/** gpcrParser.c - Parses transmembrane cooridnates, outputs to xml file. */

/* Copyright (C) 2011 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
#include "common.h"
#include "memalloc.h"
#include "dystring.h"


/** Method prototypes */
void catSeqFile(FILE* outfile, char* filename);
void getTransFromFile(FILE* infile, char *path);
FILE* createXMLFile(char* proteinID, char *path);
void populateXMLFile(FILE *outfile, int tmNumber, char *proteinID, char *path);
void addCoordinatesToXMLFile(FILE *outfile, int start, int end, char* mapTo, int count);
void finishXMLFile(FILE *outfile, char *proteinID, int seqLength);
void usage(char **argv);

void usage(char **argv)
{
   if(argv[1] == NULL) 
        {
        errAbort(
          "gpcrParser - Create xml files for gpcr snakeplots.\n"
          "usage:\n   gpcrParser TMHMMresult.htm [path]\n"
          "    The first parameter is the html output from www.cbs.dtu.dk\n"
          "    Path is the working directory holding the seq files needed to\n"
          "    create the xml files. The xml files will be created in the path location.\n"
          "    If no path location is entered, the seq files should be in your cwd\n"
           );
         }
}

void catSeqFile(FILE* outfile, char* filename)
/** Copies contents of one file to another file */
{
FILE* infile;
char* line = NULL;
infile = mustOpen(filename, "r");
     while( (line = readLine(infile))  != NULL )
     {
     fprintf(outfile, "\t\t%s\n", line);
     freeMem(line);
     }
carefulClose(&infile);
}

void finishXMLFile(FILE *outfile, char *proteinID, int seqLength)
/** Add the closing lines to the file */
{
fprintf(outfile, 
   "\t\t\n</secondary-structure>\n\n\t</protein>\n\n\t<diagram>\n\n\t\t<colors>\n\n"
   "\t\t\t<define color=\"white\" red=\"255\" green=\"255\" blue=\"255\"/>\n\n"
   "\t\t\t<define color=\"red\" red=\"255\" green=\"0\" blue=\"0\"/>\n\n"
   "\t\t\t<color-scheme name=\"GPCRDB\">\n\n"
   "\t\t\t\t<residue-background color=\"white\"/>\n\n\t\t\t</color-scheme>\n\n"
   "\t\t\t<residue-color position=\"20\" color=\"white\"/>\n\n"
   "\t\t\t<residue-color position=\"21\" color=\"red\"/>\n\n"
   "\t\t</colors>\n\n\t\t<elipses>\n\n"
   "\t\t\t<exclude residueRange=\"1-%d\" />\n\n"
   "\t\t\t<include residueRange=\"1-1\"/>\n\n\t\t</elipses>\n\n"
   "\t\t<output>\n\n\t\t\t<image format=\"GIF\" filename=\"%s.gif\"/>\n\n"
   "\t\t\t<page template=\"H:\\dev\\crover\\nrdb\\sample-template.xsl\""
   "filename=\"gpcr-rbdg-out.xml\" diagram-name=\"gpcr\"/>\n\n"
   "\t\t\t<image-map filename=\"%s.map\"/>\n\n\t\t</output>\n\n"
   "\t</diagram>\n\n</rbde-diagram>", 
    seqLength-1, proteinID, proteinID
       );
}

void addCoordinatesToXMLFile(FILE *outfile, int start, int end, char* mapTo, int count)
/** Add each coordinate for the gpcr */
{
fprintf(outfile, "\t\t\t");
   if( sameString(mapTo, "TM") )
       {
       fprintf(outfile, 
           "<segment start=\"%d\" end=\"%d\" mapto=\"%s%d\" />\n", 
           start, end, mapTo, count);
       }
       else
       {
       fprintf( outfile, 
           "<segment start=\"%d\" end=\"%d\" mapto=\"%s\" />\n",
           start, end, mapTo );
       }
}

void populateXMLFile(FILE *outfile, int tmNumber, char *proteinID, char *path)
/** Adds the number of TM helices and sequence the the xml file */
{
struct dyString *filename = dyStringNew(128);
    if(path == NULL)
        dyStringPrintf(filename, "%s.seq", proteinID);
    else
        dyStringPrintf(filename, "%s%s.seq", path, proteinID);
fprintf(outfile, 
    "%d\" id-prefix=\"TM\" nterm-id=\"N-term\" cterm-id=\"C-term\" direction=\"down\" />\n\n"
    "\t</diagram-layout>\n\n\t<protein>\n\n\t\t<name>%s</name>\n\n\t\t<residue-codes>\n\n", 
    tmNumber, proteinID
       );
catSeqFile(outfile, filename->string);
fprintf(outfile, "\n\n\t\t</residue-codes>\n\n\t\t<secondary-structure>\n\n");
dyStringFree(&filename);
}

FILE* createXMLFile(char* proteinID, char *path)
{
FILE* outfile;
struct dyString *filename = dyStringNew(128);
    if(path == NULL)
        dyStringPrintf(filename, "%s.xml", proteinID);
    else
        dyStringPrintf(filename, "%s%s.xml", path, proteinID);
outfile = mustOpen(filename->string, "w");
fprintf(outfile, 
    "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\n\n"
    "<rbde-diagram xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\""
    " xsi:noNamespaceSchemaLocation=\"H:\\dev\\crover\\xml\\xsd\\residue-based-diagram.xsd\">\n\n"
    "\t<diagram-layout>\n\n\t\t<tm-bundle tm-number=\""
       );
dyStringFree(&filename);
return outfile;
}

void getTransFromFile(FILE* infile, char *path)
{
FILE* outfile = NULL;
int start, end, tmNumber, count, seqLength;
char *line, *token;
struct dyString *proteinID = dyStringNew(24);
start = end = tmNumber = count = seqLength = 0;
while( ( line  = readLine(infile) ) != NULL )
    {  /*grab the protein ID after each <PRE> tag*/
    while( (token = nextWord(&line)) != NULL )
        {
   	    if( sameString(token,"<PRE>#"))
                {  /*create a new xml file*/
                token = nextWord(&line);
       	        dyStringAppend(proteinID, token);
                token = lastWordInLine(line);
                seqLength = atoi(token);
                }
            if( sameString(token,"predicted") )
                {   /*grab the number of transmembrane helices*/
                token = lastWordInLine(line);
                tmNumber = atoi(token);
                    if(tmNumber > 0)
                        {
                        outfile = createXMLFile(proteinID->string, path);
                        populateXMLFile(outfile, tmNumber, proteinID->string, path);
                        }
                }
            if( sameString(token,"</PRE>") )
                {  /*close the xml file*/
                carefulClose(&outfile);
  	        dyStringClear(proteinID);
                count = 0;
                }
            if( sameString(token,"TMhelix") )
                {
                    if( (token = nextWord(&line)) != NULL )
                         {  /*get the start*/
                         start = atoi(token);
                              if( (token = nextWord(&line)) != NULL  )
                                  end = atoi(token);
                         }
                    if( count == 0)
                        addCoordinatesToXMLFile(outfile, 1, start-1, "N-term", count);
                    count++;
                    addCoordinatesToXMLFile(outfile, start, end, "TM", count);
                    if( count == tmNumber && outfile != NULL )
                        {
                        addCoordinatesToXMLFile(outfile,end+1,seqLength,"C-term",count);
                        finishXMLFile(outfile, proteinID->string, seqLength);
                        }
                }
        } /*end inner while*/
    }   /*end outer while*/
    freeMem(line);
    dyStringFree(&proteinID);
}

int main(int argc, char** argv)
{
FILE *infile;
struct dyString *path = dyStringNew(128);
usage(argv);
    if(argv[2] != NULL)
        {
        dyStringAppend(path, argv[2]);
        if(!endsWith(path->string, "/"))
            dyStringAppend(path, "/");
        }
infile = mustOpen(argv[1], "r");
getTransFromFile(infile, path->string);
carefulClose(&infile);
dyStringFree(&path);
return 0;
}