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")