/*
- * 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 2.8.2)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
{ 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()))
+ {
;
+ }
+ }
}
try
{
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
{
for (Iterator dbr = feature.dbRefs.iterator(); dbr.hasNext(); dna
.addDBRef((DBRefEntry) dbr.next()))
+ {
;
+ }
}
}
}
}
}
Sequence product = null;
- int origxon[], sxpos = -1, sxstart, sxstop;
- // 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;
- }
- }
+ exon = adjustForPrStart(prstart, exon);
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
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... !");
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!");
}
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[]
- { 1, prseq.length() }, 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, prseq.length() },
- new int[]
- { 1 + (prstart - 1),
- (prstart - 1) + 3 * prseq.length() }, 1, 3);
+ { 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);
+ }
}
}
sf.setEnd(exon[xint + 1]);
sf.setType(feature.getName());
sf.setFeatureGroup(sourceDb);
- sf.setDescription("Exon " + (1 + (int) (xint / 2))
+ 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)
{
- Enumeration kv = vals.elements();
+ Enumeration kv = vals.keys();
while (kv.hasMoreElements())
{
Object key = kv.nextElement();
if (key != null)
+ {
sf.setValue(key.toString(), vals.get(key));
+ }
}
}
dna.addSequenceFeature(sf);
}
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