# BioPerl module for Bio::Matrix::PhylipDist
#
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon <shawnh@fugu-sg.org>
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Matrix::PhylipDist - A Phylip Distance Matrix object
=head1 SYNOPSIS
use Bio::Tools::Phylo::Phylip::ProtDist;
my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
-file=>"protdist.out",
-program=>"ProtDist");
#or
my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
-fh=>"protdist.out",
-program=>"ProtDist");
#get specific entries
my $distance_value = $dist->get_entry('ALPHA','BETA');
my @columns = $dist->get_column('ALPHA');
my @rows = $dist->get_row('BETA');
my @diagonal = $dist->get_diagonal();
#print the matrix in phylip numerical format
print $dist->print_matrix;
=head1 DESCRIPTION
Simple object for holding Distance Matrices generated by the following Phylip programs:
1) dnadist
2) protdist
3) restdist
It currently handles parsing of the matrix without the data output option.
5
Alpha 0.00000 4.23419 3.63330 6.20865 3.45431
Beta 4.23419 0.00000 3.49289 3.36540 4.29179
Gamma 3.63330 3.49289 0.00000 3.68733 5.84929
Delta 6.20865 3.36540 3.68733 0.00000 4.43345
Epsilon 3.45431 4.29179 5.84929 4.43345 0.00000
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 CONTRIBUTORS
Jason Stajich, jason-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
# Let the code begin...
package Bio::Matrix::PhylipDist;
use strict;
use base qw(Bio::Root::Root Bio::Matrix::MatrixI);
=head2 new
Title : new
Usage : my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",
-program=>"protdist");
Function: Constructor for PhylipDist Object
Returns : L<Bio::Matrix::PhylipDist>
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($matrix,$values, $names,
$program,$matname,
$matid) = $self->_rearrange([qw(MATRIX
VALUES
NAMES
PROGRAM
MATRIX_NAME
MATRIX_ID
)],@args);
($matrix && $values && $names) ||
$self->throw("Need matrix, values, and names fields all provided!");
$program && $self->matrix_name($program) if defined $program;
$self->_matrix($matrix) if ref($matrix) =~ /HASH/i;
$self->_values($values) if ref($values) =~ /ARRAY/i;
$self->names($names) if ref($names) =~ /ARRAY/i;
$self->matrix_name($matname) if defined $matname;
$self->matrix_id ($matid) if defined $matid;
return $self;
}
=head2 get_entry
Title : get_entry
Usage : $matrix->get_entry();
Function: returns a particular entry
Returns : a float
Arguments: string id1, string id2
=cut
sub get_entry {
my ($self,$row,$column) = @_;
$row && $column || $self->throw("Need at least 2 ids");
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
if(ref $matrix{$row}{$column}){
my ($i,$j) = @{$matrix{$row}{$column}};
return $values[$i][$j];
}
return;
}
=head2 get_row
Title : get_row
Usage : $matrix->get_row('ALPHA');
Function: returns a particular row
Returns : an array of float
Arguments: string id1
=cut
sub get_row {
my ($self,$row) = @_;
$row || $self->throw("Need at least a row id");
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
my @names = @{$self->names};
$matrix{$row} || return;
my ($val) = values %{$matrix{$row}};
my $row_pointer = $val->[0];
my $index = scalar(@names)-1;
return @{$values[$row_pointer]}[0..$index];
}
=head2 get_column
Title : get_column
Usage : $matrix->get_column('ALPHA');
Function: returns a particular column
Returns : an array of floats
Arguments: string id1
=cut
sub get_column {
my ($self,$column) = @_;
$column || $self->throw("Need at least a column id");
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
my @names = @{$self->names};
$matrix{$column} || return ();
my ($val) = values %{$matrix{$column}};
my $row_pointer = $val->[0];
my @ret;
for(my $i=0; $i < scalar(@names); $i++) {
push @ret, $values[$i][$row_pointer];
}
return @ret;
}
=head2 get_diagonal
Title : get_diagonal
Usage : $matrix->get_diagonal();
Function: returns the diagonal of the matrix
Returns : an array of float
Arguments: string id1
=cut
sub get_diagonal {
my ($self) = @_;
my %matrix = %{$self->_matrix};
my @values = @{$self->_values};
my @return;
foreach my $name (@{$self->names}){
my ($i,$j) = @{$matrix{$name}{$name}};
push @return,$values[$i][$j];
}
return @return;
}
=head2 print_matrix
Title : print_matrix
Usage : $matrix->print_matrix();
Function: returns a string of the matrix in phylip format
Returns : a string
Arguments:
=cut
sub print_matrix {
my ($self) = @_;
