X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=reversecommand.cpp;h=7a87a99a9720f3f5c8bc04e77bac39d5eabf5ea0;hb=ee1d3ba3f314f05ea50c07c881fa41ce257da77a;hp=9be29152445487dea77a36e62c01812aa617e1ea;hpb=986663e2220f6b043ee83d1699cfa081dc49cbed;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 9be2915..7a87a99 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -13,19 +13,53 @@
 
 //***************************************************************************************************************
 
-ReverseSeqsCommand::ReverseSeqsCommand(){
+ReverseSeqsCommand::ReverseSeqsCommand(string option){
 	try {
-		globaldata = GlobalData::getInstance();
-		if(globaldata->getFastaFile() == "")		{	cout << "you need to at least enter a fasta file name" << endl;	}
+		abort = false;
+		
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"fasta"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
+		
+			//check to make sure all parameters are valid for command
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//check for required parameters
+			fasta = validParameter.validFile(parameters, "fasta", true);
+			if (fasta == "not open") { abort = true; }
+			else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true;  }	
+			
+		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void ReverseSeqsCommand::help(){
+	try {
+		mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+		mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+		mothurOut("The reverse.seqs command should be in the following format: \n");
+		mothurOut("reverse.seqs(fasta=yourFastaFile) \n");	
+	}
+	catch(exception& e) {
+		errorOut(e, "ReverseSeqsCommand", "help");
 		exit(1);
-	}	
+	}
 }
 
 //***************************************************************************************************************
@@ -38,11 +72,13 @@ ReverseSeqsCommand::~ReverseSeqsCommand(){	/*	do nothing	*/	}
 int ReverseSeqsCommand::execute(){
 	try{
 		
+		if (abort == true) { return 0; }
+		
 		ifstream inFASTA;
-		openInputFile(globaldata->getFastaFile(), inFASTA);
+		openInputFile(fasta, inFASTA);
 		
 		ofstream outFASTA;
-		string reverseFile = getRootName(globaldata->getFastaFile()) + "rc" + getExtension(globaldata->getFastaFile());
+		string reverseFile = getRootName(fasta) + "rc" + getExtension(fasta);
 		openOutputFile(reverseFile, outFASTA);
 		
 		while(!inFASTA.eof()){
@@ -57,11 +93,7 @@ int ReverseSeqsCommand::execute(){
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		errorOut(e, "ReverseSeqsCommand", "execute");
 		exit(1);
 	}
 }