}
}
//**********************************************************************************************************************
+string LibShuffCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "coverage") { outputFileName = "libshuff.coverage"; }
+ else if (type == "libshuffsummary") { outputFileName = "libshuff.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LibShuffCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
LibShuffCommand::LibShuffCommand(){
try {
abort = true; calledHelp = true;
string temp;
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "10000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "1.0"; }
- convert(temp, cutOff);
+ m->mothurConvert(temp, cutOff);
temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.01"; }
- convert(temp, step);
+ m->mothurConvert(temp, step);
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
sim = m->isTrue(temp);
try {
ofstream outCov;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.coverage";
+ summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("coverage");
m->openOutputFile(summaryFile, outCov);
outputNames.push_back(summaryFile); outputTypes["coverage"].push_back(summaryFile);
outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
try {
ofstream outSum;
- summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "libshuff.summary";
+ summaryFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("libshuffsummary");
m->openOutputFile(summaryFile, outSum);
outputNames.push_back(summaryFile); outputTypes["libshuffsummary"].push_back(summaryFile);