#include <PamLevel2.h>
//--------------------------------------
//
//
//--------------------------------------
/**
 * Default constructor 
 */
PamTrack::PamTrack(){
    trk_track  = this->TrkTrack::GetTrkTrack();
    calo_track = this->CaloTrkVar::GetCaloTrkVar();
    tof_track  = this->ToFTrkVar::GetToFTrkVar();
};
//--------------------------------------
//
//
//--------------------------------------
/**
 * Constructor 
 */
PamTrack::PamTrack(TrkTrack* t, CaloTrkVar* c, ToFTrkVar* o){ 
    trk_track  = this->TrkTrack::GetTrkTrack();
    calo_track = this->CaloTrkVar::GetCaloTrkVar();
    tof_track  = this->ToFTrkVar::GetToFTrkVar();
    if(t) *trk_track  = *t;
    if(c) *calo_track = *c;
    if(o) *tof_track  = *o;	
};

//--------------------------------------
//
//
//--------------------------------------
/**
 * Constructor 
 */
PamLevel2::PamLevel2(){
	
    trk_l1_obj  = this->TrkLevel1::GetTrkLevel1();	
    trk_obj     = this->TrkLevel2::GetTrkLevel2();
    calo_obj    = this->CaloLevel2::GetCaloLevel2();
    tof_obj     = this->ToFLevel2::GetToFLevel2();
    trig_obj    = this->TrigLevel2::GetTrigLevel2();
    s4_obj      = this->S4Level2::GetS4Level2();
    nd_obj      = this->NDLevel2::GetNDLevel2();
    ac_obj      = this->AcLevel2::GetAcLevel2();
    orb_obj     = this->OrbitalInfo::GetOrbitalInfo();

    run_obj     = new GL_RUN();
    
    sorted_tracks = new TRefArray();
    
    CAL = true;
    TRK = true;
    TRG = true;
    TOF = true;
    S4  = true;
    ND  = true;
    AC  = true;
    ORB = true;
    
    TRK_L1 = false;
    
    Tout  = NULL;
};
/**
 * Destructor 
 */
PamLevel2::~PamLevel2(){
		
    TrkLevel1::Clear();
    
    TrkLevel2::Clear();
    CaloLevel2::Clear();
    ToFLevel2::Clear();
    TrigLevel2::Clear();
    S4Level2::Clear();
    NDLevel2::Clear();
    AcLevel2::Clear();
    OrbitalInfo::Clear();
    
    delete run_obj;
    
//	delete sorted_tracks;
    sorted_tracks->Delete(); // clean the reference array
	
    if(Tout)Tout->Delete(); // delete loaded tree from memory
	
};
/**
 * Clear the event
 */
void PamLevel2::Clear(){
	
    TrkLevel1::Clear();
	
    TrkLevel2::Clear();
    CaloLevel2::Clear();
    ToFLevel2::Clear();
    TrigLevel2::Clear();
    S4Level2::Clear();
    NDLevel2::Clear();
    AcLevel2::Clear();
    OrbitalInfo::Clear();
    
    sorted_tracks->Delete(); // clean the reference array
    
};


//--------------------------------------
//
//
//--------------------------------------
/**
 * Retrieves the calorimeter track matching the seqno-th tracker stored track. 
 * (If seqno = -1 retrieves the self-trigger calorimeter track)
 */
 CaloTrkVar *PamLevel2::GetCaloStoredTrack(int seqno){
	 
     if( CaloLevel2::ntrk()==0 ){
	 cout << "PamLevel2::GetCaloStoredTrack(int) : requested tracker SeqNo "<< seqno <<" but no Calorimeter tracks are stored"<<endl;
	 return NULL;
     };
     
     CaloTrkVar *c = 0;
     Int_t it_calo=0;
     
     do{ 
	 c = CaloLevel2::GetCaloTrkVar(it_calo);
	 it_calo++; 
     } while( c && seqno != c->trkseqno && it_calo < CaloLevel2::ntrk());	
     
     if(!c || seqno != c->trkseqno){
	 c = 0;
	 if(seqno!=-1)cout << "PamLevel2::GetCaloStoredTrack(int) : requested tracker SeqNo "<< seqno <<" does not match Calorimeter stored tracks"<<endl;
     };
     return c;
     
 };
//--------------------------------------
 //
 //
//--------------------------------------
/**
  * Retrieves the ToF track matching the seqno-th tracker stored track. 
  * (If seqno = -1 retrieves the tracker-independent tof track)
 */
 ToFTrkVar *PamLevel2::GetToFStoredTrack(int seqno){
	 
     if( ToFLevel2::ntrk()==0 ){
	 cout << "PamLevel2::GetToFStoredTrack(int) : requested tracker SeqNo "<< seqno <<" but no ToF tracks are stored"<<endl;
	 return NULL;
     };
     
