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  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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source/FORMAT/FastaIteratorIntern.C
 
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// -*- mode: C++; tab-width: 2; -*-
 
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// vi: set ts=2:
 
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//
 
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// --------------------------------------------------------------------------
 
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//                   OpenMS Mass Spectrometry Framework
 
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// --------------------------------------------------------------------------
 
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//  Copyright (C) 2003-2011 -- Oliver Kohlbacher, Knut Reinert
 
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//
 
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//  This library is free software; you can redistribute it and/or
 
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//  modify it under the terms of the GNU Lesser General Public
 
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//  License as published by the Free Software Foundation; either
 
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//  version 2.1 of the License, or (at your option) any later version.
 
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//
 
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//  This library is distributed in the hope that it will be useful,
 
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//  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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//  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 
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//  Lesser General Public License for more details.
 
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//
 
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//  You should have received a copy of the GNU Lesser General Public
 
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//  License along with this library; if not, write to the Free Software
 
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//  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
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//
 
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// --------------------------------------------------------------------------
 
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// $Maintainer: Clemens Groepl,Andreas Bertsch$
 
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// $Authors: $
 
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// --------------------------------------------------------------------------
 
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#include <OpenMS/FORMAT/FastaIteratorIntern.h>
 
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#include <OpenMS/FORMAT/FASTAFile.h>
 
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#include <vector>
 
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namespace OpenMS
 
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{
 
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        typedef std::pair<String,String> FASTAEntry;
 
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        FastaIteratorIntern::FastaIteratorIntern() :
 
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                fasta_file_("")
 
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        {
 
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        }
 
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        FastaIteratorIntern::~FastaIteratorIntern()
 
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        {
 
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        }
 
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        FastaIteratorIntern::FastaIteratorIntern(const FastaIteratorIntern & source) :
 
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                PepIterator (source),
 
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                fasta_file_(source.fasta_file_),
 
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                entrys_(source.entrys_),
 
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                it_(source.it_)
 
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        {
 
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        }
 
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        FASTAEntry FastaIteratorIntern::operator*()
 
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        {
 
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                if (fasta_file_=="")
 
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                {
 
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                        throw Exception::InvalidIterator(__FILE__, __LINE__, __PRETTY_FUNCTION__);
 
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                }
 
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                return *it_;
 
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        }
 
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        PepIterator & FastaIteratorIntern::operator++()
 
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        {
 
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                if (fasta_file_=="")
 
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                {
 
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                        throw Exception::InvalidIterator(__FILE__, __LINE__, __PRETTY_FUNCTION__);
 
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                }
 
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                ++it_;
 
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                return *this;
 
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        }
 
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        PepIterator * FastaIteratorIntern::operator++(int)
 
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        {
 
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                if (fasta_file_=="")
 
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                {
 
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                        throw Exception::InvalidIterator(__FILE__, __LINE__, __PRETTY_FUNCTION__);
 
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                }
 
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                PepIterator * old = new FastaIteratorIntern (*this);
 
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                ++it_;
 
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                return old;
 
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        }
 
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        void FastaIteratorIntern::setFastaFile (const String & f)
 
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        {
 
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                FASTAFile ffile;
 
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                std::vector<FASTAFile::FASTAEntry> entries;
 
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                ffile.load (f,entries);
 
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                entrys_.clear();
 
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                entrys_.resize(entries.size(), std::make_pair("", ""));
 
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                for (Size i = 0; i < entries.size(); ++i)
 
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                {
 
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                        entrys_[i].first = (entries[i].identifier + " " + entries[i].description);
 
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                        entrys_[i].second = entries[i].sequence;
 
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                }               
 
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                fasta_file_ = f;
 
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                it_ = entrys_.begin();
 
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        }
 
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        String FastaIteratorIntern::getFastaFile ()
 
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        {
 
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                return (fasta_file_);
 
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        }
 
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        bool FastaIteratorIntern::begin ()
 
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        {
 
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                if (fasta_file_=="")
 
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                {
 
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                        throw Exception::InvalidIterator(__FILE__, __LINE__, __PRETTY_FUNCTION__);
 
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                }
 
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                return true;
 
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        }
 
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        bool FastaIteratorIntern::isAtEnd ()
 
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        {
 
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                return (it_ == entrys_.end());
 
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        }
 
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}