String outputHeader = String.format("%s of %s%nJob details%n",
submitGaps ? "Re-alignment" : "Alignment", alnTitle);
SequenceI[][] conmsa = msa.getVisibleContigs('-');
String outputHeader = String.format("%s of %s%nJob details%n",
submitGaps ? "Re-alignment" : "Alignment", alnTitle);
SequenceI[][] conmsa = msa.getVisibleContigs('-');