/**
* Set the region of sequence space to draw
*
* @param oneMin
* @param oneMax
* @param twoMin
* @param twoMax
*/
public void setSequenceBounds(int oneMin, int oneMax, int twoMin, int twoMax) {
sequenceOneMin = Math.max(oneMin, 0);
sequenceTwoMin = Math.max(twoMin, 0);
sequenceOneMax = Math.min(oneMax, sequenceOne.length());
sequenceTwoMax = Math.min(twoMax, sequenceTwo.length());
redrawImage = true;
}
/**
* Recompute the substring buffers, this needs to happen anytime the sequences are changed or the
* block width changes...and results in a tiny speedup
*/
private void recalcSubstrs() {
substrs1.clear();
substrs2.clear();
for (int i = 0; i < Math.min(sequenceOne.length(), sequenceTwo.length()); i++) {
substrs1.add(
sequenceOne.toString().substring(i, Math.min(i + blockWidth, sequenceOne.length())));
substrs2.add(
sequenceTwo.toString().substring(i, Math.min(i + blockWidth, sequenceTwo.length())));
}
}
public void setSequences(Sequence seq1, Sequence seq2) {
sequenceOne = seq1;
sequenceTwo = seq2;
int minLength = Math.min(seq1.length(), seq2.length());
sequenceOneMin = 0;
sequenceTwoMin = 0;
sequenceOneMax = minLength;
sequenceTwoMax = minLength;
recalcSubstrs();
redrawImage = true;
}
/**
* Returns the amino acid that corresponds to the codon beginning at site i in this sequence
*
* @param sequence
* @param site
* @return
*/
public AminoAcid translate(Sequence sequence, int site) {
if (site >= (sequence.length() - 2)) {
throw new IllegalArgumentException(
"Cannot translate codon site #"
+ site
+ " because sequence is only "
+ sequence.length()
+ " sites long.");
} else {
AminoAcid aa = translate(sequence.toString().substring(site, site + 3));
if (aa == null) {
System.out.println(
"Cannot translate codon :" + sequence.toString().substring(site, site + 3));
}
return aa;
}
}