qname.equals("translation")) + { + StringBuilder prsq = new StringBuilder(q.getValues()[0]); + int p = prsq.indexOf(" "); + while (p > -1) { - for (Iterator quals = feature.getQualifiers().iterator(); quals - .hasNext();) - { - Qualifier q = (Qualifier) quals.next(); - if (q.getName().equals("translation")) - { - prseq = q.getValues()[0]; - } - 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 - vals.put(q.getName(), q.getValues().toString()); - } - } + prsq.deleteCharAt(p); + p = prsq.indexOf(" ", p); } - Sequence product = null; - if (prseq != null && prname != null && prid != null) + prseq = prsq.toString(); + prsq = null; + + } + else if (qname.equals("protein_id")) + { + prid = q.getValues()[0]; + } + else if (qname.equals("codon_start")) + { + prstart = Integer.parseInt(q.getValues()[0]); + } + else if (qname.equals("product")) + { + prname = q.getValues()[0]; + } + else + { + // throw anything else into the additional properties hash + String[] s = q.getValues(); + StringBuilder sb = new StringBuilder(); + if (s != null) { - // extract proteins. - if (!noPeptide) + for (int i = 0; i < s.length; i++) { - product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid - + "|" + prname, prseq, prstart, prstart - + prseq.length() - 1); - product.setDescription("Protein Product from " + sourceDb); - seqs.add(product); - } - // we have everything - create the mapping and perhaps the protein - // sequence - map = new jalview.datamodel.Mapping(product, exon, new int[] - { prstart, prstart + prseq.length() - 1 }, 3, 1); - // add cds feature to dna seq - this may include the stop codon - for (int xint = 0; xint < exon.length; xint += 2) - { - SequenceFeature sf = new SequenceFeature(); - sf.setBegin(exon[xint]); - sf.setEnd(exon[xint + 1]); - sf.setType(feature.getName()); - sf.setFeatureGroup(jalview.datamodel.DBRefSource.EMBL); - sf.setDescription("Exon " + (1 + xint) + " for protein '" - + prname + "' EMBLCDS:" + prid); - 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); + sb.append(s[i]); + sb.append("\n"); } } - // add dbRefs to sequence - if (feature.dbRefs != null && feature.dbRefs.size() > 0) + vals.put(qname, sb.toString()); + } + } + } + Sequence product = null; + DBRefEntry protEMBLCDS = null; + exon = adjustForPrStart(prstart, exon); + boolean noProteinDbref = true; + + if (prseq != null && prname != null && prid != null) + { + // extract proteins. + product = new Sequence(prid, prseq, 1, prseq.length()); + 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 == (1 - prstart + dna.getSequence().length)) + { + System.err + .println("Not allowing for additional stop codon at end of cDNA fragment... !"); + // this might occur for CDS sequences where no features are + // marked. + exon = new int[] { dna.getStart() + (prstart - 1), dna.getEnd() }; + map = new jalview.datamodel.Mapping(product, exon, new int[] { 1, + prseq.length() }, 3, 1); + } + if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length)) + { + System.err + .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!"); + exon = new int[] { dna.getStart() + (prstart - 1), + dna.getEnd() - 3 }; + map = new jalview.datamodel.Mapping(product, exon, new int[] { 1, + prseq.length() }, 3, 1); + } + } + else + { + // Trim the exon mapping if necessary - the given product may only be a + // fragment of a larger protein. (EMBL:AY043181 is an example) + + 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 + { + // final product length trunctation check + + map = new jalview.datamodel.Mapping(product, + adjustForProteinLength(prseq.length(), exon), new int[] { + 1, prseq.length() }, 3, 1); + // reconstruct the EMBLCDS entry + // TODO: this is only necessary when there codon annotation is + // complete (I think JBPNote) + 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, + prseq.length() }, new int[] { 1 + (prstart - 1), + (prstart - 1) + 3 * prseq.length() }, 1, 3); + // { 1 + (prstart - 1) * 3, + // 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[] + // { 1prstart, prstart + prseq.length() - 1 }, 3, 1); + pcdnaref.setMap(new Mapping(mp)); + if (product != null) + { + product.addDBRef(pcdnaref); + protEMBLCDS = new DBRefEntry(pcdnaref); + protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct); + product.addDBRef(protEMBLCDS); + + } + + } + } + // 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 / 2) + " for protein '" + + prname + "' EMBLCDS:" + prid); + sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint)); + sf.setValue(FeatureProperties.EXONPRODUCT, prname); + if (vals != null) + { + for (Entry val : vals.entrySet()) + { + sf.setValue(val.getKey(), val.getValue()); + } + } + dna.addSequenceFeature(sf); + } + } + // add dbRefs to sequence + if (feature.dbRefs != null) + { + for (DBRefEntry ref : feature.dbRefs) + { + 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) { - for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();) + map.getTo().addDBRef( + new DBRefEntry(ref.getSource(), ref.getVersion(), ref + .getAccessionId())); // don't copy map over. + if (map.getTo().getName().indexOf(prid) == 0) { - DBRefEntry ref = (DBRefEntry) dbr.next(); - ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref - .getSource())); - if (ref.getSource().equals( - jalview.datamodel.DBRefSource.UNIPROT)) - { - ref.setMap(map); - } - if (product != null) - { - DBRefEntry pref = new DBRefEntry(ref.getSource(), ref - .getVersion(), ref.getAccessionId()); - pref.setMap(null); // reference is direct - } - dna.addDBRef(ref); + map.getTo().setName( + jalview.datamodel.DBRefSource.UNIPROT + "|" + + ref.getAccessionId()); } } - + noProteinDbref = false; } - else + if (product != null) { - // General feature type. - if (!noNa) + 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) { - if (feature.dbRefs != null && feature.dbRefs.size() > 0) + Mapping pmap = new Mapping(dna, map.getMap().getInverse()); + pref = new DBRefEntry(sourceDb, getVersion(), + this.getAccession()); + pref.setMap(pmap); + if (map.getTo() != null) { - for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna - .addDBRef((DBRefEntry) dbr.next())) - ; + map.getTo().addDBRef(pref); } } } + dna.addDBRef(ref); + } + if (noProteinDbref && product != null) + { + // add protein coding reference to dna sequence so xref matches + if (protEMBLCDS == null) + { + protEMBLCDS = new DBRefEntry(); + protEMBLCDS.setAccessionId(prid); + protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct); + protEMBLCDS.setVersion(getVersion()); + protEMBLCDS + .setMap(new Mapping(product, map.getMap().getInverse())); + } + product.addDBRef(protEMBLCDS); + + // Add converse mapping reference + if (map != null) + { + Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap() + .getInverse()); + DBRefEntry ncMap = new DBRefEntry(protEMBLCDS); + ncMap.setMap(pmap); + if (map.getTo() != null) + { + dna.addDBRef(ncMap); + } + } } - } 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) + } + + private int[] adjustForPrStart(int prstart, int[] exon) + { + + int origxon[], sxpos = -1; + int sxstart, sxstop; // unnecessary variables used for debugging + // first adjust range for codon start attribute + if (prstart > 1) { - seqs.add(dna); + origxon = new int[exon.length]; + System.arraycopy(exon, 0, origxon, 0, exon.length); + int cdspos = 0; + for (int x = 0; x < exon.length && sxpos == -1; x += 2) + { + cdspos += exon[x + 1] - exon[x] + 1; + if (prstart <= cdspos) + { + sxpos = x; + sxstart = exon[x]; + sxstop = exon[x + 1]; + // and adjust start boundary of first exon. + exon[x] = exon[x + 1] - cdspos + prstart; + break; + } + } + + if (sxpos > 0) + { + int[] nxon = new int[exon.length - sxpos]; + System.arraycopy(exon, sxpos, nxon, 0, exon.length - sxpos); + exon = nxon; + } } - SequenceI[] sqs = new SequenceI[seqs.size()]; - for (int i = 0, j = seqs.size(); i < j; i++) + return exon; + } + + /** + * truncate the last exon interval to the prlength'th codon + * + * @param prlength + * @param exon + * @return new exon + */ + private int[] adjustForProteinLength(int prlength, int[] exon) + { + + int origxon[], sxpos = -1, endxon = 0, cdslength = prlength * 3; + int sxstart, sxstop; // unnecessary variables used for debugging + // first adjust range for codon start attribute + if (prlength >= 1 && exon != null) { - sqs[i] = (SequenceI) seqs.elementAt(i); - seqs.set(i, null); + origxon = new int[exon.length]; + System.arraycopy(exon, 0, origxon, 0, exon.length); + int cdspos = 0; + for (int x = 0; x < exon.length && sxpos == -1; x += 2) + { + cdspos += exon[x + 1] - exon[x] + 1; + if (cdslength <= cdspos) + { + // advanced beyond last codon. + sxpos = x; + sxstart = exon[x]; + sxstop = exon[x + 1]; + if (cdslength != cdspos) + { + System.err + .println("Truncating final exon interval on region by " + + (cdspos - cdslength)); + } + // locate the new end boundary of final exon as endxon + endxon = exon[x + 1] - cdspos + cdslength; + break; + } + } + + if (sxpos != -1) + { + // and trim the exon interval set if necessary + int[] nxon = new int[sxpos + 2]; + System.arraycopy(exon, 0, nxon, 0, sxpos + 2); + nxon[sxpos + 1] = endxon; // update the end boundary for the new exon + // set + exon = nxon; + } } - return sqs; + return exon; } }