(SequenceI) selsubset.elementAt(j), "pep");\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
- as.printAlignment();\r
+ as.printAlignment(System.out);\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
totscore = totscore + scores[i][j];\r
\r