NCBI C++ ToolKit
omssascore.hpp
Go to the documentation of this file.

Go to the SVN repository for this file.

1 /*
2  * ===========================================================================
3  *
4  * PUBLIC DOMAIN NOTICE
5  * National Center for Biotechnology Information
6  *
7  * This software/database is a "United States Government Work" under the
8  * terms of the United States Copyright Act. It was written as part of
9  * the author's official duties as a United States Government employee and
10  * thus cannot be copyrighted. This software/database is freely available
11  * to the public for use. The National Library of Medicine and the U.S.
12  * Government have not placed any restriction on its use or reproduction.
13  *
14  * Although all reasonable efforts have been taken to ensure the accuracy
15  * and reliability of the software and data, the NLM and the U.S.
16  * Government do not and cannot warrant the performance or results that
17  * may be obtained by using this software or data. The NLM and the U.S.
18  * Government disclaim all warranties, express or implied, including
19  * warranties of performance, merchantability or fitness for any particular
20  * purpose.
21  *
22  * Please cite the authors in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Authors: Lewis Y. Geer
27  *
28  * File Description:
29  * code to do mass spec scoring
30  *
31  * ===========================================================================
32  */
33 
34 
35 #ifndef OMSSASCORE__HPP
36 #define OMSSASCORE__HPP
37 
39 
40 // for log of gamma fcn
41 #include <util/math/miscmath.h>
42 // for erf fcn
44 
45 #define BEGIN_OMSSA_SCOPE \
46  BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) BEGIN_SCOPE(omssa)
47 #define END_OMSSA_SCOPE END_NCBI_SCOPE END_SCOPE(objects) END_SCOPE(omssa)
48 
49 #define USING_OMSSA_SCOPE \
50  USING_NCBI_SCOPE; USING_SCOPE(objects); USING_SCOPE(omssa);
51 
53 
54 /** m/z type */
55 typedef int TMSMZ;
56 
57 /** intensity type */
58 typedef unsigned TMSIntensity;
59 
60 /** ion type, e.g. eMSIonTypeA */
61 typedef signed char TMSIonSeries;
62 
63 /** charge type */
64 typedef signed char TMSCharge;
65 
66 /** ion sequence number, starting from 0. */
67 typedef short TMSNumber;
68 
69 /** density of experimental ions type */
70 typedef double TMSExpIons;
71 
72 /** intensity rank */
73 typedef int TMSRank;
74 
75 #define MSLNGAMMA BLAST_LnGammaInt
76 #define MSERF NCBI_Erf
77 
78 // define convergence delta for scoring
79 #define MSDOUBLELIMIT 1e-300L
80 
82 
83 // this is a wrapper for msscore.hpp so that msscore.hpp can be ncbi toolkit independent
84 #include "msscore.hpp"
85 
86 #endif
87 
Prototypes for portable math library (ported from C Toolkit)
signed char TMSCharge
charge type
Definition: omssascore.hpp:64
int TMSMZ
m/z type
Definition: omssascore.hpp:55
#define END_OMSSA_SCOPE
Definition: omssascore.hpp:47
#define BEGIN_OMSSA_SCOPE
Definition: omssascore.hpp:45
short TMSNumber
ion sequence number, starting from 0.
Definition: omssascore.hpp:67
signed char TMSIonSeries
ion type, e.g.
Definition: omssascore.hpp:61
int TMSRank
intensity rank
Definition: omssascore.hpp:73
double TMSExpIons
density of experimental ions type
Definition: omssascore.hpp:70
unsigned TMSIntensity
intensity type
Definition: omssascore.hpp:58
Modified on Wed Apr 24 14:15:15 2024 by modify_doxy.py rev. 669887