--- /dev/null
+/*
+ * 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);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff