Bio::LiveSeq ChainI
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Summary
Bio::LiveSeq::ChainI - Double linked chain data structure
Package variables
No package variables defined.
Included modules
Bio::LiveSeq::Chain
Carp qw ( croak )
strict
Synopsis
  #documentation needed
Description
This class generates and manipulates generic double linked list, chain,
that can be used to manage biological sequences.
The advantages over strings or plain arrays is the ease of tracking
changes (mutations) in the elements (sequence). The other side of the
coin is that these structures need consideraly more memory, but that
is cheap and constantly inceasing resource in computers.
Methods
newDescriptionCode
string2chain
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array2chain
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chain2string
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down_chain2string
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up_chain2string
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chain2string_verbose
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down_chain2string_verbose
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up_chain2string_verbose
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invert_chain
No description
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mutate_element
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down_labels
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up_labels
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start
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end
No description
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label_exists
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get_value_at_pos
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down_get_value_at_pos
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up_get_value_at_pos
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set_value_at_pos
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down_set_value_at_pos
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up_set_value_at_pos
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get_value_at_label
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set_value_at_label
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get_label_at_pos
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up_get_label_at_pos
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down_get_label_at_pos
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get_pos_of_label
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up_get_pos_of_label
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down_get_pos_of_label
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preinsert_string
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preinsert_array
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praeinsert_string
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postinsert_string
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praeinsert_array
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postinsert_array
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down_element
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up_element
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is_downstream
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is_upstream
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check_chain
No description
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chain_length
No description
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splice_chain
No description
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pos_of_element
No description
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up_pos_of_element
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down_pos_of_element
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subchain_length
No description
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down_subchain_length
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up_subchain_length
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elements
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up_elements
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down_elements
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Methods description
newcode    nextTop
  Title   : new
Usage : $chain = Bio::LiveSeq::ChainI->new(-string => "thequickbrownfoxjumpsoverthelazydog",
-offset => 3 );
OR $chain = Bio::LiveSeq::ChainI->new(-array => \@array,
-offset => 3 );
Function: generates a new Bio::LiveSeq:ChainI
Returns : a new Chain
Args : string
OR arrayreference
AND optional offset to create element labels
Methods code
newdescriptionprevnextTop
sub new {
  my ($thing, %args) = @_;
  my $class = ref($thing) || $thing;
  my $obj;

  if ($args{-string}) {
    $obj = $thing->string2chain($args{-string}, $args{-offset});
  } elsif ($args{-array}) {
    $obj = $thing->array2chain($args{-array}, $args{-offset});
  } else {
    croak "$class not initialized properly";
  }

  $obj = bless $obj, $class;
  return $obj;
}

# added as of 1.9
}
string2chaindescriptionprevnextTop
sub string2chain {
  shift @_; # so that it doesn't pass the object reference
return Bio::LiveSeq::Chain::string2chain(@_);
}
array2chaindescriptionprevnextTop
sub array2chain {
  shift @_; # so that it doesn't pass the object reference
return Bio::LiveSeq::Chain::array2chain(@_); } #
}
chain2stringdescriptionprevnextTop
sub chain2string {
  croak "ambiguous method call. Explicit down_ or up_";
}
down_chain2stringdescriptionprevnextTop
sub down_chain2string {
  return Bio::LiveSeq::Chain::down_chain2string(@_);
}
up_chain2stringdescriptionprevnextTop
sub up_chain2string {
  return Bio::LiveSeq::Chain::up_chain2string(@_);
}
chain2string_verbosedescriptionprevnextTop
sub chain2string_verbose {
  croak "ambiguous method call. Explicit down_ or up_";
}
down_chain2string_verbosedescriptionprevnextTop
sub down_chain2string_verbose {
  return Bio::LiveSeq::Chain::down_chain2string_verbose(@_);
}
up_chain2string_verbosedescriptionprevnextTop
sub up_chain2string_verbose {
  return Bio::LiveSeq::Chain::up_chain2string_verbose(@_);
}
invert_chaindescriptionprevnextTop
sub invert_chain {
  return Bio::LiveSeq::Chain::invert_chain(@_);
}
mutate_elementdescriptionprevnextTop
sub mutate_element {
  croak "Old method name, please update code to: set_value_at_label";
}

# new as of version 2.33 of Chain.pm
}
down_labelsdescriptionprevnextTop
sub down_labels {
  return Bio::LiveSeq::Chain::down_labels(@_);
}
up_labelsdescriptionprevnextTop
sub up_labels {
  return Bio::LiveSeq::Chain::up_labels(@_);
}
startdescriptionprevnextTop
sub start {
  return Bio::LiveSeq::Chain::start(@_);
}
enddescriptionprevnextTop
sub end {
  return Bio::LiveSeq::Chain::end(@_);
}
label_existsdescriptionprevnextTop
sub label_exists {
  return Bio::LiveSeq::Chain::label_exists(@_);
}
get_value_at_posdescriptionprevnextTop
sub get_value_at_pos {
  croak "ambiguous method call. Explicit down_ or up_";
}
down_get_value_at_posdescriptionprevnextTop
sub down_get_value_at_pos {
  return Bio::LiveSeq::Chain::down_get_value_at_pos(@_);
}
up_get_value_at_posdescriptionprevnextTop
sub up_get_value_at_pos {
  return Bio::LiveSeq::Chain::up_get_value_at_pos(@_);
}
set_value_at_posdescriptionprevnextTop
sub set_value_at_pos {
  croak "ambiguous method call. Explicit down_ or up_";
}
down_set_value_at_posdescriptionprevnextTop
sub down_set_value_at_pos {
  return Bio::LiveSeq::Chain::down_set_value_at_pos(@_);
}
up_set_value_at_posdescriptionprevnextTop
sub up_set_value_at_pos {
  return Bio::LiveSeq::Chain::up_set_value_at_pos(@_);
}
get_value_at_labeldescriptionprevnextTop
sub get_value_at_label {
  return Bio::LiveSeq::Chain::get_value_at_label(@_);
}
set_value_at_labeldescriptionprevnextTop
sub set_value_at_label {
  return Bio::LiveSeq::Chain::set_value_at_label(@_);
}
get_label_at_posdescriptionprevnextTop
sub get_label_at_pos {
  croak "ambiguous method call. Explicit down_ or up_";
}
up_get_label_at_posdescriptionprevnextTop
sub up_get_label_at_pos {
  return Bio::LiveSeq::Chain::up_get_label_at_pos(@_);
}
down_get_label_at_posdescriptionprevnextTop
sub down_get_label_at_pos {
  return Bio::LiveSeq::Chain::down_get_label_at_pos(@_);
}
get_pos_of_labeldescriptionprevnextTop
sub get_pos_of_label {
  croak "ambiguous method call. Explicit down_ or up_";
}
up_get_pos_of_labeldescriptionprevnextTop
sub up_get_pos_of_label {
  return Bio::LiveSeq::Chain::up_get_pos_of_label(@_);
}
down_get_pos_of_labeldescriptionprevnextTop
sub down_get_pos_of_label {
  return Bio::LiveSeq::Chain::down_get_pos_of_label(@_);
}
#
}
preinsert_stringdescriptionprevnextTop
sub preinsert_string {
  return Bio::LiveSeq::Chain::praeinsert_string(@_);
}
preinsert_arraydescriptionprevnextTop
sub preinsert_array {
  return Bio::LiveSeq::Chain::praeinsert_array(@_);
}
praeinsert_stringdescriptionprevnextTop
sub praeinsert_string {
  return Bio::LiveSeq::Chain::praeinsert_string(@_);
}
postinsert_stringdescriptionprevnextTop
sub postinsert_string {
  return Bio::LiveSeq::Chain::postinsert_string(@_);
}
praeinsert_arraydescriptionprevnextTop
sub praeinsert_array {
  return Bio::LiveSeq::Chain::praeinsert_array(@_);
}
postinsert_arraydescriptionprevnextTop
sub postinsert_array {
  return Bio::LiveSeq::Chain::postinsert_array(@_);
}
down_elementdescriptionprevnextTop
sub down_element {
  return Bio::LiveSeq::Chain::down_element(@_);
}
up_elementdescriptionprevnextTop
sub up_element {
  return Bio::LiveSeq::Chain::up_element(@_);
}
is_downstreamdescriptionprevnextTop
sub is_downstream {
  return Bio::LiveSeq::Chain::is_downstream(@_);
}
is_upstreamdescriptionprevnextTop
sub is_upstream {
  return Bio::LiveSeq::Chain::is_upstream(@_);
}
check_chaindescriptionprevnextTop
sub check_chain {
  return Bio::LiveSeq::Chain::check_chain(@_);
}
chain_lengthdescriptionprevnextTop
sub chain_length {
  return Bio::LiveSeq::Chain::chain_length(@_);
}
splice_chaindescriptionprevnextTop
sub splice_chain {
  return Bio::LiveSeq::Chain::splice_chain(@_);
}
pos_of_elementdescriptionprevnextTop
sub pos_of_element {
  croak "ambiguous and old method name. use: down_pos_of_label";
}
up_pos_of_elementdescriptionprevnextTop
sub up_pos_of_element {
  croak "old method name. use: down_pos_of_label";
  return Bio::LiveSeq::Chain::up_pos_of_element(@_);
}
down_pos_of_elementdescriptionprevnextTop
sub down_pos_of_element {
  croak "old method name. use: up_pos_of_label";
  return Bio::LiveSeq::Chain::down_pos_of_element(@_);
}
subchain_lengthdescriptionprevnextTop
sub subchain_length {
  croak "ambiguous method call. Explicit down_ or up_";
}
down_subchain_lengthdescriptionprevnextTop
sub down_subchain_length {
  return Bio::LiveSeq::Chain::down_subchain_length(@_);
}
up_subchain_lengthdescriptionprevnextTop
sub up_subchain_length {
  return Bio::LiveSeq::Chain::up_subchain_length(@_);
}

# these have to be deleted and changed names to conform to terminology
}
elementsdescriptionprevnextTop
sub elements {
  return Bio::LiveSeq::Chain::down_elements(@_);
}
up_elementsdescriptionprevnextTop
sub up_elements {
  return Bio::LiveSeq::Chain::up_elements(@_);
}
down_elementsdescriptionprevnextTop
sub down_elements {
  return Bio::LiveSeq::Chain::down_elements(@_);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Joseph A.L. InsanaTop
Email: Insana@ebi.ac.uk, jinsana@gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _