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/*
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: urkcnsrt.h
*
* Author(s): John Kuzio
*
* Version Creation Date: 98-01-01
*
* $Revision: 6.8 $
*
* File Description: consort header
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* --------------------------------------------------------------------------
* $Log: urkcnsrt.h,v $
* Revision 6.8 1998/10/13 17:16:37 kuzio
* additional Markov setup
*
* Revision 6.7 1998/10/05 13:35:16 kuzio
* start markov chains and codon bias
*
* Revision 6.6 1998/09/28 16:36:11 kuzio
* no met orf check
*
* Revision 6.5 1998/09/16 17:46:44 kuzio
* cvs logging
*
*
* ==========================================================================
*/
#ifndef _CONSORT__
#define _CONSORT__
#include <ncbi.h>
#include <accentr.h>
#include <urktree.h>
#ifdef __cplusplus
extern "C" {
#endif
#define CONMATSIZE 512
typedef struct FrequencyStructure
{
Int4Ptr frame0trip, frame1trip, frame2trip;
Int4Ptr frame0cdnobs, frame1cdnobs, frame2cdnobs;
Int4Ptr frame0cdn, frame1cdn, frame2cdn;
Int4Ptr frame0leftdi, frame1leftdi, frame2leftdi;
Int4Ptr frame0rightdi, frame1rightdi, frame2rightdi;
FloatHiPtr frame0exp, frame1exp, frame2exp;
FloatHiPtr frame0std, frame1std, frame2std;
Int4Ptr globalcdnobs;
} Freq, PNTR FreqPtr;
/* codon usage tree from genome */
extern TreeNodePtr ConsortSeqEntry (SeqEntryPtr sep);
extern Int4Ptr ConformSeqEntry (SeqEntryPtr sep);
/* exploration: ORFs related by codon usage */
extern Int4Ptr NewCodonTable (void);
extern Int4Ptr FreeCodonTable (Int4Ptr cutp);
extern Int4Ptr CodonTableFromSeqLoc (BioseqPtr bsp, SeqLocPtr slp);
extern void AddSeqLocToCodonTable (Int4Ptr cutp, BioseqPtr bsp,
SeqLocPtr slp, Boolean flagAdd);
extern Int4Ptr MergeCodonTables (Int4Ptr cutp1, Int4Ptr cutp2);
extern FloatHi Confide (Int4Ptr cutgene, Int4Ptr cutgbl);
extern void Conform (Int4Ptr freq, FILE *fn);
extern ValNodePtr ClearNonMetOrfs (ValNodePtr orflist);
extern FreqPtr FreqNew (void);
extern FreqPtr FreqFree (FreqPtr frqp);
extern FreqPtr ConKovCDSNtFreqs (BioseqPtr bsp, SeqLocPtr slp);
extern Boolean ConKovCDSGlobalNtFreqs (BioseqPtr bsp, FreqPtr frqp);
extern FreqPtr ConKovTrainCDS (BioseqPtr bsp, SeqLocPtr slp);
#ifdef __cplusplus
}
#endif
#endif
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