boolean ungapped[] = new boolean[sequences.length];
int msflen=0;
for (int i=0,j=sequences.length; i<j;i++) {
- String tempseq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequences[i].getSequence());
+ String tempseq = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ sequences[i].getSequenceAsString());
+
if (tempseq.length()==0)
ungapped[i]=false;
else {