/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
{
SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
viscontigs, codons, gapCharacter,
- (product != null) ? product[s] : null, false); // possibly anonymous
+ (product != null) ? product[s] : null, false); // possibly
+ // anonymous
// product
if (newseq != null)
{
* Definition of global ORF alignment reference frame
* @param gapCharacter
* @return sequence ready to be added to alignment.
- * @deprecated Use {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)} instead
+ * @deprecated Use
+ * {@link #translateCodingRegion(SequenceI,String,int[],AlignedCodonFrame,char,DBRefEntry,boolean)}
+ * instead
*/
public static SequenceI translateCodingRegion(SequenceI selection,
String seqstring, int[] viscontigs, AlignedCodonFrame codons,
* @param codons
* Definition of global ORF alignment reference frame
* @param gapCharacter
- * @param starForStop when true stop codons will translate as '*', otherwise as 'X'
+ * @param starForStop
+ * when true stop codons will translate as '*', otherwise as 'X'
* @return sequence ready to be added to alignment.
*/
public static SequenceI translateCodingRegion(SequenceI selection,
// edit scontigs
skipint[0] = vismapping.shift(skipint[0]);
skipint[1] = vismapping.shift(skipint[1]);
- for (vc = 0; vc < scontigs.length; )
+ for (vc = 0; vc < scontigs.length;)
{
if (scontigs[vc + 1] < skipint[0])
{
vc += 2;
continue;
}
- if (scontigs[vc]>skipint[1])
+ if (scontigs[vc] > skipint[1])
{
// finished editing so
break;
}
- // Edit the contig list to include the skipped region which did not translate
+ // Edit the contig list to include the skipped region which did
+ // not translate
int[] t;
// from : s1 e1 s2 e2 s3 e3
- // to s: s1 e1 s2 k0 k1 e2 s3 e3
- // list increases by one unless one boundary (s2==k0 or e2==k1) matches, and decreases by one if skipint intersects whole visible contig
+ // to s: s1 e1 s2 k0 k1 e2 s3 e3
+ // list increases by one unless one boundary (s2==k0 or e2==k1)
+ // matches, and decreases by one if skipint intersects whole
+ // visible contig
if (scontigs[vc] <= skipint[0])
{
if (skipint[0] == scontigs[vc])
if (scontigs[vc + 1] > skipint[1])
{
scontigs[vc] = skipint[1];
- vc+=2;
+ vc += 2;
}
else
{
- if (scontigs[vc+1]==skipint[1])
+ if (scontigs[vc + 1] == skipint[1])
{
// remove the contig
t = new int[scontigs.length - 2];
if (vc + 2 < t.length)
{
System.arraycopy(scontigs, vc + 2, t, vc, t.length
- - vc + 2);
+ - vc + 2);
}
- scontigs=t;
- } else {
+ scontigs = t;
+ }
+ else
+ {
// truncate contig to before the skipint region
- scontigs[vc+1] = skipint[0]-1;
- vc+=2;
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
}
}
}
else
{
// scontig starts before start of skipint
- if (scontigs[vc+1]<skipint[1]) {
+ if (scontigs[vc + 1] < skipint[1])
+ {
// skipint truncates end of scontig
- scontigs[vc+1] = skipint[0]-1;
- vc+=2;
- } else {
+ scontigs[vc + 1] = skipint[0] - 1;
+ vc += 2;
+ }
+ else
+ {
// divide region to new contigs
t = new int[scontigs.length + 2];
- System.arraycopy(scontigs, 0, t, 0, vc +1);
- t[vc+1] = skipint[0];
- t[vc+2] = skipint[1];
- System.arraycopy(scontigs, vc + 1, t, vc+3, scontigs.length-(vc+1));
- scontigs=t;
- vc+=4;
+ System.arraycopy(scontigs, 0, t, 0, vc + 1);
+ t[vc + 1] = skipint[0];
+ t[vc + 2] = skipint[1];
+ System.arraycopy(scontigs, vc + 1, t, vc + 3,
+ scontigs.length - (vc + 1));
+ scontigs = t;
+ vc += 4;
}
}
}
protein.toString());
if (rf != 0)
{
- if (jalview.bin.Cache.log!=null) {
- jalview.bin.Cache.log.debug("trimming contigs for incomplete terminal codon.");
- } else {
- System.err.println("trimming contigs for incomplete terminal codon.");
+ if (jalview.bin.Cache.log != null)
+ {
+ jalview.bin.Cache.log
+ .debug("trimming contigs for incomplete terminal codon.");
+ }
+ else
+ {
+ System.err
+ .println("trimming contigs for incomplete terminal codon.");
}
// map and trim contigs to ORF region
vc = scontigs.length - 1;
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
MapList map, Hashtable featureTypes, Hashtable featureGroups)
{
- SequenceFeature[] sf = (dna.getDatasetSequence()!=null ? dna.getDatasetSequence() : dna).getSequenceFeatures();
+ SequenceFeature[] sf = (dna.getDatasetSequence() != null ? dna
+ .getDatasetSequence() : dna).getSequenceFeatures();
Boolean fgstate;
jalview.datamodel.DBRefEntry[] dnarefs = jalview.util.DBRefUtils
.selectRefs(dna.getDBRef(),
git://source.jalview.org / jalview.git / blobdiff