=head1 NAME

sw_wrap module - part of the Wise2 package

=head1 SYNOPSIS

This module contains helper functions for the Wise2 package

=head1 DESCRIPTION

=over

=item Align_strings_ProteinSmithWaterman

&Wise2::Align_strings_ProteinSmithWaterman(one,two,comp,gap,ext,dpri)

  This is the most *stupidly* abstracted view of two sequences
  getting aligned, being two strings.

  It would be much better if you used Sequence objects or Protein
  objects to carry the proteins.



  Argument one          [UNKN ] string of the first sequence [char *]
  Argument two          [UNKN ] string of the second sequence [char *]
  Argument comp         [UNKN ] Comparison Matrix [CompMat *]
  Argument gap          [UNKN ] gap penalty [int]
  Argument ext          [UNKN ] extension penalty [int]
  Argument dpri         [UNKN ] Undocumented argument [DPRunImpl *]
  Return [UNKN ] Undocumented return value [AlnBlock *]


=item Align_Sequences_ProteinSmithWaterman

&Wise2::Align_Sequences_ProteinSmithWaterman(one,two,comp,gap,ext,dpri)

  This function is a mid-level abstraction of
  comparing two sequences, which could be
  generic types (eg DNA!). This is tested
  for and warnings are given but the alignment
  is still calculated. To prevent this test
  warning either make sure the Sequence types
  are set to PROTEIN or, better still, use the
  high level abstraction Align_Proteins_SmithWaterman

  Otherwise this performs a standard smith waterman
  protein alignment...

  To display the alignment use  write_pretty_seq_align



  Argument one          [READ ] First sequence to compare [Sequence *]
  Argument two          [READ ] Second sequecne to compare [Sequence *]
  Argument comp         [READ ] Comparison matrix to use [CompMat *]
  Argument gap          [UNKN ] gap penalty. Must be negative or 0 [int]
  Argument ext          [UNKN ] ext penalty. Must be negative or 0 [int]
  Argument dpri         [UNKN ] Undocumented argument [DPRunImpl *]
  Return [OWNER] new AlnBlock structure representing the alignment [AlnBlock *]


=item Align_Proteins_SmithWaterman

&Wise2::Align_Proteins_SmithWaterman(one,two,comp,gap,ext,dpri)

  This is the most correct way of aligning two Proteins,
  using Protein objects, which can be assummed to be
  proteins with no objections

  To display the alignment use write_pretty_Protein_align




  Argument one          [UNKN ] Protein to align [Protein *]
  Argument two          [UNKN ] Protein to align [Protein *]
  Argument comp         [UNKN ] Comparison Matrix [CompMat *]
  Argument gap          [UNKN ] gap penalty [int]
  Argument ext          [UNKN ] extension penalty [int]
  Argument dpri         [UNKN ] Undocumented argument [DPRunImpl *]
  Return [UNKN ] Undocumented return value [AlnBlock *]


=item Align_Proteins_ABC

&Wise2::Align_Proteins_ABC(one,two,comp,a,b,c,dpri)

  Analogous to Align_Proteins_SmithWaterman for ABC model



  Argument one          [UNKN ] protein to align [Protein *]
  Argument two          [UNKN ] protein to align [Protein *]
  Argument comp         [UNKN ] comparison matrix [CompMat *]
  Argument a            [UNKN ] generalized affine gap cost a [int]
  Argument b            [UNKN ] generalized affine gap cost b [int]
  Argument c            [UNKN ] generalized affine gap cost c [int]
  Argument dpri         [UNKN ] Undocumented argument [DPRunImpl *]
  Return [UNKN ] Undocumented return value [AlnBlock *]


=item Align_Sequences_ProteinABC

&Wise2::Align_Sequences_ProteinABC(one,two,comp,a,b,c,dpri)

  Align_Sequences_ProteinABC
  this function is analogous to Align_Sequences_ProteinSmithWaterman
  but using the abc model



  Argument one          [UNKN ] Sequence to align [Sequence *]
  Argument two          [UNKN ] Sequence to align [Sequence *]
  Argument comp         [UNKN ] Comparison Matrix [CompMat *]
  Argument a            [UNKN ] genearlized affine gap cost  [int]
  Argument b            [UNKN ] genearlized affine gap cost  [int]
  Argument c            [UNKN ] genearlized affine gap cost  [int]
  Argument dpri         [UNKN ] Undocumented argument [DPRunImpl *]
  Return [UNKN ] Undocumented return value [AlnBlock *]


=item Hscore_from_ProteinSW

&Wise2::Hscore_from_ProteinSW(querydb,targetdb,comp,gap,ext,bits_cutoff,report_level,die_on_error,dbsi)

  Runs a database psw search 



  Argument querydb      [UNKN ] query database  [ProteinDB*]
  Argument targetdb     [UNKN ] target database [ProteinDB*]
  Argument comp         [UNKN ] comparison matrix [CompMat*]
  Argument gap          [UNKN ] gap penalty [int]
  Argument ext          [UNKN ] extension penalty [int]
  Argument bits_cutoff  [UNKN ]  [double]
  Argument report_level [UNKN ]  [int]
  Argument die_on_error [UNKN ]  [boolean]
  Argument dbsi         [UNKN ]  [DBSearchImpl*]
  Return [UNKN ] Undocumented return value [Hscore *]


=item Hscore_from_ProteinABC

&Wise2::Hscore_from_ProteinABC(querydb,targetdb,comp,a,b,c,bits_cutoff,report_level,die_on_error,dbsi)

  Runs a database abc search 



  Argument querydb      [UNKN ] query database  [ProteinDB*]
  Argument targetdb     [UNKN ] target database [ProteinDB*]
  Argument comp         [UNKN ] comparison matrix [CompMat*]
  Argument a            [UNKN ] generalized affine gap cost a [int]
  Argument b            [UNKN ] generalized affine gap cost b [int]
  Argument c            [UNKN ] generalized affine gap cost c [int]
  Argument bits_cutoff  [UNKN ]  [double]
  Argument report_level [UNKN ]  [int]
  Argument die_on_error [UNKN ]  [boolean]
  Argument dbsi         [UNKN ]  [DBSearchImpl*]
  Return [UNKN ] Undocumented return value [Hscore *]


=item Hscore_from_ProteinBA

&Wise2::Hscore_from_ProteinBA(querydb,targetdb,comp,bentry,bexit,bfor_trans,b_self_trans,b3exit,bits_cutoff,report_level,dbsi)

  Runs a database pba search



  Argument querydb      [UNKN ] query database [ProteinDB*]
  Argument targetdb     [UNKN ] target database [ProteinDB*]
  Argument comp         [UNKN ] comparison matrix [CompMat*]
  Argument bentry       [UNKN ]  [Score]
  Argument bexit        [UNKN ]  [Score]
  Argument bfor_trans   [UNKN ]  [Score]
  Argument b_self_trans [UNKN ]  [Score]
  Argument b3exit       [UNKN ]  [Score]
  Argument bits_cutoff  [UNKN ]  [double]
  Argument report_level [UNKN ]  [int]
  Argument dbsi         [UNKN ]  [DBSearchImpl*]
  Return [UNKN ] Undocumented return value [Hscore *]


=back