X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=b9b907d903752d8a93979680d361c2ea683c7cab;hb=f6a58db15cdc7b90a601f8bf9c9d3b69d642f85d;hp=2f67123a88c9795c362fac6cc4a428fc8e961d46;hpb=0e051b4cfda410b0d441da6ff2f96d4bbe1d9e5a;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 2f67123..b9b907d 100644
--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -12,9 +12,9 @@
 //**********************************************************************************************************************
 vector<string> GetCurrentCommand::setParameters(){	
 	try {
-		CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pclear("clear", "String", "", "", "", "", "","",false,false); parameters.push_back(pclear);
+		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);		}
@@ -59,6 +59,7 @@ GetCurrentCommand::GetCurrentCommand(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();
@@ -89,7 +90,9 @@ int GetCurrentCommand::execute(){
 	try {
 		
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-		
+        
+		cFactory = CommandFactory::getInstance();
+        
 		//user wants to clear a type
 		if (types.size() != 0) {
 			for (int i = 0; i < types.size(); i++) {
@@ -135,6 +138,16 @@ int GetCurrentCommand::execute(){
 					m->setAccnosFile("");
 				}else if (types[i] == "taxonomy") {
 					m->setTaxonomyFile("");
+				}else if (types[i] == "flow") {
+					m->setFlowFile("");
+                }else if (types[i] == "biom") {
+					m->setBiomFile("");
+                }else if (types[i] == "count") {
+					m->setCountTableFile("");
+                }else if (types[i] == "summary") {
+					m->setSummaryFile("");
+				}else if (types[i] == "processors") {
+					m->setProcessors("1");
 				}else if (types[i] == "all") {
 					m->clearCurrentFiles();
 				}else {
@@ -143,10 +156,35 @@ int GetCurrentCommand::execute(){
 			}
 		}
 		
-		m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
-		m->printCurrentFiles();
+		if (m->hasCurrentFiles()) {
+			m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+			m->printCurrentFiles();
+		}
+        
+        string inputDir = cFactory->getInputDir();
+        if (inputDir != "") {
+            m->mothurOutEndLine(); m->mothurOut("Current input directory saved by mothur: " + inputDir); m->mothurOutEndLine();
+        }
+        
+        string outputDir = cFactory->getOutputDir();
+        if (outputDir != "") {
+            m->mothurOutEndLine(); m->mothurOut("Current output directory saved by mothur: " + outputDir); m->mothurOutEndLine();
+        }
+        string defaultPath = m->getDefaultPath();
+        if (defaultPath != "") {
+            m->mothurOutEndLine(); m->mothurOut("Current default directory saved by mothur: " + defaultPath); m->mothurOutEndLine();
+        }
+        
+        
+        string temp = "./";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+            temp = ".\\";
+#endif
+        temp = m->getFullPathName(temp);
+        m->mothurOutEndLine(); m->mothurOut("Current working directory: " + temp); m->mothurOutEndLine();
 		
-		return 0;	
+		return 0;
 	}
 	
 	catch(exception& e) {