Bio::Matrix PhylipDist
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Summary
Bio::Matrix::PhylipDist - A Phylip Distance Matrix object
Package variables
No package variables defined.
Inherit
Bio::Matrix::MatrixI Bio::Root::Root
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
newDescriptionCode
get_entryDescriptionCode
get_rowDescriptionCode
get_columnDescriptionCode
get_diagonalDescriptionCode
print_matrixDescriptionCode
_matrixDescriptionCode
namesDescriptionCode
programDescriptionCode
_valuesDescriptionCode
matrix_idDescriptionCode
matrix_nameDescriptionCode
column_headerDescriptionCode
row_headerDescriptionCode
column_num_for_nameDescriptionCode
row_num_for_nameDescriptionCode
num_rowsDescriptionCode
num_columnsDescriptionCode
row_namesDescriptionCode
column_namesDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $family = Bio::Matrix::PhylipDist->new(-file=>"protdist.out",
-program=>"protdist");
Function: Constructor for PhylipDist Object
Returns : Bio::Matrix::PhylipDist
get_entrycodeprevnextTop
 Title   : get_entry
Usage : $matrix->get_entry();
Function: returns a particular entry
Returns : a float
Arguments: string id1, string id2
get_rowcodeprevnextTop
 Title   : get_row
Usage : $matrix->get_row('ALPHA');
Function: returns a particular row
Returns : an array of float
Arguments: string id1
get_columncodeprevnextTop
 Title   : get_column
Usage : $matrix->get_column('ALPHA');
Function: returns a particular column
Returns : an array of floats
Arguments: string id1
get_diagonalcodeprevnextTop
 Title   : get_diagonal
Usage : $matrix->get_diagonal();
Function: returns the diagonal of the matrix
Returns : an array of float
Arguments: string id1
print_matrixcodeprevnextTop
 Title   : print_matrix
Usage : $matrix->print_matrix();
Function: returns a string of the matrix in phylip format
Returns : a string
Arguments:
_matrixcodeprevnextTop
 Title   : _matrix
Usage : $matrix->_matrix();
Function: get/set for hash reference of the pointers
to the value matrix
Returns : hash reference
Arguments: hash reference
namescodeprevnextTop
 Title   : names
Usage : $matrix->names();
Function: get/set for array ref of names of sequences
Returns : an array reference
Arguments: an array reference
programcodeprevnextTop
 Title   : program
Usage : $matrix->program();
Function: get/set for the program name generating this
matrix
Returns : string
Arguments: string
_valuescodeprevnextTop
 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
matrix_idcodeprevnextTop
 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
matrix_namecodeprevnextTop
 Title   : matrix_name
Usage : my $name = $matrix->matrix_name();
Function: Get/Set the matrix name
Returns : scalar value
Args : [optional] new matrix name value
column_headercodeprevnextTop
 Title   : column_header
Usage : my $name = $matrix->column_header(0)
Function: Gets the column header for a particular column number
Returns : string
Args : integer
row_headercodeprevnextTop
 Title   : row_header
Usage : my $name = $matrix->row_header(0)
Function: Gets the row header for a particular row number
Returns : string
Args : integer
column_num_for_namecodeprevnextTop
 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
row_num_for_namecodeprevnextTop
 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
num_rowscodeprevnextTop
 Title   : num_rows
Usage : my $rowcount = $matrix->num_rows;
Function: Get the number of rows
Returns : integer
Args : none
num_columnscodeprevnextTop
 Title   : num_columns
Usage : my $colcount = $matrix->num_columns
Function: Get the number of columns
Returns : integer
Args : none
row_namescodeprevnextTop
 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
column_namescodeprevnextTop
 Title   : column_names
Usage : my @columns = $matrix->column_names
Function: The names of all the columns
Returns : array in array context, arrayref in scalar context
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($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 $self;
}
get_entrydescriptionprevnextTop
sub get_entry {
  my ($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][$j];
  }
  return;
}
get_rowdescriptionprevnextTop
sub get_row {
    my ($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];
}
get_columndescriptionprevnextTop
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][$row_pointer];
    }
    return @ret;
}
get_diagonaldescriptionprevnextTop
sub get_diagonal {
  my ($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;
}
print_matrixdescriptionprevnextTop
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 $str;
}
_matrixdescriptionprevnextTop
sub _matrix {
  my ($self,$val) = @_;
  if($val){
    $self->{'_matrix'} = $val;
  }
  return $self->{'_matrix'};
}
namesdescriptionprevnextTop
sub names {
  my ($self,$val) = @_;
  if($val){
    $self->{'_names'} = $val;
  }
  return $self->{'_names'};
}
programdescriptionprevnextTop
sub program {
  my ($self) = shift;
  return $self->matrix_name(@_);
}
_valuesdescriptionprevnextTop
sub _values {
  my ($self,$val) = @_;
  if($val){
    $self->{'_values'} = $val;
  }
  return $self->{'_values'};
}
matrix_iddescriptionprevnextTop
sub matrix_id {
   my $self = shift;
   return $self->{'_matid'} = shift if @_;
   return $self->{'_matid'};
}
matrix_namedescriptionprevnextTop
sub matrix_name {
   my $self = shift;
   return $self->{'_matname'} = shift if @_;
   return $self->{'_matname'};
}
column_headerdescriptionprevnextTop
sub column_header {
    my ($self,$num) = @_;
    my @coln = $self->column_names;
    return $coln[$num];
}
row_headerdescriptionprevnextTop
sub row_header {
    my ($self,$num) = @_;
    my @rown = $self->row_names;
   return $rown[$num];
}
column_num_for_namedescriptionprevnextTop
sub column_num_for_name {
   my ($self,$name) = @_;
   my $ct = 0;
   foreach my $n ( $self->column_names ) {
       return $ct if $n eq $name;
       $ct++;
   }
   return;
}
row_num_for_namedescriptionprevnextTop
sub row_num_for_name {
   my ($self,$name) = @_;
   my $ct = 0;
   foreach my $n ( $self->row_names ) {
       return $ct if $n eq $name;
       $ct++;
   }
}
num_rowsdescriptionprevnextTop
sub num_rows {
return scalar @{shift->names}
}
num_columnsdescriptionprevnextTop
sub num_columns {
   return scalar @{shift->names};
}
row_namesdescriptionprevnextTop
sub row_names {
return @{shift->names}
}
column_namesdescriptionprevnextTop
sub column_names {
return @{shift->names}
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Shawn HoonTop
Email shawnh@fugu-sg.org
CONTRIBUTORSTop
Jason Stajich, jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
Bio::Matrix::MatrixI implementationTop