libStatGen Software  1
GlfRefSection.h
1 /*
2  * Copyright (C) 2010 Regents of the University of Michigan
3  *
4  * This program is free software: you can redistribute it and/or modify
5  * it under the terms of the GNU General Public License as published by
6  * the Free Software Foundation, either version 3 of the License, or
7  * (at your option) any later version.
8  *
9  * This program is distributed in the hope that it will be useful,
10  * but WITHOUT ANY WARRANTY; without even the implied warranty of
11  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12  * GNU General Public License for more details.
13  *
14  * You should have received a copy of the GNU General Public License
15  * along with this program. If not, see <http://www.gnu.org/licenses/>.
16  */
17 
18 #ifndef __GLF_REFSECTION_H__
19 #define __GLF_REFSECTION_H__
20 
21 #include <stdint.h>
22 
23 #include "InputFile.h"
24 #include "CharBuffer.h"
25 
26 ///This class allows a user to easily get/set the fields in a
27 /// GLF section/chromosome header.
28 /// The GlfRefSection contains:
29 /// - Reference Sequence Name
30 /// - Reference Sequence Length
32 {
33 public:
34  GlfRefSection();
35  ~GlfRefSection();
36 
37  /// Copy Constructor
38  /// \param refSection reference section to copy into this one.
39  GlfRefSection(const GlfRefSection& refSection);
40 
41  /// Overload operator= to copy the passed in refSection into this one.
42  /// \param refSection reference section to copy into this one.
43  GlfRefSection & operator = (const GlfRefSection& refSection);
44 
45  /// Copy the passed in refSection into this refSection.
46  /// \param refSection reference section to copy into this one.
47  bool copy(const GlfRefSection& refSection);
48 
49  /// Clear this reference section back to the default setting.
50  void resetRefSection();
51 
52  /// Read the refSection from the specified file (file MUST be in
53  /// the correct position for reading a refSection).
54  /// \param filePtr file to read from that is in the correct position.
55  /// \return true if the reference section was successfully read from the
56  /// file, false if not.
57  bool read(IFILE filePtr);
58 
59  /// Write the refSection to the specified file.
60  /// \param filePtr file to write to that is in the correct position.
61  /// \return true if the reference section was successfully written to the
62  /// file, false if not.
63  bool write(IFILE filePtr) const;
64 
65  /////////////
66  // Accessors.
67 
68  /// Get the reference name.
69  /// \param name string to populate with the reference name.
70  /// \return true if the name was successfully returned, false if not.
71  bool getName(std::string& name) const;
72 
73  /// Get the length of the reference sequence.
74  /// \return reference sequence length for this reference section.
75  uint32_t getRefLen() const;
76 
77  /// Set the reference name.
78  /// \param name reference name to set this section to.
79  /// \return true if the name was successfully set, false if not.
80  bool setName(const std::string& name);
81  /// Set the length of the reference sequence.
82  /// \param refLen reference sequence length to set this section to.
83  /// \return true if the length was successfully set, false if not.
84  bool setRefLen(uint32_t refLen);
85 
86  /// Print the reference section in a readable format.
87  void print() const;
88 
89 private:
90  CharBuffer myRefName;
91  uint32_t myRefLen;
92 };
93 
94 #endif
95 
This class allows a user to easily get/set the fields in a GLF section/chromosome header.
Definition: GlfRefSection.h:32
void resetRefSection()
Clear this reference section back to the default setting.
bool setName(const std::string &name)
Set the reference name.
bool copy(const GlfRefSection &refSection)
Copy the passed in refSection into this refSection.
bool read(IFILE filePtr)
Read the refSection from the specified file (file MUST be in the correct position for reading a refSe...
GlfRefSection & operator=(const GlfRefSection &refSection)
Overload operator= to copy the passed in refSection into this one.
void print() const
Print the reference section in a readable format.
bool write(IFILE filePtr) const
Write the refSection to the specified file.
bool setRefLen(uint32_t refLen)
Set the length of the reference sequence.
uint32_t getRefLen() const
Get the length of the reference sequence.
bool getName(std::string &name) const
Get the reference name.
Class for easily reading/writing files without having to worry about file type (uncompressed,...
Definition: InputFile.h:37