Bio::Assembly Contig
SummaryIncluded librariesPackage variablesDescriptionGeneral documentationMethods
Summary
Bio::Assembly::Contig - Perl module to hold and manipulate
sequence assembly contigs.
Package variables
No package variables defined.
Included modules
Bio::Align::AlignI
Bio::Root::Root
Bio::Seq::PrimaryQual
Bio::SeqFeature::Collection
Inherit
Bio::Align::AlignI Bio::Root::Root
Synopsis
No synopsis!
Description
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 one. 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 agains 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 refer.
Methods
newDescriptionCode
sourceDescriptionCode
assemblyDescriptionCode
strandDescriptionCode
upstream_neighborDescriptionCode
downstream_neighborDescriptionCode
add_featuresDescriptionCode
remove_featuresDescriptionCode
get_features_collectionDescriptionCode
change_coordDescriptionCode
get_seq_coordDescriptionCode
set_seq_coordDescriptionCode
set_consensus_sequenceDescriptionCode
set_consensus_qualityDescriptionCode
get_consensus_lengthDescriptionCode
get_consensus_sequenceDescriptionCode
get_consensus_qualityDescriptionCode
set_seq_qualDescriptionCode
get_seq_idsDescriptionCode
get_seq_feat_by_tagDescriptionCode
get_seq_by_nameDescriptionCode
get_qual_by_nameDescriptionCode
add_seqDescriptionCode
remove_seqDescriptionCode
purgeDescriptionCode
sort_alphabeticallyDescriptionCode
each_seqDescriptionCode
each_alphabeticallyDescriptionCode
each_seq_with_idDescriptionCode
get_seq_by_posDescriptionCode
selectDescriptionCode
select_noncontDescriptionCode
sliceDescriptionCode
map_charsDescriptionCode
uppercaseDescriptionCode
match_lineDescriptionCode
matchDescriptionCode
unmatchDescriptionCode
idDescriptionCode
missing_charDescriptionCode
match_charDescriptionCode
gap_charDescriptionCode
symbol_charsDescriptionCode
consensus_stringDescriptionCode
consensus_iupacDescriptionCode
is_flushDescriptionCode
lengthDescriptionCode
maxname_length
No description
Code
no_residuesDescriptionCode
no_sequencesDescriptionCode
percentage_identityDescriptionCode
overall_percentage_identityDescriptionCode
average_percentage_identityDescriptionCode
column_from_residue_numberDescriptionCode
displaynameDescriptionCode
set_displayname_countDescriptionCode
set_displayname_flatDescriptionCode
set_displayname_normalDescriptionCode
_binary_searchDescriptionCode
_compareDescriptionCode
_nof_gapsDescriptionCode
_padded_unpaddedDescriptionCode
_unpadded_paddedDescriptionCode
_register_gapsDescriptionCode
Methods description
newcode    nextTop
 Title     : new
 Usage     : my $contig = new Bio::Assembly::Contig();
 Function  : Creates a new contig object
 Returns   : Bio::Assembly::Contig
 Args      : -source => string representing the source
                        program where this contig came
                        from
             -id => contig unique ID
sourcecodeprevnextTop
 Title     : source
 Usage     : $contig->source($program);
 Function  : Get/Set program used to build this contig
 Returns   : string
 Argument  : [optional] string
assemblycodeprevnextTop
 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
strandcodeprevnextTop
 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
upstream_neighborcodeprevnextTop
 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
downstream_neighborcodeprevnextTop
 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
add_featurescodeprevnextTop
 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
             attched 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()
             method.

 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.
remove_featurescodeprevnextTop
 Title     : remove_features
 Usage     : $contig->remove_features(@feat)
 Function  : Remove an array of contig features
 Returns   : number of features removed.
 Argument  : An array of Bio::SeqFeatureI
get_features_collectioncodeprevnextTop
 Title     : get_features_collection
 Usage     : $contig->get_features_collection()
 Function  : Get the collection of all contig features
 Returns   : Bio::SeqFeature::Collection
 Argument  : none
change_coordcodeprevnextTop
 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
get_seq_coordcodeprevnextTop
 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::LocatabaleSeq object
set_seq_coordcodeprevnextTop
 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
             contig.

 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::LocatabaleSeq object
set_consensus_sequencecodeprevnextTop
 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
set_consensus_qualitycodeprevnextTop
 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
get_consensus_lengthcodeprevnextTop
 Title     : get_consensus_length
 Usage     : $contig->get_consensus_length()
 Function  : Get consensus sequence length
 Returns   : integer
 Argument  : none
get_consensus_sequencecodeprevnextTop
 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
get_consensus_qualitycodeprevnextTop
 Title     : get_consensus_quality
 Usage     : $contig->get_consensus_quality()
 Function  : Get a reference to the consensus quality object
             for this contig.
 Returns   : A Bio::QualI object
 Argument  : none
set_seq_qualcodeprevnextTop
 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.
get_seq_idscodeprevnextTop
 Title     : get_seq_ids
 Usage     : $contig->get_seq_ids(-start=>$start,
				  -end=>$end,
				  -type=>"gapped A0QR67B08.b");
 Function  : Get list of sequence IDs overlapping inteval [$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 avaliable 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
get_seq_feat_by_tagcodeprevnextTop
 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.
             When you add 

 Returns   : a Bio::SeqFeature object
 Argument  : a Bio::LocatableSeq and a string (feature primary tag)
get_seq_by_namecodeprevnextTop
 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
get_qual_by_namecodeprevnextTop
 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
add_seqcodeprevnextTop
 Title     : add_seq
 Usage     : $contig->add_seq($newseq);
 Function  :

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

 Returns   : nothing
 Argument  : a Bio::LocatableSeq object
See Bio::LocatableSeq for more information.
remove_seqcodeprevnextTop
 Title     : remove_seq
 Usage     : $contig->remove_seq($seq);
 Function  : Removes a single sequence from an alignment
 Returns   : 1 on success, 0 otherwise
 Argument  : a Bio::LocatableSeq object
purgecodeprevnextTop
 Title   : purge
 Usage   : $contig->purge(0.7);
 Function:

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

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

 Returns   : 
 Argument  :
each_seqcodeprevnextTop
 Title     : each_seq
 Usage     : foreach $seq ( $contig->each_seq() ) 
 Function  : Gets an array of Seq objects from the alignment
 Returns   : an array
 Argument  :
each_alphabeticallycodeprevnextTop
 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  :
each_seq_with_idcodeprevnextTop
 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
get_seq_by_poscodeprevnextTop
 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
             no_sequences() will thow an error.

 Returns   : a Bio::LocatableSeq object
 Argument  : positive integer for the sequence osition
selectcodeprevnextTop
 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 no_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)
select_noncontcodeprevnextTop
 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 no_sequences() will thow an error.

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

 Returns   : a Bio::Assembly::Contig object
 Argument  : positive integer for start column 
             positive integer for end column
map_charscodeprevnextTop
 Title     : map_chars
 Usage     : $contig->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
             $contig->map_chars('.','-') wont do what you want)

 Returns   : 
 Argument  : 'from' rexexp
             'to' string
uppercasecodeprevnextTop
 Title     : uppercase()
 Usage     : $contig->uppercase()
 Function  : Sets all the sequences to uppercase
 Returns   : 
 Argument  :
match_linecodeprevnextTop
 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)
matchcodeprevnextTop
 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
             it.

 Returns   : 1
 Argument  : a match character, optional, defaults to '.'
unmatchcodeprevnextTop
 Title     : unmatch()
 Usage     : $contig->unmatch()
 Function  : 

             Undoes the effect of method match. Unsets match_char.

