Bio::Matrix
Generic
Summary
Bio::Matrix::Generic - A generic matrix implementation
Package variables
No package variables defined.
Inherit
Synopsis
# A matrix has columns and rows
my $matrix = Bio::Matrix::Generic->new;
$matrix->add_column(1,$column1);
$matrix->add_column(2,$column2);
my $element = $matrix->entry_by_num(1,2);
$matrix->entry_by_num(1,2,$newval);
my $entry = $matrix->entry('human', 'mouse');
$matrix->entry('human','mouse', $newval);
Description
This is a general purpose matrix object for dealing with row+column
data which is typical when enumerating all the pairwise combinations
and desiring to get slices of the data.
Data can be accessed by column and row names or indexes. Matrix
indexes start at 0.
Methods
Methods description
Title : new
Usage : my $obj = new Bio::Matrix::Generic();
Function: Builds a new Bio::Matrix::Generic object
Returns : an instance of Bio::Matrix::Generic
Args : -values => arrayref of arrayrefs of data initialization
-rownames => arrayref of row names
-colnames => arrayref of col names
-matrix_id => id of the matrix
-matrix_name=> name of the matrix
-matrix_init_value => default value to initialize empty cells |
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 : entry
Usage : my $entry = $matrix->entry($row,$col)
Function: Get the value for a specific cell as specified
by the row and column names
Returns : scalar value or undef if row or col does not
exist
Args : $rowname - name of the row
$colname - column name |
Title : get_entry
Usage : my $entry = $matrix->get_entry($rowname,$columname)
Function: Get the entry for a given row,column pair
Returns : scalar
Args : $row name
$column name |
Title : entry_by_num
Usage : my $entry = $matrix->entry_by_num($rownum,$colnum)
Function: Get an entry by row and column numbers instead of by name
(rows and columns start at 0)
Returns : scalar value or undef if row or column name does not
exist
Args : $row - row number
$col - column number
[optional] $newvalue to store at this cell |
Title : column
Usage : my @col = $matrix->column('ALPHA');
OR
$matrix->column('ALPHA', \@col);
Function: Get/Set a particular column
Returns : Array (in array context) or arrayref (in scalar context)
of values.
For setting will warn if the new column is of a different
length from the rest of the columns.
Args : name of the column
[optional] new column to store here |
Title : get_column
Usage : my @row = $matrix->get_column('ALPHA');
Function: Get a particular column
Returns : Array (in array context) or arrayref (in scalar context)
of values
Args : name of the column |
Title : column_by_num
Usage : my @col = $matrix->column_by_num(1);
OR
$matrix->column_by_num(1,\@newcol);
Function: Get/Set a column by its number instead of name
(cols/rows start at 0)
Returns : Array (in array context) or arrayref (in scalar context)
of values
Args : name of the column
[optional] new value to store for a particular column |
Title : row
Usage : my @row = $matrix->row($rowname);
OR
$matrix->row($rowname,\@rowvalues);
Function: Get/Set the row of the matrix
Returns : Array (in array context) or arrayref (in scalar context)
Args : rowname
[optional] new value of row to store |
Title : get_row
Usage : my @row = $matrix->get_row('ALPHA');
Function: Get a particular row
Returns : Array (in array context) or arrayref (in scalar context)
of values
Args : name of the row |
Title : row_by_num
Usage : my @row = $matrix->row_by_num($rownum);
OR
$matrix->row($rownum,\@rowvalues);
Function: Get/Set the row of the matrix
Returns : Array (in array context) or arrayref (in scalar context)
Args : rowname
[optional] new value of row to store |
Title : add_row
Usage : $matrix->add_row($index,\@newrow);
Function: Adds a row at particular location in the matrix.
If $index < the rowcount will shift all the rows down
by the number of new rows.
