Bio::EnsEMBL::Analysis::PairAlign Class Reference

Public Member Functions
public	new ()
public	addFeaturePair ()
public Array	eachFeaturePair ()
public	get_hstrand ()
public Int	genomic2cDNA ()
public Int	cDNA2genomic ()
public	find_Pair ()
public Array	convert_cDNA_feature ()
public	convert_FeaturePair ()
public	create_FeaturePair ()
public	create_Feature ()

Detailed Description

Synopsis

#To convert between coordinates:
 
  my $cdna_coord = $pair->genomic2cDNA($gen_coord);
  my $gen_coord  = $pair->cDNA2genomic($cdna_coord);

Description

Contains list of sub alignments making up a dna-dna alignment

Creation:

  my $pair = new Bio::EnsEMBL::FeaturePair(
    -start  => $qstart,
    -end    => $qend,
    -strand => $qstrand,
    -hstart => $hstart,
    -hend   => $hend,
    -hend   => $hstrand,
  );

  my $pairaln = new Bio::EnsEMBL::Analysis::PairAlign;
  $pairaln->addFeaturePair($pair);

Any number of pair alignments can be added to the PairAlign object

Definition at line 34 of file PairAlign.pm.

Member Function Documentation

addFeaturePair()

public Bio::EnsEMBL::Analysis::PairAlign::addFeaturePair

(

)

Undocumented method

Code:

cDNA2genomic()

public Int Bio::EnsEMBL::Analysis::PairAlign::cDNA2genomic

(

)

 Title   : cDNA2genomic
 Usage   : my $gen_coord = $pair->genomic2cDNA($cdna_coord)
 Function: Converts a cdna coordinate to a genomic coordinate
 Example :

 Returns : int
 Args    : int

Code:

convert_cDNA_feature()

public Array Bio::EnsEMBL::Analysis::PairAlign::convert_cDNA_feature

(

)

 Title   : convert_cDNA_feature
 Usage   : my @newfeatures = $self->convert_cDNA_feature($f);
 Function: Converts a feature on the cDNA into an array of 
           features on the genomic (for features that span across introns);
 Returns : Array of Bio::EnsEMBL::FeaturePair
 Args    : Bio::EnsEMBL::FeaturePair

Code:

convert_FeaturePair()

public Bio::EnsEMBL::Analysis::PairAlign::convert_FeaturePair

(

)

Undocumented method

Code:

create_Feature()

public Bio::EnsEMBL::Analysis::PairAlign::create_Feature

(

)

Undocumented method

Code:

create_FeaturePair()

public Bio::EnsEMBL::Analysis::PairAlign::create_FeaturePair

(

)

Undocumented method

Code:

eachFeaturePair()

public Array Bio::EnsEMBL::Analysis::PairAlign::eachFeaturePair

(

)

 Title   : eachFeaturePair 
 Example :

my @pairs = $pair->eachFeaturePair

 Returns : Array of Bio::SeqFeature::FeaturePair
 Args    : none
 

Code:

find_Pair()

public Bio::EnsEMBL::Analysis::PairAlign::find_Pair

(

)

Undocumented method

Code:

genomic2cDNA()

public Int Bio::EnsEMBL::Analysis::PairAlign::genomic2cDNA

(

)

 Title   : genomic2cDNA
 Usage   : my $cdna_coord = $pair->genomic2cDNA($gen_coord)
 Function: Converts a genomic coordinate to a cdna coordinate
 Returns : int
 Args    : int
 

Code:

get_hstrand()

public Bio::EnsEMBL::Analysis::PairAlign::get_hstrand

(

)

Undocumented method

Code:

new()

public Bio::EnsEMBL::Analysis::PairAlign::new

(

)

Undocumented method

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Analysis/PairAlign.pm