X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=31efd8497f96b8da4ccfafbfeef31689b7930367;hb=dea32f71ff7f8a80cc8494864b6605921d81fafa;hp=65090633a7106c72f9949972e99913fc339258e9;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 6509063..31efd84 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -77,7 +77,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                         (SequenceI) selsubset.elementAt(j), "pep");
                 as.calcScoreMatrix();
                 as.traceAlignment();
-                as.printAlignment();
+                as.printAlignment(System.out);
                 scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
                 totscore = totscore + scores[i][j];