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Bio::EnsEMBL::Compara::GenomicAlignBlock Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::GenomicAlignBlock:

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::GenomicAlignBlock;
  
  my $genomic_align_block = new Bio::EnsEMBL::Compara::GenomicAlignBlock(
          -adaptor =\> $genomic_align_block_adaptor,
          -method_link_species_set =\> $method_link_species_set,
          -score =\> 56.2,
          -length =\> 1203,
          -genomic_align_array =\> [$genomic_align1, $genomic_align2...]
      );

SET VALUES
  $genomic_align_block-\>adaptor($gen_ali_blk_adaptor);
  $genomic_align_block-\>dbID(12);
  $genomic_align_block-\>method_link_species_set($method_link_species_set);
  $genomic_align_block-\>reference_genomic_align_id(35123);
  $genomic_align_block-\>genomic_align_array([$genomic_align1, $genomic_align2]);
  $genomic_align_block-\>reference_slice($reference_slice);
  $genomic_align_block-\>reference_slice_start(1035);
  $genomic_align_block-\>reference_slice_end(1283);
  $genomic_align_block-\>score(56.2);
  $genomic_align_block-\>length(562);

GET VALUES
  my $genomic_align_block_adaptor = $genomic_align_block-\>adaptor();
  my $dbID = $genomic_align_block-\>dbID();
  my $method_link_species_set = $genomic_align_block-\>method_link_species_set;
  my $genomic_aligns = $genomic_align_block-\>genomic_align_array();
  my $reference_genomic_align = $genomic_align_block-\>reference_genomic_align();
  my $non_reference_genomic_aligns = $genomic_align_block-\>get_all_non_reference_genomic_aligns();
  my $reference_slice = $genomic_align_block-\>reference_slice();
  my $reference_slice_start = $genomic_align_block-\>reference_slice_start();
  my $reference_slice_end = $genomic_align_block-\>reference_slice_end();
  my $score = $genomic_align_block-\>score();
  my $length = $genomic_align_block-\>length;
  my alignment_strings = $genomic_align_block-\>alignment_strings;
  my $genomic_align_block_is_on_the_original_strand =
      $genomic_align_block-\>get_original_strand;

Description

The GenomicAlignBlock object stores information about an alignment comprising of two or more pieces of genomic DNA.
 

Definition at line 57 of file GenomicAlignBlock.pm.

Available Methods

protected
Bio::EnsEMBL::Compara::GenomicAlignBlock 
_create_from_a_list_of_ungapped_genomic_align_blocks ()
protected void _print ()
public
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor 
adaptor ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
add_GenomicAlign ()
public Array alignment_strings ()
public Int dbID ()
public Int end ()
public Array genomic_align_array ()
public Array get_all_GenomicAligns ()
public A get_all_non_reference_genomic_aligns ()
public Listref get_all_ungapped_GenomicAlignBlocks ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
get_old_consensus_genomic_align ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
get_old_query_genomic_align ()
public void get_original_strand ()
public A get_SimpleAlign ()
public Int group_id ()
public Int length ()
public Int level_id ()
public
Bio::EnsEMBL::Compara::MethodLinkSpeciesSet 
method_link_species_set ()
public Int method_link_species_set_id ()
public
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlock 
new ()
public new_fast ()
public Double perc_id ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
reference_genomic_align ()
public Int reference_genomic_align_id ()
public Bio::EnsEMBL::Slice reference_slice ()
public Int reference_slice_end ()
public Int reference_slice_start ()
public Int reference_slice_strand ()
public Bio::EnsEMBL::Slice requesting_slice ()
public
Bio::EnsEMBL::Compara::GenomicAlignBlock 
restrict_between_alignment_positions ()
public
Bio::EnsEMBL::Compara::GenomicAlignBlock 
restrict_between_reference_positions ()
public A resulting_genomic_aligns ()
public void reverse_complement ()
public Double score ()
public Bio::EnsEMBL::Slice slice ()
public Int start ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
starting_genomic_align ()
public void starting_genomic_align_id ()
public Int strand ()