 Returns   : 1
 Argument  : a match character, optional, defaults to '.'
idcodeprevnextTop
 Title     : id
 Usage     : $contig->id("Ig")
 Function  : Gets/sets the id field of the alignment
 Returns   : An id string
 Argument  : An id string (optional)
missing_charcodeprevnextTop
 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)
match_charcodeprevnextTop
 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)
gap_charcodeprevnextTop
 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)
symbol_charscodeprevnextTop
 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
consensus_stringcodeprevnextTop
 Title     : consensus_string
 Usage     : $str = $contig->consensus_string($threshold_percent)
 Function  : Makes a strict consensus 
 Returns   : 
 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_iupaccodeprevnextTop
 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
is_flushcodeprevnextTop
 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  :
lengthcodeprevnextTop
 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  :
no_residuescodeprevnextTop
 Title     : no_residues
 Usage     : $no = $contig->no_residues
 Function  : number of residues in total in the alignment
 Returns   : integer
 Argument  :
no_sequencescodeprevnextTop
 Title     : no_sequences
 Usage     : $depth = $contig->no_sequences
 Function  : number of sequence in the sequence alignment
 Returns   : integer
 Argument  : None
percentage_identitycodeprevnextTop
 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 
						     implementation)
 Argument: None
overall_percentage_identitycodeprevnextTop
 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
average_percentage_identitycodeprevnextTop
 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
column_from_residue_numbercodeprevnextTop
 Title   : column_from_residue_number
 Usage   : $col = $contig->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.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)
displaynamecodeprevnextTop
 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)
set_displayname_countcodeprevnextTop
 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
set_displayname_flatcodeprevnextTop
 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
set_displayname_normalcodeprevnextTop
 Title     : set_displayname_normal
 Usage     : $contig->set_displayname_normal() 
 Function  : Makes all the sequences be displayed as name/start-end
 Returns   : None
 Argument  : None
_binary_searchcodeprevnextTop
 Title     : _binary_search
 Usage     : _binary_search($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
             mean:

             -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
             $query : integer
_comparecodeprevnextTop
    Title   : _compare
    Usage   : _compare($arg1,$arg2)
    Function: Perform numeric or string comparisons
    Returns : integer (0, 1 or -1)
    Args    : values to be compared
_nof_gapscodeprevnextTop
    Title   : _nof_gaps
    Usage   : _nof_gaps($array_ref, $query)
    Function: number of gaps found before position $query
    Returns : integer
    Args    : 
              $array_ref : gap registry reference
              $query     : [integer] a position in a sequence
_padded_unpaddedcodeprevnextTop
    Title   : _padded_unpadded
    Usage   : _padded_unpadded($array_ref, $query)
    Function: 

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

    Returns : integer
    Args    : 
              $array_ref : reference to this gap registry
              $query     : [integer] coordionate to change
_unpadded_paddedcodeprevnextTop
    Title   : _unpadded_padded
    Usage   : _unpadded_padded($array_ref, $query)
    Function: 

              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
_register_gapscodeprevnextTop
    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
              $array_ref : a reference to an array,
                           where gap locations will
                           be stored
Methods code
newdescriptionprevnextTop
sub new {
#-----------
    my ($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    my ($src, $id) = $self->_rearrange([qw(SOURCE ID)], @args);
    $src && $self->source($src);
    ($id && $self->id($id)) || ($self->{'_id'} = 'NoName'); # Alignment (contig) name
    ($id && $self->id($id)) || ($self->{'_source'} = 'Unknown'); # Program used to build the contig
    # we need to set up internal hashes first!

    # Bio::SimpleAlign derived fields (check which ones are needed for AlignI compatibility)
    $self->{'_elem'} = {}; # contig elements: aligned sequence objects (keyed by ID)
    $self->{'_order'} = {}; # store sequence order
#    $self->{'start_end_lists'} = {}; # References to entries in {'_seq'}. Keyed by seq ids.
#    $self->{'_dis_name'} = {}; # Display names for each sequence
    $self->{'_symbols'} = {}; # List of symbols

    #Contig specific slots
    $self->{'_consensus_sequence'} = undef;
    $self->{'_consensus_quality'} = undef;
    $self->{'_nof_residues'} = 0;
    $self->{'_nof_seqs'} = 0;
#    $self->{'_nof_segments'} = 0; # Let's not make it heavier than needed by now...
    $self->{'_sfc'} = Bio::SeqFeature::Collection->new();

    # Assembly specifcs
    $self->{'_assembly'} = undef; # Reference to a Bio::Assembly::Scaffold object, if contig belongs to one.
    $self->{'_strand'} = 0; # Reverse (-1) or forward (1), if contig is in a scaffold. 0 otherwise
    $self->{'_neighbor_start'} = undef; # Will hold a reference to another contig
    $self->{'_neighbor_end'} = undef; # Will hold a reference to another contig

    return $self; # success - we hope!
}
sourcedescriptionprevnextTop
sub source {
    my $self = shift;
    my $source = shift;

