=head1 NAME

estwrap module - part of the Wise2 package

=head1 SYNOPSIS

This module contains helper functions for the Wise2 package

=head1 DESCRIPTION

=over

=item Hscore_from_TSM_estwise

&Wise2::Hscore_from_TSM_estwise(tdb,cdb,cp,cm,rmd,use_syn,alg,bits_cutoff,allN,flat_insert,report_level,die_on_error,dbsi)

  Runs a database search for the estwise set
  of algorithms



  Argument tdb          [READ ] a three state model database [ThreeStateDB *]
  Argument cdb          [READ ] a dna sequence database [cDNADB *]
  Argument cp           [READ ] the codon parser for this comparison [cDNAParser *]
  Argument cm           [READ ] the codon mapper for this comparison [CodonMapper *]
  Argument rmd          [READ ] random model used for the dna sequence comparison [RandomModelDNA *]
  Argument use_syn      [UNKN ] whether a synchronous coding model should be used or not [boolean]
  Argument alg          [UNKN ] algorithm to use [int]
  Argument bits_cutoff  [UNKN ] Undocumented argument [double]
  Argument allN         [UNKN ] Undocumented argument [Probability]
  Argument flat_insert  [UNKN ] Undocumented argument [boolean]
  Argument report_level [UNKN ] Undocumented argument [int]
  Argument die_on_error [UNKN ] if true, dies if there is an error [boolean]
  Argument dbsi         [UNKN ] Undocumented argument [DBSearchImpl *]
  Return [OWNER] a newly allocated Hscore structure of the search [Hscore *]


=item AlnBlock_from_Protein_estwise_wrap

&Wise2::AlnBlock_from_Protein_estwise_wrap(pro,cdna,cp,cm,ct,comp,gap,ext,is_global,rmd,alg,rm,use_syn,allN,dpri,palpoi)

  This function is the guts for the est single alignment
  mode.

  It uses /AlnBlock_from_TSM_estwise_wrap for the
  heavy part of the call



  Argument pro          [READ ] protein to be used in the comparison [Protein *]
  Argument cdna         [READ ] cdna to be compared to [cDNA *]
  Argument cp           [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser *]
  Argument cm           [READ ] codon mapper indicating substitution errors etc [CodonMapper *]
  Argument ct           [READ ] codon table for the codon->amino acid mappings [CodonTable *]
  Argument comp         [READ ] comparison matrix to use [CompMat *]
  Argument gap          [UNKN ] gap penalty [int]
  Argument ext          [UNKN ] extension penalty [int]
  Argument is_global    [UNKN ] if true, global start-end in protein is used [boolean]
  Argument rmd          [UNKN ] random model of dna to use [RandomModelDNA *]
  Argument alg          [UNKN ] est algorithm type to use [int]
  Argument rm           [UNKN ] random protein model for use with compmat [RandomModel *]
  Argument use_syn      [UNKN ] if true, uses a synchronous coding model [boolean]
  Argument allN         [UNKN ] Undocumented argument [Probability]
  Argument dpri         [UNKN ] Undocumented argument [DPRunImpl *]
  Argument palpoi       [WRITE] the raw packed alignment output if wanted [PackAln **]
  Return [UNKN ] Undocumented return value [AlnBlock *]


=item AlnBlock_from_TSM_estwise_wrap

&Wise2::AlnBlock_from_TSM_estwise_wrap(tsm,cdna,cp,cm,ct,rmd,alg,use_syn,force_flat_insert,allN,dpri,palpoi)

  This function is the basic wrap for Protein models
  vs cDNA sequences.



  Argument tsm          [READ ] threestatemodel to be compared to the dna [ThreeStateModel *]
  Argument cdna         [READ ] cdna to be compared to [cDNA *]
  Argument cp           [READ ] cdna parser indicating insertion deletion probabilities [cDNAParser *]
  Argument cm           [READ ] codon mapper indicating substitution errors etc [CodonMapper *]
  Argument ct           [READ ] codon table for the codon->amino acid mappings [CodonTable *]
  Argument rmd          [UNKN ] random model of dna to use [RandomModelDNA *]
  Argument alg          [UNKN ] est algorithm type to use [int]
  Argument use_syn      [UNKN ] if true, uses a synchronous coding model [boolean]
  Argument force_flat_insert [UNKN ] Undocumented argument [boolean]
  Argument allN         [UNKN ] Undocumented argument [Probability]
  Argument dpri         [UNKN ] Undocumented argument [DPRunImpl *]
  Argument palpoi       [WRITE] the raw packed alignment output if wanted [PackAln **]
  Return [UNKN ] Undocumented return value [AlnBlock *]


=item alg_estwrap_from_string

&Wise2::alg_estwrap_from_string(str)

  This function returns the algorithm type
  for an est search from the string



  Argument str          [UNKN ] Undocumented argument [char *]
  Return [UNKN ] Undocumented return value [int]


=back