NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
bidir.h
Go to the documentation of this file.
1 /*
2  * nvbio
3  * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
4  *
5  * Redistribution and use in source and binary forms, with or without
6  * modification, are permitted provided that the following conditions are met:
7  * * Redistributions of source code must retain the above copyright
8  * notice, this list of conditions and the following disclaimer.
9  * * Redistributions in binary form must reproduce the above copyright
10  * notice, this list of conditions and the following disclaimer in the
11  * documentation and/or other materials provided with the distribution.
12  * * Neither the name of the NVIDIA CORPORATION nor the
13  * names of its contributors may be used to endorse or promote products
14  * derived from this software without specific prior written permission.
15  *
16  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
17  * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
18  * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
19  * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
20  * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
21  * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
22  * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
23  * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
24  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
25  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
26  */
27 
28 #pragma once
29 
30 #include <nvbio/fmindex/fmindex.h>
31 
32 namespace nvbio {
33 
36 
50 template <
51  typename TRankDictionary1,
52  typename TSuffixArray1,
53  typename TRankDictionary2,
54  typename TSuffixArray2>
56 void extend_forward(
57  const fm_index<TRankDictionary1,TSuffixArray1>& f_fmi,
58  const fm_index<TRankDictionary2,TSuffixArray2>& r_fmi,
59  typename fm_index<TRankDictionary1,TSuffixArray1>::range_type& f_range,
60  typename fm_index<TRankDictionary2,TSuffixArray2>::range_type& r_range,
61  uint8 c);
62 
76 template <
77  typename TRankDictionary1,
78  typename TSuffixArray1,
79  typename TRankDictionary2,
80  typename TSuffixArray2>
82 void extend_backwards(
83  const fm_index<TRankDictionary1,TSuffixArray1>& f_fmi,
84  const fm_index<TRankDictionary2,TSuffixArray2>& r_fmi,
85  typename fm_index<TRankDictionary1,TSuffixArray1>::range_type& f_range,
86  typename fm_index<TRankDictionary2,TSuffixArray2>::range_type& r_range,
87  uint8 c);
88 
90 
91 } // namespace nvbio
92