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 _

  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

 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)

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

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

 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

 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

 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

 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

 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

 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.

 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.

 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

 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

 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)

  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)

  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)

 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.

 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

  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")