private void constructPatterns() {
patterns.clear();
State[][] seqs = new State[sequences.size()][];
int i = 0;
int maxLen = 0;
for (Sequence seq : getSequenceList()) {
seqs[i] = seq.getStates();
if (seqs[i].length > maxLen) {
maxLen = seqs[i].length;
}
i++;
}
for (int j = 0; j < maxLen; j++) {
List<State> states = new ArrayList<State>();
for (i = 0; i < seqs.length; i++) {
if (j < seqs[i].length) {
states.add(seqs[i][j]);
} else {
states.add(sequenceType.getGapState());
}
}
patterns.add(new BasicPattern(states));
}
}
private void put(Sequence sequence) {
if (sequenceType == null) {
sequenceType = sequence.getSequenceType();
}
if (sequenceType != sequence.getSequenceType()) {
throw new IllegalArgumentException(
"Type of sequence "
+ sequence.getTaxon().getName()
+ " does not match that of other sequences in the alignment"
+ " (data type = "
+ sequence.getSequenceType().getName()
+ ", but expected "
+ sequenceType.getName()
+ ").");
}
if (taxonList.indexOf(sequence.getTaxon()) >= 0) {
throw new IllegalArgumentException("duplicate sequence name " + sequence.getTaxon());
}
sequences.put(sequence.getTaxon(), sequence);
taxonList.add(sequence.getTaxon());
}