X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.cpp;h=9051a5d94ffd07d1ba5444f5d777556faf7fab77;hb=8742edef7a51b82834289e570d336f5a81ba1f2b;hp=cf5140a1c7a03db5603cd2358ea7797ea80701f6;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index cf5140a..9051a5d 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -153,27 +153,27 @@ HeatMapCommand::HeatMapCommand(string option) {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else {  format = "list"; inputfile = listfile; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
 			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
 			else if (sabundfile == "not found") { sabundfile = ""; }
-			else {  format = "sabund"; inputfile = sabundfile; }
+			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
-			else {  format = "rabund"; inputfile = rabundfile; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  format = "sharedfile"; inputfile = sharedfile; }
+			else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 			
 			relabundfile = validParameter.validFile(parameters, "relabund", true);
 			if (relabundfile == "not open") { relabundfile = ""; abort = true; }	
 			else if (relabundfile == "not found") { relabundfile = ""; }
-			else {  format = "relabund"; inputfile = relabundfile; }
+			else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
 			
 			
 			if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) { 
@@ -286,7 +286,7 @@ 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();
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 					m->Groups.clear(); 
 					delete input; delete heatmap; return 0;
 				}
@@ -329,7 +329,7 @@ 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();
 				m->Groups.clear(); 
 				delete input; delete heatmap; return 0;
 			}
@@ -365,7 +365,7 @@ int HeatMapCommand::execute(){
 	
 			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;
 			}
 
@@ -439,7 +439,7 @@ 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();
+					for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 					m->Groups.clear(); 
 					delete input; delete heatmap; return 0;
 				}
@@ -481,7 +481,7 @@ 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();
 				m->Groups.clear(); 
 				delete input; delete heatmap; return 0;
 			}
@@ -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();