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revision 1.33, Wed Aug 4 19:42:10 2004 UTC revision 1.34, Wed Aug 4 23:00:05 2004 UTC
# Line 1  Line 1 
1    # -*- perl -*-
2    
3  use FIG;  use FIG;
4  my $fig = new FIG;  my $fig = new FIG;
# Line 2138  Line 2139 
2139          push(@$html,"<pre>\n");          push(@$html,"<pre>\n");
2140          my %org = map { ( $_, $fig->org_of($_) ) } @checked;          my %org = map { ( $_, $fig->org_of($_) ) } @checked;
2141          #  Modified by GJO to compress tree and add organism names to tree:          #  Modified by GJO to compress tree and add organism names to tree:
2142          #  push(@$html,`$FIG_Config::bin/align_with_clustal -tree \'$checked\'`);          #  push(@$html,`$FIG_Config::bin/align_with_clustal -org -func -tree \'$checked\'`);
2143    
2144          #  Simpler version          #  Simpler version
2145          # push @$html, map { chomp;          # push @$html, map { chomp;
# Line 2147  Line 2148 
2148          #                    : /- ([a-z]+\|\S+):/ && defined( $org{$1} ) # tree id?          #                    : /- ([a-z]+\|\S+):/ && defined( $org{$1} ) # tree id?
2149          #                    ? "$_ [$org{$1}]\n"  # add the name          #                    ? "$_ [$org{$1}]\n"  # add the name
2150          #                    : "$_\n"             # otherwise leave unmodified          #                    : "$_\n"             # otherwise leave unmodified
2151          #                  } `$FIG_Config::bin/align_with_clustal -tree \'$checked\'`;          #                  } `$FIG_Config::bin/align_with_clustal -org -func -tree \'$checked\'`;
2152    
2153          #  More complex version the preserves double spaced tree tips          #  More complex version the preserves double spaced tree tips
2154          my $tip = 0;          my $tip = 0;
2155          my @out = ();          my @out = ();
2156    
2157          foreach ( `$FIG_Config::bin/align_with_clustal -tree \'$checked\'` )          foreach ( `$FIG_Config::bin/align_with_clustal -org -func -tree \'$checked\'` )
2158          {          {
2159              chomp;              chomp;
2160              if    ( /^   *\|[ |]*$/ ) {}  # line that adds only tree height              if    ( /^   *\|[ |]*$/ ) {}  # line that adds only tree height

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