/ 
BioPerl-1.7.8
River stage two • 61 direct dependents • 66 total dependents
/ Bio::SimpleAlign

NAME

Bio::SimpleAlign - Multiple alignments held as a set of sequences

SYNOPSIS

# Use Bio::AlignIO to read in the alignment
$str = Bio::AlignIO->new(-file => 't/data/testaln.pfam');
$aln = $str->next_aln();

# Describe
print $aln->length;
print $aln->num_residues;
print $aln->is_flush;
print $aln->num_sequences;
print $aln->score;
print $aln->percentage_identity;
print $aln->consensus_string(50);

# Find the position in the alignment for a sequence location
$pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6;

# Extract sequences and check values for the alignment column $pos
foreach $seq ($aln->each_seq) {
    $res = $seq->subseq($pos, $pos);
    $count{$res}++;
}
foreach $res (keys %count) {
    printf "Res: %s  Count: %2d\n", $res, $count{$res};
}

# Manipulate
$aln->remove_seq($seq);
$mini_aln = $aln->slice(20,30);  # get a block of columns
$mini_aln = $aln->select_noncont(1,3,5,7,11); # select certain sequences
$new_aln = $aln->remove_columns([20,30]); # remove by position
$new_aln = $aln->remove_columns(['mismatch']); # remove by property

# Analyze
$str = $aln->consensus_string($threshold_percent);
$str = $aln->match_line();
$str = $aln->cigar_line();
$id = $aln->percentage_identity;

# See the module documentation for details and more methods.

DESCRIPTION

SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipulations and methods for reading and writing alignments.

SimpleAlign uses Bio::LocatableSeq, a subclass of Bio::PrimarySeq, to store its sequences. These are subsequences with a start and end positions in the parent reference sequence. Each sequence in the SimpleAlign object is a Bio::LocatableSeq.

SimpleAlign expects the combination of name, start, and end for a given sequence to be unique in the alignment, and this is the key for the internal hashes (name, start, end are abbreviated nse in the code). However, in some cases people do not want the name/start-end to be displayed: either multiple names in an alignment or names specific to the alignment (ROA1_HUMAN_1, ROA1_HUMAN_2 etc). These names are called displayname, and generally is what is used to print out the alignment. They default to name/start-end.

The SimpleAlign Module is derived from the Align module by Ewan Birney.

FEEDBACK

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

Support

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 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://github.com/bioperl/bioperl-live/issues

AUTHOR

Ewan Birney, birney@ebi.ac.uk

CONTRIBUTORS

Allen Day, allenday-at-ucla.edu, Richard Adams, Richard.Adams-at-ed.ac.uk, David J. Evans, David.Evans-at-vir.gla.ac.uk, Heikki Lehvaslaiho, heikki-at-bioperl-dot-org, Allen Smith, allens-at-cpan.org, Jason Stajich, jason-at-bioperl.org, Anthony Underwood, aunderwood-at-phls.org.uk, Xintao Wei & Giri Narasimhan, giri-at-cs.fiu.edu Brian Osborne, bosborne at alum.mit.edu Weigang Qiu, Weigang at GENECTR-HUNTER-CUNY-EDU Hongyu Zhang, forward at hongyu.org Jay Hannah, jay at jays.net Alexandr Bezginov, albezg at gmail.com

SEE ALSO

Bio::LocatableSeq

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title     : new
Usage     : my $aln = Bio::SimpleAlign->new();
Function  : Creates a new simple align object
Returns   : Bio::SimpleAlign
Args      : -source     => string representing the source program
                           where this alignment came from
            -annotation => Bio::AnnotationCollectionI
            -seq_annotation => Bio::AnnotationCollectionI for sequences (requires -annotation also be set)
            -seqs       => array ref containing Bio::LocatableSeq or Bio::Seq::Meta
            -consensus  => consensus string
            -consensus_meta  => Bio::Seq::Meta object containing consensus met information (kludge)

