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Bio::EnsEMBL::Analysis::PairAlign Class Reference
Inheritance diagram for Bio::EnsEMBL::Analysis::PairAlign:

List of all members.


Class Summary

Synopsis

Give standard usage here

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

Definition at line 39 of file PairAlign.pm.

Available Methods

protected _rearrange ()
public addFeaturePair ()
public Int cDNA2genomic ()
public convert_cDNA_feature ()
public convert_FeaturePair ()
public create_Feature ()
public create_FeaturePair ()
public Array eachFeaturePair ()
public find_Pair ()
public Int genomic2cDNA ()
public get_hstrand ()
public new ()
public stack_trace ()
public stack_trace_dump ()
public throw ()
public verbose ()
public warn ()

Method Documentation

protected Bio::EnsEMBL::Root::_rearrange ( ) [inherited]
Deprecated:
 
Code:
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public Bio::EnsEMBL::Analysis::PairAlign::addFeaturePair ( )

Undocumented method

Code:
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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:
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public 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);
 Example : 
 Returns : @Bio::EnsEMBL::FeaturePair
 Args    : Bio::EnsEMBL::FeaturePair
 
Code:
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public Bio::EnsEMBL::Analysis::PairAlign::convert_FeaturePair ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Analysis::PairAlign::create_Feature ( )

Undocumented method

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public Bio::EnsEMBL::Analysis::PairAlign::create_FeaturePair ( )

Undocumented method

Code:
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public Array Bio::EnsEMBL::Analysis::PairAlign::eachFeaturePair ( )
 Title   : eachFeaturePait
 Usage   : my @pairs = $pair->eachFeaturePair
 Function: 
 Example : 
 Returns : Array of Bio::SeqFeature::FeaturePair
 Args    : none
 
Code:
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public Bio::EnsEMBL::Analysis::PairAlign::find_Pair ( )

Undocumented method

Code:
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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
 Example : 
 Returns : int
 Args    : int
 
Code:
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public Bio::EnsEMBL::Analysis::PairAlign::get_hstrand ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Analysis::PairAlign::new ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Root.

public Bio::EnsEMBL::Root::stack_trace ( ) [inherited]
Deprecated:
 
Code:
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public Bio::EnsEMBL::Root::stack_trace_dump ( ) [inherited]
Deprecated:
 
Code:
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public Bio::EnsEMBL::Root::throw ( ) [inherited]
Deprecated:
 
Code:
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public Bio::EnsEMBL::Root::verbose ( ) [inherited]
Deprecated:
 
Code:
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public Bio::EnsEMBL::Root::warn ( ) [inherited]
Deprecated:
 
Code:
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The documentation for this class was generated from the following file: