/usr/include/ncbi/urkbias.h is in libncbi6-dev 6.1.20120620-10.
This file is owned by root:root, with mode 0o644.
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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: urkbias.h
*
* Author(s): John Kuzio
*
* Version Creation Date: 98-01-01
*
* $Revision: 6.5 $
*
* File Description: codon bias header
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* --------------------------------------------------------------------------
* $Log: urkbias.h,v $
* Revision 6.5 1998/09/16 17:46:43 kuzio
* cvs logging
*
*
* ==========================================================================
*/
#ifndef _URKBIAS__
#define _URKBIAS__
#include <ncbi.h>
#ifdef __cplusplus
extern "C" {
#endif
typedef struct Gather_Cds
{
Int4Ptr tableGlobal, tableRefine;
SeqLocPtr slpGlobal, slpRefine, slpAll, slpHit, slpFound;
Int4 stdcount, globalcount, refinecount, findcount;
FloatHi stdev, HIscore, LOscore, mean;
FloatHi scorecut;
} Gather_CDS, PNTR Gather_CDSPtr;
extern Gather_CDSPtr GatherCDSNew (void);
extern Gather_CDSPtr GatherCDSFree (Gather_CDSPtr gcdsp);
extern SeqLocPtr SeqLocDup (SeqLocPtr slpold);
extern SeqLocPtr SeqLocDupAll (SeqLocPtr slpold);
extern SeqLocPtr SeqLocLink (SeqLocPtr PNTR slph, SeqLocPtr slp);
extern Boolean SeqLocMatch (SeqLocPtr slplist, SeqLocPtr slpnew);
extern void UniqueOrfs (SeqLocPtr PNTR pslpFound);
extern void SortByLocOrfs (SeqLocPtr PNTR pslpFound);
extern void RemoveInternalOrfs (SeqLocPtr PNTR slpFound);
extern SeqLocPtr FindSimilarBiasOrfs (SeqEntryPtr sep, FloatHi probcut,
Int4 clustmin, Int4 findmin,
SeqLocPtr slpKnown,
SeqLocPtr slpPotential);
extern FloatHiPtr BiasScoreBioseq (BioseqPtr bsp, Int4Ptr globaltable,
Int4 tripletwindow, Int4 xframe,
Uint1 xstrand);
#ifdef __cplusplus
}
#endif
#endif
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