/**
* Called by the GUI when a key event is received, triggers an action in the
* controller.
*
*/
void Controller::receive_gui_event(const char *event,const char *value) {
if(m_sleeping) return;
//TODO: Fix this total mess, refactor into switch, break conditions out into methods.
if(strcmp(event,"Sleep" ) == 0) event_sleep(event,value); else
if(strcmp(event,"KEYPRESS" ) == 0) m_powerup=true; else
if(strcmp(event,"TOTALTIMER" ) == 0) event_totaltimer(event,value); else
if(strcmp(event,"Save:PulseWidth") == 0) event_save_pulsewidth(event,value); else
if(strcmp(event,"Save:Calib" ) == 0) event_save_calibration(); else
if(strcmp(event,"Save:Becq" ) == 0) event_save_becq(event,value); else
if(strcmp(event,"Save:UTCOff" ) == 0) event_save_utcoff(event,value); else
if(strcmp(event,"Save:Time" ) == 0) save_time(); else
if(strcmp(event,"Save:Date" ) == 0) save_date(); else
if(strcmp(event,"Save:WarnCPM" ) == 0) save_warncpm(); else
if(strcmp(event,"Japanese" ) == 0) event_japanese(event,value); else
if(strcmp(event,"Never Dim" ) == 0) event_neverdim(event,value); else
if(strcmp(event,"English" ) == 0) event_english(event,value); else
if(strcmp(event,"CPM/CPS Auto" ) == 0) event_cpm_cps_auto(event,value); else
if(strcmp(event,"Geiger Beep" ) == 0) event_geiger_beep(event,value); else
if(strcmp(event,"\x80Sv" ) == 0) event_usv(event,value); else
if(strcmp(event,"\x80R" ) == 0) event_rem(event,value); else
if(strcmp(event,"Clear Log" ) == 0) event_clear_log(event,value); else
if(strcmp(event,"Save:Brightness") == 0) event_save_brightness(event,value); else
if(strcmp(event,"Save:LogInter" ) == 0) save_loginterval(); else
if(strcmp(event,"CALIBRATE" ) == 0) initialise_calibration(); else
if(strcmp(event,"UTCSCREEN" ) == 0) event_utcscreen(event,value); else
if(strcmp(event,"TIMESCREEN" ) == 0) event_timescreen(event,value); else
if(strcmp(event,"BECQSCREEN" ) == 0) event_becqscreen(event,value); else
if(strcmp(event,"LOGINTERVAL" ) == 0) event_loginterval(event,value); else
if(strcmp(event,"WARNSCREEN" ) == 0) event_warnscreen(event,value); else
if(strcmp(event,"DATESCREEN" ) == 0) event_datescreen(event,value); else
if(strcmp(event,"BrightnessSCN" ) == 0) event_brightnessscn(event,value); else
if(strcmp(event,"LeftBrightness" ) == 0) event_leftbrightness(event,value); else
if(strcmp(event,"QR Transfer" ) == 0) qr_logxfer(); else
if(strcmp(event,"Audio Xfer" ) == 0) event_audioxfer(event,value); else
if(strcmp(event,"QR Tweet" ) == 0) event_qrtweet(event,value); else
if(strcmp(event,"varnumchange" ) == 0) {
if(strcmp ("BRIGHTNESS",value) == 0) event_varnum_brightness(event,value); else
if(strcmpl("CAL" ,value,3) ) update_calibration(); else
if(strcmpl("DATE" ,value,4) ) event_varnum_date(event,value); else
if(strcmpl("TIME" ,value,4) ) event_varnum_time(event,value);
}
}
/*------------------------------------------------------------------------------
Call a user-supplied weight function,
or read a user-supplied file,
to determine the weight of the region at angular position az, el in deg.
================================================================================
In c, the user-supplied function should take the form:
double weight(double *az, double *el)
verbose is available as a global variable that can be declared with
extern int verbose;
or you can use the msg() routine for printing messages.
================================================================================
In fortran, the same user-supplied function should take the form
(note the trailing _ added to the function name, as is standard when
calling fortran routines from c):
real*8 function weight_(az, el)
real*8 az, el
================================================================================
Input: az, el = azimuth, elevation in degrees.
survey = name of survey, or name of file containing list of weights.
Output: weight at angular position az, el;
if survey is null, then weight is set to 1.
*/
double weight_fn(double az, double el, char *survey)
{
double weight;
/* null survey */
if (!survey) {
weight = 1.;
/* 2dF 10k quasar survey */
} else if (strcmpl(survey, "2QZ10k") == 0) {
weight = twoqz_(&az, &el, &verbose);
/* 2dF 100k galaxy survey */
} else if (strcmpl(survey, "2dF100k") == 0) {
weight = twodf_(&az, &el);
/* try reading weights from file */
} else {
weight = rdweight(survey);
}
return(weight);
}
void ReadATrait(quanttrait *traitp)
{
char *s;
s = getstr();
// Checking if it has the sysmiss symbol
if (!strcmpl(SYSMISS,s))
{
traitp->sysmiss = 1;
traitp->value = 0;
}
else
{
traitp->sysmiss = 0;
traitp->value = atof(s);
}
return;
}
int ExportMerlinPedigree (individual *indlist)
{
individual *ind;
markerlist *marker;
namelist *pedlist, *pedigr;
quanttrait *qt;
int fndr, i, pednr;
// Checks that data exists
if (!listlen(indlist))
{
return -1;
}
cfopen ("merlin.ped","w");
pedigr = MakePedigreeList(indlist);
// Run through each pedigree
for (pedlist = pedigr, pednr=1; pedlist; pedlist = pedlist ->next, pednr++) {
// First select all founders then all offspring
for (fndr = 1; fndr >= 0; fndr--) {
for (ind = indlist; ind; ind = ind->next) {
// First prints the founders from right pedigree
if ((founder(ind)==fndr) && (!strcmpl(ind->pedigree, pedlist->name))) {
// Converts ID's to simple numbers
fprintf(F, "%-5d %-12d", pednr, ind->globalid);
if (ind->father)
fprintf(F, "%-12d", ind->father->globalid);
else
fprintf(F, "%-12d", 0);
if (ind->mother)
fprintf(F, "%-12d", ind->mother->globalid);
else
fprintf(F, "%-12d", 0);
fprintf(F, "%-2d", ind->sex);
// Print marker info
for (marker = ind->marker, i=1; marker; marker = marker->next, i++) {
#ifdef XGH
if (options->Index[O_XLINKED] && ind->sex == S_MALE ) {
fprintf(F, " %2d %2d ", NumberOfAlleles(i)+1, marker->allele2);
}
else
fprintf(F, " %2d %2d ", marker->allele1, marker->allele2);
#else
fprintf(F, " %2d %2d ", marker->allele1, marker->allele2);
#endif
}
// Print traits
for (qt = ind->qttrait; qt; qt = qt->next) {
if (qt->sysmiss)
fprintf(F, " %-6s ", "x");
else
fprintf(F, " %-6f ", qt->value);
}
fprintf(F, "\n");
}
}
}
}
fclose(F);
printf("Created MERLIN pedigree file\n");
freelist(pedigrees);
pedigrees = 0;
return(0);
}
void ExportLinkagePedigree (individual *indlist, int aff)
{
individual *ind;
markerlist *marker;
namelist *pedlist, *pedigr;
quanttrait *qt;
int fndr, i;
if (aff==1)
cfopen ("gh.ped","w");
else
cfopen ("linkage.ped","w");
pedigr = MakePedigreeList(indlist);
for (pedlist = pedigr; pedlist; pedlist = pedlist ->next)
{
for (fndr = 1; fndr >= 0; fndr--) {
for (ind = indlist; ind; ind = ind->next)
{
// First prints the founders from right pedigree
if ((founder(ind)==fndr) && (!strcmpl(ind->pedigree, pedlist->name)))
{
// Converts GeneHunter ID number to simple numbers
if (aff == 1) {
fprintf(F, "%-7s %-12d", ind->pedigree, ind->globalid);
if (ind->father)
fprintf(F, "%-12d", ind->father->globalid);
else
fprintf(F, "%-12d", 0);
if (ind->mother)
fprintf(F, "%-12d", ind->mother->globalid);
else
fprintf(F, "%-12d", 0);
}
else {
fprintf(F, "%-7s %-12s", ind->pedigree, ind->id);
if (ind->father)
fprintf(F, "%-12s", ind->father->id);
else
fprintf(F, "%-12d", 0);
if (ind->mother)
fprintf(F, "%-12s", ind->mother->id);
else
fprintf(F, "%-12d", 0);
}
fprintf(F, "%-2d", ind->sex);
if (aff)
fprintf(F, "1 ");
for (marker = ind->marker, i=1; marker; marker = marker->next, i++)
{
#ifdef XGH
if (options->Index[O_XLINKED] && ind->sex == S_MALE ) {
fprintf(F, " %2d %2d ", NumberOfAlleles(i)+1, marker->allele2);
}
else
fprintf(F, " %2d %2d ", marker->allele1, marker->allele2);
#else
fprintf(F, " %2d %2d ", marker->allele1, marker->allele2);
#endif
}
for (qt = ind->qttrait; qt; qt = qt->next)
{
if (qt->sysmiss)
fprintf(F, " %s ", SYSMISS);
else
fprintf(F, " %f ", qt->value);
}
fprintf(F, "\n");
}
}
}
}
fclose(F);
if (aff)
printf("Created GeneHunter pedigree file\n");
else
printf("Created LINKAGE pedigree file\n");
freelist(pedigrees);
pedigrees = 0;
}
void ExportMendelPedigree (individual *indlist)
{
int i;
namelist *pedigree, *pedlist;
markerlist *marker;
individual *ind;
pedlist = MakePedigreeList(indlist);
cfopen ("mendel.ped", "w");
fprintf(F, "(I4,A15,A8)\n");
fprintf(F, "(3A11,3A2");
// Add marker info
if (numberofmarkers()>0)
fprintf(F, ",%d(1X,A7)", numberofmarkers());
if (numberoftraits()>0)
fprintf(F, ",%d(1X,A8)", numberoftraits());
fprintf(F, ")\n");
for (pedigree = pedlist; pedigree; pedigree = pedigree ->next) {
fprintf(F, "%-4d%-15s\n",FamilySize(indlist, pedigree->name), pedigree->name);
for (ind = indlist; ind; ind = ind->next)
{
if (!strcmpl(pedigree->name, ind->pedigree)) {
if (founder(ind)) {
fprintf(F, "%-11s%-11s%-11s", ind->id, "","");
}
else {
fprintf(F, "%-11s%-11s%-11s", ind->id, ind->father->id, ind->mother->id);
}
// Spaces here for non-existing disease status and monozygotic twin status?
fprintf(F, "%2s ", ind->sex==S_MALE ? "M" : "F");
// Now write the marker information
for (i=1; i<=numberofmarkers(); i++) {
marker = markernumber(ind, order[i]);
if (marker->allele1 == 0 || marker->allele2 == 0) {
fprintf(F, " %7s", "");
}
else {
// fprintf(F, " %3d/%-3d", marker->allele1, marker->allele2);
fprintf(F, " %3c/%-3c", 64+marker->allele1, 64+marker->allele2);
}
}
// Then write the trait information
for (i=1; i<=numberoftraits(); i++) {
if (!traitmiss(ind, i))
fprintf(F, " %8f", trait(ind, i));
else
fprintf(F, " %8s", "");
}
fprintf(F, "\n");
}
}
}
freelist(pedlist);
fclose(F);
}
int ExportCRIMAPGen(individual *indlist, int xlinked)
{
individual *ind;
namelist *pedigree, *ped;
markerlist *mkr;
char mkrname[NAMESIZE], tempstr[NAMESIZE];
int nFamilies, nLoci, i, nInternalID, nMembers, al1, al2, pseudoal;
nLoci = listlen(indlist->marker);
pedigree = MakePedigreeList(indlist);
nFamilies = listlen(pedigree);
cfopen ("crimap.gen", "w");
fprintf(F, "%d %d", nFamilies, nLoci); // The first line
// Prints the markers in the correct order
for (i = 1; i<= nLoci; i++)
{
// Remove white spaces in marker name
