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Bio::EnsEMBL::Utils::CigarString Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::CigarString:

List of all members.


Class Summary

Description

Sequence alignment hits were previously stored within the core database
as ungapped alignments. This imposed 2 major constraints on alignments:
a) alignments for a single hit record would require multiple rows in the
   database, and
b) it was not possible to accurately retrieve the exact original
   alignment.
Therefore, in the new branch sequence alignments are now stored as
ungapped alignments in the cigar line format (where CIGAR stands for
Concise Idiosyncratic Gapped Alignment Report).
In the cigar line format alignments are sotred as follows:
  M: Match
  D: Deletino
  I: Insertion
An example of an alignment for a hypthetical protein match is shown
below:
  Query:   42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
              PG    P    G     GP   R      PLGP
  Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...
protein_align_feature table as the following cigar line:
  7M4D12M2I2MD7M
 

Definition at line 38 of file CigarString.pm.

Available Methods

protected _findIncrements ()
protected _findStrands ()
protected _findTypes ()
protected _rearrange ()
protected _sub_cigar_string ()
public A generate_cigar_string ()
public A generate_cigar_string_by_hsp ()
public new ()
public A split_hsp ()
public stack_trace ()
public stack_trace_dump ()
public throw ()
public verbose ()
public warn ()

Method Documentation

protected Bio::EnsEMBL::Utils::CigarString::_findIncrements ( )

Undocumented method

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protected Bio::EnsEMBL::Utils::CigarString::_findStrands ( )

Undocumented method

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protected Bio::EnsEMBL::Utils::CigarString::_findTypes ( )

Undocumented method

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protected Bio::EnsEMBL::Root::_rearrange ( ) [inherited]
Deprecated:
 
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protected Bio::EnsEMBL::Utils::CigarString::_sub_cigar_string ( )

Undocumented method

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public A Bio::EnsEMBL::Utils::CigarString::generate_cigar_string ( )
  Name : generate_cigar_string
  Usage: $cigar_string = $self->generate_cigar_string(\@qchars, \@hchars);
  Function: generate the cigar string for a piece of alignment.
  Args:     2 array references. The lengths of 2 arrays are the same
  Return:   a cigar string
 
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public A Bio::EnsEMBL::Utils::CigarString::generate_cigar_string_by_hsp ( )
  
  Name :    generate_cigar_string_by_hsp
  Usage :   my $hsp; # a ready GenericHSP object
my $cigar_string = $self->generate_cigar_string_by_hsp($hsp);
  Function: generate a cigar string by given HSP object.
  Args :    a GenericHSP object
  Returns:  a text string of cigar string
 
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public Bio::EnsEMBL::Root::new ( ) [inherited]
public A Bio::EnsEMBL::Utils::CigarString::split_hsp ( )
    Name  : split_hsp (this name is derived from the original sub in BlastWorn)
    Usage : my $hsp; # a ready Bio::Search::HSP::GenericHSP object.
my $factory = new Bio::EnsEMBL::Utils::CigarString;
my $cigar_string = $factory->split_hsp($hsp);
    Function: generate cigar string.
    Argument: a HSP object.
    Returns : a text string.
 
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public Bio::EnsEMBL::Root::stack_trace ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::stack_trace_dump ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::throw ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::verbose ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::warn ( ) [inherited]
Deprecated:
 
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The documentation for this class was generated from the following file: