X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mergefilecommand.cpp;h=0a8c0d8cda62808664a83f46c44cebb770e14f4a;hb=a218321731df14d231bbc08e79906f757cf1540d;hp=497d535e4810fac221b6ae399d59a7b1ff457d46;hpb=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index 497d535..0a8c0d8 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -21,7 +21,7 @@ MergeFileCommand::MergeFileCommand(string option){
 		}
 		else {
 			//valid paramters for this command
-			string Array[] =  {"input", "output"};
+			string Array[] =  {"input", "output","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -34,36 +34,47 @@ MergeFileCommand::MergeFileCommand(string option){
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//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;  }
+			if(fileList == "not found") { mothurOut("you must enter two or more file names"); mothurOutEndLine();  abort=true;  }
 			else{ 	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;
+				mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) +  " file names"); mothurOutEndLine();
 				abort=true;  
 			}
 			else{
 				for(int i=0;i<numInputFiles;i++){
+					if (inputDir != "") {
+						string path = 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(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") { mothurOut("you must enter an output file name"); mothurOutEndLine();  abort=true;  }
+			else if (outputDir != "") { outputFileName = outputDir + 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";
+		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);
-	}	
 }
 
 //**********************************************************************************************************************
@@ -79,12 +90,17 @@ int MergeFileCommand::execute(){
 		ofstream outputFile;
 		openOutputFile(outputFileName, outputFile);
 		
-		ifstream inputFile;
 		char c;
 		for(int i=0;i<numInputFiles;i++){
+			ifstream inputFile; //declaration must be inside for loop of windows throws an error
+			
 			openInputFile(fileNames[i], inputFile);
 			
-			while(!inputFile.eof()){	c = inputFile.get(); outputFile << c;	}
+			while(!inputFile.eof()){	
+				c = inputFile.get(); 
+				//-1 is eof char
+				if (int(c) != -1) { outputFile << c; }   
+			}
 			
 			inputFile.close();
 		}
@@ -93,31 +109,21 @@ int MergeFileCommand::execute(){
 		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";
+		errorOut(e, "MergeFileCommand", "execute");
 		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);
-	}	
-	
 }
 
 //**********************************************************************************************************************
 
 void MergeFileCommand::help(){
 	try {
-		cout << "The merge.file command..." << endl;
+		mothurOut("The merge.file command..."); mothurOutEndLine();
 	}
 	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";
+		errorOut(e, "MergeFileCommand", "help");
 		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);
-	}	
-	
 }
 
 //**********************************************************************************************************************