Algorithm-Cluster

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perl/examples/ex1_kcluster  view on Meta::CPAN

#!/usr/perl/perl580/bin/perl -w

use strict;
use Algorithm::Cluster qw/kcluster/;

my $file = "../../data/cyano.txt";
my $i = 0;
my $j = 0;
my (@orfname,@orfdata,@weight,@mask);

open(DATA,"<$file") or die "Can't open file $file: $!";


#------------------
# Read in the data file, and save the data to @orfdata
# We know that the file is intact and has no holes, 
# so just set the mask to 1 for every item.
# We don't check for errors in this case, because the file
# is short and we can spot errors by eye. 
#
my $firstline = <DATA>;  # Skip the title line
while(<DATA>) {
    chomp(my $line = $_);
    my @field     = split /\t/, $line;
    $orfname[$i]  =   $field[0];
    $orfdata[$i]  = [ @field[2..5] ];
    $mask[$i]     = [ 1,1,1,1 ];
    ++$i;
}
close(DATA);

#------------------
# Make a reverse-lookup index of the @orfnames hash:
#
my %orfname_by_rowid;
$i=0;
$orfname_by_rowid{$i++} = $_, foreach(@orfname);

@weight = (1.0) x 4;

perl/examples/ex8_kmedoids  view on Meta::CPAN

#!/usr/perl/perl580/bin/perl -w

use strict;
use Algorithm::Cluster qw/kmedoids distancematrix/;

my $file = "../../data/cyano.txt";
my $i = 0;
my $j = 0;
my (@orfname,@orfdata,@weight,@mask);

open(DATA,"<$file") or die "Can't open file $file: $!";


#------------------
# Read in the data file, and save the data to @orfdata
# We know that the file is intact and has no holes, 
# so just set the mask to 1 for every item.
# We don't check for errors in this case, because the file
# is short and we can spot errors by eye. 
#
my $firstline = <DATA>;  # Skip the title line
while(<DATA>) {
    chomp(my $line = $_);
    my @field     = split /\t/, $line;
    $orfname[$i]  =   $field[0];
    $orfdata[$i]  = [ @field[2..5] ];
    $mask[$i]     = [ 1,1,1,1 ];
    ++$i;
}
close(DATA);

#------------------
# Make a reverse-lookup index of the @orfnames hash:
#
my %orfname_by_rowid;
$i=0;
$orfname_by_rowid{$i++} = $_, foreach(@orfname);

@weight = (1.0) x 4;

src/cluster.c  view on Meta::CPAN

 * permission notice appear in supporting documentation, and that the
 * names of the contributors or copyright holders not be used in
 * advertising or publicity pertaining to distribution of the software
 * without specific prior permission.
 *
 * THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
 * WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
 * CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
 * OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
 * OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
 * OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
 * OR PERFORMANCE OF THIS SOFTWARE.
 *
 */

#include <time.h>
#include <stdlib.h>
#include <math.h>
#include <float.h>
#include <limits.h>

src/cluster.h  view on Meta::CPAN

 * permission notice appear in supporting documentation, and that the
 * names of the contributors or copyright holders not be used in
 * advertising or publicity pertaining to distribution of the software
 * without specific prior permission.
 *
 * THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
 * WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
 * CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
 * OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
 * OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
 * OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
 * OR PERFORMANCE OF THIS SOFTWARE.
 *
 */

#ifndef min
#define min(x, y)	((x) < (y) ? (x) : (y))
#endif
#ifndef max
#define	max(x, y)	((x) > (y) ? (x) : (y))