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
|
/* $Id: stsmatch.cpp,v 1.5 2004/06/03 23:37:22 rotmistr Exp $
* ===========================================================================
*
* 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.
*
* =========================================================================
*
* Author: Kirill Rotmistrovsky
*
* ========================================================================= */
#include <epcr/defaults.h>
#include <epcr/hashset.hpp>
#include <epcr/stsmatch.hpp>
#include <errno.h>
#include <ctype.h>
#include <cstdio>
#include <stdexcept>
USING_NCBI_SCOPE;
USING_SCOPE(EPCR_SCOPE);
////////////////////////////////////////////////////////////////////////
CStsFileCallbackDefault::CStsFileCallbackDefault()
{
Start();
}
bool CStsFileCallbackDefault::Start()
{
m_String="";
m_Length=0;
m_Line=0;
memset(m_Bad,0,sizeof(m_Bad));
return true;
}
bool CStsFileCallbackDefault::NextLine(const char * s, int l)
{
m_String=s;
m_Length=l;
++m_Line;
return true;
}
const char * errorMessage(IStsFileCallback::EError e)
{
switch(e){
case IStsFileCallback::eErrOK:return "OK";
case IStsFileCallback::eErrShortPrimer:return "short primer";
case IStsFileCallback::eErrAmbiquosPrimer:return "ambiquities in primer";
case IStsFileCallback::eErrBadLine:return "bad line";
default: return "unknown error";
}
}
bool CStsFileCallbackDefault::Error(EError err)
{
const char * msg="OK";
switch(err) {
case eErrTOTAL: throw logic_error("err can't be eErrTOTAL here");
case eErrOK: return true;
case eErrBadLine: m_Bad[0]++; msg="bad line"; break;
case eErrShortPrimer: m_Bad[1]++; msg="short primer"; break;
case eErrAmbiquosPrimer: m_Bad[2]++; msg="ambiquity in primer"; break;
case eErrSystem:
throw runtime_error(string("STS file error: ")+strerror(errno));
}
return true;
}
bool CStsFileCallbackDefault::Done()
{
if(m_Bad[0])
fprintf(stderr,"WARNING: %d STSs have incomplete description line\n",
m_Bad[0]);
if(m_Bad[1])
fprintf(stderr,"WARNING: %d STSs have primer shorter than W\n",
m_Bad[1]);
if(m_Bad[2])
fprintf(stderr,
"WARNING: %d STSs have ambiguities within W of 3\' end\n",
m_Bad[2]);
return true;
}
////////////////////////////////////////////////////////////////////////
/*
* $Log: stsmatch.cpp,v $
* Revision 1.5 2004/06/03 23:37:22 rotmistr
* New aligner added.
*
* Revision 1.4 2004/05/27 20:35:48 rotmistr
* Version 2.1.0 with appropriate changes (see Changes) is ready for tests.
*
* Revision 1.3 2004/04/01 05:57:53 rotmistr
* Compilable with borland C++
*
* Revision 1.2 2004/03/29 21:25:40 rotmistr
* Dist files are prepared
*
* Revision 1.1.1.1 2003/12/23 18:17:28 rotmistr
* Package that includes e-PCR, reverse e-PCR, and sequence data preparation
* program for reverse e-PCR looks ready
*
*/
|