To add a single empty row, simply call
$matrix->add_row($index,undef);
Returns : the updated number of total rows in the matrix
Args : index to store
name of the row (header)
newrow to add, if this is undef will add a single
row with all values set to undef |
Title : remove_row
Usage : $matrix->remove_row($colnum)
Function: remove a row from the matrix shifting all the rows
up by one
Returns : Updated number of rows in the matrix
Args : row index |
Title : add_column
Usage : $matrix->add_column($index,$colname,\@newcol);
Function: Adds a column at particular location in the matrix.
If $index < the colcount will shift all the columns right
by the number of new columns.
To add a single empty column, simply call
$matrix->add_column($index,undef);
Returns : the updated number of total columns in the matrix
Args : index to store
name of the column (header)
newcolumn to add, if this is undef will add a single
column with all values set to undef |
Title : remove_column
Usage : $matrix->remove_column($colnum)
Function: remove a column from the matrix shifting all the columns
to the left by one
Returns : Updated number of columns in the matrix
Args : column index |
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
Function: Gets the row number for a particular row name
Returns : integer
Args : string |
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 : 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 |
Title : _values
Usage : $matrix->_values();
Function: get/set for array ref of the matrix containing
distance values
Returns : an array reference
Args : an array reference |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($values, $rownames, $colnames,
$id,$name,$init_val) =
$self->_rearrange([qw(VALUES ROWNAMES COLNAMES
MATRIX_ID MATRIX_NAME
MATRIX_INIT_VALUE)],@args);
$self->matrix_id($id) if defined $id;
$self->matrix_name($name) if defined $name;
if( defined $rownames && defined $colnames ) {
if( ref($rownames) !~ /ARRAY/i ) {
$self->throw("need an arrayref for the -rownames option");
}
$self->{'_rownames'} = [ @$rownames ];
my $count = 0;
%{$self->{'_rownamesmap'}} = map { $_ => $count++ } @$rownames;
if( ref($colnames) !~ /ARRAY/i ) {
$self->throw("need an arrayref for the -colnames option");
}
$self->{'_colnames'} = [ @$colnames ];
$count = 0;
%{$self->{'_colnamesmap'}} = map { $_ => $count++ } @$colnames;
$self->{'_values'} = [];
if( defined $values ) {
if( ref($values) !~ /ARRAY/i ) {
$self->throw("Need an arrayref of arrayrefs (matrix) for -values option");
}
for my $v ( @$values ) {
if( ref($v) !~ /ARRAY/i ) {
$self->throw("Need and array of arrayrefs (matrix) for -values option");
}
push @{$self->{'_values'}}, [@$v];
}
} else {
my @fill = ($init_val) x scalar @$colnames;
for ( @$rownames ) {
push @{$self->{'_values'}}, [@fill];
}
}
} elsif( ! defined $rownames && ! defined $colnames && ! defined $values ) {
$self->{'_values'} = [];
$self->{'_rownames'} = [];
$self->{'_colnames'} = [];
} else {
$self->throw("Must have either provided no values/colnames/rownames or provided all three");
}
return $self;} | 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 $self->{'_matname'};} | sub entry
{ my ($self,$row,$column,$newvalue) = @_;
if( ! defined $row || ! defined $column ) {
$self->throw("Need at least 2 ids");
}
my ($rownum) = $self->row_num_for_name($row);
my ($colnum) = $self->column_num_for_name($column);
return $self->entry_by_num($rownum,$colnum,$newvalue);} | sub get_entry
{$_[0]->entry($_[1],$_[2]) } | sub entry_by_num
{ my ($self,$row,$col,$newvalue) = @_;
