Bio::SimpleAlign(3pm)

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)