Modifier methods

These methods modify the MSA by adding, removing or shuffling complete sequences.

add_seq

Title     : add_seq
Usage     : $myalign->add_seq($newseq);
            $myalign->add_seq(-SEQ=>$newseq, -ORDER=>5);
Function  : Adds another sequence to the alignment. *Does not* align
            it - just adds it to the hashes.
            If -ORDER is specified, the sequence is inserted at the
            the position spec'd by -ORDER, and existing sequences
            are pushed down the storage array.
Returns   : nothing
Args      : A Bio::LocatableSeq object
            Positive integer for the sequence position (optional)

See Bio::LocatableSeq for more information

remove_seq

Title     : remove_seq
Usage     : $aln->remove_seq($seq);
Function  : Removes a single sequence from an alignment
Returns   :
Argument  : a Bio::LocatableSeq object

purge

Title   : purge
Usage   : $aln->purge(0.7);
Function: Removes sequences above given sequence similarity
          This function will grind on large alignments. Beware!
Example :
Returns : An array of the removed sequences
Args    : float, threshold for similarity

sort_alphabetically

Title     : sort_alphabetically
Usage     : $ali->sort_alphabetically
Function  : Changes the order of the alignment to alphabetical on name
            followed by numerical by number.
Returns   :
Argument  :

sort_by_list

Title     : sort_by_list
Usage     : $aln_ordered=$aln->sort_by_list($list_file)
Function  : Arbitrarily order sequences in an alignment
Returns   : A new Bio::SimpleAlign object
Argument  : a file listing sequence names in intended order (one name per line)

set_new_reference

Title     : set_new_reference
Usage     : $aln->set_new_reference(3 or 'B31'):  Select the 3rd sequence, or
            the sequence whoes name is "B31" (full, exact, and case-sensitive),
            as the reference (1st) sequence
Function  : Change/Set a new reference (i.e., the first) sequence
Returns   : a new Bio::SimpleAlign object.
            Throws an exception if designated sequence not found
Argument  : a positive integer of sequence order, or a sequence name
            in the original alignment

uniq_seq

Title     : uniq_seq
Usage     : $aln->uniq_seq():  Remove identical sequences in
            in the alignment.  Ambiguous base ("N", "n") and
            leading and ending gaps ("-") are NOT counted as
            differences.
Function  : Make a new alignment of unique sequence types (STs)
Returns   : 1a. if called in a scalar context, 
               a new Bio::SimpleAlign object (all sequences renamed as "ST")
            1b. if called in an array context, 
               a new Bio::SimpleAlign object, and a hashref whose keys
               are sequence types, and whose values are arrayrefs to 
               lists of sequence ids within the corresponding sequence type
            2. if $aln->verbose > 0, ST of each sequence is sent to 
               STDERR (in a tabular format)
Argument  : None

Sequence selection methods

Methods returning one or more sequences objects.

each_seq

Title     : each_seq
Usage     : foreach $seq ( $align->each_seq() )
Function  : Gets a Seq object from the alignment
Returns   : Seq object
Argument  :

each_alphabetically

Title     : each_alphabetically
Usage     : foreach $seq ( $ali->each_alphabetically() )
Function  : Returns a sequence object, but the objects are returned
            in alphabetically sorted order.
            Does not change the order of the alignment.
Returns   : Seq object
Argument  :

each_seq_with_id

Title     : each_seq_with_id
Usage     : foreach $seq ( $align->each_seq_with_id() )
Function  : Gets a Seq objects from the alignment, the contents
            being those sequences with the given name (there may be
            more than one)
Returns   : Seq object
Argument  : a seq name

get_seq_by_pos

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
            num_sequences() will throw an error.
Returns   : a Bio::LocatableSeq object
Args      : positive integer for the sequence position

get_seq_by_id

Title     : get_seq_by_id
Usage     : $seq = $aln->get_seq_by_id($name) # seq named $name
Function  : Gets a sequence based on its name.
            Sequences that do not exist will warn and return undef
Returns   : a Bio::LocatableSeq object
Args      : string for sequence name

seq_with_features

Title   : seq_with_features
Usage   : $seq = $aln->seq_with_features(-pos => 1,
                                         -consensus => 60
                                         -mask =>
          sub { my $consensus = shift;

                for my $i (1..5){
                   my $n = 'N' x $i;
                   my $q = '\?' x $i;
                   while($consensus =~ /[^?]$q[^?]/){
                      $consensus =~ s/([^?])$q([^?])/$1$n$2/;
                   }
                 }
                return $consensus;
              }
                                        );
Function: produces a Bio::Seq object by first splicing gaps from -pos
          (by means of a splice_by_seq_pos() call), then creating
          features using non-? chars (by means of a consensus_string()
          call with stringency -consensus).
Returns : a Bio::Seq object
Args    : -pos : required. sequence from which to build the Bio::Seq
            object
          -consensus : optional, defaults to consensus_string()'s
            default cutoff value
          -mask : optional, a coderef to apply to consensus_string()'s
            output before building features.  this may be useful for
            closing gaps of 1 bp by masking over them with N, for
            instance

Create new alignments

The result of these methods are horizontal or vertical subsets of the current MSA.

select

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 num_sequences() will throw an error.
Returns   : a Bio::SimpleAlign object
Args      : positive integer for the first sequence
            positive integer for the last sequence to include (optional)

select_noncont

Title     : select_noncont
Usage     : # 1st and 3rd sequences, sorted
            $aln2 = $aln->select_noncont(1, 3)

            # 1st and 3rd sequences, sorted (same as first)
            $aln2 = $aln->select_noncont(3, 1)

            # 1st and 3rd sequences, unsorted
            $aln2 = $aln->select_noncont('nosort',3, 1)

Function  : Creates a new alignment from a subset of sequences.  Numbering
            starts from 1.  Sequence positions larger than num_sequences() will
            throw an error.  Sorts the order added to new alignment by default,
            to prevent sorting pass 'nosort' as the first argument in the list.
Returns   : a Bio::SimpleAlign object
Args      : array of integers for the sequences.  If the string 'nosort' is
            passed as the first argument, the sequences will not be sorted
            in the new alignment but will appear in the order listed.

select_noncont_by_name

Title     : select_noncont_by_name
Usage     : my $aln2 = $aln->select_noncont_by_name('A123', 'B456');
Function  : Creates a new alignment from a subset of sequences which are
            selected by name (sequence ID).
Returns   : a Bio::SimpleAlign object
Args      : array of names (i.e., identifiers) for the sequences.

slice

Title     : slice
Usage     : $aln2 = $aln->slice(20,30)
Function  : Creates a slice from the alignment inclusive of start and
            end columns, and the first column in the alignment is denoted 1.
            Sequences with no residues in the slice are excluded from the
            new alignment and a warning is printed. Slice beyond the length of
            the sequence does not do padding.
Returns   : A Bio::SimpleAlign object
Args      : Positive integer for start column, positive integer for end column,
            optional boolean which if true will keep gap-only columns in the newly
            created slice. Example:

            $aln2 = $aln->slice(20,30,1)

remove_columns

Title     : remove_columns
Usage     : $aln2 = $aln->remove_columns(['mismatch','weak']) or
            $aln2 = $aln->remove_columns([0,0],[6,8])
Function  : Creates an aligment with columns removed corresponding to
            the specified type or by specifying the columns by number.
Returns   : Bio::SimpleAlign object
Args      : Array ref of types ('match'|'weak'|'strong'|'mismatch'|'gaps'|
            'all_gaps_columns') or array ref where the referenced array
            contains a pair of integers that specify a range.
            The first column is 0

remove_gaps

Title     : remove_gaps
Usage     : $aln2 = $aln->remove_gaps
Function  : Creates an aligment with gaps removed
Returns   : a Bio::SimpleAlign object
Args      : a gap character(optional) if none specified taken
               from $self->gap_char,
            [optional] $all_gaps_columns flag (1 or 0, default is 0)
                       indicates that only all-gaps columns should be deleted

Used from method remove_columns in most cases. Set gap character using gap_char().

Change sequences within the MSA

These methods affect characters in all sequences without changing the alignment.

splice_by_seq_pos

Title   : splice_by_seq_pos
Usage   : $status = splice_by_seq_pos(1);
Function: splices all aligned sequences where the specified sequence
          has gaps.
Example :
Returns : 1 on success
Args    : position of sequence to splice by

map_chars

Title     : map_chars
Usage     : $ali->map_chars('\.','-')
Function  : Does a s/$arg1/$arg2/ on the sequences. Useful for gap
            characters.

            Note that the first argument is interpreted as a regexp
            so be careful and escape any wild card characters (e.g.
            do $ali->map_chars('\.','-') to replace periods with dashes.
Returns   : 1 on success
Argument  : A regexp and a string

uppercase

Title     : uppercase()
Usage     : $ali->uppercase()
Function  : Sets all the sequences to uppercase
Returns   : 1 on success
Argument  :

cigar_line

Title    : cigar_line()
Usage    : %cigars = $align->cigar_line()
Function : Generates a "cigar" (Compact Idiosyncratic Gapped Alignment
           Report) line for each sequence in the alignment. Examples are
           "1,60" or "5,10:12,58", where the numbers refer to conserved
           positions within the alignment. The keys of the hash are the
           NSEs (name/start/end) assigned to each sequence.
Args     : threshold (optional, defaults to 100)
Returns  : Hash of strings (cigar lines)

match_line

Title    : match_line()
Usage    : $line = $align->match_line()
Function : Generates a match line - much like consensus string
           except that a line indicating the '*' for a match.
Args     : (optional) Match line characters ('*' by default)
           (optional) Strong match char (':' by default)
           (optional) Weak match char ('.' by default)
Returns  : String

gap_line

Title    : gap_line()
Usage    : $line = $align->gap_line()
Function : Generates a gap line - much like consensus string
           except that a line where '-' represents gap
Args     : (optional) gap line characters ('-' by default)
Returns  : string

all_gap_line

Title    : all_gap_line()
Usage    : $line = $align->all_gap_line()
Function : Generates a gap line - much like consensus string
           except that a line where '-' represents all-gap column
Args     : (optional) gap line characters ('-' by default)
Returns  : string

gap_col_matrix

Title    : gap_col_matrix()
Usage    : my $cols = $align->gap_col_matrix()
Function : Generates an array where each element in the array is a 
           hash reference with a key of the sequence name and a
           value of 1 if the sequence has a gap at that column
Returns  : Reference to an array
Args     : Optional: gap line character ($aln->gap_char or '-' by default)

match

Title     : match()
Usage     : $ali->match()
Function  : Goes through all columns and changes residues that are
            identical to residue in first sequence to match '.'
            character. Sets match_char.

            USE WITH CARE: Most MSA formats do not support match
            characters in sequences, so this is mostly for output
            only. NEXUS format (Bio::AlignIO::nexus) can handle
            it.
Returns   : 1 on success
Argument  : a match character, optional, defaults to '.'

unmatch

Title     : unmatch()
Usage     : $ali->unmatch()
Function  : Undoes the effect of method match. Unsets match_char.
Returns   : 1 on success
Argument  : a match character, optional, defaults to '.'

See match and match_char

MSA attributes

Methods for setting and reading the MSA attributes.

Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string ('').

id

Title     : id
Usage     : $myalign->id("Ig")
Function  : Gets/sets the id field of the alignment
Returns   : An id string
Argument  : An id string (optional)

accession

Title     : accession
Usage     : $myalign->accession("PF00244")
Function  : Gets/sets the accession field of the alignment
Returns   : An acc string
Argument  : An acc string (optional)

description

Title     : description
Usage     : $myalign->description("14-3-3 proteins")
Function  : Gets/sets the description field of the alignment
Returns   : An description string
Argument  : An description string (optional)

missing_char

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)

match_char

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)

gap_char

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)

symbol_chars

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
Args    : boolean to include the gap/missing/match characters

Alignment descriptors

These read only methods describe the MSA in various ways.

score

Title     : score
Usage     : $str = $ali->score()
Function  : get/set a score of the alignment
Returns   : a score for the alignment
Argument  : an optional score to set

consensus_string

Title     : consensus_string
Usage     : $str = $ali->consensus_string($threshold_percent)
Function  : Makes a strict consensus
Returns   : Consensus string
Argument  : Optional threshold ranging from 0 to 100.
            The consensus residue has to appear at least threshold %
            of the sequences at a given location, otherwise a '?'
            character will be placed at that location.
            (Default value = 0%)

consensus_conservation

Title     : consensus_conservation
Usage     : @conservation = $ali->consensus_conservation();
Function  : Conservation (as a percent) of each position of alignment
Returns   : Array of percentages [0-100]. Gap columns are 0% conserved.
Argument  :

consensus_iupac

Title     : consensus_iupac
Usage     : $str = $ali->consensus_iupac()
Function  : Makes a consensus using IUPAC ambiguity codes from DNA
            and RNA. The output is in upper case except when gaps in
            a column force output to be in lower case.

            Note that if your alignment sequences contain a lot of
            IUPAC ambiquity codes you often have to manually set
            alphabet.  Bio::PrimarySeq::_guess_type thinks they
            indicate a protein sequence.
Returns   : consensus string
Argument  : none
Throws    : on protein sequences

consensus_meta

Title     : consensus_meta
Usage     : $seqmeta = $ali->consensus_meta()
Function  : Returns a Bio::Seq::Meta object containing the consensus
            strings derived from meta data analysis.
Returns   : Bio::Seq::Meta 
Argument  : Bio::Seq::Meta 
Throws    : non-MetaI object

is_flush

Title     : is_flush
Usage     : if ( $ali->is_flush() )
Function  : Tells you whether the alignment
          : is flush, i.e. all of the same length
Returns   : 1 or 0
Argument  :

length

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   : Integer
Argument  :

maxdisplayname_length

Title     : maxdisplayname_length
Usage     : $ali->maxdisplayname_length()
Function  : Gets the maximum length of the displayname in the
            alignment. Used in writing out various MSA formats.
Returns   : integer
Argument  :

max_metaname_length

Title     : max_metaname_length
Usage     : $ali->max_metaname_length()
Function  : Gets the maximum length of the meta name tags in the
            alignment for the sequences and for the alignment.
            Used in writing out various MSA formats.
Returns   : integer
Argument  : None

num_residues

Title     : num_residues
Usage     : $no = $ali->num_residues
Function  : number of residues in total in the alignment
Returns   : integer
Argument  :
Note      : replaces no_residues()

num_sequences

Title     : num_sequences
Usage     : $depth = $ali->num_sequences
Function  : number of sequence in the sequence alignment
Returns   : integer
Argument  : none
Note      : replaces no_sequences()

average_percentage_identity

Title   : average_percentage_identity
Usage   : $id = $align->average_percentage_identity
Function: The function uses a fast method to calculate the average
          percentage identity of the alignment
Returns : The average percentage identity of the alignment
Args    : None
Notes   : This method implemented by Kevin Howe calculates a figure that is
          designed to be similar to the average pairwise identity of the
          alignment (identical in the absence of gaps), without having to
          explicitly calculate pairwise identities proposed by Richard Durbin.
          Validated by Ewan Birney ad Alex Bateman.

percentage_identity

Title   : percentage_identity
Usage   : $id = $align->percentage_identity
Function: The function calculates the average percentage identity
          (aliased to average_percentage_identity)
Returns : The average percentage identity
Args    : None

overall_percentage_identity

Title   : overall_percentage_identity
Usage   : $id = $align->overall_percentage_identity
          $id = $align->overall_percentage_identity('short')
Function: The function calculates the percentage identity of
          the conserved columns
Returns : The percentage identity of the conserved columns
Args    : length value to use, optional defaults to alignment length
                possible values: 'align', 'short', 'long'

The argument values 'short' and 'long' refer to shortest and longest sequence in the alignment. Method modification code by Hongyu Zhang.

Alignment positions

Methods to map a sequence position into an alignment column and back. column_from_residue_number() does the former. The latter is really a property of the sequence object and can done using Bio::LocatableSeq::location_from_column:

# select somehow a sequence from the alignment, e.g.
my $seq = $aln->get_seq_by_pos(1);
#$loc is undef or Bio::LocationI object
my $loc = $seq->location_from_column(5);

column_from_residue_number

 Title   : column_from_residue_number
 Usage   : $col = $ali->column_from_residue_number( $seqname, $resnumber)
 Function: This function gives the position in the alignment
           (i.e. column number) of the given residue number in the
           sequence with the given name. For example, for the
           alignment

    	     Seq1/91-97 AC..DEF.GH.
   	     Seq2/24-30 ACGG.RTY...
  	        Seq3/43-51 AC.DDEF.GHI

           column_from_residue_number( "Seq1", 94 ) returns 6.
           column_from_residue_number( "Seq2", 25 ) returns 2.
           column_from_residue_number( "Seq3", 50 ) returns 10.

           An exception is thrown if the residue number would lie
           outside the length of the aligment
           (e.g. column_from_residue_number( "Seq2", 22 )

      	  Note: If the the parent sequence is represented by more than
	        one alignment sequence and the residue number is present in
	        them, this method finds only the first one.

 Returns : A column number for the position in the alignment of the
           given residue in the given sequence (1 = first column)
 Args    : A sequence id/name (not a name/start-end)
           A residue number in the whole sequence (not just that
           segment of it in the alignment)

Sequence names

Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways.

displayname

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)

set_displayname_count

Title     : set_displayname_count
Usage     : $ali->set_displayname_count
Function  : Sets the names to be name_# where # is the number of
            times this name has been used.
Returns   : 1, on success
Argument  :

set_displayname_flat

Title     : set_displayname_flat
Usage     : $ali->set_displayname_flat()
Function  : Makes all the sequences be displayed as just their name,
            not name/start-end (NSE)
Returns   : 1
Argument  :

set_displayname_normal

Title     : set_displayname_normal
Usage     : $ali->set_displayname_normal()
Function  : Makes all the sequences be displayed as name/start-end (NSE)
Returns   : 1, on success
Argument  :

source

Title   : source
Usage   : $obj->source($newval)
Function: sets the Alignment source program
Example :
Returns : value of source
Args    : newvalue (optional)

set_displayname_safe

Title     : set_displayname_safe
Usage     : ($new_aln, $ref_name)=$ali->set_displayname_safe(4)
Function  : Assign machine-generated serial names to sequences in input order.
            Designed to protect names during PHYLIP runs. Assign 10-char string
            in the form of "S000000001" to "S999999999". Restore the original
            names using "restore_displayname".
Returns   : 1. a new $aln with system names;
            2. a hash ref for restoring names
Argument  : Number for id length (default 10)

restore_displayname

Title     : restore_displayname
Usage     : $aln_name_restored=$ali->restore_displayname($hash_ref)
Function  : Restore original sequence names (after running
            $ali->set_displayname_safe)
Returns   : a new $aln with names restored.
Argument  : a hash reference of names from "set_displayname_safe".

sort_by_start

Title     : sort_by_start
Usage     : $ali->sort_by_start
Function  : Changes the order of the alignment to the start position of each
            subalignment    
Returns   : 1 on success
Argument  :

bracket_string

Title     : bracket_string
Usage     : my @params = (-refseq     => 'testseq',
                          -allele1    => 'allele1',
                          -allele2    => 'allele2',
                          -delimiters => '{}',
                          -separator  => '/');
            $str = $aln->bracket_string(@params)

Function :  When supplied with a list of parameters (see below), returns a
            string in BIC format. This is used for allelic comparisons.
            Briefly, if either allele contains a base change when compared to
            the refseq, the base or gap for each allele is represented in
            brackets in the order present in the 'alleles' parameter.

