#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 {
+ //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){
+MergeFileCommand::MergeFileCommand(string option) {
try {
abort = false;
}
else {
//valid paramters for this command
- string Array[] = {"input", "output"};
+ string Array[] = {"input", "output","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(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") { 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);
- }
}
//**********************************************************************************************************************
if (abort == true) { return 0; }
ofstream outputFile;
- openOutputFile(outputFileName, outputFile);
+ m->openOutputFile(outputFileName, outputFile);
- ifstream inputFile;
char c;
for(int i=0;i<numInputFiles;i++){
- openInputFile(fileNames[i], inputFile);
+ ifstream inputFile; //declaration must be inside for loop of windows throws an error
+
+ m->openInputFile(fileNames[i], inputFile);
- while(!inputFile.eof()){ c = inputFile.get(); outputFile << c; }
+ 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; }
+ }
inputFile.close();
}
+
+ 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(); outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
+ m->mothurOutEndLine();
+
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";
+ m->errorOut(e, "MergeFileCommand", "execute");
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);
- }
-
}
//**********************************************************************************************************************
void MergeFileCommand::help(){
try {
- cout << "The merge.file command..." << endl;
+ m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
}
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", "help");
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