X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastatscommand.cpp;h=b7aa7e5fcb3bcc809c89ac3cc82c1ecae9d6272a;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=1aaa41e91a3d15eb9d07bb73723ae7514c9b1216;hpb=fc1ed1ae1b022719176910ab71993bd6535810ad;p=mothur.git

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 1aaa41e..b7aa7e5 100644
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -167,7 +167,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
 			else { 
 				pickedGroups = true;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			sets = validParameter.validFile(parameters, "sets", false);			
@@ -178,14 +178,14 @@ MetaStatsCommand::MetaStatsCommand(string option) {
 
 			
 			string temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "threshold", false);			if (temp == "not found") { temp = "0.05"; }
-			convert(temp, threshold); 
+			m->mothurConvert(temp, threshold); 
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 		}
 
 	}
@@ -215,8 +215,9 @@ int MetaStatsCommand::execute(){
 		//setup the pairwise comparions of sets for metastats
 		//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 		//make sure sets are all in designMap
-		SharedUtil* util = new SharedUtil();  
-		util->setGroups(Sets, designMap->namesOfGroups);  
+		SharedUtil* util = new SharedUtil(); 
+		vector<string> dGroups = designMap->getNamesOfGroups();
+		util->setGroups(Sets, dGroups);  
 		delete util;
 		
 		int numGroups = Sets.size();
@@ -250,7 +251,7 @@ int MetaStatsCommand::execute(){
 		//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) {  outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 	
 			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
 
@@ -281,13 +282,13 @@ int MetaStatsCommand::execute(){
 			//prevent memory leak
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 			
-			if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear(); delete input;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); m->clearGroups(); delete input;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } return 0; }
 
 			//get next line to process
 			lookup = input->getSharedRAbundVectors();				
 		}
 		
-		if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }  return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }  return 0; }
 
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -315,7 +316,7 @@ int MetaStatsCommand::execute(){
 		}
 	
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		delete input; 
 		delete designMap;
 		
@@ -393,7 +394,7 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
 			//get set names
 			string setA = namesOfGroupCombos[c][0]; 
 			string setB = namesOfGroupCombos[c][1];
-		
+		//cout << setA << '\t' << setB << endl;
 			//get filename
 			string outputFileName = outputDir +  m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
 			outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
@@ -424,7 +425,8 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
 				}
 			}
 			
-			//for (int i = 0; i < subset.size(); i++) { cout << subset[i]->getGroup() << endl; }
+			//for (int i = 0; i < subset.size(); i++) { cout << designMap->getGroup(subset[i]->getGroup()) << endl; }
+			//cout << setACount << endl;
 			
 			if ((setACount == 0) || (setBCount == 0))  { 
 				m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine();