libncbi6-dev 6.1.20120620-7 / usr / include / ncbi / seg.h

This file is indexed.

/usr/include/ncbi/seg.h is in libncbi6-dev 6.1.20120620-7.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
/*  seg.h
 * ===========================================================================
 *
 *                            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:  seg.h
 *
 * Author:  Scott Federhen
 *
 * Version Creation Date: 4/24/98
 *
 * $Revision: 6.8 $
 *
 * File Description:  low-complexity filter 'seg'
 *
 * Modifications:
 * --------------------------------------------------------------------------
 * Date     Name        Description of modification
 * -------  ----------  -----------------------------------------------------
 *
 *
 * ==========================================================================
 */

#ifndef __SEGSTR__
#define __SEGSTR__

#include <stdio.h>
#include <fcntl.h>
#include <ctype.h>
#include <math.h>

#include <ncbierr.h>
#include <ncbibs.h>
#include <sequtil.h>
#include <seqport.h>

#ifdef __cplusplus
extern "C" {
#endif


/*-----------------------------------------------------(alphabet defines)---*/

#define NA4     1
#define AA20    2

#define LN20    2.9957322735539909
#define LN4     1.3862943611198906

#define CHAR_SET 128

/*--------------------------------------------------------------(structs)---*/

typedef struct segm
  {
   int begin;
   int end;
   struct segm *next;
  } Seg, PNTR SegPtr;

typedef struct alpha
  {
   Int4 alphabet;
   Int4 alphasize;
   FloatHi lnalphasize;
   Int4Ptr alphaindex;
   BytePtr alphaflag;
   CharPtr alphachar;
  } Alpha, PNTR AlphaPtr;

typedef struct segparams
  {
   Int4 window;
   FloatHi locut;
   FloatHi hicut;
   Int4 period;
   Int4 hilenmin;
   Boolean overlaps;	/* merge overlapping pieces if TRUE. */
   Int4 maxtrim;
   Int4 maxbogus;
   AlphaPtr palpha;
  } SegParams, PNTR SegParamsPtr;

typedef struct sequence
  {
   struct sequence PNTR parent;
   CharPtr seq;
   AlphaPtr palpha;
   Int4 start;
   Int4 length;
   Int4 bogus;
   Boolean punctuation;
   Int4 PNTR composition;
   Int4 PNTR state;
   FloatHi entropy;
  } Sequence, PNTR SequencePtr;

/*---------------------------------------------------------------(protos)---*/

SeqLocPtr BioseqSeg (BioseqPtr bsp, SegParamsPtr sparamsp);
SeqLocPtr BioseqSegNa (BioseqPtr bsp, SegParamsPtr sparamsp);
SeqLocPtr BioseqSegAa (BioseqPtr bsp, SegParamsPtr sparamsp);
SeqLocPtr SeqlocSegNa (SeqLocPtr slp, SegParamsPtr sparamsp);
SeqLocPtr SeqlocSegAa (SeqLocPtr slp, SegParamsPtr sparamsp);
SegParamsPtr SegParamsNewAa(void);
SegParamsPtr SegParamsNewNa(void);
void SegParamsCheck (SegParamsPtr sparamsp);

void SegSeq(SequencePtr seq, SegParamsPtr sparamsp, SegPtr *segs,
            Int4 offset);
SequencePtr SeqNew(void);
void SeqFree(SequencePtr seq);
void SegFree(SegPtr segs);

void SegParamsFree(SegParamsPtr sparamsp);

extern void lower(CharPtr string, size_t len);
extern void upper(CharPtr string, size_t len);

/*--------------------------------------------------------------------------*/

#ifdef __cplusplus
}
#endif
#endif

APT Browse - Built by Thomas Orozco.