=head1 NAME alnrange module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item AlnRange =item AlnRangeSet =back =head1 DESCRIPTION =head2 Object AlnRange =over =item starti Type [int] Scalar No documentation =item startj Type [int] Scalar No documentation =item startstate Type [int] Scalar No documentation =item stopi Type [int] Scalar No documentation =item stopj Type [int] Scalar No documentation =item stopstate Type [int] Scalar No documentation =item startscore Type [int] Scalar No documentation =item stopscore Type [int] Scalar No documentation =back No documentation for AlnRange =head2 Member functions of AlnRange =over =item hard_link_AlnRange &Wise2::AlnRange::hard_link_AlnRange(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [AlnRange *] Return [UNKN ] Undocumented return value [AlnRange *] =item alloc &Wise2::AlnRange::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [AlnRange *] =item set_starti &Wise2::AlnRange::set_starti(obj,starti) Replace member variable starti For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument starti [OWNER] New value of the variable [int] Return [SOFT ] member variable starti [boolean] =item starti &Wise2::AlnRange::starti(obj) Access member variable starti For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable starti [int] =item set_startj &Wise2::AlnRange::set_startj(obj,startj) Replace member variable startj For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument startj [OWNER] New value of the variable [int] Return [SOFT ] member variable startj [boolean] =item startj &Wise2::AlnRange::startj(obj) Access member variable startj For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable startj [int] =item set_startstate &Wise2::AlnRange::set_startstate(obj,startstate) Replace member variable startstate For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument startstate [OWNER] New value of the variable [int] Return [SOFT ] member variable startstate [boolean] =item startstate &Wise2::AlnRange::startstate(obj) Access member variable startstate For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable startstate [int] =item set_stopi &Wise2::AlnRange::set_stopi(obj,stopi) Replace member variable stopi For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument stopi [OWNER] New value of the variable [int] Return [SOFT ] member variable stopi [boolean] =item stopi &Wise2::AlnRange::stopi(obj) Access member variable stopi For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable stopi [int] =item set_stopj &Wise2::AlnRange::set_stopj(obj,stopj) Replace member variable stopj For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument stopj [OWNER] New value of the variable [int] Return [SOFT ] member variable stopj [boolean] =item stopj &Wise2::AlnRange::stopj(obj) Access member variable stopj For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable stopj [int] =item set_stopstate &Wise2::AlnRange::set_stopstate(obj,stopstate) Replace member variable stopstate For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument stopstate [OWNER] New value of the variable [int] Return [SOFT ] member variable stopstate [boolean] =item stopstate &Wise2::AlnRange::stopstate(obj) Access member variable stopstate For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable stopstate [int] =item set_startscore &Wise2::AlnRange::set_startscore(obj,startscore) Replace member variable startscore For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument startscore [OWNER] New value of the variable [int] Return [SOFT ] member variable startscore [boolean] =item startscore &Wise2::AlnRange::startscore(obj) Access member variable startscore For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable startscore [int] =item set_stopscore &Wise2::AlnRange::set_stopscore(obj,stopscore) Replace member variable stopscore For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Argument stopscore [OWNER] New value of the variable [int] Return [SOFT ] member variable stopscore [boolean] =item stopscore &Wise2::AlnRange::stopscore(obj) Access member variable stopscore For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRange *] Return [SOFT ] member variable stopscore [int] =back =head2 Object AlnRangeSet =over =item score Type [int] Scalar over complete alignment =item alr Type [AlnRange **] List No documentation =back No documentation for AlnRangeSet =head2 Member functions of AlnRangeSet =over =item hard_link_AlnRangeSet &Wise2::AlnRangeSet::hard_link_AlnRangeSet(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [AlnRangeSet *] Return [UNKN ] Undocumented return value [AlnRangeSet *] =item AlnRangeSet_alloc_std &Wise2::AlnRangeSet::AlnRangeSet_alloc_std(void) Equivalent to AlnRangeSet_alloc_len(AlnRangeSetLISTLENGTH) Return [UNKN ] Undocumented return value [AlnRangeSet *] =item set_score &Wise2::AlnRangeSet::set_score(obj,score) Replace member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRangeSet *] Argument score [OWNER] New value of the variable [int] Return [SOFT ] member variable score [boolean] =item score &Wise2::AlnRangeSet::score(obj) Access member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [AlnRangeSet *] Return [SOFT ] member variable score [int] =item alr &Wise2::AlnRangeSet::alr(obj,i) Access members stored in the alr list For use principly by API functions Argument obj [UNKN ] Object holding the list [AlnRangeSet *] Argument i [UNKN ] Position in the list [int] Return [SOFT ] Element of the list [AlnRange *] =item length_alr &Wise2::AlnRangeSet::length_alr(obj) discover the length of the list For use principly by API functions Argument obj [UNKN ] Object holding the list [AlnRangeSet *] Return [UNKN ] length of the list [int] =item flush_alr &Wise2::AlnRangeSet::flush_alr(obj) Frees the list elements, sets length to 0 If you want to save some elements, use hard_link_xxx to protect them from being actually destroyed in the free Argument obj [UNKN ] Object which contains the list [AlnRangeSet *] Return [UNKN ] Undocumented return value [int] =item add_alr &Wise2::AlnRangeSet::add_alr(obj,add) Adds another object to the list. It will expand the list if necessary Argument obj [UNKN ] Object which contains the list [AlnRangeSet *] Argument add [OWNER] Object to add to the list [AlnRange *] Return [UNKN ] Undocumented return value [boolean] =back