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EdwardsLippertIterator.h (Maintainer: Chris Bauer)

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00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 // --------------------------------------------------------------------------
00005 //                   OpenMS Mass Spectrometry Framework
00006 // --------------------------------------------------------------------------
00007 //  Copyright (C) 2003-2008 -- Oliver Kohlbacher, Knut Reinert
00008 //
00009 //  This library is free software; you can redistribute it and/or
00010 //  modify it under the terms of the GNU Lesser General Public
00011 //  License as published by the Free Software Foundation; either
00012 //  version 2.1 of the License, or (at your option) any later version.
00013 //
00014 //  This library is distributed in the hope that it will be useful,
00015 //  but WITHOUT ANY WARRANTY; without even the implied warranty of
00016 //  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
00017 //  Lesser General Public License for more details.
00018 //
00019 //  You should have received a copy of the GNU Lesser General Public
00020 //  License along with this library; if not, write to the Free Software
00021 //  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
00022 //
00023 // --------------------------------------------------------------------------
00024 // $Maintainer: Chris Bauer$
00025 // --------------------------------------------------------------------------
00026 
00027 #ifndef OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
00028 #define OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
00029 
00030 #include <OpenMS/CHEMISTRY/PepIterator.h>
00031 #include <OpenMS/CONCEPT/Exception.h>
00032 
00033 namespace OpenMS {
00039 class EdwardsLippertIterator : public PepIterator
00040 {
00041   
00042   public:
00043   
00044   typedef std::pair<String,String> FASTAEntry;  
00048   EdwardsLippertIterator();
00052   EdwardsLippertIterator (const EdwardsLippertIterator &);
00056   virtual ~EdwardsLippertIterator ();
00057   
00063   virtual FASTAEntry operator*() throw (Exception::InvalidIterator);
00064   
00070   virtual PepIterator & operator++() throw (Exception::InvalidIterator);
00071   
00077   virtual PepIterator * operator++(int i) throw (Exception::InvalidIterator);
00078 
00084   virtual void setFastaFile (const String & f) throw (Exception::FileNotFound);
00085   
00090   virtual String getFastaFile();
00091 
00097   virtual void setTolerance (float t) throw (Exception::InvalidValue);
00098   
00103   virtual float getTolerance ();
00104 
00110   virtual void setSpectrum (const std::vector<float> & s) throw (Exception::InvalidValue);
00111 
00116   virtual const std::vector<float> & getSpectrum ();
00117 
00122   virtual bool begin () throw (Exception::InvalidIterator);
00123 
00129   virtual bool isAtEnd ();
00130   
00135   virtual bool isDigestingEnd (char, char);
00136   
00141   static const std::string getName()
00142   {
00143     return "EdwardsLippertIterator";
00144   }
00145 
00150   static PepIterator* create()
00151   {
00152     return new EdwardsLippertIterator;
00153   }
00154   
00155   
00156   
00157   protected:
00162     virtual std::string next_ ();
00163   
00168     bool hasNext_();
00169   
00173     void goToNextAA_ ();
00174 
00179     virtual bool isInSpectrum_ (float & mass);
00180 
00181     String f_file_; 
00182 
00183     std::string actual_pep_; 
00184 
00185     std::vector<float> spec_; 
00186 
00187     float tol_; 
00188 
00189     float masse_[255]; 
00190 
00191     bool is_at_end_; 
00192 
00193     PepIterator * f_iterator_; 
00194 
00195     FASTAEntry f_entry_; 
00196 
00197     unsigned int b_,e_; 
00198 
00199     float m_, massMax_; 
00200   
00201   
00202 };
00203 
00204 }
00205 #endif //OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H

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