- memf += r.totalMemory()-r.freeMemory();
- System.out.println("Read took "+(t1/1000.0)+" seconds.");
- System.out.println("Difference between free memory now and before is "+(memf/(1024.0*1024.0)*1.0)+" MB");
-
+ memf += r.totalMemory() - r.freeMemory();
+ if (al != null)
+ {
+ System.out.println("Alignment contains " + al.getHeight()
+ + " sequences and " + al.getWidth() + " columns.");
+ try {
+ System.out.println(new AppletFormatAdapter().formatSequences("FASTA", al, true));
+ } catch (Exception e)
+ {
+ System.err.println("Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
+ }
+ }
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+ System.out
+ .println("Difference between free memory now and before is "
+ + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
+