     ToFTrkVar *c = 0;
     Int_t it_tof=0;
     
     do{ 
	 c = ToFLevel2::GetToFTrkVar(it_tof);
	 it_tof++; 
     } while( c && seqno != c->trkseqno && it_tof < ToFLevel2::ntrk());	
     
     if(!c || seqno != c->trkseqno){
	 c = 0;
	 if(seqno!=-1)cout << "PamLevel2::GetToFStoredTrack(int) : requested tracker SeqNo "<< seqno <<" does not match ToF stored tracks"<<endl;
     };
     return c;
     
 };

//--------------------------------------
 //
 //
//--------------------------------------
/**
 * Give the pamela track associated to a tracker track, retrieving related calorimeter and tof track information. 
 */
 PamTrack* PamLevel2::GetPamTrackAlong(TrkTrack* t){
	 
     CaloTrkVar *c = 0;
     ToFTrkVar  *o = 0;
     
     if(CAL) c = GetCaloStoredTrack(t->GetSeqNo());
     if(TOF) o = GetToFStoredTrack(t->GetSeqNo());
     
//    if(t && c && o)track = new PamTrack(t,c,o);
     PamTrack *track = new PamTrack(t,c,o);
     
     return track;
 
 };
//--------------------------------------
//
//
//--------------------------------------
/**
 * Retrieves the it-th stored track. 
 * It override TrkLevel2::GetTrack(int it). 
 * @param itrk Track number, ranging from 0 to GetNTracks().
 */

PamTrack* PamLevel2::GetStoredTrack(Int_t itrk){
    
    PamTrack *track = 0;
    
    if( itrk >=0 && itrk < TrkLevel2::ntrk() ){
	
	TrkTrack *t = TrkLevel2::GetStoredTrack(itrk);
	track = GetPamTrackAlong(t);
	
    }else{
	cout << "PamLevel2::GetStoredTrack(int) : tracker track SeqNo "<< itrk <<" does not exist (GetNTracks() = "<<TrkLevel2::GetNTracks()<<")"<<endl;
    };
    
    return track;
    
}
//--------------------------------------
//
//
//--------------------------------------
/**
 * Sort physical (tracker) tracks and stores them in the TRefArray (of TrkTrack objects) which pointer is  PamLevel2::sorted_tracks.
 * @param how String to set the sorting cryterium (es: "CAL" or "TRK+CAL+TOF" ecc...).
 * Sorting cryteria:
 * TRK: lower chi**2
 * CAL: lower Y spatial residual on the first calorimeter plane
 * TOF: bigger numebr of hit PMTs along the track, on S12 S21 S32 (where paddles are along the Y axis).
 * The default sorting cryterium is "TOF+CAL".
 * 
 * The total number of physical tracks is always given by GetNTracks() and the it-th physical track can be retrieved by means of the methods GetTrack(int it) and GetTrack(int it, TString how).
 */
void PamLevel2::SortTracks(TString how){

  //Save current Object count
    Int_t ObjectNumber = TProcessID::GetObjectCount();
    
    sorted_tracks->Delete(); //temporaneo???
	
    // loop over the tracks sorted by the tracker
    Bool_t use_TRK = how.Contains("TRK", TString::kIgnoreCase);
    Bool_t use_CAL = how.Contains("CAL", TString::kIgnoreCase);
    Bool_t use_TOF = how.Contains("TOF", TString::kIgnoreCase);
    
    if( !CAL &&  use_CAL) use_CAL = false;
    if( !TOF &&  use_TOF) use_TOF = false;
    
    if( !TRK ){
	cout << "SortTracks() : without tracker does not work!!! (not yet)" << endl;
	return;
    };
    
    for(Int_t i=0; i < TrkLevel2::GetNTracks(); i++){
	
	TrkTrack *ts = 0;
	
	// get tracker tracks
	TrkTrack   *tp = TrkLevel2::GetTrack(i);                    //tracker
//		CaloTrkVar *cp = GetCaloStoredTrack(tp->GetSeqNo());
//		ToFTrkVar  *op = GetToFStoredTrack(tp->GetSeqNo());
	CaloTrkVar *cp = 0;
	ToFTrkVar  *op = 0;
	
	// if track has an image, check image selection
	if(tp->HasImage()){
	    
	    TrkTrack   *ti = TrkLevel2::GetTrackImage(i);              //tracker (image)
//			CaloTrkVar *ci = GetCaloStoredTrack(ti->GetSeqNo());
//			ToFTrkVar  *oi = GetToFStoredTrack(ti->GetSeqNo());
	    CaloTrkVar *ci = 0;
	    ToFTrkVar  *oi = 0;
	    
