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::GeneGroup(3pm) User Contributed Perl Documentation SWISS::GeneGroup(3pm)Name
SWISS::GeneGroup.pm
Description
A SWISS::GeneGroup object contain all synonyms for a given gene name. See SWISS::GNs for a description of the gene name format.
Inherits from
SWISS::BaseClass.pm
(also implements many methods from SWISS::ListBase.pm)
Attributes
"Names"
Each list element is a SWISS::GN object, describing a primary name
or synonym. Concatenation of Name and Synonyms lists.
"OLN"
Each list element is a SWISS::GN object, describing an
OrderedLocusName.
"ORFNames"
Each list element is a SWISS::GN object, describing an ORFName.
Methods
Standard methods
new
fromText
toText
Specific methods
Name
Returns the Name (primary name).
Synonyms
Returns the Synonyms.
elements
Concatenates all elements from Names, OLN and ORFNames in
a single array.
List manipulation methods
Since GeneGroup was a previous implementation of SWISS::ListBase, the list manipulation methods below are provided to facilitate
compatibility.
size
isEmpty
elements
filter
get (deprecated)
head (deprecated)
tail (deprecated)
item (deprecated)
push (deprecated)
pop (deprecated)
shift (deprecated)
splice (deprecated)
unshift (deprecated)
set (deprecated)
add (deprecated)
perl v5.10.1 2006-01-26 SWISS::GeneGroup(3pm)
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