/*
 * dcmerge.c		Jim Piper		23-09-86
 * (from comptype.old)
 *
 * Get chromosomes, dicentrics and composites from two files:
 *	(1) Original unsegmented file
 *	(2) File of segmented chromosomes (only) with biological typing.
 * Pass all these objects to standard output.
 */

#include <stdio.h>
#include <wstruct.h>
#include <chromanal.h>
#include <otypes.h>



main(argc,argv)
char **argv;
{
	struct chromosome *obj, *objl[MAXOBJS], *pobj, *readobj();
	struct chromplist *makechromplist();
	FILE *in1, *in2;
	int i,j,k,num,numorig,pnum,ccount[MAXOBJS];
	
	in1 = fopen(argv[1],"r");
	if (in1 == NULL) {
		fprintf(stderr,"Cannot open first file %s\n",argv[1]);
		exit(1);
	}
	in2 = fopen(argv[2],"r");
	if (in2 == NULL) {
		fprintf(stderr,"Cannot open second file %s\n",argv[2]);
		exit(1);
	}

	for (i=0; i<MAXOBJS; i++) {
		ccount[i] = 0;
		objl[i] = NULL;
	}

	num = 0;
	/* read original objects */
	while ((obj = readobj(in1)) != NULL) {
		if (obj->plist == NULL)
			obj->plist = makechromplist();
			obj->plist->number = num+1;
			obj->plist->otype = 5;	/* force noise */
		objl[num++] = obj;
	}
	numorig = num;
	/* read derived objects */
	while ((obj = readobj(in2)) != NULL) {
		num = obj->plist->number - 1;
		if (objl[num] != NULL)
			freeobj(objl[num]);
		objl[num] = obj;
	}

	/* count offspring, make parents composites */
	for (i=0; i<=num; i++) {
		obj = objl[i];
		if (obj != NULL) {
			if (obj->plist->pnumber > 0) {
				pnum = obj->plist->pnumber - 1;
				pobj = objl[pnum];
				if (pobj != NULL) {
					ccount[pnum]++;
					pobj->plist->history[1] = obj->plist->history[0];
					switch(obj->plist->history[0]) {
						case 1:
						case 8:
						default:
							pobj->plist->otype = 2;
							pobj->plist->Cotype = 2;
							break;
						case 2:
							pobj->plist->otype = 3;
							pobj->plist->Cotype = 3;
							break;
						case 4:
							pobj->plist->otype = 4;
							pobj->plist->Cotype = 4;
							break;
					}
				}
			}
		}
	}

	/* classify and write away */
	for (i=0; i<=num; i++) {
		obj = objl[i];
		if (obj != NULL) {
			if (obj->plist->otype <= 3) {
				writeobj(stdout,obj);
			}
		}
	}
}