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root/PrimerMatch/sts_io.h
Revision: 1.1
Committed: Wed Dec 22 21:37:18 2004 UTC (13 years, 5 months ago) by nje01
Branch point for: MAIN
Log Message:
Initial revision

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1 nje01 1.1 /**************************************************************************
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