static void
delete_membership_internal(int conf, int uid)
{
struct membership_store *mb, *omb;
struct person_store *pp;
if ((pp = findperson(uid)) == 0)
return; /* Nothing in cache */
if (pp->confs) {
free(pp->confs);
pp->confs = NULL;
}
if (pp->next == 0)
return;
if (pp->next->mid == conf) {
mb = pp->next->next;
free(pp->next);
pp->next = mb;
return;
}
omb = pp->next;
mb = pp->next->next;
while (mb) {
if (mb->mid == conf) {
omb->next = mb->next;
free(mb);
return;
}
omb = mb;
mb = mb->next;
}
}
individual *newperson (void)
{
individual *ind;
ind = cmalloc (sizeof (individual));
memset (ind,0,sizeof (individual));
ind->sex = S_UNKNOWN;
if (findperson(ind->id))
{
printf("Not possible to create a new person as ID already exists\n");
return findperson(ind->id);
}
else
addlist (&individuals,ind);
return ind;
}
struct rk_membership *
rk_membership(u_int32_t uid, u_int32_t conf)
{
struct membership_store *mb;
struct rk_membership *m;
struct person_store *pp;
int len;
/* First, force the user into the cache */
if (rk_persinfo(uid) == NULL)
return NULL; /* The person do not exist, or something */
pp = findperson(uid);
if (pp->next) {
mb = findmember(conf, pp->next);
if (mb)
return &mb->member;
}
/* No, we failed cache search. Fetch from server. */
if (send_reply("98 %d %d\n", uid, conf)) {
komerr = get_int();
get_eat('\n');
return NULL;
}
mb = calloc(sizeof(struct membership_store), 1);
m = &mb->member;
m->rm_position = get_int();
read_in_time(&m->rm_last_time_read);
m->rm_conference = get_int();
m->rm_priority = get_int();
m->rm_last_text_read = get_int();
len = m->rm_read_texts_len = get_int();
if (len) {
int *txts, j;
txts = malloc(sizeof(int) * len);
get_accept('{');
for (j = 0; j < len; j++)
txts[j] = get_int();
get_accept('}');
m->rm_read_texts_val = txts;
} else
get_accept('*');
m->rm_added_by = get_int();
read_in_time(&m->rm_added_at);
m->rm_type = get_int();
mb->mid = m->rm_conference;
mb->next = pp->next;
pp->next = mb;
get_accept('\n');
return m;
}
/*
* XXX - should remember the membership structs also.
*/
u_int32_t *
rk_memberconf(u_int32_t uid)
{
struct person_store *ps;
int i, nconfs;
ps = findperson(uid);
if (ps == 0) {
if (rk_persinfo(uid) == NULL)
return NULL;
ps = findperson(uid); /* Cannot fail here */
if (ps == 0)
printf("EEEK! Person %d finns inte!\n", uid);
}
if (ps->confs == NULL) {
if (send_reply("46 %d 0 65535 0\n", uid)) {
komerr = get_int();
get_eat('\n');
return NULL;
}
nconfs = get_int();
ps->confs = calloc(sizeof(u_int32_t), nconfs+1);
if (nconfs) {
get_accept('{');
for (i = 0; i < nconfs; i++) {
struct rk_time t;
read_in_time(&t);
ps->confs[i] = get_int();
get_int();get_int();get_int();get_accept('*');
}
get_accept('}');
} else
get_accept('*');
get_accept('\n');
}
return ps->confs;
}
void
newname(int uid)
{
struct person_store *pp;
struct get_conf_stat_store *walker;
pp = findperson(uid);
if (pp == 0)
return;
walker = findconf(uid);
if (walker == 0)
return;
free(pp->person.rp_username);
pp->person.rp_username = strdup(walker->confer.rc_name);
}
static void
set_last_read_internal(int conf, int local)
{
struct membership_store *mb;
struct person_store *pp;
if ((pp = findperson(myuid)) == 0)
return; /* Nothing in cache */
if (pp->next) {
mb = findmember(conf, pp->next);
if (mb == 0)
return;
mb->member.rm_last_text_read = local;
if (mb->member.rm_read_texts_len) {
free(mb->member.rm_read_texts_val);
mb->member.rm_read_texts_val = NULL;
}
mb->member.rm_read_texts_len = 0;
}
}
/*
* Return the person struct.
*/
struct rk_person *
rk_persinfo(u_int32_t uid)
{
struct person_store *pp;
struct rk_person *p;
if ((pp = findperson(uid)))
return &pp->person;
if (send_reply("49 %d\n", uid)) {
komerr = get_int();
get_eat('\n');
return NULL;
}
pp = calloc(sizeof(struct person_store), 1);
pp->uid = uid;
p = &pp->person;
p->rp_username = get_string();
p->rp_privileges = get_int();
p->rp_flags = get_int();
read_in_time(&p->rp_last_login);
p->rp_user_area = get_int();
p->rp_total_time_present = get_int();
p->rp_sessions = get_int();
p->rp_created_lines = get_int();
p->rp_created_bytes = get_int();
p->rp_read_texts = get_int();
p->rp_no_of_text_fetches = get_int();
p->rp_created_persons = get_int();
p->rp_created_confs = get_int();
p->rp_first_created_local_no = get_int();
p->rp_no_of_created_texts = get_int();
p->rp_no_of_marks = get_int();
p->rp_no_of_confs = get_int();
get_accept('\n');
pp->nextp = gps;
gps = pp;
return p;
}
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);
}
