{
return false;
}
- char[][] letters = new char[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
- {
- if (seqs[i] != null)
- {
- char[] sequence = seqs[i].getSequence();
- if (sequence != null)
- {
- letters[i] = sequence;
- }
- }
- }
-
- return areNucleotide(letters);
- }
- /**
- * Answers true if more than 85% of the sequence residues (ignoring gaps) are
- * A, G, C, T or U, else false. This is just a heuristic guess and may give a
- * wrong answer (as AGCT are also amino acid codes).
- *
- * @param letters
- * @return
- */
- static final boolean areNucleotide(char[][] letters)
- {
int ntCount = 0;
int aaCount = 0;
- for (char[] seq : letters)
+ for (SequenceI seq : seqs)
{
if (seq == null)
{
}
// TODO could possibly make an informed guess just from the first sequence
// to save a lengthy calculation
- for (char c : seq)
+ int len = seq.getLength();
+ for (int i = 0; i < len; i++)
{
+ char c = seq.getCharAt(i);
if (isNucleotide(c))
{
ntCount++;