Method Documentation

protected Bio::EnsEMBL::Compara::GenomicAlignBlock Bio::EnsEMBL::Compara::GenomicAlignBlock::_create_from_a_list_of_ungapped_genomic_align_blocks ( )
  Args       : listref of ungapped Bio::EnsEMBL::Compara::GenomicAlignBlocks
  Example    : $new_genomic_align_block =
                  $self->_create_from_a_list_of_ungapped_genomic_align_blocks(
                      $ungapped_genomic_align_blocks
                  );
  Description: Takes a list of ungapped Bio::EnsEMBL::Compara::GenomicAlignBlock
               objects and creates a new Bio::EnsEMBL::Compara::GenomicAlignBlock
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object
  Exceptions : lots...
  Caller     : new()
  Status     : At risk
 
Code:
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protected void Bio::EnsEMBL::Compara::GenomicAlignBlock::_print ( )
  Arg [1]    : none
  Example    : $genomic_align->_print
  Description: print attributes of the object to the STDOUT. Used for debuging purposes.
  Returntype : none
  Exceptions : 
  Caller     : object::methodname
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor Bio::EnsEMBL::Compara::GenomicAlignBlock::adaptor ( )
  Arg [1]    : Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor $adaptor
  Example    : my $gen_ali_blk_adaptor = $genomic_align_block->adaptor();
  Example    : $genomic_align_block->adaptor($gen_ali_blk_adaptor);
  Description: Getter/Setter for the adaptor this object uses for database
               interaction.
  Returntype : Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor object
  Exceptions : thrown if $adaptor is not a
               Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor object
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::GenomicAlignBlock::add_GenomicAlign ( )
  Arg [1]    : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
  Example    : $genomic_align_block->add_GenomicAlign($genomic_align);
  Description: adds another Bio::EnsEMBL::Compara::GenomicAlign object to the set of
               Bio::EnsEMBL::Compara::GenomicAlign objects in the attribute
               genomic_align_array.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : thrown if wrong argument
  Caller     : general
  Status     : Stable
 
Code:
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public Array Bio::EnsEMBL::Compara::GenomicAlignBlock::alignment_strings ( )
  Arg [1]    : none
  Example    : $genomic_align_block->alignment_strings
  Description: Returns the alignment string of all the sequences in the
               alignment
  Returntype : array reference containing several strings
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignBlock::dbID ( )
  Arg [1]    : integer $dbID
  Example    : my $dbID = $genomic_align_block->dbID();
  Example    : $genomic_align_block->dbID(12);
  Description: Getter/Setter for the attribute dbID
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::end ( ) [inherited]
  Arg [1]    : (optional) integer $end
  Example    : my $end = $genomic_align_block->end;
  Example    : $genomic_align_block->end(1283);
  Description: get/set for attribute reference_slice_end. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
 
Code:
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public Array Bio::EnsEMBL::Compara::GenomicAlignBlock::genomic_align_array ( )
  Arg [1]    : array reference containing Bio::EnsEMBL::Compara::GenomicAlign objects
  Example    : $genomic_aligns = $genomic_align_block->genomic_align_array();
               $genomic_align_block->genomic_align_array([$genomic_align1, $genomic_align2]);
  Description: get/set for attribute genomic_align_array. If no argument is given, the
               genomic_align_array is not defined but both the dbID and the adaptor are,
               it tries to fetch the data from the database using the dbID of the
               Bio::EnsEMBL::Compara::GenomicAlignBlock object.
               You can unset all cached GenomicAlign using 0 as argument. They will be
               loaded again from the database if needed.
  Returntype : array reference containing Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Array Bio::EnsEMBL::Compara::GenomicAlignBlock::get_all_GenomicAligns ( )
  Arg [1]    : none
  Example    : $genomic_aligns = $genomic_align_block->get_all_GenomicAligns();
  Description: returns the set of Bio::EnsEMBL::Compara::GenomicAlign objects in
               the attribute genomic_align_array.
  Returntype : array reference containing Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public A Bio::EnsEMBL::Compara::GenomicAlignBlock::get_all_non_reference_genomic_aligns ( )
  Arg [1]    : (none)
  Example    : $genomic_aligns = $genomic_align_block->get_all_non_reference_genomic_aligns();
  Description: get the non_reference_genomic_aligns. When looking for genomic alignments in
               a given slice or dnafrag, the reference_genomic_align corresponds to the
               Bio::EnsEMBL::Compara::GenomicAlign included in the starting slice or
               dnafrag. The reference_genomic_align_id is the dbID corresponding to the
               reference_genomic_align. All remaining Bio::EnsEMBL::Compara::GenomicAlign
               objects included in the Bio::EnsEMBL::Compara::GenomicAlignBlock are the
               non_reference_genomic_aligns.
  Returntype : a ref. to an array of Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : warns if no reference_genomic_align_id has been set and returns a ref.
               to an empty array
  Exceptions : warns if no genomic_align_array has been set and returns a ref.
               to an empty array
  Caller     : $genomic_align_block->non_reference_genomic_aligns()
  Status     : Stable
 
