bionic (3) SWISS::DE.3pm.gz

Name

       SWISS::DE.pm

Description

       Each DE object represents one protein name. The container object for all names of an entry is SWISS::DEs

Inherits from

       SWISS::BaseClass

Attributes

       "text"
           The raw text of the protein name.  Note: as SwissKnife works with both new and old DE line formats,
           for backward rcompatibility, with both formats everything is parsed and stored the same way as it was
           with the old format. Therefore the raw text for a name of type 'EC' e.g.  6.3.5.5 will be "EC
           6.3.5.5" (instead of "6.3.5.5"). Other strings only present in old DE line text format ('precursor'
           flag and 'Allergen', 'antigen' strings) are also added in the stored raw text.  The safe method to
           get the DE text is "toText" (with both the new and old DE line format), which for "EC=6.3.5.5" (new
           DE line format), will return "6.3.5.5" (DE object of 'EC' type). For "(EC 6.3.5.5)" (old DE line
           format), will return "EC 6.3.5.5"

       "category"
           The category of the protein name: 'RecName', 'AltName', 'SubName' (TrEMBL only)

            DE   RecName: Full=CAD protein;
            DE            Short=CAD;

            Here both names (DE objects), are of category 'RecName'

           Category can be set/modified using "category(string)"

           Note: with the old DE line format, this field is undef

       "type"
           The type of the protein name: 'Full', 'Short', 'EC' 'Allergen', 'CD_antigen', 'Biotech','INN'

            DE   RecName: Full=CAD protein;
            DE            Short=CAD;

            Here the first name (DE object), is of type 'Full', the second one
            is of type 'Short'

           Type can be set/modified using "type(string)"

           Note: with the old DE line format, this field is undef

   Standard methods
       new
       fromText
       toText ($addParen)
            addParen : (meaningful only with old DE line format) if set to true,
            the name will be surrounded by parentheses, but not the evidence
            tags, e.g. : '(UMP SYNTHASE){E1}'.

Evidence Tags

       Each protein name (DE object) can have independent evidence tags.

        DE   SubName: Full=Histone H3{EI1};
        DE            EC=3.4.21.9{EC3};
        DE   AltName: Full=Enterokinase{EC5};

       The following methods have their prototype defined in SWISS::BaseClass instead of the direct parent of
       SWISS::DEs, SWISS::ListBase :

        addEvidenceTag
        deleteEvidenceTags
        getEvidenceTags
        getEvidenceTagsString
        hasEvidenceTag
        setEvidenceTags

       example :

        $evidenceTag = $entry->Stars->EV->addEvidence('P', 'DEfix', '-', 'v1.3');
        $entry->DEs->head->addEvidenceTag($evidenceTag);

       The easiest way to read the evidence tags of a protein name is to use c<getEvidenceTagsString> that will
       return the evidence tags as a string with the enclosing {} brackets. If there are no evidence tags, will
       return an empty string.

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 165:
           =back doesn't take any parameters, but you said =back  =head1 Methods