X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=b9b907d903752d8a93979680d361c2ea683c7cab;hb=f3e0de2c55da5c524abb3b404f77cb84aa1ddd34;hp=ca832314d66dbe371e314db292ab6f441d2ee351;hpb=d2390ede25cc211f95f99e377d5654bad7e6950e;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index ca83231..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);		}
@@ -90,7 +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++) {
@@ -140,6 +142,10 @@ int GetCurrentCommand::execute(){
 					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") {
@@ -154,8 +160,31 @@ int GetCurrentCommand::execute(){
 			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) {