X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.cpp;h=7d9b482564287916f599b0f3148ee4d6a80861f2;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=0d8c5b03df532dc83e23f030e93d906c727842e3;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 0d8c5b0..7d9b482 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -222,14 +222,14 @@ HeatMapCommand::HeatMapCommand(string option) {
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			string temp = validParameter.validFile(parameters, "numotu", false);		if (temp == "not found") { temp = "0"; }
-			convert(temp, numOTU);
+			m->mothurConvert(temp, numOTU);
 			
 			temp = validParameter.validFile(parameters, "fontsize", false);				if (temp == "not found") { temp = "24"; }
-			convert(temp, fontSize);
+			m->mothurConvert(temp, fontSize);
 			
 			sorted = validParameter.validFile(parameters, "sorted", false);				
 			if (sorted == "not found") { 
@@ -286,8 +286,8 @@ int HeatMapCommand::execute(){
 			while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				if (m->control_pressed) {
 					for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
-					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-					m->Groups.clear(); 
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+					m->clearGroups(); 
 					delete input; delete heatmap; return 0;
 				}
 		
@@ -329,8 +329,8 @@ int HeatMapCommand::execute(){
 			
 			
 			if (m->control_pressed) {
-				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-				m->Groups.clear(); 
+				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+				m->clearGroups(); 
 				delete input; delete heatmap; return 0;
 			}
 
@@ -359,13 +359,13 @@ int HeatMapCommand::execute(){
 			}
 		
 			//reset groups parameter
-			m->Groups.clear();  
+			m->clearGroups();  
 			
 		}else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 	
 			while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				if (m->control_pressed) {   
-					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 					delete rabund;  delete input; delete heatmap; return 0;	
 				}
 
@@ -404,7 +404,7 @@ int HeatMapCommand::execute(){
 			}
 			
 			if (m->control_pressed) {
-				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 				delete input; delete heatmap; return 0;
 			}
 
@@ -439,8 +439,8 @@ int HeatMapCommand::execute(){
 			while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				if (m->control_pressed) {
 					for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
-					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-					m->Groups.clear(); 
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+					m->clearGroups(); 
 					delete input; delete heatmap; return 0;
 				}
 		
@@ -481,8 +481,8 @@ int HeatMapCommand::execute(){
 			
 			
 			if (m->control_pressed) {
-				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
-				m->Groups.clear(); 
+				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
+				m->clearGroups(); 
 				delete input; delete heatmap; return 0;
 			}
 
@@ -511,7 +511,7 @@ int HeatMapCommand::execute(){
 			}
 		
 			//reset groups parameter
-			m->Groups.clear();  
+			m->clearGroups();  
 
 		}
 		
@@ -519,7 +519,7 @@ int HeatMapCommand::execute(){
 		delete heatmap;
 		
 		if (m->control_pressed) {
-			for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear(); return 0;
+			for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear(); return 0;
 		}
 		
 		m->mothurOutEndLine();