swiss::entry(3pm) [debian man page]
SWISS::Entry(3pm) User Contributed Perl Documentation SWISS::Entry(3pm) Name SWISS::Entry Description Main module to handle SWISS-PROT entries. One Entry object represents one SWISS-PROT entry and provides an API for its modification. The basic concept is the idea of lazy parsing. If an Entry object is created from the entry in flat file format, the text is simply stored in the private text attribute of the entry object. The member objects of the entry are only created if they are dereferenced. Example This minimum program reads entries from a file in SWISS-PROT format and prints the primary accession number for each of the entries. Attributes The following attributes represent member objects. They can be accessed like e.g. $entry->IDs IDs ID line object ACs DTs DEs GNs OSs OCs Refs The reference block object CCs KWs DRs FTs Stars Object for the annotator's section stored in the ** lines. SQs The sequence object. Methods new Return a new Entry object initialize Initialise an Entry object and return it. update [force] Update an entry. The content of the member objects is written back into the private text attribute of the entry if necessary. If $force is true, an update of all member objects is forced. reformat Reformat all fields of an entry. fromText $text [, $fullParse[, $removeInternalComments]] Create an Entry object from the text $text. If $fullParse is true, the entry is parsed at creation time. Otherwise the individual line objects are only created if they are dereferenced. If $removeInternalComments is true, wild comments and indentation will be removed from the text before the parsing is done. [NOTE: wild comments are lines starting with a double asterisk located outside the Stars section, and indented lines are lines starting with spaces. Both are used internally by SWISS-PROT annotators during their work and excluded from internal and external releases.] toText [$insertInternalComments] Return the entry in flat file text format. If internal comments and indentation have been removed as specified in the parameters to fromText(), you may wish to reinsert them in the text output by setting $insertInternalComments to true. toFasta Return the entry in Fasta format. equal Returns True if two entries are equal, False otherwise The following methods are provided for your convenience. They are shortcuts for methods of the individual line objects. ID Returns the primary ID of the entry. AC Returns the primary AC of the entry. SQ Returns the sequence of the entry. EV Returns the EV (evidence) object of an entry. SWISS-PROT internal method. Data access methods text Returns the current text of the entry. Quick and dirty! No update of the text is performed before. database_code Is it a SWISS-PROT, TREMBL or TREMBLNEW entry? database_code tries to find it out. Return values are S for SWISS-PROT, 3 for TREMBL, Q for TREMBLNEW, ? for unknown. isFragment Returns true if the DE line indicates a fragment, or of the entry contains a NON_CONS or NON_TER feature. isCurated Returns 1 if the entry is a curated entry, 0 otherwise. SWISS-PROT internal use only. perl v5.10.1 2008-07-16 SWISS::Entry(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)