if( ! defined $row || ! defined $col ||
$row !~ /^\d+$/ ||
$col !~ /^\d+$/ ) {
$self->warn("expected to get 2 number for entry_by_num");
return;
}
if( defined $newvalue ) {
return $self->_values->[$row][$col] = $newvalue;
} else {
return $self->_values->[$row][$col];
}} | sub get_element
{ my $self = shift;
$self->entry(@_);} | sub column
{ my ($self,$column,$newcol) = @_;
if( ! defined $column ) {
$self->warn("Need at least a column id");
return;
}
my $colnum = $self->column_num_for_name($column);
if( ! defined $colnum ) {
$self->warn("could not find column number for $column");
return;
}
return $self->column_by_num($colnum,$newcol);} | sub get_column
{ $_[0]->column($_[1]) } | sub column_by_num
{ my ($self,$colnum,$newcol) = @_;
if( ! defined $colnum ) {
$self->warn("need at least a column number");
return;
}
my $rowcount = $self->num_rows;
my $colcount = $self->num_columns;
my $ret;
if( defined $newcol ) {
if( ref($newcol) !~ /ARRAY/i) {
$self->warn("expected a valid arrayref for resetting a column");
return;
}
if( scalar @$newcol != $rowcount ) {
$self->warn("new column is not the correct length ($rowcount) - call add or remove row to shrink or grow the number of rows first");
return;
}
for(my $i=0; $i < $rowcount; $i++) {
$self->entry_by_num($i,$colnum,$newcol->[$i]);
}
$ret = $newcol;
} else {
$ret = [];
for(my $i=0; $i < $rowcount; $i++) {
push @$ret,$self->entry_by_num($i,$colnum);
}
}
if( wantarray ) { return @$ret }
return $ret;} | sub row
{ my ($self,$row,$newrow) = @_;
if( ! defined $row) {
$self->warn("Need at least a row id");
return;
}
my $rownum = $self->row_num_for_name($row);
return $self->row_by_num($rownum,$newrow);} | sub get_row
{ $_[0]->row($_[1]) } | sub row_by_num
{ my ($self,$rownum,$newrow) = @_;
if( ! defined $rownum ) {
$self->warn("need at least a row number");
return;
}
my $colcount = $self->num_columns;
my $ret;
if( defined $newrow ) {
if( ref($newrow) !~ /ARRAY/i) {
$self->warn("expected a valid arrayref for resetting a row");
return;
}
if( scalar @$newrow != $colcount ) {
$self->warn("new row is not the correct length ($colcount) - call add or remove column to shrink or grow the number of columns first");
return;
}
for(my $i=0; $i < $colcount; $i++) {
$self->entry_by_num($rownum,$i, $newrow->[$i]);
}
$ret = $newrow;
} else {
$ret = [];
for(my $i=0; $i < $colcount; $i++) {
push @$ret, $self->entry_by_num($rownum,$i);
}
}
if( wantarray ) { return @$ret }
return $ret;} | sub get_diagonal
{ my ($self) = @_;
my @diag;
my $rowcount = $self->num_rows;
my $colcount = $self->num_columns;
for(my $i = 0; $i < $rowcount; $i++ ) {
push @diag, $self->entry_by_num($i,$i);
}
return @diag;} | sub add_row
{ my ($self,$index,$name,$newrow) = @_;
if( !defined $index ||
$index !~ /^\d+$/ ) {
$self->warn("expected a valid row index in add_row");
return;
} elsif( ! defined $name) {
$self->warn("Need a row name or heading");
return;
} elsif( defined $self->row_num_for_name($name) ) {
$self->warn("Need a unqiue name for the column heading, $name is already used");
return;
}
my $colcount = $self->num_columns;
my $rowcount = $self->num_rows;
if( $index > $rowcount ) {
$self->warn("cannot add a row beyond 1+last row at the end ($rowcount) not $index - adding at $rowcount instead");
$index = $rowcount;
}
if( ! defined $newrow ) {
$newrow = [];
$newrow->[$colcount] = undef;
} elsif( ref($newrow) !~ /ARRAY/i ) {
$self->throw("Expected either undef or a valid arrayref for add_row");
}
splice(@{$self->{'_values'}}, $index,0,[]);
for( my $i = 0; $i < $colcount; $i++ ) {
$self->entry_by_num($index,$i,$newrow->[$i]);
}
