=head1 NAME dnaalign module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item DnaStartEnd =back =head1 DESCRIPTION =head2 Object DnaStartEnd =over =item trans[DSE_NUMBER] Type [int] Scalar start/end points possibilities =back No documentation for DnaStartEnd =head2 Member functions of DnaStartEnd =over =item hard_link_DnaStartEnd &Wise2::DnaStartEnd::hard_link_DnaStartEnd(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [DnaStartEnd *] Return [UNKN ] Undocumented return value [DnaStartEnd *] =item alloc &Wise2::DnaStartEnd::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [DnaStartEnd *] =back =over =item make_align_dnaalign &Wise2::make_align_dnaalign(one,two,mat,se,qgap,qext,tgap,text,dpri) Makes an alignment out of two DNA sequences Argument one [READ ] first sequence to align [Sequence *] Argument two [READ ] second sequence to align [Sequence *] Argument mat [READ ] DnaMatrix for the matching [DnaMatrix *] Argument se [READ ] DnaStartEnd policy [DnaStartEnd *] Argument qgap [READ ] gap open penalty in query (one) coordinate [int] Argument qext [READ ] gap extension penalty in query (one) coordinate [int] Argument tgap [READ ] gap open penalty in target (two) coordinate [int] Argument text [READ ] gap extension penalty in target (two) coordinate [int] Argument dpri [READ ] DPRunImpl structure [DPRunImpl *] Return [UNKN ] an alb structure of the alignment [AlnBlock *] =item DnaStartEnd_from_policy &Wise2::DnaStartEnd_from_policy(policy) Makes a DnaStartEnd from a particular string. Possible strings are: local - fully local global - fully global edge - aligns only to edges Argument policy [UNKN ] Undocumented argument [char *] Return [UNKN ] Undocumented return value [DnaStartEnd *] =back