my @names = @{$self->names};
my @values = @{$self->_values};
my %matrix = %{$self->_matrix};
my $str;
$str.= (" "x 4). scalar(@names)."\n";
foreach my $name (@names){
my $newname = $name. (" " x (15-length($name)));
if( length($name) >= 15 ) { $newname .= " " }
$str.=$newname;
my $count = 0;
foreach my $n (@names) {
my ($i,$j) = @{$matrix{$name}{$n}};
if($count < $#names){
$str .= $values[$i][$j]. " ";
}
else {
if( ! defined $values[$i][$j] ) {
$self->debug("no value for $i,$j cell\n");
} else {
$str .= $values[$i][$j];
}
}
$count++;
}
$str.="\n";
}
return $str;
}
=head2 _matrix
Title : _matrix
Usage : $matrix->_matrix();
Function: get/set for hash reference of the pointers
to the value matrix
Returns : hash reference
Arguments: hash reference
=cut
sub _matrix {
my ($self,$val) = @_;
if($val){
$self->{'_matrix'} = $val;
}
return $self->{'_matrix'};
}
=head2 names
Title : names
Usage : $matrix->names();
Function: get/set for array ref of names of sequences
Returns : an array reference
Arguments: an array reference
=cut
sub names {
my ($self,$val) = @_;
if($val){
$self->{'_names'} = $val;
}
return $self->{'_names'};
}
=head2 program
Title : program
Usage : $matrix->program();
Function: get/set for the program name generating this
matrix
Returns : string
Arguments: string
=cut
sub program {
my ($self) = shift;
return $self->matrix_name(@_);
}
=head2 _values
Title : _values
Usage : $matrix->_values();
Function: get/set for array ref of the matrix containing
distance values
Returns : an array reference
Arguments: an array reference
=cut
sub _values {
my ($self,$val) = @_;
if($val){
$self->{'_values'} = $val;
}
return $self->{'_values'};
}
=head1 L<Bio::Matrix::MatrixI> implementation
=head2 matrix_id
Title : matrix_id
Usage : my $id = $matrix->matrix_id
Function: Get/Set the matrix ID
Returns : scalar value
Args : [optional] new id value to store
=cut
sub matrix_id{
my $self = shift;
return $self->{'_matid'} = shift if @_;
return $self->{'_matid'};
}
=head2 matrix_name
Title : matrix_name
Usage : my $name = $matrix->matrix_name();
Function: Get/Set the matrix name
Returns : scalar value
Args : [optional] new matrix name value
=cut
sub matrix_name{
my $self = shift;
return $self->{'_matname'} = shift if @_;
return $self->{'_matname'};
}
=head2 column_header
Title : column_header
Usage : my $name = $matrix->column_header(0)
Function: Gets the column header for a particular column number
Returns : string
Args : integer
=cut
sub column_header{
my ($self,$num) = @_;
my @coln = $self->column_names;
return $coln[$num];
}
=head2 row_header
Title : row_header
Usage : my $name = $matrix->row_header(0)
Function: Gets the row header for a particular row number
Returns : string
Args : integer
=cut
sub row_header{
my ($self,$num) = @_;
my @rown = $self->row_names;
return $rown[$num];
}
=head2 column_num_for_name
Title : column_num_for_name
Usage : my $num = $matrix->column_num_for_name($name)
Function: Gets the column number for a particular column name
Returns : integer
Args : string
=cut
sub column_num_for_name{
my ($self,$name) = @_;
my $ct = 0;
foreach my $n ( $self->column_names ) {
return $ct if $n eq $name;
$ct++;
}
return;
}
=head2 row_num_for_name
Title : row_num_for_name
Usage : my $num = $matrix->row_num_for_name($name)
Function: Gets the row number for a particular row name
Returns : integer
Args : string
=cut
sub row_num_for_name{
my ($self,$name) = @_;
my $ct = 0;
foreach my $n ( $self->row_names ) {
return $ct if $n eq $name;
$ct++;
}
}
=head2 num_rows
Title : num_rows
Usage : my $rowcount = $matrix->num_rows;
Function: Get the number of rows
Returns : integer
Args : none
=cut
sub num_rows{ return scalar @{shift->names} }
=head2 num_columns
Title : num_columns
Usage : my $colcount = $matrix->num_columns
Function: Get the number of columns
Returns : integer
Args : none
=cut
sub num_columns{
return scalar @{shift->names};
}
=head2 row_names
Title : row_names
Usage : my @rows = $matrix->row_names
Function: The names of all the rows
Returns : array in array context, arrayref in scalar context
Args : none
=cut
sub row_names{ return @{shift->names} }
=head2 column_names
Title : column_names
Usage : my @columns = $matrix->column_names
Function: The names of all the columns
Returns : array in array context, arrayref in scalar context
Args : none
=cut
sub column_names{ return @{shift->names} }
1;