{
if ((i + (j * len)) < astr1.length())
{
- if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
+ boolean sameChar = Comparison.compareChars(
+ astr1.charAt(i + (j * len)), astr2.charAt(i + (j * len)),
+ false);
+ if (sameChar
&& !jalview.util.Comparison.isGap(astr1.charAt(i
+ (j * len))))
{
}
pid = pid / (aseq1.length - count) * 100;
- output = output.append(new Format("Percentage ID = %2.2f\n")
- .form(pid));
+ output = output.append(new Format("Percentage ID = %2.2f\n").form(pid));
try
{
os.print(output.toString());