// Globals.cc
// Kevin Karplus
// 22 Nov 1995

#include <fstream>
#include <sys/resource.h>	// for getrusage

#include "Input/Input.h"
#include "NamedClass/NameToPtr.h"
#include "Regularizer/BackgroundProbs.h"
#include "gen_sequence/GenSequence.h"

#include "Globals.h"
#include "TrainSet.h"
#include "InterfaceDescription.h"
#include "NeuralNet.h"
#include "NetActivation.h"
#include "NetQuality.h"
#include "OneChain.h"

vector<NeuralNet *>Globals::NNs;
vector <bool> Globals::FreezeTheseColumns;
vector <bool> Globals::ChangeTheseColumns;

TrainSet *Globals::training= 0;
TrainSet *Globals::cross_training= 0;
TrainSet *Globals::testing= 0;
TrainSet *Globals::predicting= 0;
TrainSet *Globals::which_set_to_add_to=predicting;

NameToPtr Globals::BackgroundProbsByName(97);

vector <OneChain *> Globals::design_chains;

GenSequence *Globals::SequenceGenerator=NULL;

struct timeval Globals::StartWallTime;
struct timeval Globals::StartCpuTime;

ofstream* Globals::ReportSequenceWeightsTo=0;

ofstream* Globals::ReportNetQualityForTrainTo=0;
ofstream* Globals::ReportNetQualityForCrossTrainTo=0;
ofstream* Globals::ReportNetQualityForTestTo=0;

ofstream* Globals::ReportNetQualityForTestChainTo=0;
ofstream* Globals::ReportNetQualityForTrainChainTo=0;
ofstream* Globals::ReportNetQualityForCrossTrainChainTo=0;

ofstream* Globals::ReportUnitUsageTo=0;
ofstream* Globals::ReportQvsPhatTo=0;

void Globals::clear_all(void)
{
    clear_design_chains();
    if (ReportSequenceWeightsTo)
    {	ReportSequenceWeightsTo->close();
	delete ReportSequenceWeightsTo;
	ReportSequenceWeightsTo =0;
    }
    if (ReportNetQualityForTrainTo)
    {	ReportNetQualityForTrainTo->close();
	delete ReportNetQualityForTrainTo;
	ReportNetQualityForTrainTo =0;
    }
    if (ReportNetQualityForCrossTrainTo)
    {	ReportNetQualityForCrossTrainTo->close();
	delete ReportNetQualityForCrossTrainTo;
	ReportNetQualityForCrossTrainTo =0;
    }
    if (ReportNetQualityForTestChainTo)
    {	ReportNetQualityForTestChainTo->close();
	delete ReportNetQualityForTestChainTo;
	ReportNetQualityForTestChainTo =0;
    }
    if (ReportNetQualityForTrainChainTo)
    {	ReportNetQualityForTrainChainTo->close();
	delete ReportNetQualityForTrainChainTo;
	ReportNetQualityForTrainChainTo =0;
    }
    if (ReportNetQualityForCrossTrainChainTo)
    {	ReportNetQualityForCrossTrainChainTo->close();
	delete ReportNetQualityForCrossTrainChainTo;
	ReportNetQualityForCrossTrainChainTo =0;
    }
    if (ReportUnitUsageTo)
    {   ReportUnitUsageTo->close();
        delete ReportUnitUsageTo;
	ReportUnitUsageTo=0;
    }
    if (ReportQvsPhatTo)
    {   ReportQvsPhatTo->close();
        delete ReportQvsPhatTo;
	ReportQvsPhatTo=0;
    }
    delete training;	training=0;
    delete cross_training;	cross_training=0;
    delete testing;	testing=0;
    
    for(int i=NNs.size()-1; i>=0; i--)
    {   NeuralNet *NN = NNs[i];
	if (NN != NULL)
    	{    // Although NeuralNet does not own the Regularizers in the
	    // InterfaceDescriptions, there are no other pointers left when
	    // clearing all Globals, so let's delete them now.
	    // This may have to change if we start registering all Regularizers
	    // and sharing them.
	    for (int i=NN->num_interfaces()-1; i>=0; i--)
	    {   NN->interface(i)->delete_regularizers();
	    }
	}
	delete NN;	NNs[i]=NULL;
    }
}

