=head1 NAME complexsequence module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item ComplexSequence =item ComplexSequenceEvalSet =back =head1 DESCRIPTION =head2 Object ComplexSequence =over =item type Type [int] Scalar No documentation =item seq Type [Sequence *] Scalar No documentation =item data Type [int *] Scalar No documentation =item datastore Type [int *] Scalar No documentation =item depth Type [int] Scalar No documentation =item length Type [int] Scalar No documentation =item creator Type [ComplexSequenceEvalSet *] Scalar what made it =back A ComplexSequence is an abstraction of a Sequence which can be handily made using ComplexSequenceEval functions and is efficiently laid out in memory. =head2 Member functions of ComplexSequence =over =item hard_link_ComplexSequence &Wise2::ComplexSequence::hard_link_ComplexSequence(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [ComplexSequence *] Return [UNKN ] Undocumented return value [ComplexSequence *] =item alloc &Wise2::ComplexSequence::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [ComplexSequence *] =item set_type &Wise2::ComplexSequence::set_type(obj,type) Replace member variable type For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequence *] Argument type [OWNER] New value of the variable [int] Return [SOFT ] member variable type [boolean] =item type &Wise2::ComplexSequence::type(obj) Access member variable type For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequence *] Return [SOFT ] member variable type [int] =item set_seq &Wise2::ComplexSequence::set_seq(obj,seq) Replace member variable seq For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequence *] Argument seq [OWNER] New value of the variable [Sequence *] Return [SOFT ] member variable seq [boolean] =item seq &Wise2::ComplexSequence::seq(obj) Access member variable seq For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequence *] Return [SOFT ] member variable seq [Sequence *] =back =head2 Object ComplexSequenceEvalSet =over =item type Type [int] Scalar No documentation =item has_been_prepared Type [boolean] Scalar No documentation =item left_window Type [int] Scalar overall sequence eval =item right_window Type [int] Scalar overall sequence eval =item left_lookback Type [int] Scalar overall sequence eval =item cse Type [ComplexSequenceEval **] List No documentation =back This object holds a collection of ComplexSequenceEval's. Its role is to define the sequence specific parts of a dynamic programming algorithm as computable functions. Ideally you should use pre-made ComplexSequenceEvalSets as it will save you alot of grief =head2 Member functions of ComplexSequenceEvalSet =over =item hard_link_ComplexSequenceEvalSet &Wise2::ComplexSequenceEvalSet::hard_link_ComplexSequenceEvalSet(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [ComplexSequenceEvalSet *] Return [UNKN ] Undocumented return value [ComplexSequenceEvalSet *] =item ComplexSequenceEvalSet_alloc_std &Wise2::ComplexSequenceEvalSet::ComplexSequenceEvalSet_alloc_std(void) Equivalent to ComplexSequenceEvalSet_alloc_len(ComplexSequenceEvalSetLISTLENGTH) Return [UNKN ] Undocumented return value [ComplexSequenceEvalSet *] =item set_type &Wise2::ComplexSequenceEvalSet::set_type(obj,type) Replace member variable type For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Argument type [OWNER] New value of the variable [int] Return [SOFT ] member variable type [boolean] =item type &Wise2::ComplexSequenceEvalSet::type(obj) Access member variable type For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable type [int] =item set_has_been_prepared &Wise2::ComplexSequenceEvalSet::set_has_been_prepared(obj,has_been_prepared) Replace member variable has_been_prepared For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Argument has_been_prepared [OWNER] New value of the variable [boolean] Return [SOFT ] member variable has_been_prepared [boolean] =item has_been_prepared &Wise2::ComplexSequenceEvalSet::has_been_prepared(obj) Access member variable has_been_prepared For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable has_been_prepared [boolean] =item set_left_window &Wise2::ComplexSequenceEvalSet::set_left_window(obj,left_window) Replace member variable left_window For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Argument left_window [OWNER] New value of the variable [int] Return [SOFT ] member variable left_window [boolean] =item left_window &Wise2::ComplexSequenceEvalSet::left_window(obj) Access member variable left_window For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable left_window [int] =item set_right_window &Wise2::ComplexSequenceEvalSet::set_right_window(obj,right_window) Replace member variable right_window For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Argument right_window [OWNER] New value of the variable [int] Return [SOFT ] member variable right_window [boolean] =item right_window &Wise2::ComplexSequenceEvalSet::right_window(obj) Access member variable right_window For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable right_window [int] =item set_left_lookback &Wise2::ComplexSequenceEvalSet::set_left_lookback(obj,left_lookback) Replace member variable left_lookback For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Argument left_lookback [OWNER] New value of the variable [int] Return [SOFT ] member variable left_lookback [boolean] =item left_lookback &Wise2::ComplexSequenceEvalSet::left_lookback(obj) Access member variable left_lookback For use principly by API functions Argument obj [UNKN ] Object holding the variable [ComplexSequenceEvalSet *] Return [SOFT ] member variable left_lookback [int] =back