#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;
+ //initialize outputTypes
+ 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) {
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{ splitAtDash(fileList, fileNames); }
+ 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 = ""; }
else{
for(int i=0;i<numInputFiles;i++){
if (inputDir != "") {
- string path = hasPath(fileNames[i]);
+ 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(openInputFile(fileNames[i], testFile)){ abort = true; }
+ 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 + getSimpleName(outputFileName); }
+ else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); }
}
}
if (abort == true) { return 0; }
ofstream outputFile;
- openOutputFile(outputFileName, 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
- openInputFile(fileNames[i], inputFile);
+ m->openInputFile(fileNames[i], inputFile);
while(!inputFile.eof()){
+ if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0; }
+
c = inputFile.get();
//-1 is eof char
if (int(c) != -1) { outputFile << c; }
outputFile.close();
+ 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;