=head1 NAME seqhit module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item DnaSequenceHitList =item SegmentHitList =item SegmentHit =back =head1 DESCRIPTION =head2 Object DnaSequenceHitList =over =item forward Type [SegmentHitList *] Scalar No documentation =item backward Type [SegmentHitList *] Scalar No documentation =back No documentation for DnaSequenceHitList =head2 Member functions of DnaSequenceHitList =over =item show_DnaSequenceHitList &Wise2::DnaSequenceHitList::show_DnaSequenceHitList(dsl,ofp) shows a DnaSequenceHitsList - only really useful for debugging Argument dsl [UNKN ] Undocumented argument [DnaSequenceHitList *] Argument ofp [UNKN ] Undocumented argument [FILE *] Return [UNKN ] Undocumented return value [void] =item read_MSPcrunch_DnaSequenceHitList &Wise2::DnaSequenceHitList::read_MSPcrunch_DnaSequenceHitList(ifp) Reads a MSPcrunch -x output file Argument ifp [UNKN ] input file to read [FILE *] Return [UNKN ] newly allocated structure [DnaSequenceHitList *] =item hard_link_DnaSequenceHitList &Wise2::DnaSequenceHitList::hard_link_DnaSequenceHitList(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [DnaSequenceHitList *] Return [UNKN ] Undocumented return value [DnaSequenceHitList *] =item alloc &Wise2::DnaSequenceHitList::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [DnaSequenceHitList *] =item set_forward &Wise2::DnaSequenceHitList::set_forward(obj,forward) Replace member variable forward For use principly by API functions Argument obj [UNKN ] Object holding the variable [DnaSequenceHitList *] Argument forward [OWNER] New value of the variable [SegmentHitList *] Return [SOFT ] member variable forward [boolean] =item forward &Wise2::DnaSequenceHitList::forward(obj) Access member variable forward For use principly by API functions Argument obj [UNKN ] Object holding the variable [DnaSequenceHitList *] Return [SOFT ] member variable forward [SegmentHitList *] =item set_backward &Wise2::DnaSequenceHitList::set_backward(obj,backward) Replace member variable backward For use principly by API functions Argument obj [UNKN ] Object holding the variable [DnaSequenceHitList *] Argument backward [OWNER] New value of the variable [SegmentHitList *] Return [SOFT ] member variable backward [boolean] =item backward &Wise2::DnaSequenceHitList::backward(obj) Access member variable backward For use principly by API functions Argument obj [UNKN ] Object holding the variable [DnaSequenceHitList *] Return [SOFT ] member variable backward [SegmentHitList *] =back =head2 Object SegmentHitList =over =item seghit Type [SegmentHit **] List No documentation =back No documentation for SegmentHitList =head2 Member functions of SegmentHitList =over =item hard_link_SegmentHitList &Wise2::SegmentHitList::hard_link_SegmentHitList(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [SegmentHitList *] Return [UNKN ] Undocumented return value [SegmentHitList *] =item SegmentHitList_alloc_std &Wise2::SegmentHitList::SegmentHitList_alloc_std(void) Equivalent to SegmentHitList_alloc_len(SegmentHitListLISTLENGTH) Return [UNKN ] Undocumented return value [SegmentHitList *] =item seghit &Wise2::SegmentHitList::seghit(obj,i) Access members stored in the seghit list For use principly by API functions Argument obj [UNKN ] Object holding the list [SegmentHitList *] Argument i [UNKN ] Position in the list [int] Return [SOFT ] Element of the list [SegmentHit *] =item length_seghit &Wise2::SegmentHitList::length_seghit(obj) discover the length of the list For use principly by API functions Argument obj [UNKN ] Object holding the list [SegmentHitList *] Return [UNKN ] length of the list [int] =item flush_seghit &Wise2::SegmentHitList::flush_seghit(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 [SegmentHitList *] Return [UNKN ] Undocumented return value [int] =item add_seghit &Wise2::SegmentHitList::add_seghit(obj,add) Adds another object to the list. It will expand the list if necessary Argument obj [UNKN ] Object which contains the list [SegmentHitList *] Argument add [OWNER] Object to add to the list [SegmentHit *] Return [UNKN ] Undocumented return value [boolean] =back =head2 Object SegmentHit =over =item name Type [char *] Scalar No documentation =item qstart Type [int] Scalar No documentation =item qend Type [int] Scalar No documentation =item tstart Type [int] Scalar No documentation =item tend Type [int] Scalar No documentation =item score Type [double] Scalar No documentation =item next_hit Type [SegmentHit *] Scalar for collecting hits together ;) =back No documentation for SegmentHit =head2 Member functions of SegmentHit =over =item hard_link_SegmentHit &Wise2::SegmentHit::hard_link_SegmentHit(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [SegmentHit *] Return [UNKN ] Undocumented return value [SegmentHit *] =item alloc &Wise2::SegmentHit::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [SegmentHit *] =item set_name &Wise2::SegmentHit::set_name(obj,name) Replace member variable name For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Argument name [OWNER] New value of the variable [char *] Return [SOFT ] member variable name [boolean] =item name &Wise2::SegmentHit::name(obj) Access member variable name For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Return [SOFT ] member variable name [char *] =item set_qstart &Wise2::SegmentHit::set_qstart(obj,qstart) Replace member variable qstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Argument qstart [OWNER] New value of the variable [int] Return [SOFT ] member variable qstart [boolean] =item qstart &Wise2::SegmentHit::qstart(obj) Access member variable qstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Return [SOFT ] member variable qstart [int] =item set_qend &Wise2::SegmentHit::set_qend(obj,qend) Replace member variable qend For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Argument qend [OWNER] New value of the variable [int] Return [SOFT ] member variable qend [boolean] =item qend &Wise2::SegmentHit::qend(obj) Access member variable qend For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Return [SOFT ] member variable qend [int] =item set_tstart &Wise2::SegmentHit::set_tstart(obj,tstart) Replace member variable tstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Argument tstart [OWNER] New value of the variable [int] Return [SOFT ] member variable tstart [boolean] =item tstart &Wise2::SegmentHit::tstart(obj) Access member variable tstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Return [SOFT ] member variable tstart [int] =item set_tend &Wise2::SegmentHit::set_tend(obj,tend) Replace member variable tend For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Argument tend [OWNER] New value of the variable [int] Return [SOFT ] member variable tend [boolean] =item tend &Wise2::SegmentHit::tend(obj) Access member variable tend For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Return [SOFT ] member variable tend [int] =item set_score &Wise2::SegmentHit::set_score(obj,score) Replace member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Argument score [OWNER] New value of the variable [double] Return [SOFT ] member variable score [boolean] =item score &Wise2::SegmentHit::score(obj) Access member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Return [SOFT ] member variable score [double] =item set_next_hit &Wise2::SegmentHit::set_next_hit(obj,next_hit) Replace member variable next_hit For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Argument next_hit [OWNER] New value of the variable [SegmentHit *] Return [SOFT ] member variable next_hit [boolean] =item next_hit &Wise2::SegmentHit::next_hit(obj) Access member variable next_hit For use principly by API functions Argument obj [UNKN ] Object holding the variable [SegmentHit *] Return [SOFT ] member variable next_hit [SegmentHit *] =back