#include "mergefilecommand.h"
+//**********************************************************************************************************************
+vector<string> MergeFileCommand::getValidParameters(){
+ try {
+ string Array[] = {"input", "output","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeFileCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MergeFileCommand::MergeFileCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["merge"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MergeFileCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"input","output"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeFileCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> MergeFileCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeFileCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
MergeFileCommand::MergeFileCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
if(option == "help") {
help();
- abort = true;
+ abort = true; calledHelp = true;
}
else {
//valid paramters for this command
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 = ""; }
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); }
+ else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); }
}
}
int MergeFileCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream outputFile;
m->openOutputFile(outputFileName, outputFile);
m->openInputFile(fileNames[i], inputFile);
while(!inputFile.eof()){
- if (m->control_pressed) { inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0; }
c = inputFile.get();
//-1 is eof char
outputFile.close();
- if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
m->mothurOutEndLine();
return 0;