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# Copyright (c) 1997-2018
# Ewgenij Gawrilow, Michael Joswig (Technische Universitaet Berlin, Germany)
# http://www.polymake.org
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 2, or (at your option) any
# later version: http://www.gnu.org/licenses/gpl.txt.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#-----------------------------------------------------------------------------
#
application 'polytope';
sub pairwise_dist {
my ($M) = @_;
my $n_taxa=$M->rows();
my $dist = new Matrix<Float>($n_taxa,$n_taxa);
for (my $i=0; $i<$n_taxa; ++$i) {
for (my $j=0; $j<$i; ++$j) {
my $diff_ij=$M->row($i)-$M->row($j);
my $dist_ij=sqrt(convert_to<Float>($diff_ij*$diff_ij));
$dist->elem($j,$i) = $dist->elem($i,$j)=$dist_ij;
}
}
return new TightSpan<Rational>(METRIC=>$dist);
}
# Local Variables:
# c-basic-offset:2
# mode: perl
# End:
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