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

Name
       SWISS::ListBase.pm

Description
       Base class for list oriented classes in the SWISS:: hierarchy. It provides a set of quite general list manipulation methods to inheriting
       classes.

Attributes
       list
	   Holds an array, the essential content of the object. Array elements can be, and are in fact frequently, arrays themselves.

Methods
   Standard methods
       new
       initialize

   Reading methods
       head
	   Return the first element of the list

       tail
	   Return all but the first element of the list

       get pattern
	   Return a list of all elements matched by $pattern. Only exact matches are returned, but you can use Perls regular expressions. Example:

	     $listBaseObject->set('EMBL', 'TREMBL', 'SWISSPROT');
	     $listBaseObject->get('.*EMBL');

	   returns ('EMBL', 'TREMBL')

       get @patternList
	   To be used if the ListBase elements are arrays. An array is returned if all its elements are matched exactly by the elements from
	   @patternList with the same index. Empty elements in @patternList always match. Example:

	    $listBaseObject->set(['EMBL', 'M1', 'G1', '-'],
				 ['EMBL', 'M2', 'A2', '-'],
				 ['EMBL', 'M2', 'G3', 'ALT_TERM'],
				 ['PROSITE', 'P00001', '1433_2', '1']);
	    $listBaseObject->get('EMBL');

	    returns (['EMBL', 'M1', 'G1', '-'],
		     ['EMBL', 'M2', 'A2', '-'],
		     ['EMBL', 'M2', 'G3', 'ALT_TERM'])

	    $listBaseObject->get('',M2);

	    returns (['EMBL', 'M2', 'A2', '-'],
		     ['EMBL', 'M2', 'G3', 'ALT_TERM']);

	   Offering get in the interface is not particularly nice because it exports implementation details into the interface, but it is a
	   powerful method which may save a lot of programming time. As an alternative, the 'filter' concept is available.

       getObject pattern
       getObject @patternList
	   Same as get, but returns the results wrapped in a new ListBase object.

       filter
	   Returns a new object containing all of the elements that match a search criteria. It takes a function as the only parameter. This
	   function should expect a list element, and return true or false depending on whether the element matches the criteria. If the object is
	   not a ListBase object but member of a subclass, a new object of that subclass will be returned.

	   Example:

	    $tmp = $entry->CCs->filter(&ccTopic('FUNCTION'));

	   returns a SWISS::CCs object containing all CC blocks from $entry which have the topic 'FUNCTION'.

	   Functions can also be anonymous functions.

       attributeEquals(string attributeName, string attributeValue)
	   Filter function. If the elements of a ListBase object are objects, they will be returned by this function if they have the attribute
	   and it equals the attributeValue.

	    Example:

	   $matchedKWs = $entry->KWs->filter(SWISS::ListBase::attributeEquals('text', $kw));

       attributeMatchedBy(string attributeName, string pattern)
	   Filter function. If the elements of a ListBase object are objects, they will be returned by this function if they have the attribute
	   and the attribute is matched by the pattern.

	    Example:

	   $matchedKWs = $entry->KWs->filter(SWISS::ListBase::attributeMatchedBy('text', $kw));

       isEmpty
       size
	   The number of list elements in the object

       elements
	   Returns the array of elements

       hasEvidenceTag $arrayPointer $tag
	   Returns true if the array pointed to by $arrayPointer has the evidence tag $tag

       getEvidenceTags $arrayPointer
	   returns the array of evidence tags of $arrayPointer

       getEvidenceTagsString $arrayPointer
	   returns a string containing the evidence tags of $arrayPointer

   Writing methods
       item offset[, newValue]
	   returns the list element at a specific offset, and optionally sets it to a new value. Negative offsets are relative to the end of the
	   list.

       push list
       pop
       shift
       unshift list
       splice [offset[, length[, list]]]
       set list
	   Sets the list attribute to @list

       add list
	   Synonym for push

       merge (ListBase)
	   Appends the elements of ListBase to the object

       sort [function]
	   Applies a sort function to the list attribute, or by default, alphabetical sorting. Should be overwritten in derived classes with an
	   adapted sort function.

       del pattern
	   Deletes all items fully matching $pattern. Example:

	     $listBaseObject->set('EMBL','TREMBL', 'SWISSPROT');
	     $listBaseObject->del('EMBL');

	     $listBaseObject->list();

	     returns ('TREMBL','SWISSPROT').

	   If you want to delete more, use something like

	     $listBaseObject->del('.*EMBL')

	   which deletes 'EMBL' and 'TREMBL'.

       del @patternList
	   To be used if the ListBase objects are arrays. An array is deleted if all its elements are matched by the elements from @patternList
	   with the same index.

	   Warning: Empty elements in @patternList always match!

	   Using the data from the get example above,

	     $listBaseObject->del('','', 'A2')

	   results in

	     (['EMBL', 'M1', 'G1', '-'],
	      ['EMBL', 'M2', 'G3', 'ALT_TERM'],
	      ['PROSITE', 'P00001', '1433_2', '1'])

       update
       unique
	   Makes sure each element is contained only once in a ListBase object. The second and subsequent occurrences of the same object are
	   deleted. Example:

	     $listBaseObject->set(EMBL, TREMBL, SWISSPROT);
	     $listBaseObject->add(EMBL, MGD, EMBL);
	     $listBaseObject->unique();

	   results in (EMBL, TREMBL, SWISSPROT, MGD)

       setEvidenceTags $arrayPointer @array
	   sets the evidence Tags of the array pointed to by $arrayPointer to the contents of @array

	   To be used if the ListBase elements are themselves arrays. A typical construct would be

	     foreach $dr ($entry->DRs->elements()) {
	       $entry->DRs->setEvidenceTags($dr, 'E2', 'E3');
	     }

	   Returns $arrayPointer.

       addEvidenceTag $arrayPointer $tag
	   adds $tag to the evidence tags of $arrayPointer

	   To be used if the ListBase elements are themselves arrays. See documentation of setEvidenceTags.

	   Returns $arrayPointer.

       deleteEvidenceTags $arrayPointer $evidenceTag
	   deletes $evidenceTag from the array pointed to by $arrayPointer

	   To be used if the ListBase elements are themselves arrays. A typical construct would be

	     foreach $dr ($entry->DRs->elements()) {
	       $entry->DRs->deleteEvidenceTags($dr, 'EC2');
	     }

	   Returns $arrayPointer.

perl v5.10.1							    2006-01-26						      SWISS::ListBase(3pm)