swiss::ccs(3pm) [debian man page]
SWISS::CCs(3pm) User Contributed Perl Documentation SWISS::CCs(3pm) Name SWISS::CCs Description SWISS::CCs represents the CC lines within a Swiss-Prot or TrEMBL entry as specified in the user manual http://www.expasy.org/sprot/userman.html . The CCs object is a container object which holds a list comprised of object of the type SWISS::CC or derived classes (see below). Code example local $/=" // "; while (<>) { my $entry = SWISS::Entry-> fromText($_); my @CCs = $entry -> CCs -> elements(); for my $CC (@CCs) { if ($CC -> topic eq 'ALTERNATIVE PRODUCTS') { # now can call methods of CCalt_prod } elsif ($CC -> topic eq 'Copyright') { # now can call methods of CCcopyright } else { # now can call methods of CC } } } Inherits from SWISS::ListBase.pm Attributes "list" Each list element is an object of one of the following classes, depending of the type of comment: topic object -------------------- -------------------- ALTERNATIVE PRODUCTS SWISS::CCalt_prod RNA EDITING SWISS::CCrna_editing BIOPHYSICOCHEMICAL PROPERTIES SWISS::CCbpc_properties INTERACTION SWISS::CCinteraction Copyright SWISS::CCcopyright (all other topics) SWISS::CC Methods Standard methods new fromText sort Sort the CC block according to the order given in Swiss-Prot annotation note ANN017. toText update Reading/Writing methods ccTopic ($topic) Returns true if entry contains a comment block with the specified topic. copyright Returns a string representation of the copyright text. del (@patternList) Deletes all comment elements whose topic matches the first element of the pattern list. The second element is the used to specify a requirement for the comment to match as well. get (@patternList) An array is returned consisting of all comment elements elements whose topic matches any elements of the pattern list. getObject (@patternList) Same as get, but returns the results wrapped in a new ListBase object. toString Returns a string representation of the CCs object. perl v5.10.1 2008-07-16 SWISS::CCs(3pm)
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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)