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comparison egglib/egglib-2.1.5/include/egglib-cpp/Staden.hpp @ 1:420b57c3c185 draft

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author dereeper
date Fri, 10 Jul 2015 04:39:30 -0400
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0:3e19d0dfcf3e 1:420b57c3c185
1 /*
2 Copyright 2008-2009 Stéphane De Mita, Mathieu Siol
3
4 This file is part of EggLib.
5
6 EggLib 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 3 of the License, or
9 (at your option) any later version.
10
11 EggLib 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 a copy of the GNU General Public License
17 along with EggLib. If not, see <http://www.gnu.org/licenses/>.
18 */
19
20 #ifndef EGGLIB_STADEN_HPP
21 #define EGGLIB_STADEN_HPP
22
23 #include <string>
24 #include <istream>
25 #include "Align.hpp"
26
27 namespace egglib {
28
29 /** \brief Parser of Staden output format
30 *
31 * \ingroup core
32 *
33 * The parser is available as a static method. It takes either a
34 * stream or a string containing data formatted by the program GAP4
35 * of the Staden package (command 'dump contig to file').
36 *
37 */
38 class Staden {
39
40 public:
41
42
43 /** \brief Parses a string
44 *
45 * \param string a string containing an alignment formatted
46 * by the program GAP4 of the Staden package.
47 *
48 * \param deleteConsensus if true, the sequence named
49 * "CONSENSUS" is deleted from the file (if it is present).
50 *
51 * \return An Align instance containing the data found in
52 * the Staden while, after recoding the character following
53 * the standard codes.
54 *
55 * This method opens a stream to the string and calls the
56 * overloaded method.
57 *
58 * The character replacement rules assume Staden default
59 * convention, as follows:
60 * - "-" codes for an unknown base and is replaced by "N".
61 * - "*" codes for an alignment gap and is replaced by "-".
62 * - A white space represents missing data and is replaced
63 * by "?".
64 *
65 */
66 static Align parse(const std::string& string, bool deleteConsensus=true);
67
68
69 /** \brief Parses an open stream
70 *
71 * \param stream the open containing an alignment formatted
72 * by the program GAP4 of the Staden package.
73 *
74 * \param deleteConsensus if true, the sequence named
75 * "CONSENSUS" is deleted from the file (if it is present).
76 *
77 * \return An Align instance containing the data found in
78 * the Staden while, after recoding the character following
79 * the standard codes.
80 *
81 * The character replacement rules assume Staden default
82 * convention, as follows:
83 * - "-" codes for an unknown base and is replaced by "N".
84 * - "*" codes for an alignment gap and is replaced by "-".
85 * - A white space represents missing data and is replaced
86 * by "?".
87 *
88 */
89 static Align parse(std::istream& stream, bool deleteConsensus=true);
90
91
92 private:
93
94 /// Not allowed to instantiate this class
95 Staden() { }
96
97 /// Not allowed to instantiate this class
98 Staden(const Staden& source) { }
99
100 /// Not allowed to instantiate this class
101 ~Staden() { }
102
103
104 /* Gets the start position of sequences
105 *
106 * The functions gives total number of characters before the start of sequences
107 * and reads through until the next backspace (ignores the first line).
108 */
109 static void getShift();
110
111 // Translates according to the Staden format
112 static char transforme(char);
113
114 // Imports one sequence
115 static bool readOneSequence();
116
117 // Imports and concatenates one sequence
118 static bool readAppendOneSequence();
119
120 // Replaces dots by the matching character from CONSENSUS
121 static void undot(bool delete_consensus=true);
122
123 // The number of characters before the start of sequences
124 static int shift;
125
126 // The dynamically filled container (will result in an aligment)
127 static Container container;
128
129 // The current position
130 static int currpos;
131
132 // The reading stream
133 static std::istream* stream;
134
135 // Stores unique 8 characters discriminating readings
136 static std::vector<std::string> ID;
137 };
138 }
139
140 #endif