#include "metastats.h"
#include "sharedutilities.h"
+//**********************************************************************************************************************
+vector<string> MetaStatsCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","label","outputdir","iters","threshold","g","design","sets","processors","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MetaStatsCommand::MetaStatsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["metastats"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "MetaStatsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MetaStatsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"design"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MetaStatsCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MetaStatsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
MetaStatsCommand::MetaStatsCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["metastats"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
//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 numGroups = Sets.size();
for (int a=0; a<numGroups; a++) {
- for (int l = a+1; l < numGroups; l++) {
+ for (int l = 0; l < a; l++) {
vector<string> groups; groups.push_back(Sets[a]); groups.push_back(Sets[l]);
namesOfGroupCombos.push_back(groups);
}
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
delete read;
delete designMap;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0;}
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
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
//get filename
string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
int nameLength = outputFileName.length();
char * output = new char[nameLength];
strcpy(output, outputFileName.c_str());
}
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);
- }
-}
-//**********************************************************************************************************************
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