X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mergefilecommand.cpp;h=643cf287bb9aded0847390aeea1091c12e95dd74;hp=3342c489d9f54a55abda3bac79b60511402eaf4c;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=cd37904452dc95b183ff313ff05720c562902487

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index 3342c48..643cf28 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -9,20 +9,63 @@
 
 #include "mergefilecommand.h"
 
+//**********************************************************************************************************************
+vector<string> MergeFileCommand::setParameters(){	
+	try {
+		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", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string MergeFileCommand::getHelpString(){	
+	try {
+		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", "getHelpString");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+MergeFileCommand::MergeFileCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["merge"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
-MergeFileCommand::MergeFileCommand(string option){
+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"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			vector<string> myArray = setParameters();
 			
 			OptionParser parser(option);
 			map<string,string> parameters = parser.getParameters();
@@ -34,88 +77,73 @@ MergeFileCommand::MergeFileCommand(string option){
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["merge"] = tempOutNames;
+			
+			//if the user changes the input directory command factory will send this info to us in the output parameter 
+			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			
 			string fileList = validParameter.validFile(parameters, "input", false);			
-			if(fileList == "not found") { cout << "you must enter two or more file names" << endl;  abort=true;  }
-			else{ 	splitAtDash(fileList, fileNames);	}
+			if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine();  abort=true;  }
+			else{ 	m->splitAtDash(fileList, fileNames);	}
+			
+			//if the user changes the output directory command factory will send this info to us in the output parameter 
+			string outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found")	{	outputDir = "";		}
+			
 			
 			numInputFiles = fileNames.size();
 			ifstream testFile;
 			if(numInputFiles == 0){
-				cout << "you must enter two or more file names and you entered " << fileNames.size() <<  " file names" << endl;
+				m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); m->mothurOutEndLine();
 				abort=true;  
 			}
 			else{
 				for(int i=0;i<numInputFiles;i++){
-					if(openInputFile(fileNames[i], testFile)){	abort = true;	}
+					if (inputDir != "") {
+						string path = m->hasPath(fileNames[i]);
+						//if the user has not given a path then, add inputdir. else leave path alone.
+						if (path == "") {	fileNames[i] = inputDir + fileNames[i];		}
+					}
+					
+					if(m->openInputFile(fileNames[i], testFile)){	abort = true;	}
 					testFile.close();
 				}
 			}   
 			
 			outputFileName = validParameter.validFile(parameters, "output", false);			
-			if (outputFileName == "not found") { cout << "you must enter an output file name" << endl;  abort=true;  }
+			if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
+			else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName);  }
 		}
 			
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the MergeFileCommand class Function MergeFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the MergeFileCommand class function MergeFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
-
-//**********************************************************************************************************************
-
-MergeFileCommand::~MergeFileCommand()	{	/*	do nothing	*/	}
-
 //**********************************************************************************************************************
 
 int MergeFileCommand::execute(){
 	try {
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
-		ofstream outputFile;
-		openOutputFile(outputFileName, outputFile);
+		m->mothurRemove(outputFileName);
+		for(int i=0;i<numInputFiles;i++){  m->appendFiles(fileNames[i], outputFileName);  }
 		
-		ifstream inputFile;
-		char c;
-		for(int i=0;i<numInputFiles;i++){
-			openInputFile(fileNames[i], inputFile);
-			
-			while(!inputFile.eof()){	c = inputFile.get(); outputFile << c;	}
-			
-			inputFile.close();
-		}
-		return 0;
-	}
-	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the BinSeqCommand class function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-	
-}
-
-//**********************************************************************************************************************
+		if (m->control_pressed) {  m->mothurRemove(outputFileName); return 0;  }
+		
+		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();
 
-void MergeFileCommand::help(){
-	try {
-		cout << "The merge.file command..." << endl;
+		return 0;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the MergeFileCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "MergeFileCommand", "execute");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the MergeFileCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-	
 }
-
 //**********************************************************************************************************************