/usr/include/seqan/find2/find_base.h is in seqan-dev 1.3-1ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 | // ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Basic definitions and types for the find module.
// ==========================================================================
#ifndef SEQAN_FIND2_FIND_BASE_H_
#define SEQAN_FIND2_FIND_BASE_H_
namespace seqan {
// Contains the state for finder and patterns.
struct FindState_ {
enum TState {
STATE_EMPTY, // Finder/pattern is empty.
STATE_INITIAL, // Finer/pattern has just been initialized.
STATE_FOUND, // Found the end position of a hit.
STATE_NOTFOUND, // No hit found, no more hits possible.
STATE_BEGIN_FOUND, // Found begin position.
STATE_BEGIN_NOTFOUND, // Found end but not begin, should not happen.
STATE_NO_HIT // Set manually to non-hit.
};
};
template <typename TNeedle, typename TSpec>
struct Pattern;
template <typename THaystack, typename TSpec = Default>
struct Finder;
template <typename TPattern>
struct Needle;
template <typename TNeedle, typename TSpec>
struct Needle<Pattern<TNeedle, TSpec> > {
typedef TNeedle Type;
};
// Metafunction for retrieving scoring schemes.
template <typename TPattern>
struct ScoringScheme;
// TODO(holtgrew): Implement HasFeature<TPattern, SetEndPosition> and HasFeature<TPattern, SetBeginPosition>, HasFeature<TPattern, ScoreLimit>, HasFeature<TPattern, Score>?
} // namespace seqan
#endif // SEQAN_FIND2_FIND_BASE_H_
|