Code:
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public Listref Bio::EnsEMBL::Compara::GenomicAlignBlock::get_all_ungapped_GenomicAlignBlocks ( )
  Args       : (optional) listref $genome_dbs
  Example    : my $ungapped_genomic_align_blocks =
                   $self->get_all_ungapped_GenomicAlignBlocks();
  Example    : my $ungapped_genomic_align_blocks =
                   $self->get_all_ungapped_GenomicAlignBlocks([$human_genome_db, $mouse_genome_db]);
  Description: split the GenomicAlignBlock object into a set of ungapped
               alignments. If a list of genome_dbs is provided, only those
               sequences will be taken into account. This can be used to extract
               ungapped pairwise alignments from multiple alignments.
  Returntype : listref of Bio::EnsEMBL::Compara::GenomicAlignBlocks objects
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::GenomicAlignBlock::get_old_consensus_genomic_align ( )
 
  Arg [1]    : none
  Example    : $old_consensus_genomic_aligns = $genomic_align_group->get_old_consensus_genomic_align();
  Description: get the Bio::EnsEMBL::Compara::GenomicAlign object following the convention for backwards
               compatibility
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : 
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::GenomicAlignBlock::get_old_query_genomic_align ( )
 
  Arg [1]    : none
  Example    : $old_query_genomic_aligns = $genomic_align_group->get_old_query_genomic_align();
  Description: get the Bio::EnsEMBL::Compara::GenomicAlign object following the convention for backwards
               compatibility
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : 
  Caller     : general
 
Code:
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public void Bio::EnsEMBL::Compara::BaseGenomicAlignSet::get_original_strand ( ) [inherited]
  Args       : none
  Example    : if (!$genomic_align_block->get_original_strand()) {
                 # original GenomicAlignBlock has been reverse-complemented
               }
  Description: getter for the _orignal_strand attribute
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public A Bio::EnsEMBL::Compara::GenomicAlignBlock::get_SimpleAlign ( )
  Arg [1]    : list of string $flags
               "translated" = by default, the sequence alignment will be on nucleotide. With "translated" flag
                              the aligned sequences are translated.
               "uc" = by default aligned sequences are given in lower cases. With "uc" flag, the aligned
                      sequences are given in upper cases.
               "display_id" = by default the name of each sequence in the alignment is $dnafrag->name. With 
                              "dispaly_id" flag the name of each sequence is defined by the 
                              Bio::EnsEMBL::Compara::GenomicAlign display_id method.
  Example    : $daf->get_SimpleAlign or
               $daf->get_SimpleAlign("translated") or
               $daf->get_SimpleAlign("translated","uc")
  Description: Allows to rebuild the alignment string of all the genomic_align objects within
               this genomic_align_block using the cigar_line information
               and access to the core database slice objects
  Returntype : a Bio::SimpleAlign object
  Exceptions :
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignBlock::group_id ( )
  Arg [1]    : integer $group_id
  Example    : my $group_id = $genomic_align_block->group_id;
  Example    : $genomic_align_block->group_id(1234);
  Description: get/set for attribute group_id. 
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignBlock::length ( )
  Arg [1]    : integer $length
  Example    : my $length = $genomic_align_block->length;
  Example    : $genomic_align_block->length(562);
  Description: get/set for attribute length. If no argument is given, the length
               is not defined but both the dbID and the adaptor are, it tries to
               fetch and set all the direct attributes from the database using the
               dbID of the Bio::EnsEMBL::Compara::GenomicAlignBlock object.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignBlock::level_id ( )
  Arg [1]    : int $level_id
  Example    : $level_id = $genomic_align->level_id;
  Example    : $genomic_align->level_id(1);
  Description: get/set for attribute level_id. If no argument is given, the level_id
               is not defined but both the dbID and the adaptor are, it tries to
               fetch and set all the direct attributes from the database using the
               dbID of the Bio::EnsEMBL::Compara::GenomicAlign object.
  Returntype : int
  Exceptions : none
  Warning    : warns if getting data from other sources fails.
  Caller     : object->methodname
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::MethodLinkSpeciesSet Bio::EnsEMBL::Compara::GenomicAlignBlock::method_link_species_set ( )
  Arg [1]    : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $method_link_species_set
  Example    : $method_link_species_set = $genomic_align_block->method_link_species_set;
  Example    : $genomic_align_block->method_link_species_set($method_link_species_set);
  Description: get/set for attribute method_link_species_set. If no
               argument is given, the method_link_species_set is not defined but
               both the method_link_species_set_id and the adaptor are, it tries
               to fetch the data using the method_link_species_set_id
  Returntype : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Exceptions : thrown if $method_link_species_set is not a
               Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object
  Caller     : general
  Status     : Stable
 
public Int Bio::EnsEMBL::Compara::GenomicAlignBlock::method_link_species_set_id ( )
  Arg [1]    : integer $method_link_species_set_id
  Example    : $method_link_species_set_id = $genomic_align_block->method_link_species_set_id;
  Example    : $genomic_align_block->method_link_species_set_id(3);
  Description: Getter/Setter for the attribute method_link_species_set_id. If no
               argument is given, the method_link_species_set_id is not defined but
               the method_link_species_set is, it tries to get the data from the
               method_link_species_set object. If this fails, it tries to get and set
               all the direct attributes from the database using the dbID of the
               Bio::Ensembl::Compara::GenomicAlignBlock object.
  Returntype : integer
  Exceptions : thrown if $method_link_species_set_id does not match a previously defined
               method_link_species_set
  Caller     : object::methodname
  Status     : Stable
 
public Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlock Bio::EnsEMBL::Compara::GenomicAlignBlock::new ( )
  Arg [-DBID] : (opt.) int $dbID (the database internal ID for this object)
  Arg [-ADAPTOR]
              : (opt.) Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor $adaptor
                (the adaptor for connecting to the database)
  Arg [-METHOD_LINK_SPECIES_SET]
              : (opt.) Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
                (this defines the type of alignment and the set of species used
                to get this GenomicAlignBlock)
  Arg [-METHOD_LINK_SPECIES_SET_ID]
              : (opt.) int $mlss_id (the database internal ID for the $mlss)
  Arg [-SCORE]: (opt.) float $score (the score of this alignment)
  Arg [-PERC_ID]
              : (opt.) int $perc_id (the percentage of identity, only used for pairwise)
  Arg [-LENGTH]
              : (opt.) int $length (the length of this alignment, taking into account
                gaps and all)
  Arg [-GROUP_ID]
              : (opt.) int $group)id (the group ID for this alignment)
  Arg [-REFERENCE_GENOMIC_ALIGN]
              : (opt.) Bio::EnsEMBL::Compara::GenomicAlign $reference_genomic_align (the
                Bio::EnsEMBL::Compara::GenomicAlign corresponding to the requesting
                Bio::EnsEMBL::Compara::DnaFrag or Bio::EnsEMBL::Slice when this
                Bio::EnsEMBL::Compara::GenomicAlignBlock has been fetched from a
                Bio::EnsEMBL::Compara::DnaFrag or a Bio::EnsEMBL::Slice)
  Arg [-REFERENCE_GENOMIC_ALIGN_ID]
              : (opt.) int $reference_genomic_align (the database internal ID of the
                $reference_genomic_align)
  Arg [-GENOMIC_ALIGN_ARRAY]
              : (opt.) array_ref $genomic_aligns (a reference to the array of
                Bio::EnsEMBL::Compara::GenomicAlign objects corresponding to this
                Bio::EnsEMBL::Compara::GenomicAlignBlock object)
  Example    : my $genomic_align_block =
                   new Bio::EnsEMBL::Compara::GenomicAlignBlock(
                       -adaptor => $gaba,
                       -method_link_species_set => $method_link_species_set,
                       -score => 56.2,
                       -length => 1203,
                       -group_id => 1234,
                       -genomic_align_array => [$genomic_align1, $genomic_align2...]
                   );
  Description: Creates a new GenomicAlignBlock object
  Returntype : Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlock
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlignBlock::new_fast ( )
  Arg [1]    : hash reference $hashref
  Example    : none
  Description: This is an ultra fast constructor which requires knowledge of
               the objects internals to be used.
  Returntype :
  Exceptions : none
  Caller     :
  Status     : Stable
 
Code:
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public Double Bio::EnsEMBL::Compara::GenomicAlignBlock::perc_id ( )
  Arg [1]    : double $perc_id
  Example    : my $perc_id = $genomic_align_block->perc_id;
  Example    : $genomic_align_block->perc_id(95.4);
  Description: get/set for attribute perc_id. If no argument is given, the perc_id
               is not defined but both the dbID and the adaptor are, it tries to
               fetch and set all the direct attributes from the database using the
               dbID of the Bio::EnsEMBL::Compara::GenomicAlignBlock object.
  Returntype : double
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::GenomicAlignBlock::reference_genomic_align ( )
  Arg [1]    : (optional) Bio::EnsEMBL::Compara::GenomicAlign $reference_genomic_align
  Example    : $genomic_align_block->reference_genomic_align($reference_genomic_align);
  Example    : $genomic_align = $genomic_align_block->reference_genomic_align();
  Description: get/set the reference_genomic_align. When looking for genomic alignments in
               a given slice or dnafrag, the reference_genomic_align corresponds to the
               Bio::EnsEMBL::Compara::GenomicAlign included in the starting slice or
               dnafrag. The reference_genomic_align_id is the dbID corresponding to the
               reference_genomic_align. All remaining Bio::EnsEMBL::Compara::GenomicAlign
               objects included in the Bio::EnsEMBL::Compara::GenomicAlignBlock are the
               non_reference_genomic_aligns.
               Synchronises reference_genomic_align and reference_genomic_align_id
               attributes.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : throw if reference_genomic_align is not a Bio::EnsEMBL::Compara::GenomicAlign
               object
  Exceptions : throw if reference_genomic_align_id does not match any of the
               Bio::EnsEMBL::Compara::GenomicAlign objects in the genomic_align_array
  Caller     : $genomic_align_block->reference_genomic_align()
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::GenomicAlignBlock::reference_genomic_align_id ( )
  Arg [1]    : integer $reference_genomic_align_id
  Example    : $genomic_align_block->reference_genomic_align_id(4321);
  Description: get/set for attribute reference_genomic_align_id. A value of 0 will set the
               reference_genomic_align_id attribute to undef. When looking for genomic
               alignments in a given slice or dnafrag, the reference_genomic_align
               corresponds to the Bio::EnsEMBL::Compara::GenomicAlign included in the
               starting slice or dnafrag. The reference_genomic_align_id is the dbID
               corresponding to the reference_genomic_align. All remaining
               Bio::EnsEMBL::Compara::GenomicAlign objects included in the
               Bio::EnsEMBL::Compara::GenomicAlignBlock are the
               non_reference_genomic_aligns.
               Synchronises reference_genomic_align and reference_genomic_align_id
               attributes.
  Returntype : integer
  Exceptions : throw if $reference_genomic_align_id id not a postive number
  Caller     : $genomic_align_block->reference_genomic_align_id(int)
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : my $reference_slice = $genomic_align_block->reference_slice;
  Example    : $genomic_align_block->reference_slice($slice);
  Description: Alias for slice method. TO BE

Deprecated:
Returntype : Bio::EnsEMBL::Slice object Exceptions : Caller : general Status : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_end ( ) [inherited]
  Arg [1]    : integer $reference_slice_end
  Example    : my $reference_slice_end = $genomic_align_block->reference_slice_end;
  Example    : $genomic_align_block->reference_slice_end(1283);
  Description: get/set for attribute reference_slice_end. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_start ( ) [inherited]
  Arg [1]    : integer $reference_slice_start
  Example    : my $reference_slice_start = $genomic_align_block->reference_slice_start;
  Example    : $genomic_align_block->reference_slice_start(1035);
  Description: get/set for attribute reference_slice_start. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::reference_slice_strand ( ) [inherited]
  Arg [1]    : integer $reference_slice_strand
  Example    : my $reference_slice_strand = $genomic_align_block->reference_slice_strand;
  Example    : $genomic_align_block->reference_slice_strand(-1);
  Description: get/set for attribute reference_slice_strand. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::GenomicAlignBlock::requesting_slice ( )
Deprecated:
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->reference_slice() method instead
  Arg [1]    : Bio::EnsEMBL::Slice $reference_slice
  Example    : my $reference_slice = $genomic_align_block->requesting_slice;
  Example    : $genomic_align_block->requesting_slice($reference_slice);
  Description: get/set for attribute reference_slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : throw if $reference_slice is not a Bio::EnsEMBL::Slice
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlignBlock Bio::EnsEMBL::Compara::GenomicAlignBlock::restrict_between_alignment_positions ( )
  Arg[1]     : [optional] int $start, refers to the start of the alignment
  Arg[2]     : [optional] int $end, refers to the start of the alignment
  Arg[3]     : [optional] boolean $skip_empty_GenomicAligns
  Example    : none
  Description: restrict this GenomicAlignBlock. It returns a new object unless no
               restriction is needed. In that case, it returns the original unchanged
               object.
               This method uses coordinates relative to the alignment itself.
               For instance if you have an alignment like:
                            1    1    2    2    3
                   1   5    0    5    0    5    0
                   AAC--CTTGTGGTA-CTACTT-----ACTTT
                   AACCCCTT-TGGTATCTACTTACCTAACTTT
               and you restrict it between 5 and 25, you will get back a
               object containing the following alignment:
                            1    1
                   1   5    0    5
                   CTTGTGGTA-CTACTT----
                   CTT-TGGTATCTACTTACCT
               See restrict_between_reference_positions() elsewhere in this document
               for an alternative method using absolute genomic coordinates.
               NB: This method works only for GenomicAlignBlock which have been
               fetched from the DB as it is adjusting the dnafrag coordinates
               and the cigar_line only and not the actual sequences stored in the
               object if any. If you want to restrict an object with no coordinates
               a simple substr() will do!
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object
  Exceptions : none
  Caller     : general
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlignBlock Bio::EnsEMBL::Compara::BaseGenomicAlignSet::restrict_between_reference_positions ( ) [inherited]
  Arg[1]     : [optional] int $start, refers to the reference_dnafrag
  Arg[2]     : [optional] int $end, refers to the reference_dnafrag
  Arg[3]     : [optional] Bio::EnsEMBL::Compara::GenomicAlign $reference_GenomicAlign
  Arg[4]     : [optional] boolean $skip_empty_GenomicAligns
  Example    : none
  Description: restrict this GenomicAlignBlock. It returns a new object unless no
               restriction is needed. In that case, it returns the original unchanged
               object
               It might be the case that the restricted region coincide with a gap
               in one or several GenomicAligns. By default these GenomicAligns are
               returned with a dnafrag_end equals to its dnafrag_start + 1. For instance,
               a GenomicAlign with dnafrag_start = 12345 and dnafrag_end = 12344
               correspond to a block which goes on this region from before 12345 to
               after 12344, ie just between 12344 and 12345. You can choose to remove
               these empty GenomicAligns by setting $skip_empty_GenomicAligns to any
               true value.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignBlock object in scalar context. In
               list context, returns the previous object and the start and end
               positions of the restriction in alignment coordinates (from 1 to
               alignment_length)
  Exceptions : return undef if reference positions lie outside of the alignment
  Caller     : general
  Status     : At risk
 
Code:
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Reimplemented in Bio::EnsEMBL::Compara::GenomicAlignTree.

public A Bio::EnsEMBL::Compara::GenomicAlignBlock::resulting_genomic_aligns ( )
Deprecated:
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->get_all_non_reference_genomic_align() method instead
  Arg [1]    : (none)
  Example    : $genomic_aligns = $genomic_align_block->resulting_genomic_aligns();
  Description: get the all the non_reference_genomic_aligns. When looking for genomic
               alignments in a given slice or dnafrag, the reference_genomic_align
               corresponds to the Bio::EnsEMBL::Compara::GenomicAlign included in the
               reference slice or dnafrag. The reference_genomic_align_id is the dbID
               corresponding to the reference_genomic_align. All remaining
               Bio::EnsEMBL::Compara::GenomicAlign objects included in the
               Bio::EnsEMBL::Compara::GenomicAlignBlock are the
               non_reference_genomic_aligns.
  Returntype : a ref. to an array of Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : warns if no reference_genomic_align_id has been set and returns a ref.
               to an empty array
  Exceptions : warns if no genomic_align_array has been set and returns a ref.
               to an empty array
  Caller     : $genomic_align_block->resulting_genomic_aligns()
 
