Bio::Phylo::Adaptor::Bioperl::Matrix - Adaptor class for bioperl compatibility
use Bio::Phylo::Matrices::Matrix;
use Bio::Phylo::Adaptor;
my $matrix = Bio::Phylo::Matrices::Matrix->new;
$Bio::Phylo::COMPAT = 'Bioperl';
my $alignment = Bio::Phylo::Adaptor->new($matrix);
print "compatible!" if $matrix->isa('Bio::Align::AlignI');
This class wraps Bio::Phylo::Matrices::Matrix objects to give them an interface compatible with bioperl.
Adds another sequence to the alignment.
Title : add_seq
Usage : $myalign->add_seq($newseq);
Function : Adds another sequence to the alignment. *Does not* align
it - just adds it to the hashes.
Returns : nothing
Argument : a Bio::LocatableSeq object
order (optional)
See Bio::LocatableSeq for more information.
Removes a single sequence from an alignment.
Title : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object
Changes the order of the alignemnt to alphabetical on name followed by numerical by number.
Title : sort_alphabetically
Usage : $ali->sort_alphabetically
Function :
Changes the order of the alignemnt to alphabetical on name
followed by numerical by number.
Returns :
Argument :
Gets an array of Seq objects from the alignment.
Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets an array of Seq objects from the alignment Returns : an array Argument :
Returns an array of sequence object sorted alphabetically.
Title : each_alphabetically
Usage : foreach $seq ( $ali->each_alphabetically() )
Function :
Returns an array of sequence object sorted alphabetically
by name and then by start point.
Does not change the order of the alignment
Returns :
Argument :
Gets an array of Seq objects from the alignment.
Title : each_seq_with_id
Usage : foreach $seq ( $align->each_seq_with_id() )
Function :
Gets an array of Seq objects from the
alignment, the contents being those sequences
with the given name (there may be more than one)
Returns : an array
Argument : a seq name
Gets a sequence based on its position in the alignment.
Title : get_seq_by_pos
Usage : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment
Function :
Gets a sequence based on its position in the alignment.
Numbering starts from 1. Sequence positions larger than
no_sequences() will thow an error.
Returns : a Bio::LocatableSeq object
Argument : positive integer for the sequence osition
Creates a new alignment from a continuous subset of sequences.
Title : select
Usage : $aln2 = $aln->select(1, 3) # three first sequences
Function :
Creates a new alignment from a continuous subset of
sequences. Numbering starts from 1. Sequence positions
larger than no_sequences() will thow an error.
Returns : a Bio::SimpleAlign object
Argument : positive integer for the first sequence
positive integer for the last sequence to include (optional)
Creates a new alignment from a subset of sequences.
Title : select_noncont
Usage : $aln2 = $aln->select_noncont(1, 3) # first and 3rd sequences
Function :
Creates a new alignment from a subset of
sequences. Numbering starts from 1. Sequence positions
larger than no_sequences() will thow an error.
Returns : a Bio::SimpleAlign object
Args : array of integers for the sequences
Gets/sets the id field of the alignment.
Title : id
Usage : $myalign->id("Ig")
Function : Gets/sets the id field of the alignment
Returns : An id string
Argument : An id string (optional)
Gets/sets the missing_char attribute of the alignment.
Title : missing_char
Usage : $myalign->missing_char("?")
Function : Gets/sets the missing_char attribute of the alignment
It is generally recommended to set it to 'n' or 'N'
for nucleotides and to 'X' for protein.
Returns : An missing_char string,
Argument : An missing_char string (optional)
Gets/sets the match_char attribute of the alignment.
Title : match_char
Usage : $myalign->match_char('.')
Function : Gets/sets the match_char attribute of the alignment
Returns : An match_char string,
Argument : An match_char string (optional)
Gets/sets the gap_char attribute of the alignment.
Title : gap_char
Usage : $myalign->gap_char('-')
Function : Gets/sets the gap_char attribute of the alignment
Returns : An gap_char string, defaults to '-'
Argument : An gap_char string (optional)
Returns all the seen symbols (other than gaps).
Title : symbol_chars Usage : my @symbolchars = $aln->symbol_chars; Function: Returns all the seen symbols (other than gaps) Returns : array of characters that are the seen symbols Argument: boolean to include the gap/missing/match characters
Tells you whether the alignment is flush, ie all of the same length
Title : is_flush
Usage : if( $ali->is_flush() )
:
:
Function : Tells you whether the alignment
: is flush, ie all of the same length
:
:
Returns : 1 or 0
Argument :
Returns the maximum length of the alignment.
Title : length()
Usage : $len = $ali->length()
Function : Returns the maximum length of the alignment.
To be sure the alignment is a block, use is_flush
Returns :
Argument :
Gets the maximum length of the displayname in the alignment.
Title : maxdisplayname_length
Usage : $ali->maxdisplayname_length()
Function :
Gets the maximum length of the displayname in the
alignment. Used in writing out various MSE formats.
Returns : integer
Argument :
Number of sequence in the sequence alignment.
Title : no_sequences Usage : $depth = $ali->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : None
Gets/sets the display name of a sequence in the alignment.
Title : displayname
Usage : $myalign->displayname("Ig", "IgA")
Function : Gets/sets the display name of a sequence in the alignment
:
Returns : A display name string
Argument : name of the sequence
displayname of the sequence (optional)
Makes all the sequences be displayed as just their name, not name/start-end
Title : set_displayname_flat
Usage : $ali->set_displayname_flat()
Function : Makes all the sequences be displayed as just their name,
not name/start-end
Returns : 1
Argument : None
The base class for the adaptor architecture, instantiates the appropriate wrapper depending on $Bio::Phylo::COMPAT
Bio::Phylo::Adaptor::Bioperl::Matrix is an adaptor that makes Bio::Phylo character matrices compatible with Bio::Align::AlignI objects.
Also see the manual: Bio::Phylo::Manual.
$Id: Matrix.pm 4265 2007-07-20 14:14:44Z rvosa $
