Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::Assembly::Contig - Perl module to hold and manipulate
                            sequence assembly contigs.


           # Module loading
           use Bio::Assembly::IO;

           # Assembly loading methods
           $aio = Bio::Assembly::IO->new(-file=>"test.ace.1",

           $assembly = $aio->next_assembly;
           foreach $contig ($assembly->all_contigs) {
             # do something

           # OR, if you want to build the contig yourself,

           use Bio::Assembly::Contig;
           $c = Bio::Assembly::Contig->new(-id=>"1");

           $ls  = Bio::LocatableSeq->new(-seq=>"ACCG-T",
           $ls2 = Bio::LocatableSeq->new(-seq=>"ACA-CG-T",

           $ls_coord = Bio::SeqFeature::Generic->new(-start=>3,
           $ls2_coord = Bio::SeqFeature::Generic->new(-start=>1,

           $con = Bio::LocatableSeq->new(-seq=>"ACACCG-T",

           $l = $c->change_coord('unaligned r2','ungapped consensus',6);
           print "6 in unaligned r2 => $l in ungapped consensus\n";


       A contig is as a set of sequences, locally aligned to each other, so that every sequence
       has overlapping regions with at least one sequence in the contig, such that a continuous
       of overlapping sequences is formed, allowing the deduction of a consensus sequence which
       may be longer than any of the sequences from which it was deduced.

       In this documentation we refer to the overlapping sequences used to build the contig as
       "aligned sequences" and to the sequence deduced from the overlap of aligned sequences as
       the "consensus". Methods to deduce the consensus sequence from aligned sequences were not
       yet implemented in this module, but its posssible to add a consensus sequence deduced by
       other means, e.g, by the assembly program used to build the alignment.

       All aligned sequences in a Bio::Assembly::Contig must be Bio::Assembly::Locatable objects
       and have a unique ID. The unique ID restriction is due to the nature of the module's
       internal data structures and is also a request of some assembly programs. If two sequences
       with the same ID are added to a contig, the first sequence added is replaced by the second

       There are four base coordinate systems in Bio::Assembly::Contig.  When you need to access
       contig elements or data that exists on a certain range or location, you may be specifying
       coordinates in relation to different sequences, which may be either the contig consensus
       or one of the aligned sequences that were used to do the assembly.

                 Name           | Referenced sequence
          "gapped consensus"    | Contig (with gaps)
          "ungapped consensus"  | Contig (without gaps)
          "aligned $seqID"      | sequence $seqID (with gaps)
          "unaligned $seqID"    | sequence $seqID (without gaps)

       "gapped consensus" refers to positions in the aligned consensus sequence, which is the
       consensus sequence including the gaps inserted to align it against the aligned sequences
       that were used to assemble the contig. So, its limits are [ 1, (consensus length + number
       of gaps in consensus) ]

       "ungapped consensus" is a coordinate system based on the consensus sequence, but excluding
       consensus gaps. This is just the coordinate system that you have when considering the
       consensus sequence alone, instead of aligned to other sequences.

       "aligned $seqID" refers to locations in the sequence $seqID after alignment of $seqID
       against the consensus sequence (reverse complementing the original sequence, if needed).
       Coordinate 1 in "aligned $seqID" is equivalent to the start location (first base) of
       $seqID in the consensus sequence, just like if the aligned sequence $seqID was a feature
       of the consensus sequence.

       "unaligned $seqID" is equivalent to a location in the isolated sequence, just like you
       would have when considering the sequence alone, out of an alignment.  When changing
       coordinates from "aligned $seq2" to "unaligned $seq2", if $seq2 was reverse complemented
       when included in the alignment, the output coordinates will be reversed to fit that fact,
       i.e. 1 will be changed to length($seq2), 2 will be length($seq)-1 and so on.

       An important note: when you change gap coordinates from a gapped system ("gapped
       consensus" or "aligned $seqID") to a system that does not include gaps ("ungapped
       consensus" or "unaligned $seqID"), the position returned will be the first location before
       all gaps neighboring the input location.

       Bio::Assembly::Contig stores much information about a contig in a
       Bio::Assembly::SeqFeature::Collection object. Relevant information on the alignment is
       accessed by selecting features based on their primary tags (e.g. all features which have a
       primary tag of the form '_aligned_coord:$seqID', where $seqID is an aligned sequence ID,
       are coordinates for sequences in the contig alignment) and, by using methods from
       Bio::Assembly::SeqFeature::Collection, it's possible to select features by overlap with
       other features.

       We suggest that you use the primary tags of features as identifiers for feature classes.
       By convention, features with primary tags starting with a '_' are generated by modules
       that populate the contig data structure and return the contig object, maybe as part of an
       assembly object, e.g.  drivers from the Bio::Assembly::IO set.

       Features in the features collection may be associated with particular aligned sequences.
       To obtain this, you must attach the sequence to the feature, using attach() seq from
       Bio::Assembly::SeqFeatureI, before you add the feature to the feature collection. We also
       suggest to add the sequence id to the primary tag, so that is easy to select feature for a
       particular sequence.

       There is only one feature class that some methods in Bio::Assembly::Contig expect to find
       in the feature collection: features with primary tags of the form '_aligned_coord:$seqID',
       where $seqID is the aligned sequence id (like returned by $seq->id()). These features
       describe the position (in "gapped consensus" coordinates) of aligned sequences, and the
       method set_seq_coord() automatically changes a feature's primary tag to this form whenever
       the feature is added to the collection by this method. Only two methods in
       Bio::Assembly::Contig will not work unless there are features from this class:
       change_coord() and get_seq_coord().

       Other feature classes will be automatically available only when Bio::Assembly::Contig
       objects are created by a specific module. Such feature classes are (or should be)
       documented in the documentation of the module which create them, to which the user should


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       your comments and suggestions preferably to the Bioperl mailing lists  Your participation
       is much appreciated.
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       Please direct usage questions or support issues to the mailing list:

       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.

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       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:

AUTHOR - Robson Francisco de Souza


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

Object creator

        Title     : new
        Usage     : my $contig = Bio::Assembly::Contig->new();
        Function  : Creates a new contig object
        Returns   : Bio::Assembly::Contig
        Args      : -id         => unique contig ID
                    -source     => string for the sequence assembly program used
                    -collection => Bio::SeqFeature::CollectionI instance

Assembly related methods

       These methods exist to enable adding information about possible relations among contigs,
       e.g. when you already have a scaffold for your assembly, describing the ordering of
       contigs in the final assembly, but no sequences covering the gaps between neighboring

        Title     : source
        Usage     : $contig->source($program);
        Function  : Get/Set program used to build this contig
        Returns   : string
        Argument  : [optional] string

        Title     : assembly
        Usage     : $contig->assembly($assembly);
        Function  : Get/Set assembly object for this contig
        Returns   : a Bio::Assembly::Scaffold object
        Argument  : a Bio::Assembly::Scaffold object

        Title     : strand
        Usage     : $contig->strand($num);
        Function  : Get/Set contig orientation in a scaffold/assembly.
                    Its equivalent to the strand property of sequence
                    objects and sets whether the contig consensus should
                    be reversed and complemented before being added to a
                    scaffold or assembly.
        Returns   : integer
        Argument  : 1 if orientaion is forward, -1 if reverse and
                    0 if none

        Title     : upstream_neighbor
        Usage     : $contig->upstream_neighbor($contig);
        Function  : Get/Set a contig neighbor for the current contig when
                    building a scaffold. The upstream neighbor is
                    located before $contig first base
        Returns   : nothing
        Argument  : Bio::Assembly::Contig

        Title     : downstream_neighbor
        Usage     : $contig->downstream_neighbor($num);
        Function  : Get/Set a contig neighbor for the current contig when
                    building a scaffold. The downstream neighbor is
                    located after $contig last base
        Returns   : nothing
        Argument  : Bio::Assembly::Contig

Contig feature collection methods

        Title     : add_features
        Usage     : $contig->add_features($feat,$flag)
        Function  :

                    Add an array of features to the contig feature
                    collection. The consensus sequence may be attached to the
                    added feature, if $flag is set to 1. If $flag is 0 and
                    the feature attached to one of the contig aligned
                    sequences, the feature is registered as an aligned
                    sequence feature. If $flag is 0 and the feature is not
                    attached to any sequence in the contig, the feature is
                    simply added to the feature collection and no attachment
                    or registration is made.

                    Note: You must attach aligned sequences to their features
                    prior to calling add_features, otherwise you won't be
                    able to access the feature through get_seq_feat_by_tag()

        Returns   : number of features added.
        Argument  :
                    $feat : A reference to an array of Bio::SeqFeatureI
                    $flag : boolean - true if consensus sequence object
                            should be attached to this feature, false if
                            no consensus attachment should be made.
                            Default: false.

        Title     : remove_features
        Usage     : $contig->remove_features(@feat)
        Function  : Remove an array of contig features
        Returns   : true if successful
        Argument  : An array of Bio::SeqFeature::Generic (Bio::SeqFeatureI)

        Title     : get_features_collection
        Usage     : $contig->get_features_collection()
        Function  : Get the collection of all contig features and seqfeatures
        Returns   : Bio::DB::SeqFeature::Store (Bio::SeqFeature::CollectionI)
        Argument  : none

        Title     : remove_features_collection
        Usage     : $contig->remove_features_collection()
        Function  : Remove the collection of all contig features. It is useful
                    to save some memory (when contig features are not needed).
        Returns   : none
        Argument  : none

Coordinate system's related methods

       See Coordinate_Systems above.

        Title     : change_coord
        Usage     : $contig->change_coord($in,$out,$query)
        Function  :

                    Change coordinate system for $query.  This method
                    transforms locations between coordinate systems described
                    in section "Coordinate Systems" of this document.

                    Note: this method will throw an exception when changing
                    coordinates between "ungapped consensus" and other
                    systems if consensus sequence was not set. It will also
                    throw exceptions when changing coordinates among aligned
                    sequence, either with or without gaps, and other systems
                    if sequence locations were not set with set_seq_coord().

        Returns   : integer
        Argument  :
                    $in    : [string]  input coordinate system
                    $out   : [string]  output coordinate system
                    $query : [integer] a position in a sequence

        Title     : get_seq_coord
        Usage     : $contig->get_seq_coord($seq);
        Function  : Get "gapped consensus" location for aligned sequence
        Returns   : Bio::SeqFeature::Generic for coordinates or undef.
                    A warning is printed if sequence coordinates were not set.
        Argument  : Bio::LocatableSeq object

        Title     : set_seq_coord
        Usage     : $contig->set_seq_coord($feat,$seq);
        Function  :

                    Set "gapped consensus" location for an aligned
                    sequence. If the sequence was previously added using
                    add_seq, its coordinates are changed/set.  Otherwise,
                    add_seq is called and the sequence is added to the

        Returns   : Bio::SeqFeature::Generic for old coordinates or undef.
        Argument  :
                    $feat  : a Bio::SeqFeature::Generic object
                             representing a location for the
                             aligned sequence, in "gapped
                             consensus" coordinates.

                    Note: the original feature primary tag will
                          be lost.

                    $seq   : a Bio::LocatableSeq object

Bio::Assembly::Contig consensus methods

        Title     : set_consensus_sequence
        Usage     : $contig->set_consensus_sequence($seq)
        Function  : Set the consensus sequence object for this contig
        Returns   : consensus length
        Argument  : Bio::LocatableSeq

        Title     : set_consensus_quality
        Usage     : $contig->set_consensus_quality($qual)
        Function  : Set the quality object for consensus sequence
        Returns   : nothing
        Argument  : Bio::Seq::QualI object

        Title     : get_consensus_length
        Usage     : $contig->get_consensus_length()
        Function  : Get consensus sequence length
        Returns   : integer
        Argument  : none

        Title     : get_consensus_sequence
        Usage     : $contig->get_consensus_sequence()
        Function  : Get a reference to the consensus sequence object
                    for this contig
        Returns   : Bio::SeqI object
        Argument  : none

        Title     : get_consensus_quality
        Usage     : $contig->get_consensus_quality()
        Function  : Get a reference to the consensus quality object
                    for this contig.
        Returns   : A Bio::Seq::QualI object
        Argument  : none

Bio::Assembly::Contig aligned sequences methods

        Title     : set_seq_qual
        Usage     : $contig->set_seq_qual($seq,$qual);
        Function  : Adds quality to an aligned sequence.
        Returns   : nothing
        Argument  : a Bio::LocatableSeq object and
                    a Bio::Seq::QualI object

       See Bio::LocatableSeq for more information.

        Title     : get_seq_ids
        Usage     : $contig->get_seq_ids( -start => $start,
                                          -end   => $end,
                                          -type  => "gapped A0QR67B08.b" );
        Function  : Get list of sequence IDs overlapping interval [$start, $end]
                    The default interval is [1,$contig->length]
                    Default coordinate system is "gapped contig"
        Returns   : An array
        Argument  : A hash with optional elements:
                    -start : consensus subsequence start
                    -end   : consensus subsequence end
                    -type  : the coordinate system type for $start and $end arguments
                             Coordinate system available are:
                             "gapped consensus"   : consensus coordinates with gaps
                             "ungapped consensus" : consensus coordinates without gaps
                             "aligned $ReadID"    : read $ReadID coordinates with gaps
                             "unaligned $ReadID"  : read $ReadID coordinates without gaps

        Title     : get_seq_feat_by_tag
        Usage     : $seq = $contig->get_seq_feat_by_tag($seq,"_aligned_coord:$seqID")
        Function  : Get a sequence feature based on its primary_tag.
        Returns   : a Bio::SeqFeature object
        Argument  : a Bio::LocatableSeq and a string (feature primary tag)

        Title     : get_seq_by_name
        Usage     : $seq = $contig->get_seq_by_name('Seq1')
        Function  : Gets a sequence based on its id.
        Returns   : a Bio::LocatableSeq object
                    undef if name is not found
        Argument  : string

        Title     : get_qual_by_name
        Usage     : $seq = $contig->get_qual_by_name('Seq1')
        Function  :

                    Gets Bio::Seq::QualI object for a sequence
                    through its id ( as given by $qual->id() ).

        Returns   : a Bio::Seq::QualI object.
                    undef if name is not found
        Argument  : string

Bio::Align::AlignI compatible methods

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

        Title     : add_seq
        Usage     : $contig->add_seq($newseq);
        Function  :

                    Adds a sequence to the contig. *Does*
                    *not* align it - just adds it to the

        Returns   : nothing
        Argument  : a Bio::LocatableSeq object

       See Bio::LocatableSeq for more information.

        Title     : remove_seq
        Usage     : $contig->remove_seq($seq);
        Function  : Removes a single sequence from a contig
        Returns   : 1 on success, 0 otherwise
        Argument  : a Bio::LocatableSeq object

        Title   : purge
        Usage   : $contig->purge(0.7);

                  Removes sequences above whatever %id.

                  This function will grind on large alignments. Beware!
                  (perhaps not ideally implemented)

        Example :
        Returns : An array of the removed sequences

        Title     : sort_alphabetically
        Usage     : $contig->sort_alphabetically
        Function  :

                    Changes the order of the alignment to alphabetical on name
                    followed by numerical by number.

        Returns   :
        Argument  :

   Sequence selection methods
       Methods returning one or more sequences objects.

        Title     : each_seq
        Usage     : foreach $seq ( $contig->each_seq() )
        Function  : Gets an array of Seq objects from the alignment
        Returns   : an array
        Argument  :

        Title     : each_alphabetically
        Usage     : foreach $seq ( $contig->each_alphabetically() )
        Function  :

                    Returns an array of sequence object sorted alphabetically
                    by name and then by start point.
                    Does not change the order of the alignment

        Returns   :
        Argument  :

        Title     : each_seq_with_id
        Usage     : foreach $seq ( $contig->each_seq_with_id() )
        Function  :

                    Gets an array of Seq objects from the
                    alignment, the contents being those sequences
                    with the given name (there may be more than one)

        Returns   : an array
        Argument  : a seq name

        Title     : get_seq_by_pos
        Usage     : $seq = $contig->get_seq_by_pos(3)
        Function  :

                    Gets a sequence based on its position in the alignment.
                    Numbering starts from 1.  Sequence positions larger than
                    num_sequences() will thow an error.

        Returns   : a Bio::LocatableSeq object
        Argument  : positive integer for the sequence osition

   Create new alignments
       The result of these methods are horizontal or vertical subsets of the current MSE.

        Title     : select
        Usage     : $contig2 = $contig->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 thow an error.

        Returns   : a Bio::Assembly::Contig object
        Argument  : positive integer for the first sequence
                    positive integer for the last sequence to include (optional)

        Title     : select_noncont
        Usage     : $contig2 = $contig->select_noncont(1, 3) # first and 3rd sequences
        Function  :

                    Creates a new alignment from a subset of
                    sequences.  Numbering starts from 1.  Sequence positions
                    larger than num_sequences() will throw an error.

        Returns   : a Bio::Assembly::Contig object
        Args      : array of integers for the sequences

        Title     : slice
        Usage     : $contig2 = $contig->slice(20, 30)
        Function  :

                    Creates a slice from the alignment inclusive of start and
                    end columns.  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

        Returns   : a Bio::Assembly::Contig object
        Argument  : positive integer for start column
                    positive integer for end column

   Change sequences within the MSE
       These methods affect characters in all sequences without changeing the alignment.

        Title     : map_chars
        Usage     : $contig->map_chars('\.','-')
        Function  :

                    Does a s/$arg1/$arg2/ on the sequences. Useful for gap

                    Notice that the from (arg1) is interpretted as a regex,
                    so be careful about quoting meta characters (eg
                    $contig->map_chars('.','-') won't do what you want)

        Returns   :
        Argument  : 'from' rexexp
                    'to' string

        Title     : uppercase()
        Usage     : $contig->uppercase()
        Function  : Sets all the sequences to uppercase
        Returns   :
        Argument  :

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

        Title     : match()
        Usage     : $contig->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 MSE formats do not support match
                    characters in sequences, so this is mostly for output
                    only. NEXUS format (Bio::AlignIO::nexus) can handle

        Returns   : 1
        Argument  : a match character, optional, defaults to '.'

        Title     : unmatch()
        Usage     : $contig->unmatch()
        Function  :

                    Undoes the effect of method match. Unsets match_char.

        Returns   : 1
        Argument  : a match character, optional, defaults to '.'

   MSE attibutes
       Methods for setting and reading the MSE 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 ('').

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

        Title     : missing_char
        Usage     : $contig->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)

        Title     : match_char
        Usage     : $contig->match_char('.')
        Function  : Gets/sets the match_char attribute of the alignment
        Returns   : An match_char string,
        Argument  : An match_char string (optional)

        Title     : gap_char
        Usage     : $contig->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)

        Title   : symbol_chars
        Usage   : my @symbolchars = $contig->symbol_chars;
        Function: Returns all the seen symbols (other than gaps)
        Returns : array of characters that are the seen symbols
        Argument: boolean to include the gap/missing/match characters

   Alignment descriptors
       These read only methods describe the MSE in various ways.

        Title     : consensus_string
        Usage     : $str = $contig->consensus_string($threshold_percent)
        Function  : Makes a strict consensus
        Returns   :
        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%)

        Title     : consensus_iupac
        Usage     : $str = $contig->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

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

        Title     : length()
        Usage     : $len = $contig->length()
        Function  : Returns the maximum length of the alignment.
                    To be sure the alignment is a block, use is_flush
        Returns   :
        Argument  :

        Title     : maxname_length
        Usage     : $contig->maxname_length()
        Function  :

                    Gets the maximum length of the displayname in the
                    alignment. Used in writing out various MSE formats.

        Returns   : integer
        Argument  :

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

        Title     : num_sequences
        Usage     : $depth = $contig->num_sequences
        Function  : number of sequence in the sequence alignment
        Returns   : integer
        Argument  : None
        Note      : replaces no_sequences

        Title   : percentage_identity
        Usage   : $id = $contig->percentage_identity
        Function: The function calculates the percentage identity of the alignment
        Returns : The percentage identity of the alignment (as defined by the
        Argument: None

        Title   : percentage_identity
        Usage   : $id = $contig->percentage_identity
        Function: The function calculates the percentage identity of
                  the conserved columns
        Returns : The percentage identity of the conserved columns
        Args    : None

        Title   : average_percentage_identity
        Usage   : $id = $contig->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

   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 = $contig->get_seq_by_pos(1);
           #$loc is undef or Bio::LocationI object
           my $loc = $seq->location_from_column(5);

        Title   : column_from_residue_number
        Usage   : $col = $contig->column_from_residue_number( $seqname, $resnumber)

                  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

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

                  column_from_residue_number( "Seq1", 94 ) returns 5.
                  column_from_residue_number( "Seq2", 25 ) returns 2.
                  column_from_residue_number( "Seq3", 50 ) returns 9.

                  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.

        Title     : displayname
        Usage     : $contig->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)

        Title     : set_displayname_count
        Usage     : $contig->set_displayname_count
        Function  :

                    Sets the names to be name_# where # is the number of
                    times this name has been used.

        Returns   : None
        Argument  : None

        Title     : set_displayname_flat
        Usage     : $contig->set_displayname_flat()
        Function  : Makes all the sequences be displayed as just their name,
                    not name/start-end
        Returns   : 1
        Argument  : None

        Title     : set_displayname_normal
        Usage     : $contig->set_displayname_normal()
        Function  : Makes all the sequences be displayed as name/start-end
        Returns   : None
        Argument  : None

Internal Methods

        Title     : _binary_search
        Usage     : _binary_search($list,$query)
        Function  :

                    Find a number in a sorted list of numbers.  Return values
                    may be on or two integers. One positive integer or zero
                    (>=0) is the index of the element that stores the queried
                    value.  Two positive integers (or zero and another
                    number) are the indexes of elements among which the
                    queried value should be placed. Negative single values

                    -1: $query is smaller than smallest element in list
                    -2: $query is greater than greatest element in list

        Returns   : array of integers
        Argument  :
                    $list  : array reference
                    $query : integer

           Title   : _compare
           Usage   : _compare($arg1,$arg2)
           Function: Perform numeric or string comparisons
           Returns : integer (0, 1 or -1)
           Args    : values to be compared

           Title   : _nof_gaps
           Usage   : _nof_gaps($array_ref, $query)
           Function: number of gaps found before position $query
           Returns : integer
           Args    :
                     $array_ref : gap registry reference
                     $query     : [integer] a position in a sequence

           Title   : _padded_unpadded
           Usage   : _padded_unpadded($array_ref, $query)

                     Returns a coordinate corresponding to
                     position $query after gaps were
                     removed from a sequence.

           Returns : integer
           Args    :
                     $array_ref : reference to this gap registry
                     $query     : [integer] coordionate to change

           Title   : _unpadded_padded
           Usage   : _unpadded_padded($array_ref, $query)

                     Returns the value corresponding to
                     ungapped position $query when gaps are
                     counted as valid sites in a sequence

           Returns :
           Args    : $array_ref = a reference to this sequence's gap registry
                     $query = [integer] location to change

           Title   : _register_gaps
           Usage   : $self->_register_gaps($seq, $array_ref)
           Function: stores gap locations for a sequence
           Returns : number of gaps found
           Args    :
                     $seq       : sequence string
                     $array_ref : a reference to an array,
                                  where gap locations will
                                  be stored

Deprecated methods

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

        Title     : no_sequences
        Usage     : $depth = $ali->no_sequences
        Function  : number of sequence in the sequence alignment
        Returns   : integer
        Argument  :
        Note      : deprecated in favor of num_sequences()