swiss::stars::ev(3pm) [debian 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)

SWISS::DE(3pm)						User Contributed Perl Documentation					    SWISS::DE(3pm)

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

perl v5.10.1							    2008-07-17							    SWISS::DE(3pm)