X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=deconvolutecommand.cpp;h=96682af26b8bcb1b62c17987c82355856cfaf919;hp=51362e55a0780ced0cfc9833a51ed8d71870edf2;hb=0470f6d037aacb3563c3f7010708120a4a67d4e6;hpb=bede5752eaeedb5a7e339439b6ba2f6670bca2b9

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 51362e5..96682af 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -10,19 +10,83 @@
 #include "deconvolutecommand.h"
 
 /**************************************************************************************/
-int DeconvoluteCommand::execute() {	
+DeconvoluteCommand::DeconvoluteCommand(string option) {	
 	try {
 		globaldata = GlobalData::getInstance();
+		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)));
+			
+			parser = new OptionParser();
+			parser->parse(option, parameters);  delete parser;
+			
+			ValidParameters* validParameter = new ValidParameters();
+		
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			//check for required parameters
+			filename = validParameter->validFile(parameters, "fasta", true);
+			if (filename == "not open") { abort = true; }
+			else if (filename == "not found") { filename = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true;  }	
+			else {  globaldata->setFastaFile(filename);  globaldata->setFormat("fasta"); 	}
+			
+			delete validParameter;
+		}
+
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the DeconvoluteCommand class function DeconvoluteCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+
+void DeconvoluteCommand::help(){
+	try {
+		cout << "The unique.seqs command reads a fastafile and creates a namesfile." << "\n";
+		cout << "It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. " << "\n";
+		cout << "If the sequence is unique the second column will just contain its name. " << "\n";
+		cout << "The unique.seqs command parameter is fasta and it is required." << "\n";
+		cout << "The unique.seqs command should be in the following format: " << "\n";
+		cout << "unique.seqs(fasta=yourFastaFile) " << "\n";	
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the DeconvoluteCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the DeconvoluteCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+/**************************************************************************************/
+int DeconvoluteCommand::execute() {	
+	try {
+		
+		if (abort == true) { return 0; }
 	
 		//prepare filenames and open files
-		filename = globaldata->getFastaFile();
 		outputFileName = (getRootName(filename) + "names");
 		outFastafile = (getRootName(filename) + "unique.fasta");
 		
 		openInputFile(filename, in);
 		openOutputFile(outputFileName, out);
 		openOutputFile(outFastafile, outFasta);
-	
+
 		//constructor reads in file and store internally
 		fastamap = new FastaMap();