X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrabundcommand.cpp;h=d5f5a8b8b8450deef538f564d59885b57647c430;hb=eb71e28b7b7afd82540f4a8f0bac9429c5b9d713;hp=570d64e34166cafcf734181a370dd9fc854e64a3;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 570d64e..d5f5a8b 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -12,12 +12,12 @@
 //**********************************************************************************************************************
 vector<string> GetRAbundCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);		
-		CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psorted);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(plist);
+		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(psabund);		
+		CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(psorted);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -39,7 +39,7 @@ string GetRAbundCommand::getHelpString(){
 		helpString += "Example get.rabund(sorted=F).\n";
 		helpString += "The default value for label is all labels in your inputfile.\n";
 		helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -47,6 +47,21 @@ string GetRAbundCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string GetRAbundCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "rabund")      {   pattern = "[filename],rabund";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetRAbundCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 
 //**********************************************************************************************************************
 GetRAbundCommand::GetRAbundCommand(){	
@@ -69,6 +84,7 @@ GetRAbundCommand::GetRAbundCommand(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();
@@ -115,12 +131,12 @@ GetRAbundCommand::GetRAbundCommand(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); }
 			
 			
 			//check for optional parameter and set defaults
@@ -172,7 +188,9 @@ int GetRAbundCommand::execute(){
 	
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "rabund";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+		filename = getOutputFileName("rabund", variables);
 		m->openOutputFile(filename, out);
 		
 		input = new InputData(inputfile, format);
@@ -183,19 +201,17 @@ int GetRAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str()); delete rabund; delete input; return 0; }
+		if (m->control_pressed) {  outputTypes.clear();  out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
 		
 		while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
 			if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 					m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 					
-					if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+					if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 					
 					if(sorted)	{   rabund->print(out);				}
 					else		{	rabund->nonSortedPrint(out);	}
-					
-					delete rabund;
 															
 					processedLabels.insert(rabund->getLabel());
 					userLabels.erase(rabund->getLabel());
@@ -209,13 +225,11 @@ int GetRAbundCommand::execute(){
 					
 					m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 					
-					if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+					if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 					
 					if(sorted)	{   rabund->print(out);				}
 					else		{	rabund->nonSortedPrint(out);	}
 
-					delete rabund;
-
 					processedLabels.insert(rabund->getLabel());
 					userLabels.erase(rabund->getLabel());
 					
@@ -249,7 +263,7 @@ int GetRAbundCommand::execute(){
 			
 			m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 					
-			if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0; }
 			
 			if(sorted)	{   rabund->print(out);				}
 			else		{	rabund->nonSortedPrint(out);	}
@@ -258,7 +272,7 @@ int GetRAbundCommand::execute(){
 		}
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(filename); m->mothurOutEndLine();	outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
 		m->mothurOutEndLine();