X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mergefilecommand.cpp;fp=mergefilecommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=04c92fae9a0d2189cb8f1ed69c9c53572fcfee2e;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
deleted file mode 100644
index 04c92fa..0000000
--- a/mergefilecommand.cpp
+++ /dev/null
@@ -1,169 +0,0 @@
-/*
- *  mergefilecommand.cpp
- *  Mothur
- *
- *  Created by Pat Schloss on 6/14/09.
- *  Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "mergefilecommand.h"
-
-//**********************************************************************************************************************
-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);
-		
-		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)  {
-	try {
-		abort = false; calledHelp = false;   
-		
-		if(option == "help") {
-			help();
-			abort = true; calledHelp = true;
-		}else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-		else {
-			vector<string> myArray = setParameters();
-			
-			OptionParser parser(option);
-			map<string,string> parameters = parser.getParameters();
-			
-			ValidParameters validParameter;
-			
-			//check to make sure all parameters are valid for command
-			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
-				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") { 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){
-				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 (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") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
-			else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName);  }
-		}
-			
-	}
-	catch(exception& e) {
-		m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-
-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(); m->mothurRemove(outputFileName); return 0;  }
-			
-				c = inputFile.get(); 
-				//-1 is eof char
-				if (int(c) != -1) { outputFile << c; }   
-			}
-			
-			inputFile.close();
-		}
-		
-		outputFile.close();
-		
-		if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0;  }
-		
-		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
-		m->mothurOutEndLine();
-
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "MergeFileCommand", "execute");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************