X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.cpp;h=d160525c70174131e8d32ac9803f5bcc756cb80f;hb=f687723a8357916e86a05116978e6869b039ce36;hp=9051a5d94ffd07d1ba5444f5d777556faf7fab77;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 9051a5d..d160525 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -61,6 +61,28 @@ string HeatMapCommand::getHelpString(){
 	}
 }
 
+//**********************************************************************************************************************
+
+string HeatMapCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "svg")            {   outputFileName =  "svg";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HeatMapCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 HeatMapCommand::HeatMapCommand(){	
 	try {
@@ -222,14 +244,14 @@ 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") { 
@@ -287,7 +309,7 @@ int HeatMapCommand::execute(){
 				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") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
-					m->Groups.clear(); 
+					m->clearGroups(); 
 					delete input; delete heatmap; return 0;
 				}
 		
@@ -330,7 +352,7 @@ int HeatMapCommand::execute(){
 			
 			if (m->control_pressed) {
 				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
-				m->Groups.clear(); 
+				m->clearGroups(); 
 				delete input; delete heatmap; return 0;
 			}
 
@@ -359,7 +381,7 @@ int HeatMapCommand::execute(){
 			}
 		
 			//reset groups parameter
-			m->Groups.clear();  
+			m->clearGroups();  
 			
 		}else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 	
@@ -440,7 +462,7 @@ int HeatMapCommand::execute(){
 				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") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
-					m->Groups.clear(); 
+					m->clearGroups(); 
 					delete input; delete heatmap; return 0;
 				}
 		
@@ -482,7 +504,7 @@ int HeatMapCommand::execute(){
 			
 			if (m->control_pressed) {
 				for (int i = 0; i < outputNames.size(); i++) {	if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
-				m->Groups.clear(); 
+				m->clearGroups(); 
 				delete input; delete heatmap; return 0;
 			}
 
@@ -511,7 +533,7 @@ int HeatMapCommand::execute(){
 			}
 		
 			//reset groups parameter
-			m->Groups.clear();  
+			m->clearGroups();  
 
 		}