Bio::LiveSeq::Chain.3pm

Langue: en

Autres versions - même langue

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::LiveSeq::Chain - DoubleChain DataStructure for Perl

SYNOPSIS

   #documentation needed
 
 

DESCRIPTION

This is a general purpose module (that's why it's not in object-oriented form) that introduces a novel datastructure in PERL. It implements the ``double linked chain''. The elements of the chain can contain basically everything. From chars to strings, from object references to arrays or hashes. It is used in the LiveSequence project to create a dynamical DNA sequence, easier to manipulate and change. It's use is mainly for sequence variation analysis but it could be used - for example - in e-cell projects. The Chain module in itself doesn't have any biological bias, so can be used for any programming purpose.

Each element of the chain (with the exclusion of the first and the last of the chain) is connected to other two elements (the PREVious and the NEXT one). There is no absolute position (like in an array), hence if positions are important, they need to be computed (methods are provided). Otherwise it's easy to keep track of the elements with their ``LABELs''. There is one LABEL (think of it as a pointer) to each ELEMENT. The labels won't change after insertions or deletions of the chain. So it's always possible to retrieve an element even if the chain has been modified by successive insertions or deletions. From this the high potential profit for bioinformatics: dealing with sequences in a way that doesn't have to rely on positions, without the need of constantly updating them if the sequence changes, even dramatically.

AUTHOR - Joseph A.L. Insana

Email: Insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_updown_chain2string

   Title   : chain2string
   Usage   : $string = Bio::LiveSeq::Chain::chain2string("down",$chain,6,9)
   Function: reads the contents of the chain, outputting a string
   Returns : a string
   Examples:
           : down_chain2string($chain) -> all the chain from begin to end
           : down_chain2string($chain,6) -> from 6 to the end
           : down_chain2string($chain,6,4) -> from 6, going on 4 elements
           : down_chain2string($chain,6,"",10) -> from 6 to 10
           : up_chain2string($chain,10,"",6) -> from 10 to 6 upstream
   Defaults: start=first element; if len undef, goes to last
             if last undef, goes to end
             if last defined, it overrides len (undefining it)
   Error code: -1
   Args    : "up"||"down" as first argument to specify the reading direction 
             reference (to the chain)
             [first] [len] [last] optional integer arguments to specify how
             much and from (and to) where to read
 
 

_updown_labels

  Title   : labels
  Usage   : @labels = Bio::LiveSeq::Chain::_updown_labels("down",$chain,4,16)
  Function: returns all the labels in a chain or those between two
            specified ones (termed "first" and "last")
  Returns : a reference to an array containing the labels
  Args    : "up"||"down" as first argument to specify the reading direction 
            reference (to the chain)
            [first] [last] (integer for the starting and eneding labels)
 
 

start

  Title   : start
  Usage   : $start = Bio::LiveSeq::Chain::start()
  Returns : the label marking the start of the chain
  Errorcode: -1
  Args    : none
 
 

end

  Title   : end
  Usage   : $end = Bio::LiveSeq::Chain::end()
  Returns : the label marking the end of the chain
  Errorcode: -1
  Args    : none
 
 

label_exists

  Title   : label_exists
  Usage   : $check = Bio::LiveSeq::Chain::label_exists($chain,$label)
  Function: It checks if a label is defined, i.e. if an element is there or
            is not there anymore
  Returns : 1 if the label exists, 0 if it is not there, -1 error
  Errorcode: -1
  Args    : reference to the chain, integer
 
 

down_get_pos_of_label

  Title   : down_get_pos_of_label
  Usage   : $position = Bio::LiveSeq::Chain::down_get_pos_of_label($chain,$label,$first)
  Function: returns the position of $label counting from $first, i.e. taking
            $first as 1 of coordinate system. If $first is not specified it will
            count from the start of the chain.
  Returns : 
  Errorcode: 0
  Args    : reference to the chain, integer (the label of interest)
            optional: integer (a different label that will be taken as the
            first one, i.e. the one to count from)
  Note:     It counts "downstream". To proceed backward use up_get_pos_of_label
 
 

down_subchain_length

  Title   : down_subchain_length
  Usage   : $length = Bio::LiveSeq::Chain::down_subchain_length($chain,$first,$last)
  Function: returns the length of the chain between the labels "first" and "last", included
  Returns : integer
  Errorcode: 0
  Args    : reference to the chain, integer, integer
  Note:     It counts "downstream". To proceed backward use up_subchain_length
 
 

invert_chain

  Title   : invert_chain
  Usage   : $errorcode=Bio::LiveSeq::Chain::invert_chain($chain)
  Function: completely inverts the order of the chain elements; begin is swapped with end and all links updated (PREV&NEXT fields swapped)
  Returns : 1 if all OK, 0 if errors
  Errorcode: 0
  Args    : reference to the chain
 
 

down_get_value_at_pos

  Title   : down_get_value_at_pos
  Usage   : $value = Bio::LiveSeq::Chain::down_get_value_at_pos($chain,$position,$first)
  Function: used to access the value of the chain at a particular position instead than directly with a label pointer. It will count the position from the start of the chain or from the label $first, if $first is specified
  Returns : whatever is stored in the element of the chain
  Errorcode: 0
  Args    : reference to the chain, integer, [integer]
  Note:     It works "downstream". To proceed backward use up_get_value_at_pos
 
 

down_set_value_at_pos

  Title   : down_set_value_at_pos
  Usage   : $errorcode = Bio::LiveSeq::Chain::down_set_value_at_pos($chain,$newvalue,$position,$first)
  Function: used to store a new value inside an element of the chain at a particular position instead than directly with a label pointer. It will count the position from the start of the chain or from the label $first, if $first is specified
  Returns : 1
  Errorcode: 0
  Args    : reference to the chain, newvalue, integer, [integer]
            (newvalue can be: integer, string, object reference, hash ref)
  Note:     It works "downstream". To proceed backward use up_set_value_at_pos
  Note2:    If the $newvalue is undef, it will delete the contents of the
            element but it won't remove the element from the chain.
 
 

down_set_value_at_label

  Title   : down_set_value_at_label
  Usage   : $errorcode = Bio::LiveSeq::Chain::down_set_value_at_label($chain,$newvalue,$label)
  Function: used to store a new value inside an element of the chain defined by its label.
  Returns : 1
  Errorcode: 0
  Args    : reference to the chain, newvalue, integer
            (newvalue can be: integer, string, object reference, hash ref)
  Note:     It works "downstream". To proceed backward use up_set_value_at_label
  Note2:    If the $newvalue is undef, it will delete the contents of the
            element but it won't remove the element from the chain.
 
 

down_get_value_at_label

  Title   : down_get_value_at_label
  Usage   : $value = Bio::LiveSeq::Chain::down_get_value_at_label($chain,$label)
  Function: used to access the value of the chain from one element defined by its label.
  Returns : whatever is stored in the element of the chain
  Errorcode: 0
  Args    : reference to the chain, integer
  Note:     It works "downstream". To proceed backward use up_get_value_at_label
 
 

down_get_label_at_pos

  Title   : down_get_label_at_pos
  Usage   : $label = Bio::LiveSeq::Chain::down_get_label_at_pos($chain,$position,$first)
  Function: used to retrieve the label of an an element of the chain at a particular position. It will count the position from the start of the chain or from the label $first, if $first is specified
  Returns : integer
  Errorcode: 0
  Args    : reference to the chain, integer, [integer]
  Note:     It works "downstream". To proceed backward use up_get_label_at_pos
 
 

_praepostinsert_array

  Title   : _praepostinsert_array
  Usage   : ($insbegin,$insend) = Bio::LiveSeq::Chain::_praepostinsert_array($chainref,"post",$arrayref,$position)
  Function: the elements of the array specified by $arrayref are inserted (creating a new subchain) in the chain specified by $chainref, before or after (depending on the "prae"||"post" keyword passed as second argument) the specified position.
  Returns : two labels: the first and the last of the inserted subchain
  Defaults: if no position is specified, the new chain will be inserted after
  (post) the first element of the chain
  Errorcode: 0
  Args    : chainref, "prae"||"post", arrayref, integer (position)
 
 

is_downstream

   Title   : is_downstream
   Usage   : Bio::LiveSeq::Chain::is_downstream($chainref,$firstlabel,$secondlabel)
   Function: checks if SECONDlabel follows FIRSTlabel
             It runs downstream the elements of the chain from FIRST searching
             for SECOND.
   Returns : 1 if SECOND is found /after/ FIRST; 0 otherwise (i.e. if it
             reaches the end of the chain without having found it)
   Errorcode -1
   Args    : two labels (integer)
 
 

is_upstream

   Title   : is_upstream
   Usage   : Bio::LiveSeq::Chain::is_upstream($chainref,$firstlabel,$secondlabel)
   Function: checks if SECONDlabel follows FIRSTlabel
             It runs upstream the elements of the chain from FIRST searching
             for SECOND.
   Returns : 1 if SECOND is found /after/ FIRST; 0 otherwise (i.e. if it
             reaches the end of the chain without having found it)
   Errorcode -1
   Args    : two labels (integer)
 
 

check_chain

  Title   : check_chain
  Usage   : @errorcodes = Bio::LiveSeq::Chain::check_chain()
  Function: a wraparound to a series of check for consistency of the chain
            It will check for boundaries, size, backlinking and forwardlinking
  Returns : array of 4 warn codes, each can be 1 (all ok) or 0 (something wrong)
  Errorcode: 0
  Args    : none
  Note    : this is slow and through. It is not really needed. It is mostly
            a code-developer tool.
 
 

splice_chain

  Title   : splice_chain
  Usage   : @errorcodes = Bio::LiveSeq::Chain::splice_chain($chainref,$first,$length,$last)
  Function: removes the elements designated by FIRST and LENGTH from a chain.
            The chain shrinks accordingly. If LENGTH is omitted, removes
            everything from FIRST onward.
            If END is specified, LENGTH is ignored and instead the removal
            occurs from FIRST to LAST.
  Returns : the elements removed as a string
  Errorcode: -1
  Args    : chainref, integer, integer, integer
 
 

array2chain

   Title   : array2chain
   Usage   : $chainref = Bio::LiveSeq::Chain::array2chain($arrayref,$offset)
   Function: creation of a double linked chain from an array
   Returns : reference to a hash containing the chain
   Defaults: OFFSET defaults to 1 if undef
   Error code: 0
   Args    : a reference to an array containing the elements to be chainlinked
             an optional integer > 0 (this will be the starting count for
             the chain labels instead than having them begin from "1")