compbio.data.sequence.FastaSequence seq;
for (int i = 0, n = 0; i < seqs.length; i++)
{
compbio.data.sequence.FastaSequence seq;
for (int i = 0, n = 0; i < seqs.length; i++)
{
if (preset != null && preset instanceof JabaWsParamSet)
{
newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
if (preset != null && preset instanceof JabaWsParamSet)
{
newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
String lastProgram = null;
SequenceI[][] results = new SequenceI[jobs.length][];
AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
String lastProgram = null;
for (int i = 0, l = alorders.size(); i < l; i++)
{
String orderName = " Region " + i;
for (int i = 0, l = alorders.size(); i < l; i++)
{
String orderName = " Region " + i;