/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
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)
{
}
try
{
- for (EmblFeature feature: features)
+ for (EmblFeature feature : features)
{
if (!noNa)
{
.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))
{
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
// final product length trunctation check
map = new jalview.datamodel.Mapping(product,
- adjustForProteinLength(prseq.length(), exon), new int[]
- { 1, prseq.length() }, 3, 1);
+ 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)
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);