# an example Jrna.pm template file

package jrna_template;

use Jrna;
use Jrna_objs;
use strict;
use warnings;

my $data = Jrna->input (
			"data/galr/Galerucinae.28S.0.03.Nex",		# full path to input file
			"data/galr/Galerucinae.Index_0.02.txt",			# full path to stem file
			"galr",							# model "name"
			248							# number taxa (n-1)
		);

# define some data partitions
my $all_data = slice->new;
$all_data->blocks(0..145); 
#$all_data->taxa(0..248);
$all_data->taxa(0..15, 17..36, 40..82, 86..121, 123..139, 141..151, 153..168, 170..181, 183..185, 187..235, 237..239, 242..246);	# taxa with 28S data


my $my_data = $all_data;		# make a working copy of the slice/partion you want to use 

$data->init();				# required
$data->init_stems($all_data);		# required for output using stems (nearly everything)

# &Jrna::mx_safenames();			# translate long taxon names to unique short ones
$data->out_web($my_data, 1, 0);	# best to start with this one as a test

#&Jrna::descr_stembpfreq(*STDOUT, $my_data, 0, 1);

#$data->out_nexus($my_data, 2);
#$data->out_phylip($my_data, 0);
#$data->out_tnt($my_data, 0);
#$data->out_poy($my_data, 2, 0, "ichs");
#$data->out_phase($my_data, 0, "ichs", 2); 
#$data->out_bayes($my_data, 0);
#$data->out_rna_translate($my_data);
#$data->out_gde($my_data);

#$data->out_inaase($my_data,1);

#&Jrna::descr_seq_length($my_data);

# methods that produce file-output:
#    	out_inaase(slice; correct data [0-no, 1-yes])
#    	*out_phylip(slice, stem mode)
#    	out_bayes(slice, stem mode)
#	out_poy(slice, poy mode [0- DO on *all* blocks; 1- DO on unbracketed, FSO on bracketed; 2- FSO on all; 3- DO on unbracketed], stem mode, fileroot)
# 	out_phase(slice, stem mode, fileroot (text name for result files), output control file(s) [0-no; 1-single RNA6A; 2-multi mode])
#    	out_nexus(slice, stem mode)
#    	*out_tnt(slice, stem mode)
#    	out_rna_translate(slice)
#    	*out_web(slice, mode, interleave size, interleave)
#    	out_gde(slice)
#
# methods that produce screen output
#	 &jrna::descr_seq_length(slice)
#	 &Jrna::descr_stembpfreq(filehandle (="*STDOUT" for screen, slice, output mode [0-text; 1-css], summary mode [0-include all taxa; 1-exclude taxa with "??"] ); 
#	 &Jrna::descr_taxa($my_data);
#	 &Jrna::debug_seq4taxa(23, $my_data);

# methods that alter slices:
# 	slice->Jrna::slice_prune_uninformative_taxa();

1;

__END__

