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revision 1.2, Fri Dec 15 00:46:54 2006 UTC revision 1.4, Sat Jan 6 17:39:41 2007 UTC
# Line 1  Line 1 
 #!/usr/bin/env /Volumes/seagate/FIGdisk/env/mac/bin/perl  
   
 BEGIN {  
     @INC = qw(  
               /Volumes/seagate/FIGdisk/dist/releases/ross/mac/lib  
               /Volumes/seagate/FIGdisk/dist/releases/ross/mac/lib/FigKernelPackages  
               /Volumes/seagate/FIGdisk/dist/ross/mac/lib  
               /Volumes/seagate/FIGdisk/dist/ross/mac/lib/FigKernelPackages  
               /Volumes/seagate/FIGdisk/env/mac/lib/perl5/5.8.7/darwin-2level  
               /Volumes/seagate/FIGdisk/env/mac/lib/perl5/5.8.7  
               /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl/5.8.7/darwin-2level  
               /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl/5.8.7  
               /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl  
               .  
               /Volumes/seagate/FIGdisk/config  
   
 );  
 }  
 use Data::Dumper;  
 use Carp;  
 use FIG_Config;  
 $ENV{'BLASTMAT'} = "/Volumes/seagate/FIGdisk/BLASTMAT";  
 $ENV{'FIG_HOME'} = "/Volumes/seagate/FIGdisk";  
 # end of tool_hdr  
1  ########################################################################  ########################################################################
2    
3    
# Line 32  Line 8 
8  use gjoseqlib;  use gjoseqlib;
9  use gjonewicklib;  use gjonewicklib;
10    
11  my $usage = "usage: insert_into_a_tree [-c CheckPointFile] Alignment Tree [TreeProg] > new.tree\n";  my $usage = "usage: insert_into_a_tree [-c CheckPointFile] [-a Alpha] Alignment Tree [TreeProg] > new.tree\n";
12    
13  my $check_point = undef;  my $check_point = undef;
14    my $alpha       = undef;
15  while ($ARGV[0] =~ /^-/)  while ($ARGV[0] =~ /^-/)
16  {  {
17      my $flag = shift @ARGV;      $_ = shift @ARGV;
18      if ( $flag =~ /^-c/ )      if ($_ =~ s/^-a//)    { $alpha = ($_ || shift @ARGV) }
19      {      elsif ($_ =~ s/^-c//) { $check_point = ($_ || shift @ARGV) }
20          $check_point = shift @ARGV;      else                  { die "Error: invalid flag $_\n$usage" }
     }  
     else  
     {  
         die "Error: invalid flag $flag\n$usage"  
     }  
21  }  }
22    
23  my($aliF,$treeF);  my($aliF,$treeF);
# Line 63  Line 35 
35  my $new_tree = &InsertIntoTree::update_old_tree_using_new_ali( align => $ali,  my $new_tree = &InsertIntoTree::update_old_tree_using_new_ali( align => $ali,
36                                                                 tree => $tree,                                                                 tree => $tree,
37                                                                 tree_prog => $tree_prog,                                                                 tree_prog => $tree_prog,
38                                                                 check_point => $check_point                                                                 check_point => $check_point,
39                                                                   alpha => $alpha
40                                                               );                                                               );
41  &gjonewicklib::writeNewickTree($new_tree);  &gjonewicklib::writeNewickTree($new_tree);
42    

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