X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mergefilecommand.cpp;h=643cf287bb9aded0847390aeea1091c12e95dd74;hp=cece52d9cd06b78950f5b197c19d2e9574b7daa8;hb=615301e57c25e241356a9c2380648d117709458d;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index cece52d..643cf28 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -12,10 +12,10 @@
 //**********************************************************************************************************************
 vector<string> MergeFileCommand::setParameters(){	
 	try {
-		CommandParameter pinput("input", "String", "", "", "", "", "",false,true); parameters.push_back(pinput);
-		CommandParameter poutput("output", "String", "", "", "", "", "",false,true); parameters.push_back(poutput);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pinput("input", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pinput);
+		CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
+		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);		}
@@ -41,7 +41,6 @@ string MergeFileCommand::getHelpString(){
 		exit(1);
 	}
 }
-
 //**********************************************************************************************************************
 MergeFileCommand::MergeFileCommand(){	
 	try {
@@ -64,7 +63,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
 		if(option == "help") {
 			help();
 			abort = true; calledHelp = true;
-		}
+		}else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		else {
 			vector<string> myArray = setParameters();
 			
@@ -130,32 +129,13 @@ int MergeFileCommand::execute(){
 	try {
 		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		ofstream outputFile;
-		m->openOutputFile(outputFileName, outputFile);
-		
-		char c;
-		for(int i=0;i<numInputFiles;i++){
-			ifstream inputFile; //declaration must be inside for loop of windows throws an error
-			
-			m->openInputFile(fileNames[i], inputFile);
-			
-			while(!inputFile.eof()){	
-				if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
-			
-				c = inputFile.get(); 
-				//-1 is eof char
-				if (int(c) != -1) { outputFile << c; }   
-			}
-			
-			inputFile.close();
-		}
-		
-		outputFile.close();
+		m->mothurRemove(outputFileName);
+		for(int i=0;i<numInputFiles;i++){  m->appendFiles(fileNames[i], outputFileName);  }
 		
-		if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0;  }
+		if (m->control_pressed) {  m->mothurRemove(outputFileName); return 0;  }
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
 		m->mothurOutEndLine();