/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * 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.
*
- * 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
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel.xdb.embl;
/**
* @param accession
- * the accession to set
+ * the accession to set
*/
public void setAccession(String accession)
{
/**
* @param dbRefs
- * the dbRefs to set
+ * the dbRefs to set
*/
public void setDbRefs(Vector dbRefs)
{
/**
* @param desc
- * the desc to set
+ * the desc to set
*/
public void setDesc(String desc)
{
/**
* @param features
- * the features to set
+ * the features to set
*/
public void setFeatures(Vector features)
{
/**
* @param keywords
- * the keywords to set
+ * the keywords to set
*/
public void setKeywords(Vector keywords)
{
/**
* @param lastUpdated
- * the lastUpdated to set
+ * the lastUpdated to set
*/
public void setLastUpdated(String lastUpdated)
{
/**
* @param refs
- * the refs to set
+ * the refs to set
*/
public void setRefs(Vector refs)
{
/**
* @param releaseCreated
- * the releaseCreated to set
+ * the releaseCreated to set
*/
public void setRcreated(String releaseCreated)
{
/**
* @param releaseLastUpdated
- * the releaseLastUpdated to set
+ * the releaseLastUpdated to set
*/
public void setRLastUpdated(String releaseLastUpdated)
{
/**
* @param sequence
- * the sequence to set
+ * the sequence to set
*/
public void setSequence(EmblSequence sequence)
{
/**
* @param taxDivision
- * the taxDivision to set
+ * the taxDivision to set
*/
public void setTaxDivision(String taxDivision)
{
/**
* @param version
- * the version to set
+ * the version to set
*/
public void setVersion(String 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
+ * 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.
*
* 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
+ * don't return nucleic acid sequences
* @param sourceDb
- * TODO
+ * TODO
* @param noProtein
- * don't return any translated protein sequences marked in
- * features
+ * 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,
// 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
* decorate it with annotations.
*
* @param feature
- * coding feature
+ * coding feature
* @param sourceDb
- * source database for the EMBLXML
+ * source database for the EMBLXML
* @param seqs
- * place where sequences go
+ * place where sequences go
* @param dna
- * parent dna sequence for this record
+ * parent dna sequence for this record
* @param noPeptide
- * flag for generation of Peptide sequence objects
+ * flag for generation of Peptide sequence objects
*/
private void parseCodingFeature(EmblFeature feature, String sourceDb,
Vector seqs, Sequence dna, boolean noPeptide)
}
}
Sequence product = null;
+ exon = adjustForPrStart(prstart, exon);
+
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));
-
+ 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
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() };
+ { dna.getStart() + (prstart - 1), dna.getEnd() };
map = new jalview.datamodel.Mapping(product, exon, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ { 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 };
+ { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
map = new jalview.datamodel.Mapping(product, exon, new int[]
- { prstart, prstart + prseq.length() - 1 }, 3, 1);
+ { 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
}
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)
product.addDBRef(pcdnaref);
}
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)
{
}
}
}
+
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff