int main(int argv, char** argc)
{
File* hw;
Marker* markers;
Marker* it;
const char* markersPath;
const char* hwPath;
FILE* outFile;
if (argv != 3)
{
printf("Usage: %s markers homeworks\n", argc[0]);
printf("markers: Markers file path.\n");
printf("files: HW files path.\n");
exit(EXIT_FAILURE);
}
markersPath = argc[1];
hwPath = argc[2];
markers = readMarkers(markersPath);
srand(time(NULL));
rand();
rand();
hw = makeFileList(hwPath);
markers = distribute(hw, markers);
markers = sortMarkers(markers, numMarkers(markers));
for (it = markers; it; it = it->next)
{
it->files = sortFiles(it->files, numFiles(it->files));
}
printMarkers(markers);
for (it = markers; it; it = it->next)
{
free((void*)it->name);
}
freeMarkers(markers);
freeFiles(hw);
return 0;
}
void writeOut(FILE *sto)
/* write out STS marker information to a file */
{
struct hashEl *mapList = NULL, *mapEl = NULL, *stsList = NULL, *stsEl = NULL;
struct hashEl *aliasList = NULL, *aliasEl = NULL;
struct zfin *zfEl = NULL;
struct sts *sts = NULL, *s = NULL, *stsVal = NULL;
struct alias *aliases = NULL;
struct aliasId *aliasId = NULL;
char *alias = NULL, *id = NULL, *al = NULL, *addName = NULL, *newName = NULL;
boolean found = FALSE, aliasFound = FALSE;
int i = 0, j = 0;
char **aliasNames = NULL;
mapList = hashElListHash(zfinMarkerHash);
stsList = hashElListHash(stsHash);
aliasList = hashElListHash(aliasByNameHash);
fprintf(sto, "UniSTS ID\tUniSTS Accession\tUniSTS Name\tZFIN name\tZFIN ID\tUniSTS Alias\tZFIN Alias\tZFIN Gb Acc\tPanel\tChrom\tPosition\tUnits\n \n");
if (mapList != NULL)
{
/* walk through list of hash elements */
for (mapEl = mapList; mapEl != NULL; mapEl = mapEl->next)
{
found = FALSE;
zfEl = (struct zfin *)mapEl->val;
/* check aliases in all combinations */
/* if this name is a key in the stsHash */
if ((sts = hashFindVal(stsHash, mapEl->name)) != NULL)
found = TRUE;
/* check by ZFIN alias instead */
else if ((zfEl->zfAlias != NULL) && (!found))
{
alias = cloneString(zfEl->zfAlias);
touppers(alias);
stsVal = NULL;
if ((stsVal = hashFindVal(stsHash, alias)) != NULL)
{
found = TRUE;
sts = stsVal;
}
}
/* check stsHash for name with extension or remove extension from zfin name */
else if (!found)
{
sts = (struct sts *)addExtensionAndSearch(mapEl->name, stsHash, FALSE);
if (sts != NULL)
found = TRUE;
}
/* check if this is an alias in alias hash keyed by alias names */
/* need to get list of aliases in all cases but if sts ID not found */
/* can find it here */
/* mapEl->name is in upper case, so get lower case, zfinEl->name */
aliasFound = FALSE;
if (((aliasId = hashFindVal(aliasByNameHash, mapEl->name))!=NULL) ||
((aliasId = hashFindVal(aliasByNameHash, zfEl->name))!=NULL))
aliasFound = TRUE;
else /* alias is not found, try different extensions */
{
aliasId = (struct aliasId *)addExtensionAndSearch(zfEl->name, aliasByNameHash, TRUE);
if (aliasId != NULL)
aliasFound = TRUE;
}
if (!found && sts != NULL)
sts = NULL;
/* all UniSTS IDs have an entry in sts and alias files so the */
/* UniSTS ID in the sts found will also be in aliases IDs list */
if (aliasFound)
{
/* go through each ID in the ids array and get sts struct */
/* and the list of aliases */
for (j = 0; j < MAXIDS; j++)
{
if (aliasId->ids[j] != NULL)
{
/* get sts and alias names */
sts = hashFindVal(stsIdHash, aliasId->ids[j]);
aliases = hashFindVal(aliasHash, aliasId->ids[j]);
printMarkers(sto, sts, zfEl, aliases->names);
}
}
}
else
printMarkers(sto, sts, zfEl, NULL);
}
}
hashElFreeList(&mapList);
hashElFreeList(&stsList);
hashElFreeList(&aliasList);
}
