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/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
============================================================================
$Id: blast_parsing.h 4714 2009-08-24 13:38:02Z weese@PCPOOL.MI.FU-BERLIN.DE $
==========================================================================*/
#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>
_parse_readAlignmentString(TFile & file, TChar& c)
{
SEQAN_CHECKPOINT
// Read word
String<char> str(c);
while (!_streamEOF(file)) {
c = _streamGet(file);
if (!_parse_isLetter(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
_parse_readQueryAndDBName(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";
//_parse_untilBeginLineOneOf(file,c,delim,2);
String<char> query = "Query";
if(_parse_untilBeginLine(file,c,query,6))
query_pos = _streamTellG(file);
else
return act_pos;
_streamSeekG(file,act_pos);
c = c_before;
String<char> database = "Database";
if(_parse_untilBeginLine(file,c,database,8))
db_pos = _streamTellG(file);
else
return act_pos;
//getQueryName
_streamSeekG(file,query_pos);
_parse_skipWhitespace(file,c);
c = _streamGet(file);
_parse_skipWhitespace(file,c);
query_name = _parse_readWord(file, c);
while (!_streamEOF(file) && c != '\n' && c != '\r')
query_name += _parse_readWord(file, c);
//getDBName
_streamSeekG(file,db_pos);
c = _streamGet(file);
_parse_skipWhitespace(file,c);
db_name = _parse_readWord(file, c);
while (!_streamEOF(file) && c != '\n' && c != '\r')
db_name += _parse_readWord(file, c);
_parse_skipWhitespace(file,c);
c = _streamGet(file);
return _streamTellG(file);
}
}// namespace SEQAN_NAMESPACE_MAIN
#endif //#ifndef SEQAN_HEADER_...
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