/**\r
* DOCUMENT ME!\r
*/\r
- public void printAlignment()\r
+ public void printAlignment(java.io.PrintStream os)\r
{\r
// Find the biggest id length for formatting purposes\r
int maxid = s1.getName().length();\r
pid = pid / (float) (aseq1.length - count) * 100;\r
output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));\r
\r
- System.out.println(output.toString());\r
+ try{\r
+ os.println(output.toString());\r
+ }catch(Exception ex){}\r
}\r
\r
/**\r