string CollectCommand::getHelpString(){
try {
string helpString = "";
+ ValidCalculators validCalculator;
helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n";
helpString += "The collect.single command should be in the following format: \n";
helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
helpString += "collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n";
helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
- helpString += validCalculator->printCalc("single");
+ helpString += validCalculator.printCalc("single");
helpString += "The label parameter is used to analyze specific labels in your input.\n";
- helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
return helpString;
}
catch(exception& e) {
allLines = 1;
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
+ if(option == "help") { help(); calledHelp = true; abort = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
- else { format = "sabund"; inputfile = sabundfile; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
- else { format = "rabund"; inputfile = rabundfile; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "sharedfile"; inputfile = sharedfile; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
- convert(temp, freq);
+ m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
- convert(temp, abund);
+ m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
- convert(temp, size);
+ m->mothurConvert(temp, size);
}
}
for (int p = 0; p < inputFileNames.size(); p++) {
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
- validCalculator = new ValidCalculators();
+ ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
+ if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
delete order;
- delete validCalculator;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
delete order;
- delete validCalculator;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
- delete validCalculator;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
- delete order;
- delete validCalculator;
- m->Groups.clear();
+ delete order;
+ m->clearGroups();
return 0;
}
delete order;
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
cDisplays.clear();
delete input;
- delete validCalculator;
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
- remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
}
projects / mothur.git / blobdiff