Bio::Matrix
PhylipDist
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Summary
Bio::Matrix::PhylipDist - A Phylip Distance Matrix object
Package variables
No package variables defined.
Inherit
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;
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
Methods
Methods description
Title : new
Usage : my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",
-program=>"protdist");
Function: Constructor for PhylipDist Object
Returns : Bio::Matrix::PhylipDist |
Title : get_entry
Usage : $matrix->get_entry();
Function: returns a particular entry
Returns : a float
Arguments: string id1, string id2 |
Title : get_row
Usage : $matrix->get_row('ALPHA');
Function: returns a particular row
Returns : an array of float
Arguments: string id1 |
Title : get_column
Usage : $matrix->get_column('ALPHA');
Function: returns a particular column
Returns : an array of floats
Arguments: string id1 |
Title : get_diagonal
Usage : $matrix->get_diagonal();
Function: returns the diagonal of the matrix
Returns : an array of float
Arguments: string id1 |
Title : print_matrix
Usage : $matrix->print_matrix();
Function: returns a string of the matrix in phylip format
Returns : a string
Arguments: |
Title : _matrix
Usage : $matrix->_matrix();
Function: get/set for hash reference of the pointers
to the value matrix
Returns : hash reference
Arguments: hash reference |
Title : names
Usage : $matrix->names();
Function: get/set for array ref of names of sequences
Returns : an array reference
Arguments: an array reference |
Title : program
Usage : $matrix->program();
Function: get/set for the program name generating this
matrix
Returns : string
Arguments: string |
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 |
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 |
Title : matrix_name
Usage : my $name = $matrix->matrix_name();
Function: Get/Set the matrix name
Returns : scalar value
Args : [optional] new matrix name value |
Title : column_header
Usage : my $name = $matrix->column_header(0)
Function: Gets the column header for a particular column number
Returns : string
Args : integer |
Title : row_header
Usage : my $name = $matrix->row_header(0)
Function: Gets the row header for a particular row number
Returns : string
Args : integer |
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 |
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 |
Title : num_rows
Usage : my $rowcount = $matrix->num_rows;
Function: Get the number of rows
Returns : integer
Args : none |
Title : num_columns
Usage : my $colcount = $matrix->num_columns
Function: Get the number of columns
Returns : integer
Args : none |
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 |
Title : column_names
Usage : my @columns = $matrix->column_names
Function: The names of all the columns
Returns : array in array context, arrayref in scalar context
Args : none |
Methods code
sub new
{ my ($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 $self;} | sub get_entry
{ my ($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][$j];
}
return;} | sub get_row
{ my ($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];} | 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][$row_pointer];
}
return @ret;} | sub get_diagonal
{ my ($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;} | 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 $str;} | sub _matrix
{ my ($self,$val) = @_;
if($val){
$self->{'_matrix'} = $val;
}
return $self->{'_matrix'};} | sub names
{ my ($self,$val) = @_;
if($val){
$self->{'_names'} = $val;
}
return $self->{'_names'};} | sub program
{ my ($self) = shift;
return $self->matrix_name(@_); } | sub _values
{ my ($self,$val) = @_;
if($val){
$self->{'_values'} = $val;
}
return $self->{'_values'};} | sub matrix_id
{ my $self = shift;
return $self->{'_matid'} = shift if @_;
return $self->{'_matid'};} | sub matrix_name
{ my $self = shift;
return $self->{'_matname'} = shift if @_;
return $self->{'_matname'};} | sub column_header
{ my ($self,$num) = @_;
my @coln = $self->column_names;
return $coln[$num];} | sub row_header
{ my ($self,$num) = @_;
my @rown = $self->row_names;
return $rown[$num];} | sub column_num_for_name
{ my ($self,$name) = @_;
my $ct = 0;
foreach my $n ( $self->column_names ) {
return $ct if $n eq $name;
$ct++;
}
return;} | sub row_num_for_name
{ my ($self,$name) = @_;
my $ct = 0;
foreach my $n ( $self->row_names ) {
return $ct if $n eq $name;
$ct++;
}} | sub num_rows
{return scalar @{shift->names}} | sub num_columns
{ return scalar @{shift->names};} | sub row_names
{return @{shift->names}} | sub column_names
{return @{shift->names}} | General documentation
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
Please direct usage questions or support issues to the mailing list:
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.
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/
Jason Stajich, jason-at-bioperl-dot-org
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".