/*
- * 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 2.6)
+ * Copyright (C) 2010 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;
}
Sequence product = null;
exon = adjustForPrStart(prstart, exon);
-
+
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
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)
-
-
+ // 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
{
// 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);
+ { 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);
}
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
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)
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;
}
}
git://source.jalview.org / jalview.git / blobdiff