X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcurrentcommand.cpp;h=d74786ce1eaaa8767164a0fbd670d06843388b44;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=7bfae208ad9eb6b1a94ba92e2ae028c2f986f24a;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/getcurrentcommand.cpp b/getcurrentcommand.cpp
index 7bfae20..d74786c 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();
@@ -134,7 +135,17 @@ int GetCurrentCommand::execute(){
 				}else if (types[i] == "accnos") {
 					m->setAccnosFile("");
 				}else if (types[i] == "taxonomy") {
-						m->setTaxonomyFile("");
+					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 {
@@ -143,8 +154,10 @@ 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();
+		}
 		
 		return 0;	
 	}