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revision 1.1, Wed Oct 27 16:21:57 2010 UTC revision 1.2, Wed Nov 10 16:55:24 2010 UTC
# Line 20  Line 20 
20    
21  use ERDB;  use ERDB;
22  use Tracer;  use Tracer;
 use SeedUtils;  
 use ServerThing;  
23    
24  use gjoalignment;  use gjoalignment;
25    
26    use AlignTree;
27    use SeedUtils;
28    use ServerThing;
29    
30  sub new {  sub new {
31      my ($class) = @_;      my ($class) = @_;
32      # Create the sapling object.      # Create the sapling object.
# Line 41  Line 43 
43    
44  use constant METHODS => [qw(  use constant METHODS => [qw(
45                              align_seqs                              align_seqs
46                                trim_ali
47                             )];                             )];
48    
49  sub methods {  sub methods {
# Line 49  Line 52 
52  }  }
53    
54  sub align_seqs {  sub align_seqs {
55      my ($self, $args) = @_;      my ($self, $opts) = @_;
56      my $rv;      my $ali = AlignTree::align_sequences($opts);
57        return { rv => $ali };
     my $program = \&align_with_clustal;  
     if ($args->{tool} =~ /muscle/i) {  
         $program = \&align_with_muscle;  
         $args->{muscle} = "/home/fangfang/bin/muscle";  
     } elsif ($args->{tool} =~ /mafft/i) {  
         $program = \&align_with_mafft;  
         $args->{mafft} = "/home/fangfang/bin/mafft";  
58      }      }
59    
60      $rv->{rv} = $program->($args->{seqs}, $args);  sub trim_ali {
61      $rv->{args} = $args;      my ($self, $opts) = @_;
62      return $rv;      my $trim = AlignTree::trim_alignment($opts);
63        return { rv => $trim };
64  }  }
65    
66  1;  1;

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