multovl  1.3
Multiple overlaps of genomic regions
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Pages
trackio.hh
Go to the documentation of this file.
1 /* <LICENSE>
2 License for the MULTOVL multiple genomic overlap tools
3 
4 Copyright (c) 2007-2012, Dr Andras Aszodi,
5 Campus Science Support Facilities GmbH (CSF),
6 Dr-Bohr-Gasse 3, A-1030 Vienna, Austria, Europe.
7 All rights reserved.
8 
9 Redistribution and use in source and binary forms, with or without
10 modification, are permitted provided that the following conditions are
11 met:
12 
13  * Redistributions of source code must retain the above copyright notice,
14  this list of conditions and the following disclaimer.
15  * Redistributions in binary form must reproduce the above copyright notice,
16  this list of conditions and the following disclaimer in the documentation
17  and/or other materials provided with the distribution.
18  * Neither the name of the Campus Science Support Facilities GmbH
19  nor the names of its contributors may be used to endorse
20  or promote products derived from this software without specific prior
21  written permission.
22 
23 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS
24 AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
25 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
26 AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL
27 THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
28 INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
29 NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
30 USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
31 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
32 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
33 THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
34 </LICENSE> */
35 #ifndef MULTOVL_TRACKIO_HEADER
36 #define MULTOVL_TRACKIO_HEADER
37 
38 // == HEADER trackio.hh ==
39 
46 // -- Standard headers --
47 
48 #include <fstream>
49 #include <string>
50 
51 // -- Boost headers --
52 
53 #include "boost/noncopyable.hpp"
54 
55 // -- Own headers --
56 
57 #include "errors.hh"
58 
59 namespace multovl {
60 
61 class Region;
62 
63 namespace io {
64 
65 // -- Input --
66 
69 class TrackReader: private boost::noncopyable
70 {
71 public:
72 
74  TrackReader(): _errors() {}
75 
82  virtual
83  std::string read_into(std::string& chrom, Region& reg) = 0;
84 
86  const Errors& errors() const { return _errors; }
87 
88  // Adds a simple error message to _errors.
89  virtual
90  void add_error(const std::string& msg)
91  {
92  _errors.add_error(msg);
93  }
94 
95  virtual
96  ~TrackReader() {}
97 
98 private:
99 
100  Errors _errors;
101 
102 }; // END OF CLASS TrackReader
103 
104 // -- Output --
105 
106 // NOTE: necessary only if various output formats are used.
107 
108 } // namespace io
109 } // namespace multovl
110 
111 #endif // MULTOVL_TRACKIO_HEADER
void add_error(const std::string &msg)
const Errors & errors() const
Definition: trackio.hh:86
Definition: trackio.hh:69
TrackReader()
default init
Definition: trackio.hh:74
virtual std::string read_into(std::string &chrom, Region &reg)=0
Instances of the Region class represent regions on a sequence. They have first and last coordinates...
Definition: region.hh:65
Simple facility to keep track of errors and warnings.
Definition: errors.hh:49