	    //assign starting scores
	    Int_t tp_score = 0;  //main track sorted by the tracker
	    Int_t ti_score = 0;  //image track
	    
	    // ------------------------
	    // calorimeter check
	    // ------------------------
	    // check the Y spatial residual on the first calorimeter plane
	    // (cut on calorimeter variables from Emiliano)
	    if(
		use_CAL            &&
		npcfit[1] > 15     &&   //no. of fit planes on Y view
		varcfit[1] < 1000. &&  //fit variance on Y view
		true){
		
		cp = GetCaloStoredTrack(tp->GetSeqNo());
		ci = GetCaloStoredTrack(ti->GetSeqNo());
		
		Float_t resy_p = cp->tbar[0][1] - cbar[0][1]; if(resy_p < 0)resy_p= - resy_p;
		Float_t resy_i = ci->tbar[0][1] - cbar[0][1]; if(resy_i < 0)resy_i= - resy_i;
		
		if(resy_p <= resy_i) tp_score++;
		else                 ti_score++;
	    };
	    // ------------------------
	    // TOF check
	    // ------------------------	    
	    // check the number of hit pmts along the track 
	    // on S12 S21 and S32, where paddles are parallel to Y axis
	    if( use_TOF ){
		
		Int_t nphit_p =0;
		Int_t nphit_i =0;
		
		op = GetToFStoredTrack(tp->GetSeqNo());
		oi = GetToFStoredTrack(ti->GetSeqNo());
		
/*				cout << "track: npmtadc "<< op->npmtadc << endl;
				cout << "track: npmttdc "<< op->npmttdc << endl;
				cout << "image: npmtadc "<< oi->npmtadc << endl;
				cout << "image: npmttdc "<< oi->npmttdc << endl;*/
		
		for (Int_t ih=0; ih < op->npmtadc; ih++){
		    Int_t pl = GetPlaneIndex( (op->pmtadc).At(ih) );
		    if(pl == 1 || pl == 2 || pl == 5)nphit_p++;
		};
		
		for (Int_t ih=0; ih < oi->npmtadc; ih++){
		    Int_t pl = GetPlaneIndex( (oi->pmtadc).At(ih) );
		    if(pl == 1 || pl == 2 || pl == 5)nphit_i++;	
		};
		
		if(
		    use_TOF            &&
		    (nphit_p+nphit_i) !=0 &&	
		    true){
		    
		    if( nphit_p >= nphit_i) tp_score++;
		    else ti_score++;
		};
	    };
	    if(tp_score == ti_score) use_TRK = true;
	    // ------------------------
	    // tracker check
	    // ------------------------
	    // chi**2 difference is not always large enough to distinguish among 
	    // the real track and its image.
	    // Tracker check will be applied always when calorimeter and tof information is ambiguous.
	    if(use_TRK){
		if(      tp->chi2 > 0 && tp->chi2 < ti->chi2 ) tp_score++ ;
		else if( ti->chi2 > 0 && ti->chi2 < tp->chi2 ) ti_score++ ;
	    };
	    
	    // ------------------------
	    // the winner is....
	    // ------------------------	    
	    if      (tp_score > ti_score) ts = tp;//the track sorted by the tracker!!
	    else if (tp_score < ti_score) ts = ti;//its image!!
	    else {
		ts = tp;
//				cout << "Warning - track image ambiguity not solved" << endl;
//				cout << ts->GetNtot() << " "<< ts->chi2 << " " << npcfit[1] << " "<< nphit_p << endl;
	    };
	    
	}else{
	    ts = tp;
	};
	
//		cout <<" SortTracks() "<<i<<" -- "<<ts<<endl;
	sorted_tracks->Add(ts);//save the track in the sorted array
//		cout << "SortTracks:: sorted_tracks->Add(it) "<<i<<" "<<ts<<endl;
	
    };
    //Restore Object count 
    //To save space in the table keeping track of all referenced objects
    //we assume that our events do not address each other. We reset the 
    //object count to what it was at the beginning of the event.
    TProcessID::SetObjectCount(ObjectNumber);
    
};
//--------------------------------------
//
//
//--------------------------------------
/**
 * This method overrides TrkLevel2::GetTracks(), where sorting is done by decreasing number of fit points and increasing chi^2.
 * PamLevel2::GetTracks() keeps the same track order given by TrkLevel2::GetTracks(), but checks image selection by using calorimeter and ToF tracking information.
 */
 TRefArray *PamLevel2::GetTracks(){
	 //
//	SortTracks("+CAL+TOF");
	 SortTracks("+CAL+TRK");//TEMP!!!!!!!!!!!!!
	//
	return sorted_tracks;
 };
//--------------------------------------
 //
 //
//--------------------------------------
/**
 * Retrieves the it-th Pamela "physical" track. 
 * It override TrkLevel2::GetTrack(int it). 
 * @param it Track number, ranging from 0 to GetNTracks().
 */
PamTrack *PamLevel2::GetTrack(int it){
	
//  *-*-*-*-*-*-*
//	SortTracks("+CAL+TOF");
    SortTracks("+CAL+TRK");//TEMP!!!!!!!!!!!!!
//  *-*-*-*-*-*-*

    PamTrack *track = 0;
    
    if( it >=0 && it < TrkLevel2::GetNTracks() && it<sorted_tracks->GetEntriesFast() ){	
	TrkTrack   *t = (TrkTrack*)sorted_tracks->At(it);
	track = GetPamTrackAlong(t);
    }else{
	cout << "PamLevel2::GetTrack(int) : tracker track SeqNo "<< it <<" does not exist (GetNTracks() = "<<TrkLevel2::GetNTracks()<<")"<<endl;
    };
    
    return track;
    
};

//--------------------------------------
//
//
//--------------------------------------
/**
 * Retrieves (if present) the image of the it-th Pamela "physical" track, sorted by the method PamLevel2::SortTracks(). 
 * @param it Track number, ranging from 0 to GetNTracks().
 */
PamTrack *PamLevel2::GetTrackImage(int it){

//	SortTracks("+CAL+TOF");
	SortTracks("+CAL+TRK");//TEMP!!!!!!!!!!!!!
	
	PamTrack *image = 0;

	if( it >=0 && it < TrkLevel2::GetNTracks() ){
		TrkTrack *temp = (TrkTrack*)sorted_tracks->At(it);
		if( temp->HasImage() ){
			TrkTrack   *t = TrkLevel2::GetStoredTrack(temp->GetImageSeqNo());
			image = GetPamTrackAlong(t);
		}else{
			cout <<"PamLevel2::GetTrackImage(int) : Track SeqNo "<<it<<" does not have image"<<endl;
		};
	}else{
		cout << "PamLevel2::GetTrackImage(int) : Tracker track SeqNo "<< it <<" does not exist (GetNTracks() = "<<TrkLevel2::GetNTracks()<<")"<<endl;
	};
    
	return image;
}

//--------------------------------------
//
//
//--------------------------------------
/**
 * Get the Pamela detector trees in a single file and make them friends.
 * @param f TFile pointer
 * @param detlist String to select trees to be included
 * @return Pointer to a TTree
 */
TTree *PamLevel2::GetPamTree(TFile *f, TString detlist="+ALL"){

//	cout << "WARNING!!! -- obsolete method -- \n";
//	cout << "better use TChain *PamLevel2::GetPamTree(TList*, TString) \n";
	
    TTree *Trout =0;
    
    SetWhichTrees(detlist);
// Tracker
    TTree *T = (TTree*)f->Get("Tracker");
    if(T && TRK) {
	if(TRK_L1){
	    T->SetBranchAddress("TrkLevel1", GetPointerToTrk(1));
	    cout << "Tracker      : set branch address TrkLevel1"<<endl;
	};
	T->SetBranchAddress("TrkLevel2", GetPointerToTrk(2));
	cout << "Tracker      : set branch address TrkLevel2"<<endl;
	Trout=T;
    }else{
        cout << "Tracker      : missing tree"<<endl;
    };
    // Calorimeter
    TTree *C = (TTree*)f->Get("Calorimeter");
    if(C && CAL) {
        C->SetBranchAddress("CaloLevel2", GetPointerToCalo());
        cout << "Calorimeter  : set branch address CaloLevel2"<<endl;
        if(!Trout)Trout=C;
        else Trout->AddFriend(C);
    }else{
        cout << "Calorimeter  : missing tree"<<endl;
    };
    // ToF    
    TTree *O = (TTree*)f->Get("ToF");
    if(O && TOF) {
        O->SetBranchAddress("ToFLevel2", GetPointerToToF());
        cout << "ToF          : set branch address ToFLevel2"<<endl;
        if(!Trout)Trout=O;
        else Trout->AddFriend(O);
    }else{
        cout << "ToF         : missing tree"<<endl;
    };
    // Trigger
    TTree *R = (TTree*)f->Get("Trigger");
    if(R && TRG) {
        R->SetBranchAddress("TrigLevel2", GetPointerToTrig());
        cout << "Trigger      : set branch address TrigLevel2"<<endl;
        if(!Trout)Trout=O;
        else Trout->AddFriend(R);
    }else{
        cout << "Trigger      : missing tree"<<endl;
    };
    // S4
    TTree *S = (TTree*)f->Get("S4");
    if(S && S4) {
        S->SetBranchAddress("S4Level2", GetPointerToS4());
        cout << "S4           : set branch address S4Level2"<<endl;
        if(!Trout)Trout=O;
        else Trout->AddFriend(S);
    }else{
        cout << "S4           : missing tree"<<endl;
    };
    // Neutron Detector
    TTree *N = (TTree*)f->Get("NeutronD");
    if(N && ND) {
        N->SetBranchAddress("NDLevel2", GetPointerToND());
        cout << "NeutronD     : set branch address NDLevel2"<<endl;
        if(!Trout)Trout=O;
        else Trout->AddFriend(N);
    }else{
        cout << "NeutronD     : missing tree"<<endl;
    };
    // Anticounters
    TTree *A = (TTree*)f->Get("Anticounter");
    if(A && AC) {
        A->SetBranchAddress("AcLevel2", GetPointerToAc());
        cout << "Anticounter  : set branch address AcLevel2"<<endl;
        if(!Trout)Trout=O;
        else Trout->AddFriend(A);
    }else{
        cout << "Anticounter  : missing tree"<<endl;
    };
    // Orbital Info
	TTree *B = (TTree*)f->Get("OrbitalInfo");
	if(B && ORB) {
		B->SetBranchAddress("OrbitalInfo", GetPointerToOrb());
		cout << "OrbitalInfo  : set branch address OrbitalInfo"<<endl;
		if(!Trout)Trout=O;
		else Trout->AddFriend(B);
	}else{
		cout << "OrbitalInfo  : missing tree"<<endl;
	};
    
	cout<<endl<<" Number of entries: "<<Trout->GetEntries()<<endl<<endl;
	
	return Trout;
    
}
//--------------------------------------
//
//
//--------------------------------------
/**
 * Get list of Level2 files.
 * @param ddir Level2 data directory.
 * @param flisttxt Name of txt file containing file list.
 * @return Pointer to a TList of TSystemFiles
 * If no input file list is given , all the Level2 files inside the directory are processed.
 */
TList*  PamLevel2::GetListOfLevel2Files(TString ddir, TString flisttxt = ""){
	
    TString wdir = gSystem->WorkingDirectory();	
    
    if(ddir=="")ddir = wdir;
//	TSystemDirectory *datadir = new TSystemDirectory(gSystem->BaseName(ddir),ddir);
    cout << "Level2 data directory : "<<  ddir << endl;
    
    TList *contents  = new TList; // create output list
    contents->SetOwner();
    
    char *fullpath;
    
    // if no input file list is given:	
    if ( flisttxt != "" ){
	
	if( !gSystem->IsFileInIncludePath(flisttxt,&fullpath) )return 0;
	
//		flisttxt = gSystem->ConcatFileName(gSystem->DirName(flisttxt),gSystem->BaseName(flisttxt));
	flisttxt = fullpath;
	
	if( !gSystem->ChangeDirectory(ddir) )return 0; 
	
	cout <<"Input file list : " << flisttxt <<endl;
	ifstream in; 
	in.open(flisttxt, ios::in); //open input file list
	while (1) {
	    TString file;
	    in >> file;
	    if (!in.good()) break;
	    if( gSystem->IsFileInIncludePath(file,&fullpath) ){
//				contents->Add(new TSystemDirectory(fullpath,ddir)); // add file to the list
//				contents->Add(new TSystemFile(fullpath,ddir)); // add file to the list
		contents->Add(new TSystemFile(fullpath,gSystem->DirName(fullpath)));// add file to the list
	    }else{
		cout << "warning! --- File "<<file<<" does not exists"<< endl;
	    };
	};
	in.close();
	
    }else{
	
	cout << "No input file list given."<<endl;
	cout << "Check for existing root files."<<endl;
//		cout << "Warking directory: "<< gSystem->WorkingDirectory()<< endl;
	
	TSystemDirectory *datadir = new TSystemDirectory(gSystem->BaseName(ddir),ddir);
	TList *temp = datadir->GetListOfFiles();
//		temp->Print();
//		cout << "*************************************" << endl;
	
	TIter next(temp);
	TSystemFile *questo = 0;
	
	
	while ( (questo = (TSystemFile*) next()) ) {
	    TString name =  questo-> GetName();
	    if( name.EndsWith(".root") ){
		char *fullpath;
		gSystem->IsFileInIncludePath(name,&fullpath);
		contents->Add(new TSystemFile(fullpath,gSystem->DirName(fullpath)));
	    };
	}
	delete temp;
	delete datadir;
	
