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) { inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0; }