splice(@{$self->{'_rownames'}}, $index,0,$name);
my $ct = 0;
%{$self->{'_rownamesmap'}} = map { $_ => $ct++} @{$self->{'_rownames'}};
return $self->num_rows;} | sub remove_row
{ my ($self,$rowindex) = @_;
my $rowcount = $self->num_rows;
if( $rowindex > $rowcount ) {
$self->warn("rowindex $rowindex is greater than number of rows $rowcount, cannot process");
return 0;
} else {
splice(@{$self->_values},$rowindex,1);
delete $self->{'_rownamesmap'}->{$self->{'_rownames'}->[$rowindex]};
splice(@{$self->{'_rownames'}},$rowindex,1);
}
my $ct = 0;
%{$self->{'_rownamesmap'}} = map { $_ => $ct++} @{$self->{'_rownames'}};
return $self->num_rows;} | sub add_column
{ my ($self,$index,$name,$newcol) = @_;
if( !defined $index ||
$index !~ /^\d+$/ ) {
$self->warn("expected a valid col index in add_column");
return;
} elsif( ! defined $name) {
$self->warn("Need a column name or heading");
return;
} elsif( defined $self->column_num_for_name($name) ) {
$self->warn("Need a unqiue name for the column heading, $name is already used");
return;
}
my $colcount = $self->num_columns;
my $rowcount = $self->num_rows;
if( $index > $colcount ) {
$self->warn("cannot add a column beyond 1+last column at the end ($colcount) not $index - adding at $colcount instead");
$index = $colcount;
}
if( ! defined $newcol ) {
$newcol = [];
$newcol->[$rowcount] = undef;
} elsif( ref($newcol) !~ /ARRAY/i ) {
$self->throw("Expected either undef or a valid arrayref for add_row");
}
for( my $i = 0; $i < $rowcount; $i++ ) {
splice(@{$self->_values->[$i]},$index,0,[]);
$self->entry_by_num($i,$index,$newcol->[$i]);
}
splice(@{$self->{'_colnames'}}, $index,0,$name);
my $ct = 0;
%{$self->{'_colnamesmap'}} = map {$_ => $ct++} @{$self->{'_colnames'}};
return $self->num_columns;} | sub remove_column
{ my ($self,$colindex) = @_;
my $colcount = $self->num_columns;
my $rowcount = $self->num_rows;
if( $colindex > $colcount ) {
$self->warn("colindex $colindex is greater than number of columns ($colcount), cannot process");
return 0;
} else {
for(my $i = 0; $i < $rowcount; $i++ ) {
splice(@{$self->_values->[$i]},$colindex,1);
}
delete $self->{'_colnamesmap'}->{$self->{'_colnames'}->[$colindex]};
splice(@{$self->{'_colnames'}},$colindex,1);
}
my $ct = 0;
%{$self->{'_colnamesmap'}} = map {$_ => $ct++} @{$self->{'_colnames'}};
return $self->num_columns;} | sub column_num_for_name
{ my ($self,$name) = @_;
return $self->{'_colnamesmap'}->{$name};} | sub row_num_for_name
{ my ($self,$name) = @_;
return $self->{'_rownamesmap'}->{$name}} | sub column_header
{ my ($self,$num) = @_;
return $self->{'_colnames'}->[$num];} | sub row_header
{ my ($self,$num) = @_;
return $self->{'_rownames'}->[$num];} | sub num_rows
{ my ($self) = @_;
return scalar @{$self->_values};} | sub num_columns
{ my ($self) = @_;
return scalar @{$self->_values->[0] || []};} | sub row_names
{ if( wantarray ) {
return @{shift->{'_rownames'}};
} else {
return shift->{'_rownames'};
}} | sub column_names
{ if( wantarray ) {
return @{shift->{'_colnames'}};
} else {
return shift->{'_colnames'};
}} | sub _values
{ my ($self,$val) = @_;
if( $val ){
$self->{'_values'} = $val;
}
return $self->{'_values'};} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
| AUTHOR - Jason Stajich | Top |
Email jason-at-bioperl-dot-org
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : diagonal
Usage : my @diagonal = $matrix->get_diagonal()
Function: Get the diagonal of a matrix
Returns : Array (in array context) or arrayref (in scalar context)
of values which lie along the diagonal
Args : none
Private methods for a Generic Matrix