    };
    gSystem->ChangeDirectory(wdir); // back to the working directory
//	cout << endl << "Selected files:" << endl;
//	contents->Print();
    cout << contents->GetEntries()<<" files selected\n";
//	cout << endl;
//	cout << "Working directory: "<< gSystem->WorkingDirectory()<< endl;
    return contents;
};
//--------------------------------------
//
//
//--------------------------------------
/**
 * Get the Pamela detector chains from a list of files and make them friends.
 * @param fl Pointer to a TList of TSystemFiles 
 * @param detlist String to select trees to be included
 * @return Pointer to a TChain
 */
TChain *PamLevel2::GetPamTree(TList *fl, TString detlist="+ALL"){

//	TChain *Tout=0;
    if(Tout)Tout->Delete();
    Tout = NULL;
    
    SetWhichTrees(detlist);
    
    TChain *T = 0;	
    TChain *C = 0;
    TChain *O = 0;
    TChain *R = 0;
    TChain *S = 0;
    TChain *N = 0;
    TChain *A = 0;
    TChain *B = 0;
    
    if(TRK) T = new TChain("Tracker");	
    if(CAL) C = new TChain("Calorimeter");
    if(TOF) O = new TChain("ToF");
    if(TRG) R = new TChain("Trigger");
    if(S4)  S = new TChain("S4");
    if(ND)  N = new TChain("NeutronD");
    if(AC)  A = new TChain("Anticounter");
    if(ORB) B = new TChain("OrbitalInfo");
    
    // loop over files and create chains	
    TIter next(fl);
    TSystemFile *questo = 0;
    while ( (questo = (TSystemFile*) next()) ) {
	TString name =  questo->GetName();
//		cout << "File: "<< name << endl;
	if( CheckLevel2File(name) ){
	    if(TRK) T->Add(name);
	    if(CAL) C->Add(name);
	    if(TOF) O->Add(name);
	    if(TRG) R->Add(name);
	    if(S4)  S->Add(name);
	    if(ND)  N->Add(name);
	    if(AC)  A->Add(name);
	    if(ORB) B->Add(name);
	};
    }
    
    cout << "done chain \n";

    // Tracker
    if(TRK) if(!Tout)Tout=T;
    // Calorimeter
    if(CAL) {		
	if(!Tout)Tout=C;
	else Tout->AddFriend("Calorimeter");
    };
    // ToF    
    if(TOF) {
	if(!Tout)Tout=O;
	else Tout->AddFriend("ToF");
    };
    // Trigger
    if(TRG) {
	if(!Tout)Tout=O;
	else Tout->AddFriend("Trigger");
    };
    // S4
    if(S4) {
	if(!Tout)Tout=O;
	else Tout->AddFriend("S4");
    };
    // Neutron Detector
    if(ND) {
	if(!Tout)Tout=O;
	else Tout->AddFriend("NeutronD");
    };
    // Anticounters
    if(AC) {
	if(!Tout)Tout=O;
	else Tout->AddFriend("Anticounter");
    };
    // OrbitalInfo
    if(ORB) {
	if(!Tout)Tout=O;
	else Tout->AddFriend("OrbitalInfo");
    };
    
//    cout<<endl<<" Number of entries: "<<Tout->GetEntries()<<endl<<endl;
    
    if( Tout->GetEntries() )PamLevel2::SetBranchAddress();
    
    return Tout;
}
//--------------------------------------
//
//
//--------------------------------------
/**
 * Set branch addresses for Pamela friend trees
 */
void PamLevel2::SetBranchAddress(){
    // Tracker
    if(TRK) {
	if(TRK_L1){
	    Tout->SetBranchAddress("TrkLevel1", GetPointerToTrk(1));
	    cout << "Tracker      : set branch address TrkLevel1"<<endl;
	};
	Tout->SetBranchAddress("TrkLevel2", GetPointerToTrk(2));
	cout << "Tracker      : set branch address TrkLevel2"<<endl;
    };
    
    // Calorimeter
    if(CAL) {
	Tout->SetBranchAddress("CaloLevel2", GetPointerToCalo());
	cout << "Calorimeter  : set branch address CaloLevel2"<<endl;
    };
    
    // ToF    
    if(TOF) {
	Tout->SetBranchAddress("ToFLevel2", GetPointerToToF());
	cout << "ToF          : set branch address ToFLevel2"<<endl;
    };
    // Trigger
    if(TRG) {
	Tout->SetBranchAddress("TrigLevel2", GetPointerToTrig());
	cout << "Trigger      : set branch address TrigLevel2"<<endl;
    };
    // S4
    if(S4) {
	Tout->SetBranchAddress("S4Level2", GetPointerToS4());
	cout << "S4           : set branch address S4Level2"<<endl;
    };
    // Neutron Detector
    if(ND) {
	Tout->SetBranchAddress("NDLevel2", GetPointerToND());
	cout << "NeutronD     : set branch address NDLevel2"<<endl;
    };
    // Anticounters
    if(AC) {
	Tout->SetBranchAddress("AcLevel2", GetPointerToAc());
	cout << "Anticounter  : set branch address AcLevel2"<<endl;
    };
    // OrbitalInfo
    if(ORB) {
	Tout->SetBranchAddress("OrbitalInfo", GetPointerToOrb());
	cout << "OrbitalInfo  : set branch address OrbitalInfo"<<endl;
    };
    
}

//--------------------------------------
//
//
//--------------------------------------
void *PamLevel2::GetPointerTo(const char* c ){
//	cout << "objname "<< objname << endl;
    TString objname = c;
    if(!objname.CompareTo("TrkLevel1"))return &trk_l1_obj;
    if(!objname.CompareTo("TrkLevel2"))return &trk_obj;
    
    return NULL;
};
//--------------------------------------
//
//
//--------------------------------------
/**
 * Get the Run tree chain from a list of files.
 * @param fl Pointer to a TList of TSystemFiles 
 * @return Pointer to a TChain
 */
TChain *PamLevel2::GetRunTree(TList *fl){
	
    TChain *R = new TChain("Run");
    
    // loop over files and create chains	
    TIter next(fl);
    TSystemFile *questo = 0;
    while ( (questo = (TSystemFile*) next()) ) {
	TString name =  questo->GetName();
//		cout << "File: "<< name << endl;
	if( CheckLevel2File(name) ){
	    R->Add(name);
	};
    }
    
    R->SetBranchAddress("RunInfo", GetPointerToRun());
    cout << "Run         : set branch address RunInfo"<<endl;
    
    return R;
    
}
//--------------------------------------
//
//
//--------------------------------------
/**
 * Get the Run tree  from a file.
 * @param f Pointer to a TFile 
 * @return Pointer to a TTree
 */
TTree *PamLevel2::GetRunTree(TFile *f){


    TTree *R = (TTree*)f->Get("Run");
    
    R->SetBranchAddress("RunInfo", GetPointerToRun());
    cout << "Run         : set branch address RunInfo"<<endl;
    
    return R;
    
}
//--------------------------------------
//
//
//--------------------------------------
/**
 * Set which trees should be analysed
 * @param detlist TString containing the sequence of trees required 
*/
void PamLevel2::SetWhichTrees(TString detlist){
	
    if(detlist.Contains("+ALL", TString::kIgnoreCase)){
	CAL = true;
	TRK = true;
	TRK_L1 = false;
	TRG = true;
	TOF = true;
	S4  = true;
	ND  = true;
	AC  = true;
	ORB = true;
    }else if( detlist.Contains("-ALL", TString::kIgnoreCase) ){
	CAL = false;
	TRK = false;
	TRK_L1 = false;
	TRG = false;
	TOF = false;
	S4  = false;
	ND  = false;
	AC  = false;
	ORB = false;
    };
    
    if( detlist.Contains("-CAL", TString::kIgnoreCase) )CAL = false;
    else if( detlist.Contains("+CAL", TString::kIgnoreCase) )CAL = true;
    
    if( detlist.Contains("-TRK", TString::kIgnoreCase) )TRK = false;
    else if( detlist.Contains("+TRK", TString::kIgnoreCase) )TRK = true;
    
    if( detlist.Contains("-TRK1", TString::kIgnoreCase) )TRK_L1 = false;
    else if( detlist.Contains("+TRK1", TString::kIgnoreCase) )TRK_L1 = true;
    
    if( detlist.Contains("-TRG", TString::kIgnoreCase) )TRG = false;
    else if( detlist.Contains("+TRG", TString::kIgnoreCase) )TRG = true;
    
    if( detlist.Contains("-TOF", TString::kIgnoreCase) )TOF = false;
    else if( detlist.Contains("+TOF", TString::kIgnoreCase) )TOF = true;
    
    if( detlist.Contains("-S4",  TString::kIgnoreCase) )S4  = false;
    else if( detlist.Contains("+S4",  TString::kIgnoreCase) )S4  = true;
    
    if( detlist.Contains("-ND",  TString::kIgnoreCase) )ND  = false;
    else if( detlist.Contains("+ND",  TString::kIgnoreCase) )ND  = true;
    
    if( detlist.Contains("-AC",  TString::kIgnoreCase) )AC  = false;
    else if( detlist.Contains("+AC",  TString::kIgnoreCase) )AC  = true;
    
    if( detlist.Contains("-ORB", TString::kIgnoreCase) )ORB = false;
    else if( detlist.Contains("+ORB", TString::kIgnoreCase) )ORB = true;
    
};
//--------------------------------------
//
//
//--------------------------------------
/**
 * Check if a file contains selected Pamela Level2 trees.
 * @param name File name
 * @return true if the file is ok.
 */
Bool_t  PamLevel2::CheckLevel2File(TString name){
	
    Bool_t CAL__ok = false;     
    Bool_t TRK__ok = false;     
    Bool_t TRK_L1__ok = false;    
    Bool_t TRG__ok = false;     
    Bool_t TOF__ok = false;     
    Bool_t S4__ok  = false;    
    Bool_t ND__ok  = false;    
    Bool_t AC__ok  = false;     
    Bool_t ORB__ok = false;    
    
    Bool_t RUN__ok = false;
    
//    cout << "Checking file: "<<name<<endl;
    TFile *f = new TFile(name.Data());
    if( !f || f->IsZombie() ){
	cout << "File: "<< f->GetName() <<" discarded ---- Non valid root file"<< endl; return false;
    }
    //   cout << "Get list of keys: "<<f<<endl;
    TList *lk = f->GetListOfKeys();
//	lk->Print();
    TIter next(lk);
    TKey *key =0;
    Int_t nev =0;
    Int_t nev_previous =0;
    while( (key = (TKey*)next()) ){
	
	nev_previous = nev;
	nev = ((TTree*)f->Get(key->GetName()))->GetEntries();
	if( key->GetClassName()=="TTree" && nev_previous && nev != nev_previous ){
	    cout << "File: "<< f->GetName() <<" discarded ---- "<< key->GetName() << " tree: n.entries does not match "<<nev<<" "<<nev_previous<< endl;
	    return false;
	};

	if( !strcmp(key->GetName(),"Calorimeter") )CAL__ok = true;
       	if( !strcmp(key->GetName(),"Trigger"    ) )TRG__ok = true;
	if( !strcmp(key->GetName(),"ToF"        ) )TOF__ok = true;
	if( !strcmp(key->GetName(),"S4"         ) )S4__ok = true;
	if( !strcmp(key->GetName(),"NeutronD"   ) )ND__ok = true;
	if( !strcmp(key->GetName(),"Anticounter") )AC__ok = true;
	if( !strcmp(key->GetName(),"OrbitalInfo") )ORB__ok = true;
	if( !strcmp(key->GetName(),"Run"        ) )RUN__ok = true;	
	if( !strcmp(key->GetName(),"Tracker"    ) ){
	    TRK__ok = true;
	    TTree *T = (TTree*)f->Get("Tracker");
	    for(Int_t i=0; i<T->GetListOfBranches()->GetEntries(); i++){
		TString name = T->GetListOfBranches()->At(i)->GetName();
		if( !name.CompareTo("TrkLevel1") )TRK_L1__ok=true;
	    };
	};
	
    };
    
    lk->Delete();
    f->Close();
    
    Bool_t FLAG = true;
    if(!RUN__ok) {
	cout << "File: "<< f->GetName() <<" discarded ---- Missing RunInfo tree"<< endl; return false;
//	FLAG = false;
    };
    if(CAL && !CAL__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing Calorimeter tree"<< endl; return false;
//	FLAG = false;
    };
    if(TRK && !TRK__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing Tracker tree"<< endl; return false;
//	FLAG = false;
    };
    if(TRK_L1 && !TRK_L1__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing Tracker Level1 Branch"<< endl; return false;
//	FLAG = false;
    };
    if(TRG && !TRG__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing Trigger tree"<< endl; return false;
//	FLAG = false;
    };
    if(TOF && !TOF__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing ToF tree"<< endl; return false;
//	FLAG = false;
    };
    if(S4 && !S4__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing S4 tree"<< endl; return false;
//	FLAG = false;
    };
    if(ND && !ND__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing ND tree"<< endl; return false;
//	FLAG = false;
    };
    if(AC && !AC__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing AC tree"<< endl; return false;
//	FLAG = false;
    };
    if(ORB && !ORB__ok){
	cout << "File: "<< f->GetName() <<" discarded ---- Missing ORB tree"<< endl; return false;
//	FLAG = false;
    };
    
    return FLAG;
	
};