void Globals::clear_design_chains(void)
{   for (unsigned int c=0; c<design_chains.size(); c++)
    {	if (design_chains[c]) 
	{   delete design_chains[c];
	    design_chains[c]= NULL;
	}
    }
    design_chains.clear();
}


double Globals::elapsed_seconds(void)
{
    struct timeval wall_time;
    gettimeofday(&wall_time,0);
    return (wall_time.tv_sec-Globals::StartWallTime.tv_sec)
	+ (wall_time.tv_usec-Globals::StartWallTime.tv_usec)*1.e-6;

}

double Globals::user_seconds(void)
{   struct rusage resources;
    getrusage(RUSAGE_SELF, &resources);
    return (resources.ru_utime.tv_sec - Globals::StartCpuTime.tv_sec) +
    	 (resources.ru_utime.tv_usec- Globals::StartCpuTime.tv_usec)*1.e-6;

}

bool Globals::add_neural_net(NeuralNet *n)
{   if (NNs.size()>0)
    {   // check for compatibility of input interfaces
    	InterfaceDescription* old_ifd=Globals::nn(0)->interface(0);
	InterfaceDescription* new_ifd=n->interface(0);
	if (!new_ifd->is_compatible(old_ifd, 
			Globals::nn(0)->name(), n->name(), &cerr))
	    return 0;
    }
    
    NNs.push_back(n);
    return 1;
}    

const BackgroundProbs* Globals::background_probs(
			const AlphabetTuple*al, OptionIfNew opt) 
{    return dynamic_cast<const BackgroundProbs*>
	(BackgroundProbsByName.FindOldName(al->name(),opt));
}




void Globals::initialize_freeze(void)
{   assert(design_chains.size()>0 && design_chains[0]!=NULL);
    FreezeTheseColumns.assign(design_chains[0]->num_cols(), false);
}
void Globals::initialize_change(void)
{   assert(design_chains.size()>0 && design_chains[0]!=NULL);
    ChangeTheseColumns.assign(design_chains[0]->num_cols(), false);
}

// CHANGE LOG:
// 21 July 1997 Kevin Karplus
//	copied from estimat-dist and removed everything related to
//	TestSet or regularizer stack.
// 23 July 1997 Kevin Karplus
//	modified open_input to try gunzipping file if the file
//	doesn't exist but the file.gz does
// 14 Sept 1997 Kevin Karplus
//	FINALLY fixed open_input to use popen and zcat if need to gunzip
// 21 March 1998 Kevin Karplus
//	Added clear_all() to clean up all globals.
// 22 March 1998 Kevin Karplus
//	Repaired damage Christian did to open_input, by providing
//	option of adding prefix and suffix or not.
// 2 May 1998 Kevin Karplus
//	Moved filename handling to Filenames.cc
// 20 July 1998 Kevin Karplus
//	Added ReportnetQualityFor...ChainTo variables.
// 21 May 2004 Sol Katzman
//	Added time functions
// Mon Jun 13 03:23:15 PDT 2005 Kevin Karplus
//	Picked up Jes Frellsen's addition of "design_chain"
// Sat Jun 18 10:54:12 PDT 2005 Kevin Karplus
//	Added BackgroundProbsByName
//	Removed some includes that were no longer needed.
// Sat Jun 18 21:57:46 PDT 2005 Kevin Karplus
//	Added background_probs()
// Sat Jun 25 20:38:13 PDT 2005 Kevin Karplus
//	Moved add_neural_net from Globals.h and added some
//	consistency checks.
// Sat Jul  9 04:36:31 PDT 2005 Kevin Karplus
//	Changed design_chain to design_chains
//	Added clear_design_chains
// Thu Jul 14 22:03:04 PDT 2005 Kevin Karplus
//	Added FreezeTheseColumns
// Thu Jul 21 17:55:20 PDT 2005 Kevin Karplus
//	added SequenceGenerator
// Sun Feb  5 02:41:02 PST 2006 Kevin Karplus
//	added ChangeTheseColumns