X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mergefilecommand.cpp;h=643cf287bb9aded0847390aeea1091c12e95dd74;hb=3914b0d6480f67df53b1e838f51c4e6155710434;hp=d431dd32ff17dcef5e267b1e93a47c8fc93b324b;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index d431dd3..643cf28 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -10,49 +10,47 @@
 #include "mergefilecommand.h"
 
 //**********************************************************************************************************************
-vector<string> MergeFileCommand::getValidParameters(){	
+vector<string> MergeFileCommand::setParameters(){	
 	try {
-		string Array[] =  {"input", "output","outputdir","inputdir"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		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);		}
 		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "MergeFileCommand", "getValidParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-MergeFileCommand::MergeFileCommand(){	
-	try {
-		//initialize outputTypes
-		vector<string> tempOutNames;
-		outputTypes["merge"] = tempOutNames;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
+		m->errorOut(e, "MergeFileCommand", "setParameters");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> MergeFileCommand::getRequiredParameters(){	
+string MergeFileCommand::getHelpString(){	
 	try {
-		string Array[] =  {"input","output"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-		return myArray;
+		string helpString = "";
+		helpString += "The merge.file command takes a list of files separated by dashes and merges them into one file."; 
+		helpString += "The merge.file command parameters are input and output."; 
+		helpString += "Example merge.file(input=small.fasta-large.fasta, output=all.fasta).";
+		helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n";
+		return helpString;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "MergeFileCommand", "getRequiredParameters");
+		m->errorOut(e, "MergeFileCommand", "getHelpString");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
-vector<string> MergeFileCommand::getRequiredFiles(){	
+MergeFileCommand::MergeFileCommand(){	
 	try {
-		vector<string> myArray;
-		return myArray;
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["merge"] = tempOutNames;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "MergeFileCommand", "getRequiredFiles");
+		m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
 		exit(1);
 	}
 }
@@ -60,16 +58,14 @@ vector<string> MergeFileCommand::getRequiredFiles(){
 
 MergeFileCommand::MergeFileCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		if(option == "help") {
 			help();
-			abort = true; 
-		}
+			abort = true; calledHelp = true;
+		}else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		else {
-			//valid paramters for this command
-			string Array[] =  {"input", "output","outputdir","inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -127,43 +123,19 @@ MergeFileCommand::MergeFileCommand(string option)  {
 		exit(1);
 	}
 }
-
-//**********************************************************************************************************************
-
-MergeFileCommand::~MergeFileCommand()	{	/*	do nothing	*/	}
-
 //**********************************************************************************************************************
 
 int MergeFileCommand::execute(){
 	try {
-		if (abort == true) {	return 0;	}
-		
-		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();
-		}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		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();
 
@@ -174,17 +146,4 @@ int MergeFileCommand::execute(){
 		exit(1);
 	}
 }
-
-//**********************************************************************************************************************
-
-void MergeFileCommand::help(){
-	try {
-		m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "MergeFileCommand", "help");
-		exit(1);
-	}
-}
-
 //**********************************************************************************************************************