X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=7116e46e0f9e96045fc3c60a717ae41819949118;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=b3b4b1869f4368c3c7555d5a711e95acb54c9283;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index b3b4b18..7116e46 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -194,7 +194,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			string temp = validParameter.validFile(parameters, "all", false);				if (temp == "not found") { temp = "false"; }
@@ -205,7 +205,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			if (abort == false) {
 			
@@ -364,23 +364,23 @@ int SummarySharedCommand::execute(){
 			for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 			
 			//close files and clean up
-			remove(outputFileName.c_str());
-			if (mult == true) { remove(outAllFileName.c_str());  }
+			m->mothurRemove(outputFileName);
+			if (mult == true) { m->mothurRemove(outAllFileName);  }
 			return 0;
 		//if you only have 2 groups you don't need a .sharedmultiple file
 		}else if ((lookup.size() == 2) && (mult == true)) { 
 			mult = false;
-			remove(outAllFileName.c_str());
+			m->mothurRemove(outAllFileName);
 			outputNames.pop_back();
 		}
 		
 		if (m->control_pressed) {
-			if (mult) {  remove(outAllFileName.c_str());  }
-			remove(outputFileName.c_str()); 
+			if (mult) {  m->mothurRemove(outAllFileName);  }
+			m->mothurRemove(outputFileName); 
 			delete input;
 			for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 			for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			return 0;
 		}
 		/******************************************************/
@@ -388,7 +388,7 @@ int SummarySharedCommand::execute(){
 		
 		/******************************************************/
 		//comparison breakup to be used by different processes later
-		numGroups = m->Groups.size();
+		numGroups = m->getNumGroups();
 		lines.resize(processors);
 		for (int i = 0; i < processors; i++) {
 			lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
@@ -403,12 +403,12 @@ int SummarySharedCommand::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) {
-				if (mult) {  remove(outAllFileName.c_str());  }
-				remove(outputFileName.c_str()); 
+				if (mult) {  m->mothurRemove(outAllFileName);  }
+				m->mothurRemove(outputFileName); 
 				delete input; 
 				for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 				for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
-				m->Groups.clear(); 
+				m->clearGroups(); 
 				return 0;
 			}
 
@@ -446,11 +446,11 @@ int SummarySharedCommand::execute(){
 		}
 		
 		if (m->control_pressed) {
-			if (mult) { remove(outAllFileName.c_str());  }
-			remove(outputFileName.c_str()); 
+			if (mult) { m->mothurRemove(outAllFileName);  }
+			m->mothurRemove(outputFileName); 
 			delete input; 
 			for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			return 0;
 		}
 
@@ -479,14 +479,14 @@ int SummarySharedCommand::execute(){
 		
 				
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		
 		for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 		delete input;  
 		
 		if (m->control_pressed) {
-			remove(outAllFileName.c_str());  
-			remove(outputFileName.c_str()); 
+			m->mothurRemove(outAllFileName);  
+			m->mothurRemove(outputFileName); 
 			return 0;
 		}
 		
@@ -515,10 +515,10 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 				if(processors == 1){
 					driver(thisLookup, 0, numGroups, sumFileName+".temp", sumAllFileName+".temp", calcDists);
 					m->appendFiles((sumFileName + ".temp"), sumFileName);
-					remove((sumFileName + ".temp").c_str());
+					m->mothurRemove((sumFileName + ".temp"));
 					if (mult) {
 						m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
-						remove((sumAllFileName + ".temp").c_str());
+						m->mothurRemove((sumAllFileName + ".temp"));
 					}
 				}else{
 					int process = 1;
@@ -561,7 +561,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 					//parent do your part
 					driver(thisLookup, lines[0].start, lines[0].end, sumFileName + toString(getpid()) + ".temp", sumAllFileName + toString(getpid()) + ".temp", calcDists);   
 					m->appendFiles((sumFileName + toString(getpid()) + ".temp"), sumFileName);
-					remove((sumFileName + toString(getpid()) + ".temp").c_str());
+					m->mothurRemove((sumFileName + toString(getpid()) + ".temp"));
 					if (mult) { m->appendFiles((sumAllFileName + toString(getpid()) + ".temp"), sumAllFileName); }
 						
 					//force parent to wait until all the processes are done
@@ -572,8 +572,8 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 					
 					for (int i = 0; i < processIDS.size(); i++) {
 						m->appendFiles((sumFileName + toString(processIDS[i]) + ".temp"), sumFileName);
-						remove((sumFileName + toString(processIDS[i]) + ".temp").c_str());
-						if (mult) {	remove((sumAllFileName + toString(processIDS[i]) + ".temp").c_str());	}
+						m->mothurRemove((sumFileName + toString(processIDS[i]) + ".temp"));
+						if (mult) {	m->mothurRemove((sumAllFileName + toString(processIDS[i]) + ".temp"));	}
 						
 						if (createPhylip) {
 							string tempdistFileName = m->getRootName(m->getSimpleName(sumFileName)) + toString(processIDS[i]) +  ".dist";
@@ -596,7 +596,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 								}
 							}
 							intemp.close();
-							remove(tempdistFileName.c_str());
+							m->mothurRemove(tempdistFileName);
 						}
 					}
 
@@ -604,10 +604,10 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 			#else
 				driver(thisLookup, 0, numGroups, (sumFileName + ".temp"), (sumAllFileName + ".temp"), calcDists);
 				m->appendFiles((sumFileName + ".temp"), sumFileName);
-				remove((sumFileName + ".temp").c_str());
+				m->mothurRemove((sumFileName + ".temp"));
 				if (mult) {
 					m->appendFiles((sumAllFileName + ".temp"), sumAllFileName);
-					remove((sumAllFileName + ".temp").c_str());
+					m->mothurRemove((sumAllFileName + ".temp"));
 				}
 			#endif