    $self->{'_source'} = $source if (defined $source);
    return $self->{'_source'};
}
assemblydescriptionprevnextTop
sub assembly {
    my $self = shift;
    my $assembly = shift;

    $self->throw("Using non Bio::Assembly::Scaffold object when assign contig to assembly")
	if (defined $assembly && ! $assembly->isa("Bio::Assembly::Scaffold"));

    $self->{'_assembly'} = $assembly if (defined $assembly);
    return $self->{'_assembly'};
}
stranddescriptionprevnextTop
sub strand {
    my $self = shift;
    my $ori = shift;

    $self->throw("Contig strand must be either 1, -1 or 0")
	unless (defined $ori && ($ori == 1 || $ori == 0 || $ori == -1));

    $self->{'_strand'} = $ori;
    return $self->{'_strand'};
}
upstream_neighbordescriptionprevnextTop
sub upstream_neighbor {
    my $self = shift;
    my $ref = shift;

    $self->throw("Trying to assign a non Bio::Assembly::Contig object to upstream contig")
	if (defined $ref && ! $ref->isa("Bio::Assembly::Contig"));

    $self->{'_neighbor_start'} = $ref if (defined $ref);
    return $self->{'_neighbor_start'};
}
downstream_neighbordescriptionprevnextTop
sub downstream_neighbor {
    my $self = shift;
    my $ref = shift;

    $self->throw("Trying to assign a non Bio::Assembly::Contig object to downstream contig")
	if (defined $ref && ! $ref->isa("Bio::Assembly::Contig"));
    $self->{'_neighbor_end'} = $ref if (defined $ref);
    return $self->{'_neighbor_end'};
}
add_featuresdescriptionprevnextTop
sub add_features {
    my ($self, $args, $flag) = @_;

    # Adding shortcuts for aligned sequence features
    $flag = 0 unless (defined $flag);
    if ($flag && defined $self->{'_consensus_sequence'}) {
	foreach my $feat (@$args) {
	    next if (defined $feat->seq);
	    $feat->attach_seq($self->{'_consensus_sequence'});
	}
    } elsif (!$flag) { # Register aligned sequence features
	foreach my $feat (@$args) {
	    if (my $seq = $feat->entire_seq()) {
		my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
		$self->warn("Adding contig feature attached to unknown sequence $seqID!")
		    unless (exists $self->{'_elem'}{$seqID});
		my $tag = $feat->primary_tag;
		$self->{'_elem'}{$seqID}{'_feat'}{$tag} = $feat;
	    }
	}
    }

    # Add feature to feature collection
    my $nof_added = $self->{'_sfc'}->add_features($args);

    return $nof_added;
}
remove_featuresdescriptionprevnextTop
sub remove_features {
    my ($self, @args) = @_;

    # Removing shortcuts for aligned sequence features
    foreach my $feat (@args) {
	if (my $seq = $feat->entire_seq()) {
	    my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
	    my $tag = $feat->primary_tag;
	    $tag =~ s/:$seqID$/$1/g;
	    delete( $self->{'_elem'}{$seqID}{'_feat'}{$tag} )
		if (exists $self->{'_elem'}{$seqID}{'_feat'}{$tag} &&
		    $self->{'_elem'}{$seqID}{'_feat'}{$tag} eq $feat);
	}
    }

    return $self->{'_sfc'}->remove_features(\@args);
}
get_features_collectiondescriptionprevnextTop
sub get_features_collection {
    my $self = shift;

    return $self->{'_sfc'};
}
change_coorddescriptionprevnextTop
sub change_coord {
    my $self     = shift;
    my $type_in  = shift;
    my $type_out = shift;
    my $query    = shift;

    # Parsing arguments
    # Loading read objects (these calls will throw exceptions whether $read_in or 
    # $read_out is not found
    my ($read_in,$read_out) = (undef,undef);
    my $in_ID  = ( split(' ',$type_in)  )[1];
    my $out_ID = ( split(' ',$type_out) )[1];

    if ($in_ID  ne 'consensus') {
	$read_in  = $self->get_seq_coord( $self->get_seq_by_name($in_ID)  );
	$self->throw("Can't change coordinates without sequence location for $in_ID") 
	    unless (defined $read_in);
    }
    if ($out_ID ne 'consensus') {
	$read_out = $self->get_seq_coord( $self->get_seq_by_name($out_ID) );
	$self->throw("Can't change coordinates without sequence location for $out_ID")
	    unless (defined $read_out);
    }

