X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=mergefilecommand.cpp;fp=mergefilecommand.cpp;h=04c92fae9a0d2189cb8f1ed69c9c53572fcfee2e;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
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--- /dev/null
+++ b/mergefilecommand.cpp
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+/*
+ *  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);
+	}
+}
+//**********************************************************************************************************************