X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getlistcountcommand.cpp;h=a4d7b83397f83bf6ae3dd21627566252035b328f;hp=4dc20634c1e53d774348559447c736f736ff4e69;hb=615301e57c25e241356a9c2380648d117709458d;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 4dc2063..a4d7b83 100644
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> GetListCountCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "",false,false); parameters.push_back(parasort);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otu",false,true, true); parameters.push_back(plist);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter parasort("sort", "Multiple", "name-otu", "otu", "", "", "","",false,false); parameters.push_back(parasort);
+		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);		}
@@ -49,6 +49,21 @@ string GetListCountCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string GetListCountCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "otu") {  pattern = "[filename],[tag],otu"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetListCountCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 GetListCountCommand::GetListCountCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -114,6 +129,7 @@ GetListCountCommand::GetListCountCommand(string option)  {
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (listfile == "not open") { abort = true; }	
+			else { m->setListFile(listfile); }
 			
 		
 			//check for optional parameter and set defaults
@@ -148,7 +164,7 @@ int GetListCountCommand::execute(){
 		set<string> processedLabels;
 		set<string> userLabels = labels;
 		
-		if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+		if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 		
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
@@ -156,7 +172,7 @@ int GetListCountCommand::execute(){
 			
 				process(list);
 				
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 							
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
@@ -170,7 +186,7 @@ int GetListCountCommand::execute(){
 				
 				process(list);
 				
-				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+				if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 
 													
 				processedLabels.insert(list->getLabel());
@@ -207,7 +223,7 @@ int GetListCountCommand::execute(){
 				
 			process(list);	
 			
-			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} return 0;  }
+			if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} return 0;  }
 			
 			delete list;  
 		}
@@ -233,7 +249,11 @@ void GetListCountCommand::process(ListVector* list) {
 	try {
 		string binnames;
 		if (outputDir == "") { outputDir += m->hasPath(listfile); }
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
+        map<string, string> variables; 
+		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = list->getLabel();
+		string outputFileName = getOutputFileName("otu", variables);
+		
 		m->openOutputFile(outputFileName, out);
 		outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);