int MergeGroupsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
designMap = new DesignMap(designfile);
if (method != "sum") {
string defaultClass = designMap->getDefaultClass();
vector<string> treatments = designMap->getCategory(defaultClass);
set<int> numGroupsPerTreatment;
for (int i = 0; i < treatments.size(); i++) {
if (m->getControl_pressed()) { break; }
map<string, vector<string> > checkTreatments;
vector<string> temp; temp.push_back(treatments[i]);
checkTreatments[defaultClass] = temp;
numGroupsPerTreatment.insert(designMap->getNumUnique(checkTreatments));
}
if (numGroupsPerTreatment.size() > 1) { m->mothurOut("[ERROR]: The median and average methods require you to have the same number of sequences in each treatment, quitting.\n"); delete designMap; return 0; }
}
if (groupfile != "") { processGroupFile(designMap); }
if (sharedfile != "") { processSharedFile(designMap); }
if (countfile != "") { processCountFile(designMap); }
//reset groups parameter
delete designMap;
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0;}
//set shared file as new current sharedfile
string currentName = "";
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setSharedFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "execute");
exit(1);
}
}
/**
* init and run the application
*/
int main(int argc, char *argv[])
{
if(argc < 2)
{
printf("signalCount: usage: signalCounter [endpoint] (trigger_interval_ms)\n");
return 1;
}
// store endpoint
strcpy(endPointUrl, argv[1]);
printf("Using [%s] as endpoint URL\n", endPointUrl);
// store trigger interval, if we have one
if(argc == 3)
{
char* p; // will be set to the "first invalid character" set by strtol
errno = 0;
triggerInterval = strtol(argv[2], &p, 10);
if (*p != '\0' || errno != 0)
{
fprintf(stderr, "invalid trigger interval [%s]\n", argv[2]);
return 1;
}
}
printf("Using [%d] for trigger interval\n", triggerInterval);
// init the wiringPi library
if (wiringPiSetup () < 0)
{
fprintf(stderr, "Unable to setup wiringPi: %s\n", strerror (errno));
return 1 ;
}
// set up an interrupt on our input pin
if (wiringPiISR(PIN_INPUT, INT_EDGE_BOTH, &signalIsr) < 0)
{
fprintf(stderr, "Unable to setup ISR: %s\n", strerror (errno));
return 1 ;
}
// configure the output pin for output. Output output output
pinMode(PIN_OUTPUT, OUTPUT);
pinMode(PIN_INPUT, INPUT);
// pull the internal logic gate down to 0v - we don't want it floating around
pullUpDnControl(PIN_INPUT, PUD_DOWN);
// blink 3 times - we're ready to go
ledBlink(300);
delay(300);
ledBlink(300);
delay(300);
ledBlink(300);
// send a test signal count with the current timestamp
fileRecordSignalCount(getCurrentMilliseconds());
printf("signalCount started\n");
for(;;) {
delay(1000);
// this thread will submit any count files that have not been sent
printf("about to run cleanup thread\n");
processCountFile();
}
return 0;
}
