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root/PrimerMatch/sts_io.h
Revision: 1.1.1.1 (vendor branch)
Committed: Wed Dec 22 21:37:18 2004 UTC (11 years, 4 months ago) by nje01
Branch: MAIN
CVS Tags: HEAD, RELEASE-20041222, HEAD
Changes since 1.1: +0 -0 lines
Log Message:
Initial primer_match import

Line File contents
1 /**************************************************************************
2 * This code is part of the supporting infrastructure for ATA Mapper.
3 * Copyright (C) 2002,2003,2004 Applera Corporation. All rights reserved.
4 * Author: Nathan Edwards
5 *
6 * This program is free software; you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation; either version 2 of the License, or
9 * (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received (LICENSE.txt) a copy of the GNU General Public
17 * License along with this program; if not, write to the Free Software
18 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
19 *************************************************************************/
20
21 #ifndef _IBPEP_STS_IO_H_
22 #define _IBPEP_STS_IO_H_
23
24 #include <assert.h>
25 #include <string>
26
27 #if !defined(NO_STD_NAMESPACE)
28 using namespace std;
29 #endif
30
31 class sts_entry {
32 std::string id_;
33 std::string forward_primer_;
34 std::string reverse_primer_;
35 long unsigned int sizelb_;
36 long unsigned int sizeub_;
37 std::string acc_;
38 std::string chrom_;
39 std::string altacc_;
40 std::string species_;
41 public:
42 sts_entry(std::string const & id="",
43 std::string const & fp="", std::string const & rp="",
44 long unsigned int sizelb=0, long unsigned int sizeub=0,
45 std::string const & accession="",std::string const & chrom="",
46 std::string const & altacc="", std::string const & species="") {
47 id_ = id;
48 forward_primer_ = fp;
49 reverse_primer_ = rp;
50 sizelb_ = sizelb;
51 sizeub_ = sizeub;
52 acc_ = accession;
53 chrom_ = chrom;
54 altacc_ = altacc;
55 species_ = species;
56 }
57 ~sts_entry() {}
58 std::string const & id() const {
59 return id_;
60 }
61 void id(std::string const & id) {
62 id_ = id;
63 }
64 std::string const & forward_primer() const {
65 return forward_primer_;
66 }
67 void forward_primer(std::string const & fp) {
68 forward_primer_ = fp;
69 }
70 std::string const & reverse_primer() const {
71 return reverse_primer_;
72 }
73 void reverse_primer(std::string const & rp) {
74 reverse_primer_ = rp;
75 }
76 long unsigned int const & sizelb() const {
77 return sizelb_;
78 }
79 void sizelb(long unsigned int const & sizelb) {
80 sizelb_ = sizelb;
81 }
82 long unsigned int const & sizeub() const {
83 return sizeub_;
84 }
85 void sizeub(long unsigned int const & sizeub) {
86 sizeub_ = sizeub;
87 }
88 std::string const & accession() const {
89 return acc_;
90 }
91 void accession(std::string const & acc) {
92 acc_ = acc;
93 }
94 std::string const & altacc() const {
95 return altacc_;
96 }
97 void altacc(std::string const & altacc) {
98 altacc_ = altacc;
99 }
100 std::string const & species() const {
101 return species_;
102 }
103 void species(std::string const & species) {
104 species_ = species;
105 }
106 std::string const & chrom() const {
107 return chrom_;
108 }
109 void chrom(std::string const & chrom) {
110 chrom_ = chrom;
111 }
112 void uppercase();
113 void lowercase();
114 void read(istream & is);
115 void write(ostream & os) const;
116 };
117
118 ostream & operator<<(ostream & os, sts_entry const & fe);
119 istream & operator>>(istream & is, sts_entry & fe);
120
121 #endif