=head1 NAME matchsum module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item MatchSummarySet =item MatchSummary =back =head1 DESCRIPTION =head2 Object MatchSummarySet =over =item ms Type [MatchSummary **] List No documentation =back This holds a set of MatchSummaries, =head2 Member functions of MatchSummarySet =over =item MatchSummarySet_from_AlnBlock_estwise &Wise2::MatchSummarySet::MatchSummarySet_from_AlnBlock_estwise(alb,qname,offset,target) Builds a MatchSummarySet from a EstWise alignment. this makes alot of assumptions about the labels setc in alb, so make sure it was a estwise alignment - however as you can notice this is exactly the same labels as found in genewise set Argument alb [UNKN ] Undocumented argument [AlnBlock *] Argument qname [UNKN ] Undocumented argument [char *] Argument offset [UNKN ] Undocumented argument [int] Argument target [UNKN ] Undocumented argument [Sequence *] Return [UNKN ] Undocumented return value [MatchSummarySet *] =item MatchSummarySet_from_AlnBlock_genewise &Wise2::MatchSummarySet::MatchSummarySet_from_AlnBlock_genewise(alb,qname,protoff,target) Builds a MatchSummarySet from a GeneWise alignment. this makes alot of assumptions about the labels setc in alb, so make sure it was a genewise alignment Argument alb [UNKN ] Undocumented argument [AlnBlock *] Argument qname [UNKN ] Undocumented argument [char *] Argument protoff [UNKN ] Undocumented argument [int] Argument target [UNKN ] Undocumented argument [Sequence *] Return [UNKN ] Undocumented return value [MatchSummarySet *] =item hard_link_MatchSummarySet &Wise2::MatchSummarySet::hard_link_MatchSummarySet(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [MatchSummarySet *] Return [UNKN ] Undocumented return value [MatchSummarySet *] =item MatchSummarySet_alloc_std &Wise2::MatchSummarySet::MatchSummarySet_alloc_std(void) Equivalent to MatchSummarySet_alloc_len(MatchSummarySetLISTLENGTH) Return [UNKN ] Undocumented return value [MatchSummarySet *] =item ms &Wise2::MatchSummarySet::ms(obj,i) Access members stored in the ms list For use principly by API functions Argument obj [UNKN ] Object holding the list [MatchSummarySet *] Argument i [UNKN ] Position in the list [int] Return [SOFT ] Element of the list [MatchSummary *] =item length_ms &Wise2::MatchSummarySet::length_ms(obj) discover the length of the list For use principly by API functions Argument obj [UNKN ] Object holding the list [MatchSummarySet *] Return [UNKN ] length of the list [int] =item flush_ms &Wise2::MatchSummarySet::flush_ms(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 [MatchSummarySet *] Return [UNKN ] Undocumented return value [int] =item add_ms &Wise2::MatchSummarySet::add_ms(obj,add) Adds another object to the list. It will expand the list if necessary Argument obj [UNKN ] Object which contains the list [MatchSummarySet *] Argument add [OWNER] Object to add to the list [MatchSummary *] Return [UNKN ] Undocumented return value [boolean] =back =head2 Object MatchSummary =over =item bits Type [double] Scalar No documentation =item qname Type [char *] Scalar No documentation =item tname 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 qintron Type [int] Scalar No documentation =item qframeshift Type [int] Scalar No documentation =item tintron Type [int] Scalar No documentation =item tframeshift Type [int] Scalar No documentation =back A Match Summary has summary statistics for a single alignment, with the two start/end ranges and the number of introns and frameshifts for each sequence (obviously, if one is a protein then neither are valid!) =head2 Member functions of MatchSummary =over =item hard_link_MatchSummary &Wise2::MatchSummary::hard_link_MatchSummary(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [MatchSummary *] Return [UNKN ] Undocumented return value [MatchSummary *] =item alloc &Wise2::MatchSummary::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [MatchSummary *] =item set_bits &Wise2::MatchSummary::set_bits(obj,bits) Replace member variable bits For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument bits [OWNER] New value of the variable [double] Return [SOFT ] member variable bits [boolean] =item bits &Wise2::MatchSummary::bits(obj) Access member variable bits For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable bits [double] =item set_qname &Wise2::MatchSummary::set_qname(obj,qname) Replace member variable qname For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument qname [OWNER] New value of the variable [char *] Return [SOFT ] member variable qname [boolean] =item qname &Wise2::MatchSummary::qname(obj) Access member variable qname For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable qname [char *] =item set_tname &Wise2::MatchSummary::set_tname(obj,tname) Replace member variable tname For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument tname [OWNER] New value of the variable [char *] Return [SOFT ] member variable tname [boolean] =item tname &Wise2::MatchSummary::tname(obj) Access member variable tname For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable tname [char *] =item set_qstart &Wise2::MatchSummary::set_qstart(obj,qstart) Replace member variable qstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument qstart [OWNER] New value of the variable [int] Return [SOFT ] member variable qstart [boolean] =item qstart &Wise2::MatchSummary::qstart(obj) Access member variable qstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable qstart [int] =item set_qend &Wise2::MatchSummary::set_qend(obj,qend) Replace member variable qend For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument qend [OWNER] New value of the variable [int] Return [SOFT ] member variable qend [boolean] =item qend &Wise2::MatchSummary::qend(obj) Access member variable qend For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable qend [int] =item set_tstart &Wise2::MatchSummary::set_tstart(obj,tstart) Replace member variable tstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument tstart [OWNER] New value of the variable [int] Return [SOFT ] member variable tstart [boolean] =item tstart &Wise2::MatchSummary::tstart(obj) Access member variable tstart For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable tstart [int] =item set_tend &Wise2::MatchSummary::set_tend(obj,tend) Replace member variable tend For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument tend [OWNER] New value of the variable [int] Return [SOFT ] member variable tend [boolean] =item tend &Wise2::MatchSummary::tend(obj) Access member variable tend For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable tend [int] =item set_qintron &Wise2::MatchSummary::set_qintron(obj,qintron) Replace member variable qintron For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument qintron [OWNER] New value of the variable [int] Return [SOFT ] member variable qintron [boolean] =item qintron &Wise2::MatchSummary::qintron(obj) Access member variable qintron For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable qintron [int] =item set_qframeshift &Wise2::MatchSummary::set_qframeshift(obj,qframeshift) Replace member variable qframeshift For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument qframeshift [OWNER] New value of the variable [int] Return [SOFT ] member variable qframeshift [boolean] =item qframeshift &Wise2::MatchSummary::qframeshift(obj) Access member variable qframeshift For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable qframeshift [int] =item set_tintron &Wise2::MatchSummary::set_tintron(obj,tintron) Replace member variable tintron For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument tintron [OWNER] New value of the variable [int] Return [SOFT ] member variable tintron [boolean] =item tintron &Wise2::MatchSummary::tintron(obj) Access member variable tintron For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable tintron [int] =item set_tframeshift &Wise2::MatchSummary::set_tframeshift(obj,tframeshift) Replace member variable tframeshift For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Argument tframeshift [OWNER] New value of the variable [int] Return [SOFT ] member variable tframeshift [boolean] =item tframeshift &Wise2::MatchSummary::tframeshift(obj) Access member variable tframeshift For use principly by API functions Argument obj [UNKN ] Object holding the variable [MatchSummary *] Return [SOFT ] member variable tframeshift [int] =back