X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblEntry.java;h=a1bf4525d9e779e4b81907da93c89c0e61163ba6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=2ee1fb2f6f2906cb44d3f170b22979e4b9ac2a66;hpb=5ecedaaa568fc4a32ea18e892249b35106ed023f;p=jalview.git diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index 2ee1fb2..a1bf452 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -1,20 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel.xdb.embl; @@ -26,11 +28,18 @@ 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; @@ -47,13 +56,11 @@ public class EmblEntry String lastUpdated; - Vector keywords; - - Vector refs; + Vector keywords; - Vector dbRefs; + Vector dbRefs; - Vector features; + Vector features; EmblSequence sequence; @@ -77,7 +84,7 @@ public class EmblEntry /** * @return the dbRefs */ - public Vector getDbRefs() + public Vector getDbRefs() { return dbRefs; } @@ -86,7 +93,7 @@ public class EmblEntry * @param dbRefs * the dbRefs to set */ - public void setDbRefs(Vector dbRefs) + public void setDbRefs(Vector dbRefs) { this.dbRefs = dbRefs; } @@ -111,7 +118,7 @@ public class EmblEntry /** * @return the features */ - public Vector getFeatures() + public Vector getFeatures() { return features; } @@ -120,7 +127,7 @@ public class EmblEntry * @param features * the features to set */ - public void setFeatures(Vector features) + public void setFeatures(Vector features) { this.features = features; } @@ -128,7 +135,7 @@ public class EmblEntry /** * @return the keywords */ - public Vector getKeywords() + public Vector getKeywords() { return keywords; } @@ -137,7 +144,7 @@ public class EmblEntry * @param keywords * the keywords to set */ - public void setKeywords(Vector keywords) + public void setKeywords(Vector keywords) { this.keywords = keywords; } @@ -160,23 +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() @@ -188,7 +178,7 @@ public class EmblEntry * @param releaseCreated * the releaseCreated to set */ - public void setRcreated(String releaseCreated) + public void setRCreated(String releaseCreated) { this.rCreated = releaseCreated; } @@ -406,7 +396,7 @@ public class EmblEntry boolean noPeptide, String sourceDb) { // TODO: ensure emblEntry.getSequences behaves correctly for returning all // cases of noNa and noPeptide - Vector seqs = new Vector(); + Vector seqs = new Vector(); Sequence dna = null; if (!noNa) { @@ -418,27 +408,30 @@ public class EmblEntry 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)); + 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) { - 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 (FeatureProperties.isCodingFeature(sourceDb, feature.getName())) @@ -448,13 +441,15 @@ public class EmblEntry else { // General feature type. + // TODO this is just duplicated code ?? 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); + } } } } @@ -475,7 +470,7 @@ public class EmblEntry SequenceI[] sqs = new SequenceI[seqs.size()]; for (int i = 0, j = seqs.size(); i < j; i++) { - sqs[i] = (SequenceI) seqs.elementAt(i); + sqs[i] = seqs.elementAt(i); seqs.set(i, null); } return sqs; @@ -497,19 +492,16 @@ public class EmblEntry * flag for generation of Peptide sequence objects */ private void parseCodingFeature(EmblFeature feature, String sourceDb, - Vector seqs, Sequence dna, boolean noPeptide) + 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) + if (feature.locations != null) { - for (Enumeration locs = feature.locations.elements(); locs - .hasMoreElements();) + for (EmblFeatureLocations loc : feature.locations) { - EmblFeatureLocations loc = (EmblFeatureLocations) locs - .nextElement(); int[] se = loc.getElementRanges(accession); if (exon == null) { @@ -527,19 +519,17 @@ public class EmblEntry String prseq = null; String prname = new String(); String prid = null; - Hashtable vals = new Hashtable(); + Hashtable vals = new Hashtable(); int prstart = 1; // get qualifiers - if (feature.getQualifiers() != null - && feature.getQualifiers().size() > 0) + if (feature.getQualifiers() != null) { - for (Iterator quals = feature.getQualifiers().iterator(); quals - .hasNext();) + for (Qualifier q : feature.getQualifiers()) { - Qualifier q = (Qualifier) quals.next(); - if (q.getName().equals("translation")) + String qname = q.getName(); + if (qname.equals("translation")) { - StringBuffer prsq = new StringBuffer(q.getValues()[0]); + StringBuilder prsq = new StringBuilder(q.getValues()[0]); int p = prsq.indexOf(" "); while (p > -1) { @@ -550,15 +540,15 @@ public class EmblEntry prsq = null; } - else if (q.getName().equals("protein_id")) + else if (qname.equals("protein_id")) { prid = q.getValues()[0]; } - else if (q.getName().equals("codon_start")) + else if (qname.equals("codon_start")) { prstart = Integer.parseInt(q.getValues()[0]); } - else if (q.getName().equals("product")) + else if (qname.equals("product")) { prname = q.getValues()[0]; } @@ -566,7 +556,7 @@ public class EmblEntry { // throw anything else into the additional properties hash String[] s = q.getValues(); - StringBuffer sb = new StringBuffer(); + StringBuilder sb = new StringBuilder(); if (s != null) { for (int i = 0; i < s.length; i++) @@ -575,21 +565,22 @@ public class EmblEntry sb.append("\n"); } } - vals.put(q.getName(), sb.toString()); + 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)); + product.setDescription(((prname.length() == 0) ? "Protein Product from " + + sourceDb + : prname)); if (!noPeptide) { // Protein is also added to vector of sequences returned @@ -602,32 +593,31 @@ 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 == (1-prstart + 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() + (prstart - 1), dna.getEnd() }; - map = new jalview.datamodel.Mapping(product, exon, new int[] - { 1, prseq.length() }, 3, 1); + 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)) + 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); + 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) - - + // 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 @@ -639,26 +629,32 @@ public class EmblEntry else { // final product length trunctation check - - map = new jalview.datamodel.Mapping(product, adjustForProteinLength(prseq.length(),exon), new int[] - { 1, prseq.length() }, 3, 1); + + 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) + // 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); + 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); + + } } } @@ -670,29 +666,25 @@ public class EmblEntry sf.setEnd(exon[xint + 1]); sf.setType(feature.getName()); sf.setFeatureGroup(sourceDb); - sf.setDescription("Exon " + (1 + (int) (xint / 2)) - + " for protein '" + prname + "' EMBLCDS:" + prid); + 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 && vals.size() > 0) + if (vals != null) { - Enumeration kv = vals.elements(); - while (kv.hasMoreElements()) + for (Entry val : vals.entrySet()) { - Object key = kv.nextElement(); - if (key != null) - sf.setValue(key.toString(), vals.get(key)); + sf.setValue(val.getKey(), val.getValue()); } } dna.addSequenceFeature(sf); } } // add dbRefs to sequence - if (feature.dbRefs != null && feature.dbRefs.size() > 0) + if (feature.dbRefs != null) { - for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext();) + for (DBRefEntry ref : feature.dbRefs) { - DBRefEntry ref = (DBRefEntry) dbr.next(); ref.setSource(jalview.util.DBRefUtils.getCanonicalName(ref .getSource())); // Hard code the kind of protein product accessions that EMBL cite @@ -711,19 +703,20 @@ public class EmblEntry + ref.getAccessionId()); } } + noProteinDbref = false; } 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) { @@ -733,6 +726,33 @@ public class EmblEntry } 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); + } + } + } } } @@ -770,8 +790,10 @@ public class EmblEntry } return exon; } + /** - * truncate the last exon interval to the prlength'th codon + * truncate the last exon interval to the prlength'th codon + * * @param prlength * @param exon * @return new exon @@ -779,15 +801,15 @@ public class EmblEntry private int[] adjustForProteinLength(int prlength, int[] exon) { - int origxon[], sxpos = -1,endxon=0,cdslength=prlength*3; + 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) + 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) + for (int x = 0; x < exon.length && sxpos == -1; x += 2) { cdspos += exon[x + 1] - exon[x] + 1; if (cdslength <= cdspos) @@ -796,21 +818,25 @@ public class EmblEntry sxpos = x; sxstart = exon[x]; sxstop = exon[x + 1]; - if (cdslength!=cdspos) { - System.err.println("Truncating final exon interval on region by "+(cdspos-cdslength)); + 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; + endxon = exon[x + 1] - cdspos + cdslength; break; } } - if (sxpos !=-1) + 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 + 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; } }