X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=a94988814fa114863eda6f37ef64661524324e94;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=906122db8f0e2fbe56115275fae416f255a27ebc;hpb=385e63c78d289d4beae9c1ad2b187c0ea311ffbc;p=jalview.git diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index 906122d..a949888 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -1,3 +1,20 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . + */ package jalview.datamodel.xdb.embl; import jalview.datamodel.DBRefEntry; @@ -247,8 +264,8 @@ 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. @@ -372,7 +389,6 @@ 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 @@ -387,15 +403,23 @@ public class EmblEntry */ 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 + 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 @@ -434,8 +458,7 @@ public class EmblEntry } } } - } - catch (Exception e) + } catch (Exception e) { System.err.println("EMBL Record Features parsing error!"); System.err @@ -458,14 +481,22 @@ public class EmblEntry } /** - * 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 + * 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) + private void parseCodingFeature(EmblFeature feature, String sourceDb, + Vector seqs, Sequence dna, boolean noPeptide) { boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS); // extract coding region(s) @@ -533,19 +564,30 @@ public class EmblEntry else { // throw anything else into the additional properties hash - vals.put(q.getName(), q.getValues().toString()); + 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; + exon = adjustForPrStart(prstart, exon); + if (prseq != null && prname != null && prid != null) { // extract proteins. - product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid - +((prname.length()==0) ? "" : " " + prname), prseq, prstart, prstart - + prseq.length() - 1); - product.setDescription("Protein Product from " + sourceDb); - + 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 @@ -558,50 +600,64 @@ public class EmblEntry 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) + 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(), dna.getEnd() }; - map = new jalview.datamodel.Mapping(product, exon, - new int[] - { prstart, prstart + prseq.length() - 1 }, 3, 1); + { 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 == dna.getSequence().length) + 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(), dna.getEnd() - 3 }; - map = new jalview.datamodel.Mapping(product, exon, - new int[] - { prstart, prstart + prseq.length() - 1 }, 3, 1); + { 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 { - map = new jalview.datamodel.Mapping(product, exon, - new int[] - { prstart, prstart + prseq.length() - 1 }, 3, 1); + // 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+(prstart-1)*3, 1+(prstart-1)*3 + (prseq.length()-1)*3 }, new int[] { prstart, prstart+prseq.length() - 1 }, 3, 1); + { 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) + if (product != null) product.addDBRef(pcdnaref); - + } } // add cds feature to dna seq - this may include the stop codon @@ -612,8 +668,8 @@ public class EmblEntry sf.setEnd(exon[xint + 1]); sf.setType(feature.getName()); sf.setFeatureGroup(sourceDb); - sf.setDescription("Exon " + (1 + xint) + " for protein '" - + prname + "' EMBLCDS:" + prid); + sf.setDescription("Exon " + (1 + (int) (xint / 2)) + + " for protein '" + prname + "' EMBLCDS:" + prid); sf.setValue(FeatureProperties.EXONPOS, new Integer(1 + xint)); sf.setValue(FeatureProperties.EXONPRODUCT, prname); if (vals != null && vals.size() > 0) @@ -638,29 +694,36 @@ public class EmblEntry 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)) + if (ref.getSource().equals(jalview.datamodel.DBRefSource.UNIPROT)) { ref.setMap(map); - /*if (map.getTo()!=null) + if (map != null && map.getTo() != null) { - map.getTo().setName(map.getTo().getName()+"|"+ref.getSource()+"|"+ref.getAccessionId()); - }*/ + 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()); + 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 = new DBRefEntry(sourceDb, getVersion(), + this.getAccession()); pref.setMap(pmap); - if (map.getTo()!=null) + if (map.getTo() != null) { map.getTo().addDBRef(pref); } @@ -670,4 +733,91 @@ public class EmblEntry } } } + + 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) + { + 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; + } + } + 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) + { + 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 exon; + } }