[Bio] / WebApplication / WebPage / AlignSeqsClustal.pm Repository:
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revision 1.1, Thu Mar 5 13:02:55 2009 UTC revision 1.2, Fri Mar 13 11:28:28 2009 UTC
# Line 100  Line 100 
100    $self->{ 'color_aln_by' } = $self->{ 'cgi' }->param( 'color_aln_by' ) || 'consensus';    $self->{ 'color_aln_by' } = $self->{ 'cgi' }->param( 'color_aln_by' ) || 'consensus';
101    $self->{ 'seq_format' }   = $self->{ 'cgi' }->param( 'seq_format' ) || 'protein';    $self->{ 'seq_format' }   = $self->{ 'cgi' }->param( 'seq_format' ) || 'protein';
102    
103      if ( $self->{ 'seq_format' } eq 'pre' ) {
104        my $firstp = $self->{ 'cgi' }->param( 'firstpoint' );
105        my $secondp = $self->{ 'cgi' }->param( 'secondpoint' );
106        if ( defined( $firstp ) && $firstp =~ /^-?\d+$/ ) {
107          $self->{ 'seq_format' } .= "_$firstp";
108        }
109        if ( defined( $secondp ) && $secondp =~ /^-?\d+$/ ) {
110          $self->{ 'seq_format' } .= "_$secondp";
111        }
112      }
113    
114    #########    #########
115    # TASKS #    # TASKS #
116    #########    #########
# Line 257  Line 268 
268    
269    my $tree = clustaltree::tree_with_clustal( \@align );    my $tree = clustaltree::tree_with_clustal( \@align );
270    my $treecont;    my $treecont;
271    if ( $self->{ 'tree_format' } eq 'newick' ) {    if ( defined( $self->{ 'tree_format' } ) && $self->{ 'tree_format' } eq 'newick' ) {
272      $treecont .= &gjonewicklib::formatNewickTree( $tree );      $treecont .= &gjonewicklib::formatNewickTree( $tree );
273    }    }
274    elsif ( $self->{ 'tree_format' } eq 'normal' ) {    elsif ( defined( $self->{ 'tree_format' } ) && $self->{ 'tree_format' } eq 'normal' ) {
275      $treecont = $self->construct_tree( \@seqs, $tree );      $treecont = $self->construct_tree( \@seqs, $tree );
276    }    }
277    else {    else {
# Line 1273  Line 1284 
1284    my $checked_newick = '';    my $checked_newick = '';
1285    my $checked_normal = '';    my $checked_normal = '';
1286    my $checked_notree = '';    my $checked_notree = '';
1287    if ( $self->{ 'tree_format' } eq 'newick' ) {    if ( defined( $self->{ 'tree_format' } ) && $self->{ 'tree_format' } eq 'newick' ) {
1288      $checked_newick = 'CHECKED';      $checked_newick = 'CHECKED';
1289    }    }
1290    elsif ( $self->{ 'tree_format' } eq 'normal' ) {    elsif ( defined( $self->{ 'tree_format' } ) && $self->{ 'tree_format' } eq 'normal' ) {
1291      $checked_normal = 'CHECKED';      $checked_normal = 'CHECKED';
1292    }    }
1293    else {    else {

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