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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *\
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
**                                                                                 **
**                                                                                 **
**                                 E N S E M B L E                                 **
**                                                                                 **
**                                   Version 2.1                                   **
**                                                                                 **
**                                                                                 **
**                   Principal Investigator: Julie D. Forman-Kay                   **
**                                                                                 **
**                           Author:  Mickaël Krzeminski                           **
**                                                                                 **
**                               Date: November 2012                               **
**                                                                                 **
**                                                                                 **
*************************************************************************************
**                                                                                 **
**                                                                                 **
**   Copyright (C) The Hospital for Sick Children, 2001                            **
**                                                                                 **
**   Distribution of substantively modified versions of this module is prohibited  **
**  without the explicit permission of the copyright holder.                       **
**                                                                                 **
**   Any use of this work or derivative works in whole or in part for any          **
**  commercial purpose or for monetary gain is prohibited.                         **
**                                                                                 **
**                                                                                 **
**                                   NO WARRANTY                                   **
**   This software package is provided 'as is' without warranty of any kind,       **
**  expressed or implied.                                                          **
**                                                                                 **
**                                                                                 **
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
\* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

/*
   COMPILATION
                gcc -O3 -lm -o combine_csp combine_csp.c
*/

#include "Include/ens.h"


enum toolsPrograms TP = __COMBINE_CDP__;


int main (int argc, char *argv[])
{
    /***********************************************************\
    |*                                                         *|
    |*                                                         *|
    |*                  Variables declaration                  *|
    |*                                                         *|
    |*                                                         *|
    \***********************************************************/
    counter count;

    unsigned int nbInpFiles = 0;
    unsigned int maxcdpInpFileNames = 0;

    char *cdpOutFileName = NULL;
    char **cdpInpFileNames = NULL;
    char fileType[4] = {'\0'};

    FILE *ENSFile;

    /***********************************************************\
    |*                                                         *|
    |*                                                         *|
    |*             Arguments  reading and checking             *|
    |*                                                         *|
    |*                                                         *|
    \***********************************************************/
    if (argc<4) __USAGE__

    for (count=1; count<argc; count++)
    {
        if (!strcmp(argv[count], "-o"))
        {
            ++count;
            if (argc>count)
            {
                if ((ENSFile = fopen(argv[count], "r")) == NULL)
                {
                    if ((cdpOutFileName = malloc((strlen(argv[count]) + 1) * CHAR_SIZE)) == NULL)
                    {
                        _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
                        fatal_error("MEMORY", "create PDBListFileName variable");
                    }
    
                    strcpy(cdpOutFileName, argv[count]);
                }
                else
                {
                    fclose(ENSFile);

                    _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
                    fatal_error("EXIST_FILE", argv[count]);
                }
            }
            else
            {
                _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
                fatal_error("NO_ARGUMENT_FLAG", "-o");
            }
        }
        else if (!strcmp(argv[count], "-h"))
        {
            _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
            __USAGE__
        }
        else
        {
            // Testing the existence and relevance of each provided CDP file
            // Opening the file
            if ((ENSFile = fopen(argv[count], "r")) == NULL)
            {
                _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
                fatal_error("NO_FILE", argv[count]);
            }
        
            // Reading in the file type
            fread(&fileType, CHAR_SIZE, 3, ENSFile);
            fclose(ENSFile);

            if (!strcmp(fileType, "Cdp"))
            {
                if (nbInpFiles == maxcdpInpFileNames)
                {
                    maxcdpInpFileNames += 10;
                    if ((cdpInpFileNames = realloc(cdpInpFileNames, maxcdpInpFileNames*sizeof(char *))) == NULL)
                    {
                        _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
                        fatal_error("MEMORY", "re-instance cdpInpFileNames variable");
                    }
                }

                if ((cdpInpFileNames[nbInpFiles] = malloc((strlen(argv[count])+1)*CHAR_SIZE)) == NULL)
                {
                    _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
                    fatal_error("MEMORY", "instance cdpInpFileNames[nbInpFiles] variable");
                }

                strcpy(cdpInpFileNames[nbInpFiles], argv[count]);
                ++nbInpFiles;
            }
            else
            {
                _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
                fatal_error("CDP_FILE", argv[count]);
            }
        }
    }

    if ((cdpInpFileNames = realloc(cdpInpFileNames, nbInpFiles*sizeof(char *))) == NULL)
    {
        _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);
        fatal_error("MEMORY", "re-allocate cdpInpFileNames variable");
    }

    if (combineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles))
    {
        printf("Cleaning up... ");

        if (remove(cdpOutFileName) == -1)
        {
            printf("Impossible to remove the file %s! Abandonning.\n\n", cdpOutFileName);
        }
        else
        {
            printf("DONE\n\n");
        }

        _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);

        return 1;
    }

    // Releasing memory
    _cleanCombineCDP(cdpOutFileName, cdpInpFileNames, nbInpFiles);


    return 0;
}