X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getlinecommand.cpp;h=5f459bf7e6a8013ee61893502c01e5c6a306c4b1;hp=df14f5123d2bd2e8c6d02380520810211e19c461;hb=0470f6d037aacb3563c3f7010708120a4a67d4e6;hpb=bede5752eaeedb5a7e339439b6ba2f6670bca2b9

diff --git a/getlinecommand.cpp b/getlinecommand.cpp
index df14f51..5f459bf 100644
--- a/getlinecommand.cpp
+++ b/getlinecommand.cpp
@@ -9,10 +9,21 @@
 
 #include "getlinecommand.h"
 
-
-GetlineCommand::GetlineCommand(){
+//**********************************************************************************************************************
+GetlineCommand::GetlineCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			if (option != "") { cout << "There are no valid parameters for the get.line command." << endl; abort = true; }
+			
+			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.line command." << endl; abort = true; }				
+		}
+
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function GetlineCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -24,6 +35,25 @@ GetlineCommand::GetlineCommand(){
 	}	
 			
 }
+//**********************************************************************************************************************
+
+void GetlineCommand::help(){
+	try {
+		cout << "The get.line command can only be executed after a successful read.otu command." << "\n";
+		cout << "You may not use any parameters with the get.line command." << "\n";
+		cout << "The get.line command should be in the following format: " << "\n";
+		cout << "get.line()" << "\n";
+		cout << "Example get.line()." << "\n";
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the GetlineCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the GetlineCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
 
 //**********************************************************************************************************************
 
@@ -34,6 +64,9 @@ GetlineCommand::~GetlineCommand(){
 
 int GetlineCommand::execute(){
 	try {
+	
+		if (abort == true) { return 0; }
+	
 		filename = globaldata->inputFileName;
 		ifstream in;
 		openInputFile(filename, in);