/* only call on an exon position */
private char getPeptide(int bp, SeqFeatureI sf) {
char base = '\0';
SequenceI peptides = null;
FeatureSetI parent = sf.getParent();
int pepPos = -1;
if (parent != null && parent.hasPeptideSequence()) {
peptides = parent.getPeptideSequence();
if (parent instanceof FeatureSet) {
FeatureSet fs = (FeatureSet) parent;
pepPos = fs.getPeptidePosForGenomicPos(bp);
}
if (pepPos >= 0 && pepPos < peptides.getLength()) {
base = peptides.getBaseAt(pepPos);
}
}
return base;
}
private boolean isShiftPosition(int bp, SeqFeatureI feature, SequenceType type) {
boolean result = false;
// Can shifts only happen on exons?
if (feature != null) {
FeatureSet fs = (FeatureSet) feature.getRefFeature();
result = fs.plus1FrameShiftPosition() == bp || fs.minus1FrameShiftPosition() == bp;
if (type == SequenceType.AA) {
bp += feature.getStrand();
result =
result || fs.plus1FrameShiftPosition() == bp || fs.minus1FrameShiftPosition() == bp;
}
if (type == SequenceType.AA) {
bp += feature.getStrand();
result =
result || fs.plus1FrameShiftPosition() == bp || fs.minus1FrameShiftPosition() == bp;
}
}
return result;
}