* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
* allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
*/
int truePos = sequencePos - (start - 1);
for (int i = 0, v = 0; i < frange.length; i += 2, v++)
{
vf[v] = new SequenceFeature(f, frange[i], frange[i + 1],
for (int i = 0, v = 0; i < frange.length; i += 2, v++)
{
vf[v] = new SequenceFeature(f, frange[i], frange[i + 1],
- copy.setMap(new MapList(from, to, map.getFromRatio(), map
- .getToRatio()));
+ copy.setMap(
+ new MapList(from, to, map.getFromRatio(), map.getToRatio()));
/**
* Returns an iterator which can serve up the aligned codon column positions
* and their corresponding peptide products
/**
* Returns an iterator which can serve up the aligned codon column positions
* and their corresponding peptide products
- return String.format("%s %s", this.map.toString(), this.to == null ? ""
- : this.to.getName());
+ return String.format("%s %s", this.map.toString(),
+ this.to == null ? "" : this.to.getName());