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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,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) {
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; }
m->mothurRemove(outputFileName);
for(int i=0;i<numInputFiles;i++){ m->appendFiles(fileNames[i], outputFileName); }
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();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeFileCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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