X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrelabundcommand.cpp;h=7c623fbfd8ced3cd88bff70b3579e893d6e6cfa0;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=6397e358de806f08695d0707c6539352a282be44;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 6397e35..7c623fb 100644
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -40,7 +40,7 @@ string GetRelAbundCommand::getHelpString(){
 		helpString += "Example get.relabund(groups=A-B-C, scale=averagegroup).\n";
 		helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
 		helpString += "The get.relabund command outputs a .relabund file.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -49,6 +49,26 @@ string GetRelAbundCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string GetRelAbundCommand::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 == "relabund")         {   outputFileName = "relabund" ;  }
+            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, "GetRelAbundCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -69,6 +89,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
 				
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -110,7 +131,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
 				sharedfile = m->getSharedFile(); 
 				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setSharedFile(sharedfile); }
 			
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -130,7 +151,7 @@ GetRelAbundCommand::GetRelAbundCommand(string option) {
 			else { 
 				pickedGroups = true;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			scale = validParameter.validFile(parameters, "scale", false);				if (scale == "not found") { scale = "totalgroup"; }
@@ -153,7 +174,7 @@ int GetRelAbundCommand::execute(){
 	
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "relabund";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("relabund");
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
@@ -169,11 +190,12 @@ int GetRelAbundCommand::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) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 	
 			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
 
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				getRelAbundance(lookup, out);
 				
 				processedLabels.insert(lookup[0]->getLabel());
@@ -186,7 +208,7 @@ int GetRelAbundCommand::execute(){
 				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  
 				lookup = input->getSharedRAbundVectors(lastLabel);
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-				
+				if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 				getRelAbundance(lookup, out);
 				
 				processedLabels.insert(lookup[0]->getLabel());
@@ -200,13 +222,13 @@ int GetRelAbundCommand::execute(){
 			//prevent memory leak
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 			
-			if (m->control_pressed) {  outputTypes.clear();  m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) {  outputTypes.clear();  m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 
 			//get next line to process
 			lookup = input->getSharedRAbundVectors();				
 		}
 		
-		if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str());  return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -227,18 +249,18 @@ int GetRelAbundCommand::execute(){
 			lookup = input->getSharedRAbundVectors(lastLabel);
 			
 			m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-			
+			if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 			getRelAbundance(lookup, out);
 			
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 		}
 	
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		delete input; 
 		out.close();
 		
-		if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();