            For the following data:

            >testseq
            GGATCCATTGCTACT
            >allele1
            GGATCCATTCCTACT
            >allele2
            GGAT--ATTCCTCCT

            the returned string with parameters 'refseq => testseq' and
            'alleles => [qw(allele1 allele2)]' would be:

            GGAT[C/-][C/-]ATT[C/C]CT[A/C]CT
Returns   : BIC-formatted string
Argument  : Required args
               refseq    : string (ID) of the reference sequence used
                           as basis for comparison
               allele1   : string (ID) of the first allele
               allele2   : string (ID) of the second allele
            Optional args
               delimiters: two symbol string of left and right delimiters.
                           Only the first two symbols are used
                           default = '[]'
               separator : string used as a separator.  Only the first
                           symbol is used
                           default = '/'
Throws    : On no refseq/alleles, or invalid refseq/alleles.

methods implementing Bio::FeatureHolderI

FeatureHolderI implementation to support labeled character sets like one would get from NEXUS represented data.

get_SeqFeatures

Usage   : @features = $aln->get_SeqFeatures
Function: Get the feature objects held by this feature holder.
Example :
Returns : an array of Bio::SeqFeatureI implementing objects
Args    : optional filter coderef, taking a Bio::SeqFeatureI 
        : as argument, returning TRUE if wanted, FALSE if 
        : unwanted

add_SeqFeature

Usage   : $aln->add_SeqFeature($subfeat);
Function: Adds a SeqFeature into the SeqFeature array. The 'EXPAND' qualifier
          (see L<Bio::FeatureHolderI>) is supported, but has no effect.
Example :
Returns : 1 on success
Args    : a Bio::SeqFeatureI object

remove_SeqFeatures

Usage   : $obj->remove_SeqFeatures
Function: Removes all SeqFeatures.  If you want to remove only a subset,
          remove that subset from the returned array, and add back the rest.
Returns : The array of Bio::SeqFeatureI features that was
          deleted from this alignment.
Args    : none

feature_count

Title   : feature_count
Usage   : $obj->feature_count()
Function: Return the number of SeqFeatures attached to the alignment
Returns : integer representing the number of SeqFeatures
Args    : None

get_all_SeqFeatures

Title   : get_all_SeqFeatures
Usage   : 
Function: Get all SeqFeatures.
Example :
Returns : an array of Bio::SeqFeatureI implementing objects
Args    : none
Note    : Falls through to Bio::FeatureHolderI implementation.

methods for Bio::AnnotatableI

AnnotatableI implementation to support sequence alignments which contain annotation (NEXUS, Stockholm).

annotation

Title   : annotation
Usage   : $ann = $aln->annotation or 
          $aln->annotation($ann)
Function: Gets or sets the annotation
Returns : Bio::AnnotationCollectionI object
Args    : None or Bio::AnnotationCollectionI object

See Bio::AnnotationCollectionI and Bio::Annotation::Collection for more information

Deprecated methods

mask_columns

Title     : mask_columns
Usage     : $aln2 = $aln->mask_columns(20,30)
Function  : Masks a slice of the alignment inclusive of start and
            end columns, and the first column in the alignment is denoted 1.
            Mask beyond the length of the sequence does not do padding.
Returns   : A Bio::SimpleAlign object
Args      : Positive integer for start column, positive integer for end column,
            optional string value use for the mask. Example:

            $aln2 = $aln->mask_columns(20,30,'?')
Note      : Masking must use a character that is not used for gaps or
            frameshifts.  These can be adjusted using the relevant global
            variables, but be aware these may be (uncontrollably) modified
            elsewhere within BioPerl (see bug 2715)