=head1 NAME packaln module - part of the Wise2 package =head1 SYNOPSIS This module contains the following objects =over =item PackAln =item PackAlnUnit =back =head1 DESCRIPTION =head2 Object PackAln =over =item pau Type [PackAlnUnit **] List list of PackAlnUnits from start to end =item score Type [int] Scalar score over the entire alignment =back This is the lowest-level of representation of a DP alignment, being the list of (i,j,state) triples taken through the DP matrix. The score for the transition to this point is held as well. This object is very low level and often a much better choice for representation is in /AlnBlock objects =head2 Member functions of PackAln =over =item show_simple_PackAln &Wise2::PackAln::show_simple_PackAln(pal,ofp) shows packaln with a pretty verbose debugging format Argument pal [UNKN ] Undocumented argument [PackAln *] Argument ofp [UNKN ] Undocumented argument [FILE *] Return [UNKN ] Undocumented return value [void] =item show_bits_and_cumlative_PackAln &Wise2::PackAln::show_bits_and_cumlative_PackAln(pal,ofp) Shows packaln as: i,j,state,score,bits,cumlative-score,cumlative-bits cumlative score and cumlative bits are useful sometimes Argument pal [UNKN ] Undocumented argument [PackAln *] Argument ofp [UNKN ] Undocumented argument [FILE *] Return [UNKN ] Undocumented return value [void] =item hard_link_PackAln &Wise2::PackAln::hard_link_PackAln(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [PackAln *] Return [UNKN ] Undocumented return value [PackAln *] =item PackAln_alloc_std &Wise2::PackAln::PackAln_alloc_std(void) Equivalent to PackAln_alloc_len(PackAlnLISTLENGTH) Return [UNKN ] Undocumented return value [PackAln *] =item pau &Wise2::PackAln::pau(obj,i) Access members stored in the pau list For use principly by API functions Argument obj [UNKN ] Object holding the list [PackAln *] Argument i [UNKN ] Position in the list [int] Return [SOFT ] Element of the list [PackAlnUnit *] =item length_pau &Wise2::PackAln::length_pau(obj) discover the length of the list For use principly by API functions Argument obj [UNKN ] Object holding the list [PackAln *] Return [UNKN ] length of the list [int] =item flush_pau &Wise2::PackAln::flush_pau(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 [PackAln *] Return [UNKN ] Undocumented return value [int] =item add_pau &Wise2::PackAln::add_pau(obj,add) Adds another object to the list. It will expand the list if necessary Argument obj [UNKN ] Object which contains the list [PackAln *] Argument add [OWNER] Object to add to the list [PackAlnUnit *] Return [UNKN ] Undocumented return value [boolean] =item set_score &Wise2::PackAln::set_score(obj,score) Replace member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAln *] Argument score [OWNER] New value of the variable [int] Return [SOFT ] member variable score [boolean] =item score &Wise2::PackAln::score(obj) Access member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAln *] Return [SOFT ] member variable score [int] =back =head2 Object PackAlnUnit =over =item i Type [int] Scalar position in query =item j Type [int] Scalar position in target =item state Type [int] Scalar state in FSM =item score Type [int] Scalar score of the transition that reached this state =back Internal object for /PackAln: A single position of an alignment as the (i,j,state) triple =head2 Member functions of PackAlnUnit =over =item hard_link_PackAlnUnit &Wise2::PackAlnUnit::hard_link_PackAlnUnit(obj) Bumps up the reference count of the object Meaning that multiple pointers can 'own' it Argument obj [UNKN ] Object to be hard linked [PackAlnUnit *] Return [UNKN ] Undocumented return value [PackAlnUnit *] =item alloc &Wise2::PackAlnUnit::alloc(void) Allocates structure: assigns defaults if given Return [UNKN ] Undocumented return value [PackAlnUnit *] =item set_i &Wise2::PackAlnUnit::set_i(obj,i) Replace member variable i For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Argument i [OWNER] New value of the variable [int] Return [SOFT ] member variable i [boolean] =item i &Wise2::PackAlnUnit::i(obj) Access member variable i For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Return [SOFT ] member variable i [int] =item set_j &Wise2::PackAlnUnit::set_j(obj,j) Replace member variable j For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Argument j [OWNER] New value of the variable [int] Return [SOFT ] member variable j [boolean] =item j &Wise2::PackAlnUnit::j(obj) Access member variable j For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Return [SOFT ] member variable j [int] =item set_state &Wise2::PackAlnUnit::set_state(obj,state) Replace member variable state For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Argument state [OWNER] New value of the variable [int] Return [SOFT ] member variable state [boolean] =item state &Wise2::PackAlnUnit::state(obj) Access member variable state For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Return [SOFT ] member variable state [int] =item set_score &Wise2::PackAlnUnit::set_score(obj,score) Replace member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Argument score [OWNER] New value of the variable [int] Return [SOFT ] member variable score [boolean] =item score &Wise2::PackAlnUnit::score(obj) Access member variable score For use principly by API functions Argument obj [UNKN ] Object holding the variable [PackAlnUnit *] Return [SOFT ] member variable score [int] =back