/usr/include/seqan/blast/blast_parsing.h is in seqan-dev 1.3-1ubuntu2.
This file is owned by root:root, with mode 0o644.
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// 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.
//
// ==========================================================================
#ifndef SEQAN_HEADER_BLAST_PARSING_H
#define SEQAN_HEADER_BLAST_PARSING_H
namespace SEQAN_NAMESPACE_MAIN
{
//////////////////////////////////////////////////////////////////////////////
// Internal Blast Parsing Functions
// remark: uses a lot of functions from graph_utility_parsing.h
//////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////
// read alignment string (letters and gaps)
// steht am ende dahinter
template<typename TFile, typename TChar>
inline String<char>
_parseReadAlignmentString(TFile & file, TChar& c)
{
SEQAN_CHECKPOINT
// Read word
String<char> str(c);
while (!_streamEOF(file)) {
c = _streamGet(file);
if (!_parseIsLetter(c) && !(c=='-')) break;
append(str, c);
}
return str;
}
////////////////////////////////////////////////////////////////////////////
// parses query and database name (file should be pointing to the beginning of the file)
template<typename TFile, typename TChar>
typename Position<TFile>::Type
_parseReadQueryAndDBName(TFile & file,
TChar & c,
String<char> & query_name,
String<char> & db_name)
{
SEQAN_CHECKPOINT
typedef typename Position<TFile>::Type TPosition;
typedef typename Value<TFile>::Type TValue;
TChar c_before = c;
TPosition act_pos = _streamTellG(file);
TPosition query_pos,db_pos;
//String<char> delim = "DQ";
//_parseUntilBeginLineOneOf(file,c,delim,2);
String<char> query = "Query";
if(_parseUntilBeginLine(file,c,query,6))
query_pos = _streamTellG(file);
else
return act_pos;
_streamSeekG(file,act_pos);
c = c_before;
String<char> database = "Database";
if(_parseUntilBeginLine(file,c,database,8))
db_pos = _streamTellG(file);
else
return act_pos;
//getQueryName
_streamSeekG(file,query_pos);
_parseSkipWhitespace(file,c);
c = _streamGet(file);
_parseSkipWhitespace(file,c);
query_name = _parseReadWord(file, c);
while (!_streamEOF(file) && c != '\n' && c != '\r')
query_name += _parseReadWord(file, c);
//getDBName
_streamSeekG(file,db_pos);
c = _streamGet(file);
_parseSkipWhitespace(file,c);
db_name = _parseReadWord(file, c);
while (!_streamEOF(file) && c != '\n' && c != '\r')
db_name += _parseReadWord(file, c);
_parseSkipWhitespace(file,c);
c = _streamGet(file);
return _streamTellG(file);
}
}// namespace SEQAN_NAMESPACE_MAIN
#endif //#ifndef SEQAN_HEADER_...
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