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.