SWISS::DE (3pm)

\s-1SWISS::DE\s0.pm

Each \s-1DE\s0 object represents one protein name. The container object for all names of an entry is SWISS::DEs

SWISS::BaseClass

The raw text of the protein name. Note: as SwissKnife works with both new and old \s-1DE\s0 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 '\s-1EC\s0' e.g. 6.3.5.5 will be \*(L"\s-1EC\s0 6.3.5.5\*(R" (instead of \*(L"6.3.5.5\*(R"). Other strings only present in old \s-1DE\s0 line text format ('precursor' flag and 'Allergen', 'antigen' strings) are also added in the stored raw text. The safe method to get the \s-1DE\s0 text is \*(C`toText\*(C' (with both the new and old \s-1DE\s0 line format), which for \*(L"EC=6.3.5.5\*(R" (new \s-1DE\s0 line format), will return \*(L"6.3.5.5\*(R" (\s-1DE\s0 object of '\s-1EC\s0' type). For \*(L"(\s-1EC\s0 6.3.5.5)\*(R" (old \s-1DE\s0 line format), will return \*(L"\s-1EC\s0 6.3.5.5\*(R" 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 \*(C`category(string)\*(C' Note: with the old \s-1DE\s0 line format, this field is undef The type of the protein name: 'Full', 'Short', '\s-1EC\s0' 'Allergen', 'CD_antigen', 'Biotech','\s-1INN\s0' 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 \*(C`type(string)\*(C' Note: with the old \s-1DE\s0 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}'.

Each protein name (\s-1DE\s0 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.

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