RemoveWhiteSpace(tempstr, GetName(markernames, order[i]));
strncpy(mkrname, tempstr, 15);
fprintf(F, " %s", mkrname);
}
fprintf(F, "\n");
// Fixes internal id's for use below
for (ped = pedigree; ped; ped = ped->next)
{
nInternalID = 1;
for (ind = indlist; ind; ind = ind->next)
{
// From the right pedigree
if (!strcmpl(ind->pedigree, ped->name))
{
ind->localid = nInternalID;
nInternalID++;
}
}
}
// Writes each family
for (ped = pedigree; ped; ped = ped->next)
{
// Family name
fprintf(F, "%s\n", ped->name);
nMembers = 0;
// Count the number of family members
for (ind = indlist; ind; ind = ind->next)
{
// From the right pedigree
if (!strcmpl(ind->pedigree, ped->name))
nMembers++;
}
fprintf(F, "%d\n", nMembers);
for (ind = indlist; ind; ind = ind->next)
{
// From the right pedigree
if (!strcmpl(ind->pedigree, ped->name))
{
if (founder(ind))
fprintf(F, "%d 0 0 ", ind->localid);
else
fprintf(F, "%d %d %d ", ind->localid, ind->father->localid, ind->mother->localid);
switch (ind->sex)
{
case S_MALE: fprintf(F, "1"); break;
case S_FEMALE: fprintf(F, "0"); break;
default: fprintf(F, "3"); break;
}
// Should now print the alleles for each locus
// If xlinked, then create a pseudo allele for each marker
// to make the males heterozygous
for (i = 1; i<= nLoci; i++)
{
mkr = markernumber(ind, order[i]);
al1 = mkr->allele1;
al2 = mkr->allele2;
if (xlinked && ind->sex == S_MALE && al1>0 && al2>0) {
pseudoal = NumberOfAlleles(order[i])+1;
al2 = pseudoal;
}
fprintf(F, " %d %d", al1, al2);
}
fprintf(F, "\n");
}
}
}
fclose(F);
printf("Created crimap gen file\n");
if (xlinked) {
printf("Pseudo-allele generated for all males\n");
}
return 0;
}
int ExportRelpairPedigree(individual *indlist)
{
int i, famsize;
namelist *pedlist, *pedigr;
individual *ind, *ind2;
markerlist *marker;
cfopen ("relpair.ped", "w");
fprintf(F, "(I4,1X,A8)\n");
fprintf(F, "(3A8,2A1");
if (numberofmarkers())
fprintf(F, ",A3");
if (numberofmarkers()>1) {
fprintf(F, ",%d(1X,A3))\n", numberofmarkers()-1);
}
pedigr = MakePedigreeList(indlist);
for (pedlist = pedigr; pedlist; pedlist = pedlist ->next) {
// Start by calculating the family size
famsize = 0;
for (ind2 = indlist; ind2; ind2 = ind2->next) {
if (!strcmpl(pedlist->name, ind2->pedigree)) {
famsize++;
}
}
fprintf(F, "%4d %s \n",famsize, pedlist->name);
for (ind = indlist; ind; ind = ind->next) {
// Pick correct pedigree
if (!strcmpl(ind->pedigree,pedlist->name)) {
fprintf(F, "%-8s", ind->id);
if (ind->father)
fprintf(F, "%-8s", ind->father->id);
else
fprintf(F, "%-8s", "0");
if (ind->mother)
fprintf(F, "%-8s", ind->mother->id);
else
fprintf(F, "%-8s", "0");
if (ind->sex == S_MALE)
fprintf(F, "M");
else
fprintf(F, "F");
fprintf(F, " "); // MZ status
// Prints the genotypes
for (i = 1; i<=numberofmarkers(); i++) {
marker = markernumber(ind, order[i]);
if (marker->allele1*marker->allele2)
fprintf(F, "%c/%c ", marker->allele1 + 64, marker->allele2 + 64);
else
fprintf(F, " ");
}
fprintf(F, "\n");
}
}
}
fclose(F);
freelist(pedigr);
printf("Created relpair pedigree file\n");
return 1;
}
