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=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
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