Code:
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public void Bio::EnsEMBL::Compara::GenomicAlignBlock::reverse_complement ( )
  Args       : none
  Example    : none
  Description: reverse complement the ,
               modifying dnafrag_strand and cigar_line of each GenomicAlign in consequence
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Double Bio::EnsEMBL::Compara::GenomicAlignBlock::score ( )
  Arg [1]    : double $score
  Example    : my $score = $genomic_align_block->score();
               $genomic_align_block->score(56.2);
  Description: get/set for attribute score. If no argument is given, the score
               is not defined but both the dbID and the adaptor are, it tries to
               fetch and set all the direct attributes from the database using the
               dbID of the Bio::EnsEMBL::Compara::GenomicAlignBlock object.
  Returntype : double
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::BaseGenomicAlignSet::slice ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::Slice $reference_slice
  Example    : my $slice = $genomic_align_block->slice;
  Example    : $genomic_align_block->slice($slice);
  Description: get/set for attribute slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : 
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::start ( ) [inherited]
  Arg [1]    : (optional) integer $start
  Example    : my $start = $genomic_align_block->start;
  Example    : $genomic_align_block->start(1035);
  Description: get/set for attribute reference_slice_start. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::GenomicAlignBlock::starting_genomic_align ( )
Deprecated:
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->reference_genomic_align() method instead
  Arg [1]    : (none)
  Example    : $genomic_align = $genomic_align_block->starting_genomic_align();
  Description: get the reference_genomic_align. When looking for genomic alignments in
               a given slice or dnafrag, the reference_genomic_align corresponds to the
               Bio::EnsEMBL::Compara::GenomicAlign included in the starting slice or
               dnafrag. The reference_genomic_align_id is the dbID corresponding to the
               reference_genomic_align. All remaining Bio::EnsEMBL::Compara::GenomicAlign
               objects included in the Bio::EnsEMBL::Compara::GenomicAlignBlock are the
               non_reference_genomic_aligns.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : warns if no reference_genomic_align_id has been set and returns a ref.
               to an empty array
  Exceptions : warns if no genomic_align_array has been set and returns a ref.
               to an empty array
  Exceptions : throw if reference_genomic_align_id does not match any of the
               Bio::EnsEMBL::Compara::GenomicAlign objects in the genomic_align_array
  Caller     : $genomic_align_block->starting_genomic_align()
 
Code:
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public void Bio::EnsEMBL::Compara::GenomicAlignBlock::starting_genomic_align_id ( )
Deprecated:
! Use Bio::EnsEMBL::Compara::GenomicAlignBlock->reference_genomic_align_id() method instead
  Arg [1]    : integer $reference_genomic_align_id
  Example    : $genomic_align_block->starting_genomic_align_id(4321);
  Description: set for attribute reference_genomic_align_id. A value of 0 will set the
               reference_genomic_align_id attribute to undef. When looking for genomic
               alignments in a given slice or dnafrag, the reference_genomic_align
               corresponds to the Bio::EnsEMBL::Compara::GenomicAlign included in the
               starting slice or dnafrag. The reference_genomic_align_id is the dbID
               corresponding to the reference_genomic_align. All remaining
               Bio::EnsEMBL::Compara::GenomicAlign objects included in the
               Bio::EnsEMBL::Compara::GenomicAlignBlock are the non_reference_genomic_aligns.
  Returntype : none
  Exceptions : throw if $reference_genomic_align_id id not a postive number
  Caller     : $genomic_align_block->starting_genomic_align_id(int)
 
Code:
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public Int Bio::EnsEMBL::Compara::BaseGenomicAlignSet::strand ( ) [inherited]
  Arg [1]    : integer $strand
  Example    : my $strand = $genomic_align_block->strand;
  Example    : $genomic_align_block->strand(-1);
  Description: get/set for attribute strand. A value of 0 will set
               the attribute to undefined.
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file: