Bio::LiveSeq::Chain - DoubleChain DataStructure for Perl #documentation needed 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. Email: Insana@ebi.ac.uk, jinsana@gmx.net Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom 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")