//**********************************************************************************************************************
MetaStatsCommand::MetaStatsCommand(){
try {
+ abort = true;
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["metastats"] = tempOutNames;
//make sure the user has already run the read.otu command
if ((globaldata->getSharedFile() == "")) {
- m->mothurOut("You must read a list and a group, or a shared file before you can use the normalize.shared command."); m->mothurOutEndLine(); abort = true;
+ m->mothurOut("You must read a list and a group, or a shared file before you can use the metastats command."); m->mothurOutEndLine(); abort = true;
}
//check for optional parameter and set defaults
int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
try {
- if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
}else if (pid == 0){
driver(lines[process].start, lines[process].num, thisLookUp);
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
//do my part
}
m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine();
-
metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
-int MetaStatsCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
- try {
-
- vector<SharedRAbundVector*> newLookup;
- for (int i = 0; i < thislookup.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thislookup[i]->getLabel());
- temp->setGroup(thislookup[i]->getGroup());
- newLookup.push_back(temp);
- }
-
- //for each bin
- for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
-
- //look at each sharedRabund and make sure they are not all zero
- bool allZero = true;
- for (int j = 0; j < thislookup.size(); j++) {
- if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
- }
-
- //if they are not all zero add this bin
- if (!allZero) {
- for (int j = 0; j < thislookup.size(); j++) {
- newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
- }
- }
- }
-
- for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
-
- thislookup = newLookup;
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "MetaStatsCommand", "eliminateZeroOTUS");
- exit(1);
- }
-}
-//**********************************************************************************************************************