#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){
+MergeFileCommand::MergeFileCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
if(option == "help") {
help();
- abort = true;
- }
+ abort = true; calledHelp = true;
+ }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"input", "output"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
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") { cout << "you must enter two or more file names" << endl; abort=true; }
- else{ splitAtDash(fileList, fileNames); }
+ 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){
- cout << "you must enter two or more file names and you entered " << fileNames.size() << " file names" << endl;
+ 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(openInputFile(fileNames[i], testFile)){ abort = true; }
+ 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") { cout << "you must enter an output file name" << endl; abort=true; }
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the MergeFileCommand class Function MergeFileCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->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);
- }
}
-
-//**********************************************************************************************************************
-
-MergeFileCommand::~MergeFileCommand() { /* do nothing */ }
-
//**********************************************************************************************************************
int MergeFileCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- ofstream outputFile;
- openOutputFile(outputFileName, outputFile);
+ m->mothurRemove(outputFileName);
+ for(int i=0;i<numInputFiles;i++){ m->appendFiles(fileNames[i], outputFileName); }
- ifstream inputFile;
- char c;
- for(int i=0;i<numInputFiles;i++){
- openInputFile(fileNames[i], inputFile);
-
- while(!inputFile.eof()){ c = inputFile.get(); outputFile << c; }
-
- inputFile.close();
- }
- 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";
- 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);
- }
-
-}
-
-//**********************************************************************************************************************
+ 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();
-void MergeFileCommand::help(){
- try {
- cout << "The merge.file command..." << endl;
+ return 0;
}
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";
+ m->errorOut(e, "MergeFileCommand", "execute");
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);
- }
-
}
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff