SWISS::RCelement(3pm) User Contributed Perl Documentation SWISS::RCelement(3pm)Name
SWISS::RCelement.pm
Description
Each RCelement object represents one element of the RC line. The container object for all RCelements of an entry is SWISS::Ref.
Inherits from
SWISS::BaseClass
Attributes
"text"
The text of the keyword.
Standard methods
new
fromText
toText
Writing methods
cleanText
Remove potentially leading "and" from text.
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 87:
=back doesn't take any parameters, but you said =back =head1 Methods
perl v5.10.1 2006-01-26 SWISS::RCelement(3pm)
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SWISS::CCs(3pm) User Contributed Perl Documentation SWISS::CCs(3pm)Name
SWISS::CCs
Description
SWISS::CCs represents the CC lines within a Swiss-Prot or TrEMBL entry as specified in the user manual
http://www.expasy.org/sprot/userman.html . The CCs object is a container object which holds a list comprised of object of the type
SWISS::CC or derived classes (see below).
Code example
local $/="
//
";
while (<>) {
my $entry = SWISS::Entry-> fromText($_);
my @CCs = $entry -> CCs -> elements();
for my $CC (@CCs) {
if ($CC -> topic eq 'ALTERNATIVE PRODUCTS') {
# now can call methods of CCalt_prod
} elsif ($CC -> topic eq 'Copyright') {
# now can call methods of CCcopyright
} else {
# now can call methods of CC
}
}
}
Inherits from
SWISS::ListBase.pm
Attributes
"list"
Each list element is an object of one of the following classes, depending of the type of comment:
topic object
----------------------------------------
ALTERNATIVE PRODUCTS SWISS::CCalt_prod
RNA EDITING SWISS::CCrna_editing
BIOPHYSICOCHEMICAL PROPERTIES SWISS::CCbpc_properties
INTERACTION SWISS::CCinteraction
Copyright SWISS::CCcopyright
(all other topics) SWISS::CC
Methods
Standard methods
new
fromText
sort
Sort the CC block according to the order given in Swiss-Prot annotation note ANN017.
toText
update
Reading/Writing methods
ccTopic ($topic)
Returns true if entry contains a comment block with the specified topic.
copyright
Returns a string representation of the copyright text.
del (@patternList)
Deletes all comment elements whose topic matches the first element of the pattern list. The second element is the used to specify a
requirement for the comment to match as well.
get (@patternList)
An array is returned consisting of all comment elements elements whose topic matches any elements of the pattern list.
getObject (@patternList)
Same as get, but returns the results wrapped in a new ListBase object.
toString
Returns a string representation of the CCs object.
perl v5.10.1 2008-07-16 SWISS::CCs(3pm)
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