X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=237506e666641ab80e263db5573aec13756e3429;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=98bdcb2cba6cb726f9d793baca1c78f785a04c00;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 98bdcb2..237506e 100644
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> GetSAbundCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);		
-		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","sabund",false,false, true); parameters.push_back(plist);
+		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","sabund",false,false, true); parameters.push_back(prabund);		
+		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);		}
@@ -37,7 +37,7 @@ string GetSAbundCommand::getHelpString(){
 		helpString += "Example get.sabund().\n";
 		helpString += "The default value for label is all labels in your inputfile.\n";
 		helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -45,7 +45,21 @@ string GetSAbundCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string GetSAbundCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "sabund")      {   pattern = "[filename],sabund";    }
+        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);
+    }
+}
 //**********************************************************************************************************************
 GetSAbundCommand::GetSAbundCommand(){	
 	try {
@@ -67,6 +81,7 @@ GetSAbundCommand::GetSAbundCommand(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();
@@ -113,12 +128,12 @@ GetSAbundCommand::GetSAbundCommand(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); }
 			
 			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); }
 			
 		
 						//check for optional parameter and set defaults
@@ -165,7 +180,9 @@ int GetSAbundCommand::execute(){
 	try {
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-		filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund";
+        map<string, string> variables; 
+		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+		filename = getOutputFileName("sabund", variables);
 		m->openOutputFile(filename, out);
 		
 		input = new InputData(inputfile, format);
@@ -177,7 +194,7 @@ int GetSAbundCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input; return 0; }
+		if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input; return 0; }
 
 		
 		while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -186,9 +203,8 @@ int GetSAbundCommand::execute(){
 					m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 					
 					sabund->print(out);
-					delete sabund;
 					
-				if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+				if (m->control_pressed) { outputTypes.clear();  out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
 					processedLabels.insert(sabund->getLabel());
 					userLabels.erase(sabund->getLabel());
@@ -202,9 +218,8 @@ int GetSAbundCommand::execute(){
 					
 					m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 					sabund->print(out);
-					delete sabund;
 					
-					if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+					if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
 					processedLabels.insert(sabund->getLabel());
 					userLabels.erase(sabund->getLabel());
@@ -242,7 +257,7 @@ int GetSAbundCommand::execute(){
 			sabund->print(out);
 			delete sabund;
 			
-			if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; return 0; }
 			
 		}
 		
@@ -250,7 +265,7 @@ int GetSAbundCommand::execute(){
 		delete input;
 		
 		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["sabund"].push_back(filename);
 		m->mothurOutEndLine();