/usr/include/ncbi/urkptpf.h is in libncbi6-dev 6.1.20120620-10.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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: urkptpf.h
*
* Author(s): John Kuzio
*
* Version Creation Date: 98-01-01
*
* $Revision: 6.20 $
*
* File Description: patterns and profiles header
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* --------------------------------------------------------------------------
* $Log: urkptpf.h,v $
* Revision 6.20 1999/07/13 13:07:05 sicotte
* prefix functions SeqAlignSort* with URK to resolve toolkit conflicts urkptpf.c
*
* Revision 6.19 1998/11/16 14:29:54 kuzio
* flagBoundaryCondition
*
* Revision 6.18 1998/09/16 17:46:46 kuzio
* cvs logging
*
*
* ==========================================================================
*/
#ifndef _URKPTPF__
#define _URKPTPF__
#include <objres.h>
#include <objseq.h>
#include <objsset.h>
#ifdef __cplusplus
extern "C" {
#endif
#define MAXMATCH 1024
#define MAXPATSIZE 4096
#define MAXPROFSIZE 128
#define MAXCHUNKSIZE 32768
typedef struct compilepattern
{
Char name[256];
Int4 min;
Int4 max;
Char res[64];
Boolean flagPalindrome;
Boolean flagNTerm, flagCTerm;
struct compilepattern PNTR prev;
struct compilepattern PNTR next;
struct compilepattern PNTR prevpattern;
struct compilepattern PNTR nextpattern;
} ComPat, PNTR ComPatPtr;
typedef struct compileprofile
{
Char name[256];
FloatHi score[64];
Int4 iscore[64];
struct compileprofile PNTR prev;
struct compileprofile PNTR next;
struct compileprofile PNTR prevprofile;
struct compileprofile PNTR nextprofile;
} ComProf, PNTR ComProfPtr;
/* patterns and profiles */
extern SeqAlignPtr MeldStrands (SeqAlignPtr sap);
extern SeqAlignPtr SeparateStrands (SeqAlignPtr sap);
/* patterns */
extern ValNodePtr ReadPatternNames (CharPtr filename);
extern ComPatPtr ReadRENPattern (CharPtr filename, Boolean flagNeedCutPos,
ValNodePtr namelist);
extern ComPatPtr ReadPrositePattern (CharPtr filename, Boolean flagStringent,
Int4 cutoff, CharPtr taxon,
ValNodePtr namelist);
extern Boolean IsProsite (CharPtr inbuff);
extern CharPtr PrositeToGBPattern (CharPtr pspat);
extern CharPtr ReadPattern (CharPtr filename);
extern void CleanPattern (CharPtr inbuff);
extern ComPatPtr ComPatNew (ComPatPtr currcpp);
extern ComPatPtr ComPatFree (ComPatPtr headcpp);
extern ComPatPtr ComPatDup (ComPatPtr cppold);
extern ComPatPtr CompilePattern (CharPtr pattern, Int2 moltype);
extern ComPatPtr InvertPattern (ComPatPtr cppold);
extern void PalindromeCheck (ComPatPtr cpph);
extern SeqAlignPtr PatternMatch (Uint1Ptr seq, Int4 seqpos, Uint1 strand,
SeqIdPtr sip, ComPatPtr cpp,
Int4 mismatch, Int2 topology,
Boolean flagFindAllMatches);
extern SeqAlignPtr PatternMatchBioseq (BioseqPtr bsp, ComPatPtr cpp,
Int4 mismatch);
/* profiles */
extern ComProfPtr ReadProfile (CharPtr filename);
extern ComProfPtr ComProfNew (ComProfPtr currppp);
extern ComProfPtr ComProfFree (ComProfPtr headppp);
extern ComProfPtr ComProfDup (ComProfPtr pppold);
extern ComProfPtr ComProfDupThis (ComProfPtr pppthis);
extern void ComProfLink (ComProfPtr PNTR ppphead, ComProfPtr pppdup);
extern void IntegerProfile (ComProfPtr ppp);
extern ComProfPtr InvertProfile (ComProfPtr pppold);
extern FloatHi ProfScoreMax (ComProfPtr ppp);
extern Int4 ProfLenMax (ComProfPtr ppp);
extern Int4 CatenateProfile (ComProfPtr ppp, Int4 proflen, Int4 icount);
extern SeqAlignPtr ProfileMatch (Uint1Ptr seq, Int4 seqpos, FloatHi cutoff,
Uint1 strand, SeqIdPtr sip, ComProfPtr ppp,
Int2 topology, Boolean flagFindAllMatches,
Boolean flagBoundaryCondition);
extern SeqAlignPtr ProfileMatchBioseq (BioseqPtr bsp, ComProfPtr ppp,
ComProfPtr ippp, FloatHi cutoff,
Boolean flagBoundaryCondition);
extern SeqAlignPtr IntProfileMatchBioseq (BioseqPtr bsp, ComProfPtr ppp,
ComProfPtr ippp, Int4 cutoff,
Boolean flagBoundaryCondition);
/* SeqAligns SeqLocs */
extern SeqLocPtr MatchSa2Sl (SeqAlignPtr PNTR saph);
extern void EmbedFragLengthInfo (SeqAlignPtr saph, Int4 length);
extern void EmbedMolecularWeightInfo (SeqAlignPtr saph, BioseqPtr bsp);
extern void URK_SeqAlignSortByStart (SeqAlignPtr PNTR sap);
extern void URK_SeqAlignSortByLength (SeqAlignPtr PNTR sap);
extern void URK_SeqAlignSortByMolWt (SeqAlignPtr PNTR sap);
extern void URK_SeqAlignSortByScore (SeqAlignPtr PNTR sap);
#ifdef __cplusplus
}
#endif
#endif
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