SWISS::Stars(3pm) User Contributed Perl Documentation SWISS::Stars(3pm)NAME
SWISS::Stars.pm
DESCRIPTION
SWISS::Stars represents the ** lines within an SWISS-PROT + TrEMBL entry. These are the lines with the line tag ** which are normally not
publicly visible.
SWISS::Stars is a master object like SWISS::Entry. It contains subobjects which represent the different line types in the ** section. Each
line type has a two letter tag in addition to the ** line tag. This module has been written to allow easy addition of new ** line types. To
use a new ** line tag, just use the tag as an object dereference. Example:
$entry->Stars->XX->add("New XX tag line.","Second new XX tag line.");
If there is no class SWISS::Stars::XX, the class of the new object will be SWISS::Stars::default, which handles lines with the
corresponding tag as an array of lines. If more specific handling is required, a new class SWISS::Stars::XX can be created following the
template of SWISS::Stars::default. An example is SWISS::Stars::aa.
Subclass names and new line tags have to be two-letter-tags. No checks are made wheter the dereferenced tag is allowed.
Access to the (old) unstructured ANNOTATOR'S SECTION is provided by the line tag 'aa'.
$entry->Stars->aa->add("Testline 1.","Second new test line.");
will add these two lines to the ANNOTATOR'S SECTION.
Inherits from
SWISS::BaseClass.pm
Attributes
No public attributes apart from the subclasses.
Methods
Standard methods
new
fromText
toText
update
perl v5.10.1 2006-01-26 SWISS::Stars(3pm)
Check Out this Related Man Page
SWISS::Stars::EV(3pm) User Contributed Perl Documentation SWISS::Stars::EV(3pm)
new
fromText
toText
sort
addEvidence($category, $type, $initials, $attributes [, $date])
Title: addEvidence
Usage: $evidenceTag = $entry->Stars->EV->addEvidence($category,
$type,
$initials,
$attributes
[, $date])
Function: adds the evidence to the EV block if it does not yet exist
or returns the correct evidence tag if the evidence already exists,
possibly with a different date.
Args: $category: the evidence category. Currently one of 'A', 'C', 'I','P'.
$type: the evidence type
$initials: The initals of the person doing the update.
For programs this should be '-'.
$attributes: the attributes of the evidence
$date: optional. If present, it must be in standard SWISS-PROT
date format. If not present the current date will be used.
Returns: The correct evidence tag.
updateEvidence($category, $type, $initials, $attributes [, $date])
Title: updateEvidence
Usage: $evidenceTag = $entry->Stars->EV->updateEvidence($category,
$type,
$initials,
$attributes
[, $date])
Function: updates the evidence to the EV block to $date or inserts it
if it does not yet exist.
Args: $category: the evidence category. Currently one of 'A', 'C', 'I','P'.
$type: the evidence type
$initials: The initals of the person doing the update.
For programs this should be '-'.
$attributes: the attributes of the evidence
$date: optional. If present, it must be in standard SWISS-PROT
date format. If not present the current date will be used.
Returns: The correct evidence tag.
Name
SWISS::Stars::EV.pm
Description
SWISS/Stars/EV.pm represents the evidence section within an SWISS-PROT + TrEMBL entry. See
http://www3.ebi.ac.uk/~sp/intern/projects/evidenceTags/index.html
For a usage example, see evTest.pl in the Swissknife package.
Inherits from SWISS::ListBase.pm
Attributes
"list" Each element of the list describes one evidence, itself represented as an array.
perl v5.10.1 2006-01-26 SWISS::Stars::EV(3pm)