/**
* mark all places that are reachable
*/
void pullAndMark(vector<string> &mark, Position b, Position p)
{
if (outOfBoundary(mark, p) || outOfBoundary(mark, b)) {
return;
}
if (mark[b.x][b.y] == 'V')
return;
if (isWall(mark[b.x][b.y]) || isWall(mark[p.x][p.y]))
return;
mark[b.x][b.y] = 'V';
for (int i = 0; i < 4; ++i) {
Position newbox(b.x + direction[i][0], b.y + direction[i][1]);
Position newperson(newbox.x + direction[i][0], newbox.y + direction[i][1]);
pullAndMark(mark, newbox, newperson);
}
}
void importlinkagepedigree (void)
{
char minibuf[NAMESIZE];
individual *ind, *ind2;
// IDlist *idlist;
markerlist *marker;
namelist *nl;
quanttrait *qt;
int i, families, persons, nmarkers, ntraits, code;
printf("Number of markers in file: ");
InputLine(buf, BUFFERSIZE);
nmarkers = atoip(buf);
printf("Number of traits in file : ");
InputLine(buf, BUFFERSIZE);
ntraits = atoip(buf);
printf ("Name of linkage pedigree file to input: ");
InputLine(buf, BUFFERSIZE);
cfopen (buf,"r");
getbuf ();
persons = 0;
families = 0;
if (options->Index[O_CONVERTLINKAGEID])
printf("WARNING: ID's are converted from number to fam-number\n");
while (buf[0] != EOF)
{
// If empty line then read next line
if (!buf[0] || !strpbrk(buf, "0123456789"))
{
getbuf ();
continue;
}
ind = newperson ();
persons++;
ind->globalid = persons;
ind->localid = persons;
strcpy(ind->pedigree, igetstr (buf));
strcpy(ind->id, getstr ());
strcpy(ind->tmpstr1, getstr ()); // Father ID
strcpy(ind->tmpstr2, getstr ()); // Mother ID
// If conversion of IDs
if (options->Index[O_CONVERTLINKAGEID]) {
sprintf(minibuf,"%s-%s", ind->pedigree,ind->id);
strcpy(ind->id,minibuf);
sprintf(minibuf, "%s-%s", ind->pedigree,ind->tmpstr1);
strcpy(ind->tmpstr1,minibuf);
sprintf(minibuf, "%s-%s", ind->pedigree,ind->tmpstr2);
strcpy(ind->tmpstr2,minibuf);
}
switch (geti ())
{
case 1 : ind->sex = S_MALE; break;
case 2 : ind->sex = S_FEMALE; break;
default : ind->sex = S_UNKNOWN;
}
// atof(getstr());
for (i = 0 ; i<nmarkers; i++)
{
marker = cmalloc (sizeof (markerlist));
memset (marker,0,sizeof (markerlist));
marker->allele1 = geti();
marker->allele2 = geti ();
addlist(&ind->marker, marker);
}
// Reading traits
for (i = 0 ; i<ntraits; i++)
{
qt = cmalloc (sizeof (quanttrait));
memset (qt,0,sizeof (quanttrait));
ReadATrait(qt);
addlist(&ind->qttrait,qt);
}
// printf("\n");
getbuf ();
}
fclose (F);
printf ("%d persons from %d pedigree(s) read\n",
persons, numberofpedigrees());
code = 0;
// Should now fix fathers and mothers
forind
{
ind->father = findperson(ind->tmpstr1);
ind->mother = findperson(ind->tmpstr2);
// if a person has a father and a mother, then add the
// person to the parents lists
if (ind->father && ind->mother)
{
adduniqueidlist (&ind->father->offspring, ind);
adduniqueidlist (&ind->father->mate, ind->mother);
adduniqueidlist (&ind->mother->offspring, ind);
adduniqueidlist (&ind->mother->mate,ind->father);
}
else if (ind->father || ind->mother) // The person has only one parent
{
code = 1;
sprintf(buf2, "%s has only one parent in pedigree file\n", ind->id);
WriteErrorMsg(buf2);
}
}
if (code)
printf("ERROR: A least one parent not found in pedigree file\n");
// Fixing sibs
forind
{
for (ind2 = ind->next; ind2; ind2 = ind2->next)
{
// If same father or mother then add to list of both
if (((ind->father == ind2->father) && (ind->father)) ||
((ind->mother == ind2->mother) && (ind->mother)))
{
adduniqueidlist(&ind->sib, ind2);
adduniqueidlist(&ind2->sib, ind);
}
}
}
// Have now read the file and made the dataset
// Should fix the missing parts
// This part definately needs some error checking
// First set the marker names:
for (i=1; i<=nmarkers; i++)
{
nl = cmalloc (sizeof (namelist));
memset (nl,0,sizeof (namelist));
sprintf(nl->name, "Marker %d",i);
addlist(&markernames, nl);
}
// Then add trait names
for (i=1; i<=ntraits; i++)
{
nl = cmalloc (sizeof (namelist));
memset (nl,0,sizeof (namelist));
sprintf(nl->name, "Trait %d",i);
addlist(&traitnames, nl);
}
InitializeFrequencies(nmarkers);
// Initialize order and distances
order = ivector(1,nmarkers);
invorder = ivector(1,nmarkers);
distance = vector(1, nmarkers-1);
for (i=1; i<=nmarkers; i++)
{
order[i] = i;
invorder[i] = i;
}
for (i=1; i<nmarkers; i++)
distance[i] = InverseMapFunction(0.1);
}