Bio::SimpleAlign.3pm

Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

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->no_residues;
   print $aln->is_flush;
   print $aln->no_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); # get single columns
   $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
 
 

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:
   http://bugzilla.open-bio.org/
 
 

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

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);
  Function  : Adds another sequence to the alignment. *Does not* align
              it - just adds it to the hashes.
  Returns   : nothing
  Args      : a Bio::LocatableSeq object
              order (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   : 1. a new Bio::SimpleAlign object (all sequences renamed as "ST")
              2. ST of each sequence in STDERR
  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
              no_sequences() will thow 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 no_sequences() will thow 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 no_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.
 
 

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
 
              Notice that the from (arg1) is interpretted as a regex,
              so be careful about quoting meta characters (eg
              $ali->map_chars('.','-') wont do what you want)
  Returns   :
  Argument  : 'from' rexexp
              'to' string
 
 

uppercase

  Title     : uppercase()
  Usage     : $ali->uppercase()
  Function  : Sets all the sequences to uppercase
  Returns   :
  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 = $align->gap_col_matrix()
  Function : Generates an array of hashes where
             each entry in the array is a hash reference
             with keys of all the sequence names and
             and value of 1 or 0 if the sequence has a gap at that column
  Args     : (optional) gap line characters ($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
  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
  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 treshold 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_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
 
 

no_residues

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

no_sequences

  Title     : no_sequences
  Usage     : $depth = $ali->no_sequences
  Function  : number of sequence in the sequence alignment
  Returns   : integer
  Argument  :
 
 

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
  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
  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   :
  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 for Bio::FeatureHolder

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

get_SeqFeatures

  Usage   :
  Function: Get the feature objects held by this feature holder.
  Example :
  Returns : an array of Bio::SeqFeatureI implementing objects
  Args    : none
 
 

At some day we may want to expand this method to allow for a feature filter to be passed in.

add_SeqFeature

  Usage   : $feat->add_SeqFeature($subfeat);
            $feat->add_SeqFeature($subfeat,'EXPAND')
  Function: adds a SeqFeature into the subSeqFeature array.
            with no 'EXPAND' qualifer, subfeat will be tested
            as to whether it lies inside the parent, and throw
            an exception if not.
 
            If EXPAND is used, the parent''s start/end/strand will
            be adjusted so that it grows to accommodate the new
            subFeature
  Example :
  Returns : nothing
  Args    : a Bio::SeqFeatureI object
 
 

remove_SeqFeatures

  Usage   : $obj->remove_SeqFeatures
  Function: Removes all sub 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 implementing sub-features that was
            deleted from this feature.
  Args    : none
 
 

feature_count

  Title   : feature_count
  Usage   : $obj->feature_count()
  Function: Return the number of SeqFeatures attached to a feature holder.
 
            This is before flattening a possible sub-feature tree.
 
            We provide a default implementation here that just counts
            the number of objects returned by get_SeqFeatures().
            Implementors may want to override this with a more
            efficient implementation.
 
  Returns : integer representing the number of SeqFeatures
  Args    : None
 
 

At some day we may want to expand this method to allow for a feature filter to be passed in.

Our default implementation allows for any number of additional arguments and will pass them on to get_SeqFeatures(). I.e., in order to support filter arguments, just support them in get_SeqFeatures().

get_all_SeqFeatures

  Title   : get_all_SeqFeatures
  Usage   :
  Function: Get the flattened tree of feature objects held by this
            feature holder. The difference to get_SeqFeatures is that
            the entire tree of sub-features will be flattened out.
 
            We provide a default implementation here, so implementors
            don''t necessarily need to implement this method.
 
  Example :
  Returns : an array of Bio::SeqFeatureI implementing objects
  Args    : none
 
 

At some day we may want to expand this method to allow for a feature filter to be passed in.

Our default implementation allows for any number of additional arguments and will pass them on to any invocation of get_SeqFeatures(), wherever a component of the tree implements FeatureHolderI. I.e., in order to support filter arguments, just support them in get_SeqFeatures().

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