    # Performing transformation between coordinates
  SWITCH1: {

      # Transformations between contig padded and contig unpadded
      (($type_in eq 'gapped consensus') && ($type_out eq 'ungapped consensus')) && do {
	  $self->throw("Can't use ungapped consensus coordinates without a consensus sequence")
	      unless (defined $self->{'_consensus_sequence'});
	  $query = &_padded_unpadded($self->{'_consensus_gaps'}, $query);
	  last SWITCH1;
      };
      (($type_in eq 'ungapped consensus') && ($type_out eq 'gapped consensus')) && do {
	  $self->throw("Can't use ungapped consensus coordinates without a consensus sequence")
	      unless (defined $self->{'_consensus_sequence'});
	  $query = &_unpadded_padded($self->{'_consensus_gaps'},$query);
	  last SWITCH1;
      };

      # Transformations between contig (padded) and read (padded)
      (($type_in  eq 'gapped consensus') &&
       ($type_out =~ /^aligned /) && defined($read_out)) && do {
	   $query = $query - $read_out->start() + 1;
	   last SWITCH1;
       };
      (($type_in =~ /^aligned /) && defined($read_in) &&
       ($type_out  eq 'gapped consensus')) && do {
	   $query = $query + $read_in->start() - 1;
	   last SWITCH1;
       };

      # Transformations between contig (unpadded) and read (padded)
      (($type_in eq 'ungapped consensus') &&
       ($type_out =~ /^aligned /) && defined($read_out)) && do {
	   $query = $self->change_coord('ungapped consensus','gapped consensus',$query);
	   $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
	   last SWITCH1;
       };
      (($type_in =~ /^aligned /) && defined($read_in) && 
       ($type_out eq 'ungapped consensus')) && do {
	   $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
	   $query = $self->change_coord('gapped consensus','ungapped consensus',$query);
	   last SWITCH1;
       };

      # Transformations between seq $read_in padded and seq $read_out padded
      (defined($read_in)  && ($type_in  =~ /^aligned /)  &&
       defined($read_out) && ($type_out =~ /^aligned /)) && do {
	   $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
	   $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
	   last SWITCH1;
       };

      # Transformations between seq $read_in padded and seq $read_out unpadded
      (defined($read_in)  && ($type_in  =~ /^aligned /)    &&
       defined($read_out) && ($type_out =~ /^unaligned /)) && do {
	   if ($read_in ne $read_out) {
	       $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
	       $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
	   }
	   my $list_out = $self->{'_elem'}{$out_ID}{'_gaps'};
	   $query = &_padded_unpadded($list_out,$query);
	   # Changing read orientation if read was reverse complemented when aligned
	   if ($read_out->strand == -1) {
	       my ($length) = $read_out->length();
	       $length = $length - &_nof_gaps($list_out,$length);
	       $query  = $length - $query + 1;
	   }
	   last SWITCH1;
       };
      (defined($read_in)  && ($type_in  =~ /^unaligned /) && 
       defined($read_out) && ($type_out =~ /^aligned /))  && do {
	   my $list_in = $self->{'_elem'}{$in_ID}{'_gaps'};
	   # Changing read orientation if read was reverse complemented when aligned
	   if ($read_in->strand == -1) {
	       my ($length) = $read_in->length();
	       $length = $length - &_nof_gaps($list_in,$length);
	       $query  = $length - $query + 1;
	   }
	   $query = &_unpadded_padded($list_in,$query);
	   if ($read_in ne $read_out) {
	       $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
	       $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
	   }
	   last SWITCH1;
       };

      # Transformations between seq $read_in unpadded and seq $read_out unpadded
      (defined($read_in)  && ($type_in  =~ /^unaligned /)    &&
       defined($read_out) && ($type_out =~ /^unaligned /)) && do {
	   $query = $self->change_coord("unaligned $in_ID","aligned $out_ID",$query);
	   $query = $self->change_coord("aligned $out_ID","unaligned $out_ID",$query);
	   last SWITCH1;
       };

      # Transformations between contig (padded) and read (unpadded)
      (($type_in eq 'gapped consensus') &&
       ($type_out =~ /^unaligned /) && defined($read_out)) && do {
	   $query = $self->change_coord('gapped consensus',"aligned $out_ID",$query);
	   $query = $self->change_coord("aligned $out_ID","unaligned $out_ID",$query);
	   last SWITCH1;
       };
      (($type_in =~ /^unaligned /) && defined($read_in) &&
       ($type_out eq 'gapped consensus')) && do {
	   $query = $self->change_coord("unaligned $in_ID","aligned $in_ID",$query);
	   $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
	   last SWITCH1;
       };

      # Transformations between contig (unpadded) and read (unpadded)
      (($type_in eq 'ungapped consensus') &&
       ($type_out =~ /^unaligned /) && defined($read_out)) && do {
	   $query = $self->change_coord('ungapped consensus','gapped consensus',$query);
	   $query = $self->change_coord('gapped consensus',"unaligned $out_ID",$query);
	   last SWITCH1;
       };
      (($type_in =~ /^unaligned /) && defined($read_in) &&
       ($type_out eq 'ungapped consensus')) && do {
	   $query = $self->change_coord("unaligned $in_ID",'gapped consensus',$query);
	   $query = $self->change_coord('gapped consensus','ungapped consensus',$query);
	   last SWITCH1;
       };

      $self->throw("Unknow coordinate system. Args: $type_in, $type_out.");
      $query = undef; # If a coordinate systems just requested is unknown
  }

    return $query;
}
get_seq_coorddescriptionprevnextTop
sub get_seq_coord {
    my ($self,$seq) = @_;

    if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
	$self->throw("$seq is not a Bio::LocatableSeq");
    }
    my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;

    unless (exists( $self->{'_elem'}{$seqID} )) {
	$self->warn("No such sequence ($seqID) in contig ".$self->id);
	return undef;
    }
    unless (exists( $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"} )) {
	$self->warn("Location not set for sequence ($seqID) in contig ".$self->id);
	return undef;
    }

    return $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"};
}
set_seq_coorddescriptionprevnextTop
sub set_seq_coord {
    my ($self,$feat,$seq) = @_;

    if( !ref $seq || ! $seq->isa('Bio::LocatableSeq') ) {
	$self->throw("Unable to process non locatable sequences [".ref($seq)."]");
    }

    # Complaining about inadequate feature object
     $self->throw("Coordinates must be a Bio::SeqFeature::Generic object!")
	unless ( $feat->isa("Bio::SeqFeature::Generic") );
    $self->throw("Sequence coordinates must have an end!")
	unless (defined $feat->end);
    $self->throw("Sequence coordinates must have a start!")
	unless (defined $feat->start);

    my $seqID = $seq->id() || $seq->display_id || $seq->primary_id;
    if (exists( $self->{'_elem'}{$seqID} ) &&
	exists( $self->{'_elem'}{$seqID}{'_seq'} ) &&
	defined( $self->{'_elem'}{$seqID}{'_seq'} ) &&
	($seq ne $self->{'_elem'}{$seqID}{'_seq'}) ) {
	$self->warn("Replacing sequence $seqID\n");
	$self->remove_seq($self->{'_elem'}{$seqID}{'_seq'});
    }
    $self->add_seq($seq);

    # Remove previous coordinates, if any
    $self->remove_features($feat);

    # Add new Bio::Generic::SeqFeature
    $feat->add_tag_value('contig',$self->id)
	unless ( $feat->has_tag('contig') );
    $feat->primary_tag("_aligned_coord:$seqID");
    $feat->attach_seq($seq);
    $self->{'_elem'}{$seqID}{'_feat'}{"_aligned_coord:$seqID"} = $feat;
    $self->add_features([ $feat ]);
}
set_consensus_sequencedescriptionprevnextTop
sub set_consensus_sequence {
    my $self = shift;
    my $seq  = shift;

    $self->throw("Consensus sequence must be a Bio::LocatableSeq!")
	unless ($seq->isa("Bio::LocatableSeq"));

    my $con_len = $seq->length;
    $seq->start(1); $seq->end($con_len);

    $self->{