BioSwissProtFt.h

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#ifndef BIOSISSPROTFT_H
#define BIOSISSPROTFT_H

using namespace std;

#include <iostream>
#include <string>
#include <iomanip>
#include <sstream>
#include <fstream>
#include <vector>

#include "BioSwptFTKSingleConflict.h"
#include "BioSwptFTKSingleVariant.h"
#include "BioSwptFTKSingleVarSplic.h"
#include "BioSwptFTKSingleMutagen.h"
#include "BioSwptFTKSingleModRes.h"

#include "BioSwptFTKSingleCarbohyd.h"
#include "BioSwptFTKSingleLipid.h"
#include "BioSwptFTKSingleDiSulfid.h"
#include "BioSwptFTKSingleCrossLnk.h"
#include "BioSwptFTKSingleSeCys.h"

#include "BioSwptFTKSingleMetal.h"
#include "BioSwptFTKSingleBinding.h"
#include "BioSwptFTKSingleSignal.h"
#include "BioSwptFTKSinglePropep.h"
#include "BioSwptFTKSingleTransit.h"

#include "BioSwptFTKSingleChain.h"
#include "BioSwptFTKSinglePeptide.h"
#include "BioSwptFTKSingleDomain.h"
#include "BioSwptFTKSingleDnaBind.h"
#include "BioSwptFTKSingleCaBind.h"

#include "BioSwptFTKSingleNpBind.h"
#include "BioSwptFTKSingleTransMem.h"
#include "BioSwptFTKSingleZnFing.h"
#include "BioSwptFTKSingleRepeat.h"
#include "BioSwptFTKSingleActSite.h"

#include "BioSwptFTKSingleSite.h"
#include "BioSwptFTKSingleInitMet.h"
#include "BioSwptFTKSingleNonTer.h"
#include "BioSwptFTKSingleNonCons.h"
#include "BioSwptFTKSingleUnsure.h"

#include "BioSwptFTKSingleTurn.h"
#include "BioSwptFTKSingleStrand.h"
#include "BioSwptFTKSingleHelix.h"

class BioSwissProtFt
{
      vector<BioSwptFTKSingleConflict> conflict_;
      vector<BioSwptFTKSingleVariant> variant_;
      vector<BioSwptFTKSingleVarSplic> varsplic_;
      vector<BioSwptFTKSingleMutagen> mutagen_;
      vector<BioSwptFTKSingleModRes>modres_;
      
      vector<BioSwptFTKSingleCarbohyd> carbohyd_;
      vector<BioSwptFTKSingleLipid> lipid_;
      vector<BioSwptFTKSingleDiSulfid> disulfid_;
      vector<BioSwptFTKSingleCrossLnk> crosslnk_;
      vector<BioSwptFTKSingleSeCys> secys_;

      vector<BioSwptFTKSingleMetal> metal_;
      vector<BioSwptFTKSingleBinding> binding_;
      vector<BioSwptFTKSingleSignal> signal_;
      vector<BioSwptFTKSinglePropep> propep_;
      vector<BioSwptFTKSingleTransit> transit_;

      vector<BioSwptFTKSingleChain> chain_;
      vector<BioSwptFTKSinglePeptide> peptide_;
      vector<BioSwptFTKSingleDomain> domain_;
      vector<BioSwptFTKSingleDnaBind> dnabind_;
      vector<BioSwptFTKSingleCaBind> cabind_;

      vector<BioSwptFTKSingleNpBind> npbind_;
      vector<BioSwptFTKSingleTransMem> transmem_;
      vector<BioSwptFTKSingleZnFing> znfing_;
      vector<BioSwptFTKSingleRepeat> repeat_;
      vector<BioSwptFTKSingleActSite> actsite_;

      vector<BioSwptFTKSingleSite> site_;
      vector<BioSwptFTKSingleInitMet> initmet_;
      vector<BioSwptFTKSingleNonTer> nonter_;
      vector<BioSwptFTKSingleNonCons> noncons_;
      vector<BioSwptFTKSingleUnsure> unsure_;

      vector<BioSwptFTKSingleTurn> turn_;
      vector<BioSwptFTKSingleStrand> strand_;
      vector<BioSwptFTKSingleHelix> helix_;

      void alignFt(string,int,int,string,ostream & = cout);
  public :
        BioSwissProtFt();
        BioSwissProtFt(const string &);
        void setFt(vector <string>);
        
        int getNumberOfConflicts();
        BioSwptFTKSingleConflict getConflict(int);

        int getNumberOfVariants();
        BioSwptFTKSingleVariant getVariant(int);

        int getNumberOfVarSplics();
        BioSwptFTKSingleVarSplic getVarSplic(int);

        int getNumberOfMutagens();
        BioSwptFTKSingleMutagen getMutagen(int);
        
        int getNumberOfModRess();
        BioSwptFTKSingleModRes getModRes(int);

        int getNumberOfCarbohyds();
        BioSwptFTKSingleCarbohyd getCarbohyd(int);

        int getNumberOfLipids();
        BioSwptFTKSingleLipid getLipid(int);

        int getNumberOfDiSulfids();
        BioSwptFTKSingleDiSulfid getDiSulfid(int);

        int getNumberOfCrossLnks();
        BioSwptFTKSingleCrossLnk getCrossLnk(int);

        int getNumberOfSeCyss();
        BioSwptFTKSingleSeCys getSeCys(int);

        int getNumberOfMetals();
        BioSwptFTKSingleMetal getMetal(int);

        int getNumberOfBindings();
        BioSwptFTKSingleBinding getBinding(int);
        
        int getNumberOfSignals();
        BioSwptFTKSingleSignal getSignal(int);
        
        int getNumberOfPropeps();
        BioSwptFTKSinglePropep getPropep(int);
        
        int getNumberOfTransits();
        BioSwptFTKSingleTransit getTransit(int);

        int getNumberOfChains();
        BioSwptFTKSingleChain getChain(int);

        int getNumberOfPeptides();
        BioSwptFTKSinglePeptide getPeptide(int);
        
        int getNumberOfDomains();
        BioSwptFTKSingleDomain getDomain(int);

        int getNumberOfDnaBinds();
        BioSwptFTKSingleDnaBind getDnaBind(int);
        
        int getNumberOfCaBinds();
        BioSwptFTKSingleCaBind getCaBind(int);

        int getNumberOfNpBinds();
        BioSwptFTKSingleNpBind getNpBind(int);

        int getNumberOfTransMems();
        BioSwptFTKSingleTransMem getTransMem(int);

        int getNumberOfRepeats();
        BioSwptFTKSingleRepeat getRepeat(int);

        int getNumberOfZnFings();
        BioSwptFTKSingleZnFing getZnFing(int);

        int getNumberOfActSites();
        BioSwptFTKSingleActSite getActSite(int);

        int getNumberOfSites();
        BioSwptFTKSingleSite getSite(int);

        int getNumberOfInitMets();
        BioSwptFTKSingleInitMet getInitMet(int);

        int getNumberOfNonTers();
        BioSwptFTKSingleNonTer getNonTer(int);

        int getNumberOfNonCons();
        BioSwptFTKSingleNonCons getNonCons(int);

        int getNumberOfUnsures();
        BioSwptFTKSingleUnsure getUnsure(int);

        int getNumberOfTurns();
        BioSwptFTKSingleTurn getTurn(int);

        int getNumberOfStrands();
        BioSwptFTKSingleStrand getStrand(int);

        int getNumberOfHelixs();
        BioSwptFTKSingleHelix getHelix(int);

        void showFt(ostream & = cout);

        void showFeatureKeys(ostream & os=cout);

};                       
                        
                        
#endif