X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=heatmapcommand.cpp;h=441eaf8a4dc4e77beb36c7e39c102f9aa13f0d53;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=57c4c86b44bf2ccf9368c2c8c26acc1e67d360af;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 57c4c86..441eaf8 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 {
@@ -151,27 +173,27 @@ HeatMapCommand::HeatMapCommand(string option) {
 			
 			//check for required parameters
 			listfile = validParameter.validFile(parameters, "list", true);
-			if (listfile == "not open") { listfile = ""; abort = true; }
+			if (listfile == "not open") { abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
 			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
-			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
+			if (sabundfile == "not open") {  abort = true; }	
 			else if (sabundfile == "not found") { sabundfile = ""; }
 			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
-			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
+			if (rabundfile == "not open") {  abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
 			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
-			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			if (sharedfile == "not open") { abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
 			else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 			
 			relabundfile = validParameter.validFile(parameters, "relabund", true);
-			if (relabundfile == "not open") { relabundfile = ""; abort = true; }	
+			if (relabundfile == "not open") {  abort = true; }	
 			else if (relabundfile == "not found") { relabundfile = ""; }
 			else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
 			
@@ -226,10 +248,10 @@ HeatMapCommand::HeatMapCommand(string option) {
 			}
 			
 			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") {