// predict-2nd.cc
// Kevin Karplus
// 22 Nov 1995

// This main program is a very simple shell for the commands in the
// *Commands.cc files

#include "Command/Command.h"
#include "Command/HelpCommand.h"
#include "EqualStrings/EqualStrings.h"
#include "Alphabet/Alph.h"
#include "NamedClass/NameToPtr.h"
#include "PrintInColumns/PrintInColumns.h"
#include "Alphabet/MultiFeatureAlphabet.h"
#include "Alphabet/FeatureRangeAlphabet.h"
#include "Alphabet/CombinedAlphabet.h"
#include "Alphabet/GaussianAlphabet.h"

#include "SeqWeight.h"		// only needed for Help command
#include "LearningParam.h"	// only needed for Help command
#include "InterfaceDescription.h" // only needed for Help command
#include "Globals.h"
#include "Regularizer/all-reg.h"

#include <sys/resource.h>
#include <unistd.h>

static DirichletReg DummyToEnsureLoading;
class NeuralLayer;


static int ExtraHelp(istream&in, const char*word, ostream&log_file)
{
    
    if (EqualStrings(word, "alphabets", 1))
    {   for (int i=0; i<Alphabet::num_alphabets(); i++)
    		log_file << Alphabet::alphabet_list(i)->name() << "\n"; 
	return 1;
    }
    
    if (EqualStrings(word, "SequenceWeightObjects", 1))
    {   PrintNames(log_file, SequenceWeightObject::weighter_table());
	return 1;
    }

    if (EqualStrings(word, "LearningParams", 1))
    {   PrintNames(log_file,  LearningParam::command_table());
	return 1;
    }

    if (EqualStrings(word, "IFcommands" , 1))
    {   PrintNames(log_file,  InterfaceDescription::command_table());
	return 1;
    }
    

    const Alphabet* al = Alphabet::name_to_alphabet(word,ZeroIfNew);
    if (al)
    {   al->describe(log_file);
	return 1;
    }
    log_file << "No help available for " << word << "\n"
	    << "Try 'help alphabets' for list of alphabets\n"
	    << "or 'help SequenceWeightObjects' for list of SequenceWeightObject\n"
	    << "or 'help LearningParams' for list of learning parameters\n"
	    << "or 'help IFCommands for list of InterfaceDescription commands\n"
	    << "or 'help command' for list of commands\n"
	    << "or 'help' with no arguments for more options\n"
	    << "Note: alphabet recognition is currently case-sensitive.\n";
    return 1;
}

void EstInitHelp(void)
{
    UnknownHelpFunction=ExtraHelp;
    AddHelpCommandTable();
    
    AddHelpCommandTable(IdObject::lookup_table(), 
		"<name of named class> (Regularizer, Alphabet, ...)");
    
    AddHelpCommandTable(SequenceWeightObject::weighter_table(),
			"<name of SequenceWeightObject>");
    
    LearningParam::init_command_table();
    AddHelpCommandTable(LearningParam::command_table(),
		"<name of learning parameter>");
    
    InterfaceDescription::init_command_table();
    AddHelpCommandTable(InterfaceDescription::command_table(),
		"<name of interface description command>");
}

int
main(int argc, const char** argv)
{
    gettimeofday(&(Globals::StartWallTime),0);
    struct rusage resources;
    getrusage(RUSAGE_SELF, &resources);
    Globals::StartCpuTime = resources.ru_utime;

    int load_default_alphabets=1;
    
    for (int i=1; i<argc; i++)
    {   if (EqualStrings(argv[i], "-noalph", 1))
    	{    load_default_alphabets=0;
	}
	else
	{    cerr << "Error: unrecognized argument " << argv[i] 
		<< " for program " << argv[0] << "\n" << flush;
	}
    }

    // to ensure MultiFeatureAlphabet is linked
    // to ensure FeatureRangeAlphabet is linked
    // to ensure GaussianAlphabet is linked
    // to ensure CombinedAlphabet is linked
    assert(FeatureRangeAlphabet::classID() !=  MultiFeatureAlphabet::classID());
    assert(FeatureRangeAlphabet::classID() !=  GaussianAlphabet::classID());
    assert(CombinedAlphabet::classID() !=  GaussianAlphabet::classID());
    

    if (load_default_alphabets)
    {	Alphabet::set_default(Alph::ExtAA());
    }
    EstInitHelp();

    Command::read_script(cin, cout, &cout);    
    Globals::clear_all();
    
    // throw out the alphabets to eliminate leak reports
    //	Note: have to cast away const
    NameToPtr * alpha_table = const_cast<NameToPtr*>(Alphabet::name_to_alphabet_table());
    alpha_table->apply_all(&DeleteNamedObject );
    delete alpha_table;
    return 0;
}

//CHANGE LOG:
// 21 July 1997 Keivn Karplus
//	Copied from estimate-dist and added EHL alphabet
// 12 March 1998 Kevin Karplus
//	Moved Globals cleanup to Globals.cc
// 30 March 1998 Kevin Karplus
//	Added DSSPAlphabet
// 2 Apr 1998 Kevin karplus
//	Added EHTLAlphabet and modified EHL so it could read
//		DSSP alphabet strings, avoiding need for derived EHL files.
// 20 Apr 1998  Melissa Cline
//      Added RBK alphabet to handle alignment columns with respect
//      to alignment trimming.  The alphabet represents the three
//      classes of alignment columns and the action to be taken on them:
//      Keep = keep it in the alignment; Remove = trim it from the
//      alignment; Borderline = either trimming or keeping would be reasonable.
// 7 June 1998 Kevin Karplus
//	Modified DSSP, EHL, and EHTL alphabets to make 'C' for coil be
//	last character, with 'L' just as alias.  This should not affect
//	any currently input files, but will change output to using C,
//	as desired for CASP3 format.
// 25 March 1999 Kevin Karplus
//	updated to use improved Alphabet class:
//	improved help slightly, and now load alphabets from file
// 21 May 2004 Sol Katzman
//	Added time functions
// 23 June 2005 Kevin Karplus
//	Eliminated preloading alphabets, other than standard ones from
//	Alph class
// 23 June 2005 Kevin Karplus
//	Added PrintNames() calls for listing SequenceWeightObjects
//	and LearningParams
// Thu Jul 16 13:31:38 PDT 2009 Kevin Karplus
//	Improved 'help' print with illegal argument.
//	Added InterfaceDescription commands to help.
// Sat Aug 22 11:58:20 PDT 2009 Kevin Karplus
//	Added asserts to make sure that Alphabet derived classes are
//	linked in.