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revision 1.37, Tue Feb 20 13:37:32 2007 UTC revision 1.38, Tue Feb 20 19:06:36 2007 UTC
# Line 353  Line 353 
353          my %in_ali = map { $_->[0] => 1 } @$ali;          my %in_ali = map { $_->[0] => 1 } @$ali;
354          foreach $seq (grep { ! $in_ali{$_->[0]} } @$seqs)          foreach $seq (grep { ! $in_ali{$_->[0]} } @$seqs)
355          {          {
356              print STDERR "adding $seq->[0] to alignment\n";  #            print STDERR "adding $seq->[0] to alignment\n";
357              $ali     = &gjoalignment::add_to_alignment($seq,$ali,1);              $ali     = &gjoalignment::add_to_alignment($seq,$ali,1);
358              &gjoseqlib::print_alignment_as_fasta("$ali_file.last",$ali);              &gjoseqlib::print_alignment_as_fasta("$ali_file.last",$ali);
359          }          }
360    
361            if (! -s "$ali_file.last")
362            {
363                &gjoseqlib::print_alignment_as_fasta($ali_file,$ali);
364            }
365            else
366            {
367          rename("$ali_file.last",$ali_file);          rename("$ali_file.last",$ali_file);
368      }      }
369        }
370    
371      if (! -s "$dir/built") { system "echo 1 > $dir/built" }      if (! -s "$dir/built") { system "echo 1 > $dir/built" }
372      bless $fam,$class;      bless $fam,$class;

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